From f4d59ac915892ccba5e5de339da8fb91b39eec6a Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 2 Jun 2021 13:07:15 -0400
Subject: [PATCH 001/105] Squashed commit of the following:

commit 4b652ea8eab2f24cbae67c5da56a6f8e7cd9349e
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Wed Jun 2 13:04:22 2021 -0400

    Fix #29

    - Analytics no longer depends on ha_area to execute.
    - With this structure, should be able to extend to other fixed variable reporting

commit 5fda15ffc981298e02a3bcb72c9f7bda951e6cd0
Merge: 923d034 0933b35
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Tue Jun 1 13:50:29 2021 -0400

    Merge bulk fixes

commit eabc95fd9d1814899e4c2d818f30b5c8e81e133a
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Tue Jun 1 12:38:07 2021 -0400

    Overall cleanup of the codebase

    * Fix pre-release versioning
    * Modify poetry configuration to use local venvs
    * Remove unneeded packages
    * Update existing packages
    * Remove v1 codebase

commit 923d034690ad2386d35c0ca79eba23f25d0fe537
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Wed Jan 27 12:12:11 2021 -0500

    Check for missing profile_id in lookup_ghr()

    * Potential KeyError crash when looking for the profile ID in the cache.

commit 52da6a2c324a0675facd08914561c08fcf4ef1fc
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Tue Jan 19 16:56:18 2021 -0500

    Remove unneeded packages

    Fix #18

commit 57611ebb8316d0b3a9d183ca3ffe492132f83c7d
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Tue Jan 19 16:29:43 2021 -0500

    Use context vs run for variable search

    * Fix #17
    * When doing a `$var` search, check the current `context`. This SHOULD
      include `run` as well, but with variables from rasters already in
      place.

commit 88c829ba4f1464e9dac30e24ab59b044082e28b6
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Tue Jan 19 16:29:23 2021 -0500

    Add logging to date conversion utils

    * Fixes #16

commit cf7c2b82d955148c7a0972d17c3f64e9180261bf
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Tue Jan 19 08:54:02 2021 -0500

    Implement GHR caching

    * Build the cache on first request to GHR.
    * Utilize the cache on each subsequent call.
    * VERY rudimentary cache implementation.

commit d6c9ea7d21f6baf5ba14e300bd3dd646d4927211
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Wed Jan 6 16:28:21 2021 -0500

    Migrate to script executable

    * Implement __main__.py to run as module
    * Implement tool.poetry.scripts to install through poetry into the
      environment.
    * Move pythia.py to pythia/cli.py for proper package layout

commit 149375e5e55024b175afe465c6b477c1373a38de
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Wed Dec 23 22:46:25 2020 -0500

    Add more details to logging for #14

commit 9bc5b45156948379a65ade6a940bf94cb88a656d
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Wed Dec 23 22:37:09 2020 -0500

    Log missing assignment for values

    Fix #14

commit a54b396e2d22cf04c990ba5f0f7094566780816a
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Thu Dec 17 16:08:43 2020 -0500

    Add datetime stamp to logfiles

commit e6c89885e02d9e46fa0c59acffca7fcdea02e801
Merge: 3637042 4913c65
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Wed Nov 25 16:36:26 2020 -0500

    Fix path issues for analytics
---
 .gitignore                 |   2 +
 .python-version            |   2 +-
 Pipfile                    |  20 --
 Pipfile.lock               | 442 -----------------------------
 bin/pythia                 |   3 +
 poetry.lock                | 552 +++++++++++++++++++++++++++++++++++++
 poetry.toml                |   3 +
 pyproject.toml             |  25 ++
 pythia/__main__.py         |   5 +
 pythia/analytics.py        |  54 ++--
 pythia/cache_manager.py    |   1 +
 pythia.py => pythia/cli.py |  12 +-
 pythia/functions.py        |  54 ++--
 pythia/util.py             |  21 +-
 v1/__init__.py             |   0
 v1/pythia.py               |  82 ------
 16 files changed, 680 insertions(+), 598 deletions(-)
 delete mode 100644 Pipfile
 delete mode 100644 Pipfile.lock
 create mode 100755 bin/pythia
 create mode 100644 poetry.lock
 create mode 100644 poetry.toml
 create mode 100644 pyproject.toml
 create mode 100644 pythia/__main__.py
 create mode 100644 pythia/cache_manager.py
 rename pythia.py => pythia/cli.py (89%)
 delete mode 100644 v1/__init__.py
 delete mode 100644 v1/pythia.py

diff --git a/.gitignore b/.gitignore
index 6ead5367..f671c910 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ work/*
 .pytest_cache/*
 docs/source/_build
 docs/build
+.venv
+dist
diff --git a/.python-version b/.python-version
index c77a7de8..f06fb9e9 100644
--- a/.python-version
+++ b/.python-version
@@ -1 +1 @@
-3.7.9
+3.7.10
diff --git a/Pipfile b/Pipfile
deleted file mode 100644
index c3b457da..00000000
--- a/Pipfile
+++ /dev/null
@@ -1,20 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-fiona = "~=1.8"
-jinja2 = "~=2.10"
-numpy = "~=1.16"
-pandas = "~=0.25"
-pillow = "~=5.4"
-rasterio = "~=1.0"
-shapely = "~=1.6"
-rtree = "~=0.8"
-
-[dev-packages]
-pytest = "~=5.1"
-
-[requires]
-python_version = "3.7"
diff --git a/Pipfile.lock b/Pipfile.lock
deleted file mode 100644
index 23eb9139..00000000
--- a/Pipfile.lock
+++ /dev/null
@@ -1,442 +0,0 @@
-{
-    "_meta": {
-        "hash": {
-            "sha256": "cdcda79c33258759b2146be4030e364383d0ce610aaac3c4d7713a6bc862f1a7"
-        },
-        "pipfile-spec": 6,
-        "requires": {
-            "python_version": "3.7"
-        },
-        "sources": [
-            {
-                "name": "pypi",
-                "url": "https://pypi.org/simple",
-                "verify_ssl": true
-            }
-        ]
-    },
-    "default": {
-        "affine": {
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-            ],
-            "version": "==2.3.0"
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-        "attrs": {
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-            "version": "==20.3.0"
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-            "version": "==7.1.2"
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-            "version": "==1.1.1"
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-            "version": "==0.7.1"
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-        "fiona": {
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diff --git a/bin/pythia b/bin/pythia
new file mode 100755
index 00000000..ed90256b
--- /dev/null
+++ b/bin/pythia
@@ -0,0 +1,3 @@
+#!/usr/bin/env sh
+
+python -m pythia $@
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 00000000..0a20c87f
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,552 @@
+[[package]]
+name = "affine"
+version = "2.3.0"
+description = "Matrices describing affine transformation of the plane."
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.extras]
+test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
+
+[[package]]
+name = "atomicwrites"
+version = "1.4.0"
+description = "Atomic file writes."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "attrs"
+version = "21.2.0"
+description = "Classes Without Boilerplate"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[package.extras]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
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diff --git a/poetry.toml b/poetry.toml
new file mode 100644
index 00000000..53b35d37
--- /dev/null
+++ b/poetry.toml
@@ -0,0 +1,3 @@
+[virtualenvs]
+create = true
+in-project = true
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..07c344a8
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,25 @@
+[tool.poetry]
+name = "pythia"
+version = "2.0.0-beta.0"
+description = "An extensible gridded modeling framework for point-based modeling."
+authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
+license = "BSD-3-Clause"
+
+[tool.poetry.dependencies]
+python = "^3.7"
+fiona = "^1.8"
+jinja2 = "^2.10"
+numpy = "^1.16"
+rasterio = "^1.0"
+shapely = "^1.6"
+rtree = "^0.8"
+
+[tool.poetry.dev-dependencies]
+pytest = "^5.1"
+
+[tool.poetry.scripts]
+pythia = "pythia.cli:main"
+
+[build-system]
+requires = ["setuptools", "poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
diff --git a/pythia/__main__.py b/pythia/__main__.py
new file mode 100644
index 00000000..06137fa9
--- /dev/null
+++ b/pythia/__main__.py
@@ -0,0 +1,5 @@
+import sys
+from pythia.cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/pythia/analytics.py b/pythia/analytics.py
index f8861b82..9b4bb46c 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -153,33 +153,39 @@ def collate_outputs(config, run):
         else:
             mode = "w"
         with open(os.path.join(current_dir, "summary.csv")) as source, open(out_file, mode) as dest:
-            # TODO Fix later, this is hacky with little checks in place
+            additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
+            ds = None
+            band = None
             if harea_info:
+                additional_headers = f'{additional_headers},HARVEST_AREA'
                 harea_tiff = harea_info.split("::")[1]
-                with rasterio.open(harea_tiff) as ds:
-                    band = ds.read(1)
-                    for i, line in enumerate(source):
-                        if i == 0:
-                            if not collected_first_line:
-                                dest.write(
-                                    "LATITUDE,LONGITUDE,HARVEST_AREA,RUN_NAME,{}\n".format(
-                                        line.strip()
-                                    )
-                                )
-                                collected_first_line = True
-                        else:
-                            harea = pythia.io.get_site_raster_value(
-                                ds, band, (float(lng), float(lat))
-                            )
-                            if harea is None:
-                                harea = 0
-                                logging.warning("%s, %s is giving an invalid harea, replacing with 0")
-                            harea_s = "{:0.2f}".format(harea)
-                            dest.write(
-                                "{},{},{},{},{}\n".format(
-                                    lat, lng, harea_s, run.get("name", ""), line.strip()
-                                )
+                ds = rasterio.open(harea_tiff)
+                band = ds.read(1)
+            for i, line in enumerate(source):
+                if i == 0:
+                    if not collected_first_line:
+                        dest.write(
+                            "{},{}\n".format(
+                                additional_headers,
+                                line.strip()
                             )
+                        )
+                        collected_first_line = True
+                else:
+                    to_write = (lat, lng, run.get("name", ""))
+                    if ds is not None and not ds.closed:
+                        harea = pythia.io.get_site_raster_value(
+                            ds, band, (float(lng), float(lat))
+                        )
+                        if harea is None:
+                            harea = 0
+                            logging.warning("%s, %s is giving an invalid harea, replacing with 0")
+                        harea_s = "{:0.2f}".format(harea)
+                        to_write = to_write + (harea_s,)
+                    to_write = to_write + (line.strip()+"\n",)
+                    dest.write(",".join(to_write))
+            if ds is not None:
+                ds.close()
     return out_file
 
 
diff --git a/pythia/cache_manager.py b/pythia/cache_manager.py
new file mode 100644
index 00000000..a4d06b03
--- /dev/null
+++ b/pythia/cache_manager.py
@@ -0,0 +1 @@
+cache = {}
\ No newline at end of file
diff --git a/pythia.py b/pythia/cli.py
similarity index 89%
rename from pythia.py
rename to pythia/cli.py
index 1397e69b..8153658e 100644
--- a/pythia.py
+++ b/pythia/cli.py
@@ -1,3 +1,4 @@
+import argparse
 import datetime
 import logging
 import os
@@ -9,13 +10,9 @@
 import pythia.peerless
 import pythia.plugin
 
-logging.getLogger("pythia_app")
-logging.basicConfig(level=logging.INFO, filename="pythia.log", filemode="w")
 
-if __name__ == "__main__":
-    import argparse
-
-    parser = argparse.ArgumentParser()
+def main():
+    parser = argparse.ArgumentParser(prog="pythia")
     parser.add_argument("config", help="JSON configuration file to run")
     parser.add_argument("--all", action="store_true", help="Run all the steps in pythia")
     parser.add_argument(
@@ -36,6 +33,9 @@
     if not args.config:
         parser.print_help()
     else:
+        now = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+        logging.getLogger("pythia_app")
+        logging.basicConfig(level=logging.INFO, filename="pythia-{}.log".format(now), filemode="w")
         config = pythia.config.load_config(args.config)
         if args is None or not config:
             print("Invalid configuration file")
diff --git a/pythia/functions.py b/pythia/functions.py
index f433d428..b1a8e2c4 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -1,6 +1,8 @@
 import datetime
 import logging
+import os
 
+from pythia.cache_manager import cache
 import pythia.io
 import pythia.soil_handler
 import pythia.template
@@ -71,32 +73,45 @@ def generate_ic_layers(k, run, context, _):
     return {k: [dict(zip(layer_labels, cl)) for cl in calculated_layers]}
 
 
-def lookup_ghr(k, run, context, config):
-    import os
+def build_ghr_cache(config):
     import sqlite3
+    with sqlite3.connect(os.path.join(config["ghr_root"], "GHR.db")) as conn:
+        cache["ghr_profiles"] = {}
+        conn.row_factory = sqlite3.Row
+        cursor = conn.cursor()
+        cursor.execute("SELECT * FROM profile_map")
+        for row in cursor.fetchall():
+            if row["profile"] == "":
+                profile = None
+            else:
+                profile = row["profile"]
+            cache["ghr_profiles"][row["id"]] = profile
+
+    pass
 
+def lookup_ghr(k, run, context, config):
     args = run[k].split("::")[1:]
     if "raster" in args:
         logging.debug("lookup_ghr - context[%s] => %s", k, context[k])
-        with sqlite3.connect(os.path.join(config["ghr_root"], "GHR.db")) as conn:
-            c = conn.cursor()
-            tif_profile_id = (int(str(context[k])),)
-            c.execute("SELECT profile from profile_map WHERE id=?", tif_profile_id)
-            id_soil = c.fetchone()
-            if id_soil and id_soil[0].strip() != "":
-                id_soil = id_soil[0]
-                sol_file = "{}.SOL".format(id_soil[:2].upper())
-                return {k: id_soil, "soilFiles": [os.path.join(config["ghr_root"], sol_file)]}
-            else:
-                logging.error("Soil NOT found")
-                logging.error(context)
-                return None
-
+        if not "ghr_profiles" in cache:
+            build_ghr_cache(config)
+        tif_profile_id = int(str(context[k]))
+        if not tif_profile_id in cache["ghr_profiles"]:
+            logging.error("Invalid soil ID (%d) at (%f,%f)", tif_profile_id, context["lng"], context["lat"])
+            return None
+        id_soil = cache["ghr_profiles"][tif_profile_id] 
+        if id_soil and id_soil.strip() != "":
+            sol_file = "{}.SOL".format(id_soil[:2].upper())
+            return {k: id_soil, "soilFiles": [os.path.join(config["ghr_root"], sol_file)]}
+        else:
+            logging.error("Soil NOT found for id: %s at (%f,%f)", tif_profile_id, context["lng"], context["lat"])
+            return None
 
 def split_fert_dap_percent(k, run, context, _):
     args = run[k].split("::")[1:]
     if args[0].startswith("$"):
-        total = run[args[0][1:]]
+        search_context = args[0][1:]
+        total = float(context[search_context])
     else:
         total = float(args[0])
     # splits = int(args[1])
@@ -129,15 +144,16 @@ def assign_by_raster_value(k, run, context, _):
     if "raster" in init_args:
         args = init_args[init_args.index("raster")+2:]
     else:
-        logging.error("Need to specify a raster for assign_by_value")
+        logging.error("Need to specify a raster for %s:assign_by_value", k)
         return None
     raster_val = [int(i) for i in args[0::2]]
     assignment = args[1::2]
     if len(raster_val) != len(assignment):
-        logging.error("The values and assignments don't pair up in assign_by_raster_value")
+        logging.error("The values and assignments don't pair up in %s:assign_by_raster_value", k)
         return None
     if context[k] in raster_val:
         rv_idx = raster_val.index(context[k])
         return {k: assignment[rv_idx]}
     else:
+        logging.error("No assignment for value %d in %s:assign_by_value", context[k], k)
         return None
diff --git a/pythia/util.py b/pythia/util.py
index 5d100320..29b0991d 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -1,25 +1,38 @@
 import datetime
+import logging
 
 import pythia.functions
 
 
 def to_julian_date(d):
-    return d.strftime("%y%j")
+    try:
+        return d.strftime("%y%j")
+    except ValueError:
+        logging.error("Unable to convert %s to a julian date", d)
 
 
 def to_iso_date(d):
-    return d.strftime("%Y-%m-%d")
+    try:
+        return d.strftime("%Y-%m-%d")
+    except ValueError:
+        logging.error("Unable to convert %s to an ISO date", d)
+        return None
 
 
 def from_julian_date(s):
-    return datetime.datetime.strptime(s, "%y%j").date()
+    try:
+        return datetime.datetime.strptime(s, "%y%j").date()
+    except ValueError:
+        logging.error("%s is not a valid julian date", s)
+        return None
 
 
 def from_iso_date(s):
     try:
         return datetime.datetime.strptime(s, "%Y-%m-%d").date()
     except ValueError:
-        pass
+        logging.error("%s is not a proper ISO date.", s)
+        return None
 
 
 def get_rasters_list(iterator):
diff --git a/v1/__init__.py b/v1/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/v1/pythia.py b/v1/pythia.py
deleted file mode 100644
index dbd238a6..00000000
--- a/v1/pythia.py
+++ /dev/null
@@ -1,82 +0,0 @@
-import argparse
-from datetime import datetime
-import math
-import os
-import numpy as np
-import pandas as pd
-import rasterio
-
-def loadRaster(raster):
-    data = {}
-    with rasterio.open(raster) as r:
-        data['nd_val'] = r.nodata
-        data['vals'] = r.read(1)
-    return data
-
-def loadSummary(d, idx, items):
-    df = pd.read_csv(os.path.join(d, 'summary.csv'), index_col=False)
-    lim =  df.filter(items=items, col_index)
-    lim.replace(-99, 0, inplace=True)
-    lim.fillna(0, inplace=True)
-    lim['adj'] = np.where((lim['ADAT'] == 0) | (lim['HDAT'] == 0), 1, 0)
-    lim.loc[lim['ADAT'] == 0, 'HDAT'] = 0
-    df = None
-    return lim
-
-def applyScale(df, scale):
-    return df*scale
-
-def applyAverage(df, col, cum):
-    return round(df[col]/cum)
-
-def applyDateAverage(df, col, cum):
-    return df[col]/(cum - df['adj'])
-
-def accumulate(acc, df):
-    if acc is None:
-        return df
-    else:
-        return acc+df
-
-def main(args):
-    scale_data = loadRaster(args.scale)
-    directories = next(os.walk(args.wd))[1]
-#    coord_list = [tuple(map(int, d.split('_'))) for d in directories]
-    scale_factors = ([scale_data['vals'][c[0]][c[1]] for c in [tuple(map(int, d.split('_'))) for d in directories]])
-    sf_cum = sum(scale_factors)
-    if args.debug:
-        print(list(zip(directories, scale_factors)))
-        print(sf_cum)
-    acc = None
-    scale_adjust = {}
-    for idx, d in enumerate(directories):
-        if args.debug:
-            print("Running {}".format(d))
-        summary = loadSummary(os.path.join(args.wd, d))
-        scaled = applyScale(summary, scale_factors[idx])
-        acc = accumulate(acc, scaled)
-    if args.debug:
-        print(acc['adj'])
-    acc['HWAM'] = (acc['HWAM'].astype(int))/1000 #hardcoded to Metric Tonnes
-    acc['PRCP'] = applyDateAverage(acc, 'PRCP', sf_cum).astype(int)
-    acc['AY'] = round(acc['HWAM']/sf_cum).astype(int)
-    acc['PDAT'] = pd.to_datetime(applyAverage(acc, 'PDAT', sf_cum).apply(math.floor).apply(str), format="%Y%j", errors='coerce')
-    acc['ADAT'] = pd.to_datetime(applyDateAverage(acc, 'ADAT', sf_cum).apply(math.floor).apply(str), format="%Y%j", errors='coerce')
-    acc['HDAT'] = pd.to_datetime(applyDateAverage(acc, 'HDAT', sf_cum).apply(math.floor).apply(str), format="%Y%j", errors='coerce')
-    acc['YEAR'] = acc.index+1984
-    acc['SCALE'] = round((acc['adj']/sf_cum)*100).astype(int)
-    acc = acc.reindex(columns=['YEAR', 'HWAM', 'AY', 'PRCP', 'PDAT', 'ADAT', 'HDAT', 'SCALE'])
-    acc.columns = ['Year', 'Production (t)', 'Average Yield (kg/ha)', 'Average Rainfall (mm)', 'Average Planting Date', 'Average Anthesis Date', 'Average Harvest Date', 'Percent Failures']
-    if args.debug or args.no_output:
-        print(acc)
-    if not args.no_output:
-        acc.to_csv(os.path.join(args.wd, 'overview.csv'), index=False)
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description='The oracle')
-    parser.add_argument('wd', help='The working directory')
-    parser.add_argument('scale', help='The raster used to scale up the results')
-    parser.add_argument('--no-output', action='store_true')
-    parser.add_argument('--debug', action='store_true')
-    args = parser.parse_args()
-    main(args)

From 76b718236a682e31316beac92399d2c5e049d8ce Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Thu, 3 Jun 2021 13:04:17 -0400
Subject: [PATCH 002/105] Add black and flake8 to development tools

---
 poetry.lock    | 224 ++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |   2 +
 2 files changed, 225 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 10d00cde..a5b84ed9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -9,6 +9,14 @@ python-versions = "*"
 [package.extras]
 test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
 
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.0"
@@ -31,6 +39,30 @@ docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
 tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
 tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
 
+[[package]]
+name = "black"
+version = "21.5b2"
+description = "The uncompromising code formatter."
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+appdirs = "*"
+click = ">=7.1.2"
+mypy-extensions = ">=0.4.3"
+pathspec = ">=0.8.1,<1"
+regex = ">=2020.1.8"
+toml = ">=0.10.1"
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
+typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"]
+python2 = ["typed-ast (>=1.4.2)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
 [[package]]
 name = "certifi"
 version = "2021.5.30"
@@ -110,6 +142,20 @@ calc = ["shapely"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["pytest (>=3)", "pytest-cov", "boto3 (>=1.2.4)", "mock"]
 
+[[package]]
+name = "flake8"
+version = "3.9.2"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[package.dependencies]
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+mccabe = ">=0.6.0,<0.7.0"
+pycodestyle = ">=2.7.0,<2.8.0"
+pyflakes = ">=2.3.0,<2.4.0"
+
 [[package]]
 name = "importlib-metadata"
 version = "4.4.0"
@@ -148,6 +194,14 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "mccabe"
+version = "0.6.1"
+description = "McCabe checker, plugin for flake8"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "more-itertools"
 version = "8.8.0"
@@ -171,6 +225,14 @@ six = "*"
 testing = ["pytest", "coverage", "astroid (>=1.5.3,<1.6.0)", "pylint (>=1.7.2,<1.8.0)", "astroid (>=2.0)", "pylint (>=2.3.1,<2.4.0)"]
 yaml = ["PyYAML (>=5.1.0)"]
 
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "numpy"
 version = "1.20.3"
@@ -190,6 +252,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 [package.dependencies]
 pyparsing = ">=2.0.2"
 
+[[package]]
+name = "pathspec"
+version = "0.8.1"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "pluggy"
 version = "0.13.1"
@@ -212,6 +282,22 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pycodestyle"
+version = "2.7.0"
+description = "Python style guide checker"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "pyflakes"
+version = "2.3.1"
+description = "passive checker of Python programs"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
 [[package]]
 name = "pyparsing"
 version = "2.4.7"
@@ -269,6 +355,14 @@ plot = ["matplotlib"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "pytest (>=2.8.2)", "shapely"]
 
+[[package]]
+name = "regex"
+version = "2021.4.4"
+description = "Alternative regular expression module, to replace re."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "rtree"
 version = "0.8.3"
@@ -313,6 +407,22 @@ pyparsing = ">=2.1.6"
 [package.extras]
 test = ["pytest", "hypothesis"]
 
+[[package]]
+name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+
+[[package]]
+name = "typed-ast"
+version = "1.4.3"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "typing-extensions"
 version = "3.10.0.0"
@@ -344,13 +454,17 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pyt
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7"
-content-hash = "fac28d8d66792f81cdf1da3abd3e60ec3f889d7e7b37f73cca7c4ecf96f155ec"
+content-hash = "765c40c0da71552294c3d49408c9cddce3e514a157c5422f9eb1d00f1e371b28"
 
 [metadata.files]
 affine = [
     {file = "affine-2.3.0-py2.py3-none-any.whl", hash = "sha256:34b05b070d954c382e56f02c207a372d8a32621a87653cc30cdd31cd7f65799f"},
     {file = "affine-2.3.0.tar.gz", hash = "sha256:2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102"},
 ]
+appdirs = [
+    {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
+    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
+]
 atomicwrites = [
     {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
@@ -359,6 +473,10 @@ attrs = [
     {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
     {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
 ]
+black = [
+    {file = "black-21.5b2-py3-none-any.whl", hash = "sha256:e5cf21ebdffc7a9b29d73912b6a6a9a4df4ce70220d523c21647da2eae0751ef"},
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+    {file = "typed_ast-1.4.3-cp36-cp36m-win_amd64.whl", hash = "sha256:bff6ad71c81b3bba8fa35f0f1921fb24ff4476235a6e94a26ada2e54370e6da7"},
+    {file = "typed_ast-1.4.3-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:0fb71b8c643187d7492c1f8352f2c15b4c4af3f6338f21681d3681b3dc31a266"},
+    {file = "typed_ast-1.4.3-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:760ad187b1041a154f0e4d0f6aae3e40fdb51d6de16e5c99aedadd9246450e9e"},
+    {file = "typed_ast-1.4.3-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:5feca99c17af94057417d744607b82dd0a664fd5e4ca98061480fd8b14b18d04"},
+    {file = "typed_ast-1.4.3-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:95431a26309a21874005845c21118c83991c63ea800dd44843e42a916aec5899"},
+    {file = "typed_ast-1.4.3-cp37-cp37m-win32.whl", hash = "sha256:aee0c1256be6c07bd3e1263ff920c325b59849dc95392a05f258bb9b259cf39c"},
+    {file = "typed_ast-1.4.3-cp37-cp37m-win_amd64.whl", hash = "sha256:9ad2c92ec681e02baf81fdfa056fe0d818645efa9af1f1cd5fd6f1bd2bdfd805"},
+    {file = "typed_ast-1.4.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:b36b4f3920103a25e1d5d024d155c504080959582b928e91cb608a65c3a49e1a"},
+    {file = "typed_ast-1.4.3-cp38-cp38-manylinux1_i686.whl", hash = "sha256:067a74454df670dcaa4e59349a2e5c81e567d8d65458d480a5b3dfecec08c5ff"},
+    {file = "typed_ast-1.4.3-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:7538e495704e2ccda9b234b82423a4038f324f3a10c43bc088a1636180f11a41"},
+    {file = "typed_ast-1.4.3-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:af3d4a73793725138d6b334d9d247ce7e5f084d96284ed23f22ee626a7b88e39"},
+    {file = "typed_ast-1.4.3-cp38-cp38-win32.whl", hash = "sha256:f2362f3cb0f3172c42938946dbc5b7843c2a28aec307c49100c8b38764eb6927"},
+    {file = "typed_ast-1.4.3-cp38-cp38-win_amd64.whl", hash = "sha256:dd4a21253f42b8d2b48410cb31fe501d32f8b9fbeb1f55063ad102fe9c425e40"},
+    {file = "typed_ast-1.4.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:f328adcfebed9f11301eaedfa48e15bdece9b519fb27e6a8c01aa52a17ec31b3"},
+    {file = "typed_ast-1.4.3-cp39-cp39-manylinux1_i686.whl", hash = "sha256:2c726c276d09fc5c414693a2de063f521052d9ea7c240ce553316f70656c84d4"},
+    {file = "typed_ast-1.4.3-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:cae53c389825d3b46fb37538441f75d6aecc4174f615d048321b716df2757fb0"},
+    {file = "typed_ast-1.4.3-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:b9574c6f03f685070d859e75c7f9eeca02d6933273b5e69572e5ff9d5e3931c3"},
+    {file = "typed_ast-1.4.3-cp39-cp39-win32.whl", hash = "sha256:209596a4ec71d990d71d5e0d312ac935d86930e6eecff6ccc7007fe54d703808"},
+    {file = "typed_ast-1.4.3-cp39-cp39-win_amd64.whl", hash = "sha256:9c6d1a54552b5330bc657b7ef0eae25d00ba7ffe85d9ea8ae6540d2197a3788c"},
+    {file = "typed_ast-1.4.3.tar.gz", hash = "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"},
+]
 typing-extensions = [
     {file = "typing_extensions-3.10.0.0-py2-none-any.whl", hash = "sha256:0ac0f89795dd19de6b97debb0c6af1c70987fd80a2d62d1958f7e56fcc31b497"},
     {file = "typing_extensions-3.10.0.0-py3-none-any.whl", hash = "sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84"},
diff --git a/pyproject.toml b/pyproject.toml
index 07c344a8..a9df6fe1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,6 +16,8 @@ rtree = "^0.8"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.1"
+black = "^21.5b2"
+flake8 = "^3.9.2"
 
 [tool.poetry.scripts]
 pythia = "pythia.cli:main"

From a9b64cc7ca40f8d6f6ce777f4f10281ae26e6c9f Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Thu, 3 Jun 2021 13:06:33 -0400
Subject: [PATCH 003/105] Add date_from_doy_raster function

- date_from_doy_raster::raster::<file>
- Raster should have Day of Year values (1 to 366)
- Uses startYear parameter for complete year
- If startYear is not a leap year and day 366 is found, it rolls over to Jan 1 of the next year.
- Support for 4 digit Julian dates in _from_julian_date() utility function.
---
 pythia/functions.py | 74 +++++++++++++++++++++++++++++++++++----------
 pythia/util.py      |  9 ++++--
 2 files changed, 65 insertions(+), 18 deletions(-)

diff --git a/pythia/functions.py b/pythia/functions.py
index b1a8e2c4..5a26c9b3 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -1,4 +1,5 @@
 import datetime
+
 import logging
 import os
 
@@ -20,8 +21,8 @@ def xy_from_vector(v):
     return pythia.io.extract_vector_coords(args[1])
 
 
-def xy_from_list(l):
-    return [tuple(x[::-1]) for x in l]
+def xy_from_list(lst):
+    return [tuple(x[::-1]) for x in lst]
 
 
 def auto_planting_window(k, run, context, _):
@@ -52,11 +53,10 @@ def lookup_hc27(k, run, context, _):
 def lookup_wth(k, run, context, _):
     args = run[k].split("::")[1:]
     finder = pythia.io.find_closest_vector_coords
+    cell_id = None
     if "vector" in args:
         idx = args.index("vector")
-        cell_id = finder(
-            args[idx + 1], context["lng"], context["lat"], args[idx + 2]
-        )
+        cell_id = finder(args[idx + 1], context["lng"], context["lat"], args[idx + 2])
     return {k: args[0], "wthFile": "{}.WTH".format(cell_id)}
 
 
@@ -66,7 +66,9 @@ def generate_ic_layers(k, run, context, _):
         profile = args[0][1:]
     else:
         profile = args[0]
-    soil_file = pythia.soil_handler.findSoilProfile(context[profile], context["soilFiles"])
+    soil_file = pythia.soil_handler.findSoilProfile(
+        context[profile], context["soilFiles"]
+    )
     layers = pythia.soil_handler.readSoilLayers(context[profile], soil_file)
     calculated_layers = pythia.soil_handler.calculateICLayerData(layers, run)
     layer_labels = ["icbl", "sh2o", "snh4", "sno3"]
@@ -75,6 +77,7 @@ def generate_ic_layers(k, run, context, _):
 
 def build_ghr_cache(config):
     import sqlite3
+
     with sqlite3.connect(os.path.join(config["ghr_root"], "GHR.db")) as conn:
         cache["ghr_profiles"] = {}
         conn.row_factory = sqlite3.Row
@@ -89,24 +92,39 @@ def build_ghr_cache(config):
 
     pass
 
+
 def lookup_ghr(k, run, context, config):
     args = run[k].split("::")[1:]
     if "raster" in args:
         logging.debug("lookup_ghr - context[%s] => %s", k, context[k])
-        if not "ghr_profiles" in cache:
+        if "ghr_profiles" not in cache:
             build_ghr_cache(config)
         tif_profile_id = int(str(context[k]))
-        if not tif_profile_id in cache["ghr_profiles"]:
-            logging.error("Invalid soil ID (%d) at (%f,%f)", tif_profile_id, context["lng"], context["lat"])
+        if tif_profile_id not in cache["ghr_profiles"]:
+            logging.error(
+                "Invalid soil ID (%d) at (%f,%f)",
+                tif_profile_id,
+                context["lng"],
+                context["lat"],
+            )
             return None
-        id_soil = cache["ghr_profiles"][tif_profile_id] 
+        id_soil = cache["ghr_profiles"][tif_profile_id]
         if id_soil and id_soil.strip() != "":
             sol_file = "{}.SOL".format(id_soil[:2].upper())
-            return {k: id_soil, "soilFiles": [os.path.join(config["ghr_root"], sol_file)]}
+            return {
+                k: id_soil,
+                "soilFiles": [os.path.join(config["ghr_root"], sol_file)],
+            }
         else:
-            logging.error("Soil NOT found for id: %s at (%f,%f)", tif_profile_id, context["lng"], context["lat"])
+            logging.error(
+                "Soil NOT found for id: %s at (%f,%f)",
+                tif_profile_id,
+                context["lng"],
+                context["lat"],
+            )
             return None
 
+
 def split_fert_dap_percent(k, run, context, _):
     args = run[k].split("::")[1:]
     if args[0].startswith("$"):
@@ -117,7 +135,9 @@ def split_fert_dap_percent(k, run, context, _):
     # splits = int(args[1])
     split_amounts = args[2:]
     if any(n.startswith("-") for n in split_amounts):
-        logging.error("No arguments for split_applications_dap_percent should be negative")
+        logging.error(
+            "No arguments for split_applications_dap_percent should be negative"
+        )
         return None
     daps = [int(i) for i in split_amounts[0::2]]
     percents = [float(i) / 100.0 for i in split_amounts[1::2]]
@@ -125,7 +145,9 @@ def split_fert_dap_percent(k, run, context, _):
         logging.error("Not enough arguments for split_applications_dap_percent")
         return None
     if sum(percents) != 1.0:
-        logging.error("The sum of all percents needs to be 100 in split_applications_dap_percent")
+        logging.error(
+            "The sum of all percents needs to be 100 in split_applications_dap_percent"
+        )
         logging.error(percents)
         return None
     if len(daps) != len(set(daps)):
@@ -142,14 +164,16 @@ def split_fert_dap_percent(k, run, context, _):
 def assign_by_raster_value(k, run, context, _):
     init_args = run[k].split("::")[1:]
     if "raster" in init_args:
-        args = init_args[init_args.index("raster")+2:]
+        args = init_args[init_args.index("raster") + 2:]
     else:
         logging.error("Need to specify a raster for %s:assign_by_value", k)
         return None
     raster_val = [int(i) for i in args[0::2]]
     assignment = args[1::2]
     if len(raster_val) != len(assignment):
-        logging.error("The values and assignments don't pair up in %s:assign_by_raster_value", k)
+        logging.error(
+            "The values and assignments don't pair up in %s:assign_by_raster_value", k
+        )
         return None
     if context[k] in raster_val:
         rv_idx = raster_val.index(context[k])
@@ -157,3 +181,21 @@ def assign_by_raster_value(k, run, context, _):
     else:
         logging.error("No assignment for value %d in %s:assign_by_value", context[k], k)
         return None
+
+
+def date_from_doy_raster(k, run, context, _):
+    init_args = run[k].split("::")[1:]
+    if "raster" not in init_args:
+        logging.error("date_from_doy_raster: No raster specified.")
+        return None
+    if context[k] < 1 or context[k] > 366:
+        logging.error(
+            "date_from_doy_raster: Invalid day of year found in raster: %d", context[k]
+        )
+        return None
+    return {
+        k: pythia.util.to_iso_date(
+            pythia.util.from_julian_date(f'{run["startYear"]}{context[k]}')
+        )
+
+    }
diff --git a/pythia/util.py b/pythia/util.py
index 29b0991d..900cf8c1 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -9,6 +9,7 @@ def to_julian_date(d):
         return d.strftime("%y%j")
     except ValueError:
         logging.error("Unable to convert %s to a julian date", d)
+        return None
 
 
 def to_iso_date(d):
@@ -23,7 +24,11 @@ def from_julian_date(s):
     try:
         return datetime.datetime.strptime(s, "%y%j").date()
     except ValueError:
-        logging.error("%s is not a valid julian date", s)
+        pass
+    try:
+        return datetime.datetime.strptime(s, "%Y%j").date()
+    except ValueError:
+        logging.error('"%s" is an invalid julian date format.', s)
         return None
 
 
@@ -31,7 +36,7 @@ def from_iso_date(s):
     try:
         return datetime.datetime.strptime(s, "%Y-%m-%d").date()
     except ValueError:
-        logging.error("%s is not a proper ISO date.", s)
+        logging.error('"%s" is an invalid ISO date format.', s)
         return None
 
 

From 3aab8848d40e53a7adf3a27c263a14a9e2d4b987 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Thu, 3 Jun 2021 13:48:10 -0400
Subject: [PATCH 004/105] Add date_offset function

- date_offset::$<variable>::<offset int>
- Currently only supports using existing variables in the context.
---
 pythia/functions.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/pythia/functions.py b/pythia/functions.py
index 5a26c9b3..87db4fe3 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -197,5 +197,27 @@ def date_from_doy_raster(k, run, context, _):
         k: pythia.util.to_iso_date(
             pythia.util.from_julian_date(f'{run["startYear"]}{context[k]}')
         )
-
     }
+
+
+def date_offset(k, run, context, _):
+    args = run[k].split("::")[1:]
+    offset_value = args[-1]
+    try:
+        offset_value = int(offset_value)
+    except ValueError:
+        logging.error("date_offset: %s is not an integer", offset_value)
+        return None
+    if args[0].startswith("$"):
+        search_context = args[0][1:]
+        if search_context not in context:
+            logging.error("date_offset: %s is not in the current context.", args[0])
+            return None
+        context_date = context[search_context]
+        cxt_date = pythia.util.from_iso_date(context_date)
+        td = datetime.timedelta(days=offset_value)
+        new_date = cxt_date + td
+        return {k: pythia.util.to_iso_date(new_date)}
+    else:
+        logging.error("date_offset only works with references variables.")
+        return None

From e2598d857bfd39f540cb9f5a4b0c2f6e224a264e Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 8 Jun 2021 15:01:13 -0400
Subject: [PATCH 005/105] Fix #32

* Add --logfile-prefix CLI argument to allow user to change the prefix of the logfile. Default is pythia.
---
 pythia/cli.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pythia/cli.py b/pythia/cli.py
index 8153658e..1f0f94f7 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -28,6 +28,8 @@ def main():
     parser.add_argument(
         "--clean-work-dir", action="store_true", help="Clean the work directory prior to run"
     )
+    parser.add_argument(
+            "--logfile-prefix", default="pythia", help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log")
     args = parser.parse_args()
 
     if not args.config:
@@ -35,7 +37,7 @@ def main():
     else:
         now = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
         logging.getLogger("pythia_app")
-        logging.basicConfig(level=logging.INFO, filename="pythia-{}.log".format(now), filemode="w")
+        logging.basicConfig(level=logging.INFO, filename="{}-{}.log".format(args.logfile_prefix, now), filemode="w")
         config = pythia.config.load_config(args.config)
         if args is None or not config:
             print("Invalid configuration file")

From 3dae9d4bb56792bb0a7ef5be2d736b02facbcc03 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Thu, 8 Jul 2021 15:25:45 -0400
Subject: [PATCH 006/105] Fix #34

Squashed commit of the following:

commit b050301ec28a7a546e619dd4cbb236d7b40dba6c
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Fri Jun 18 11:33:28 2021 -0400

    Add logging to potential error points.

    * Currently only targetting the filter and calc points
---
 pythia/analytics.py | 364 ++++++++++++++++++++++----------------------
 1 file changed, 185 insertions(+), 179 deletions(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 9b4bb46c..3ef4b53b 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -9,208 +9,214 @@
 
 
 def get_run_basedir(config, run):
-    return os.path.join(config.get("workDir", "."), run.get("name", ""))
+	return os.path.join(config.get("workDir", "."), run.get("name", ""))
 
 
 def _generated_run_files(run_path, target_file):
-    for root, subdir, files in os.walk(run_path, topdown=False):
-        if target_file in files:
-            yield root
-    pass
+	for root, subdir, files in os.walk(run_path, topdown=False):
+		if target_file in files:
+			yield root
+	pass
 
 
 def extract_ll(path):
-    ll = path.split(os.path.sep)[-2:]
-    return tuple([pythia.util.translate_news_coords(coords) for coords in ll])
+	ll = path.split(os.path.sep)[-2:]
+	return tuple([pythia.util.translate_news_coords(coords) for coords in ll])
 
 
 # Always by default keep the per_pixel_per_management file, but create a place
 # for the single output or analytics, should we have a "final outputs"
 # directory.
 def final_outputs(config, outputs):
-    analytics_config = config.get("analytics_setup", {})
-    out_files = []
-    out_dir = os.path.join(config.get("workDir", "."))
-    file_prefix = "{}_".format(analytics_config.get("per_pixel_prefix", "pp"))
-    if not os.path.exists(out_dir):
-        os.makedirs(out_dir)
-    for current_file in outputs:
-         bn = os.path.basename(current_file)
-         out_file = os.path.join(out_dir, bn[bn.find(file_prefix):])
-         shutil.copyfile(current_file, out_file)
+	analytics_config = config.get("analytics_setup", {})
+	out_files = []
+	out_dir = os.path.join(config.get("workDir", "."))
+	file_prefix = "{}_".format(analytics_config.get("per_pixel_prefix", "pp"))
+	if not os.path.exists(out_dir):
+		os.makedirs(out_dir)
+	for current_file in outputs:
+		 bn = os.path.basename(current_file)
+		 out_file = os.path.join(out_dir, bn[bn.find(file_prefix):])
+		 shutil.copyfile(current_file, out_file)
 
 def filter_columns(config, outputs):
-    analytics_config = config.get("analytics_setup", {})
-    columns = analytics_config.get("columns", [])
-    out_files = []
-    out_dir = os.path.join(config.get("workDir", "."), "scratch")
-    if not os.path.exists(out_dir):
-        os.makedirs(out_dir)
-    for current_file in outputs:
-        col_indexes = []
-        out_file = os.path.join(out_dir, "filtered_{}".format(os.path.basename(current_file)))
-        with open(current_file) as source, open(out_file, "w") as dest:
-            dssat_in = csv.reader(source)
-            dssat_out = csv.writer(dest)
-            for line in dssat_in:
-                if dssat_in.line_num == 1:
-                    for x, col in enumerate(line):
-                        if col in columns:
-                            col_indexes.append(x)
-                row = [line[idx] for idx in col_indexes]
-                dssat_out.writerow(row)
-        out_files.append(out_file)
-    return out_files
+	analytics_config = config.get("analytics_setup", {})
+	columns = analytics_config.get("columns", [])
+	out_files = []
+	out_dir = os.path.join(config.get("workDir", "."), "scratch")
+	if not os.path.exists(out_dir):
+		os.makedirs(out_dir)
+	for current_file in outputs:
+		col_indexes = []
+		out_file = os.path.join(out_dir, "filtered_{}".format(os.path.basename(current_file)))
+		with open(current_file) as source, open(out_file, "w") as dest:
+			dssat_in = csv.reader(source)
+			dssat_out = csv.writer(dest)
+			try:
+				for line in dssat_in:
+					if dssat_in.line_num == 1:
+						for x, col in enumerate(line):
+							if col in columns:
+								col_indexes.append(x)
+					row = [line[idx] for idx in col_indexes]
+					dssat_out.writerow(row)
+			except csv.Error as e:
+				logging.error("CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e)
+		out_files.append(out_file)
+	return out_files
 
 
 def calculate_columns(config, outputs):
-    analytics_config = config.get("analytics_setup", {})
-    calculations = analytics_config.get("calculatedColumns", [])
-    funs = pythia.analytic_functions.generate_funs(calculations)
-    arg_columns = []
-    for fun in funs:
-        for a in fun["args"]:
-            if a.startswith("$"):
-                if a.upper() not in arg_columns:
-                    arg_columns.append(a[1::].upper())
-    out_files = []
-    out_dir = os.path.join(config.get("workDir", "."), "scratch")
-    if not os.path.exists(out_dir):
-        os.makedirs(out_dir)
-    for current_file in outputs:
-        col_indexes = []
-        out_file = os.path.join(out_dir, "calculated_{}".format(os.path.basename(current_file)))
-        with open(current_file) as source, open(out_file, "w") as dest:
-            dssat_in = csv.reader(source)
-            dssat_out = csv.writer(dest)
-            num_cols = 0
-            for line in dssat_in:
-                if dssat_in.line_num != 1:
-                    if num_cols == 0:
-                        print("we have a problem")
-                    else:
-                        line = line[0:num_cols]
-                if dssat_in.line_num == 1:
-                    num_cols = len(line)
-                    col_indexes = [line.index(x) for x in arg_columns]
-                    for fun in funs:
-                        line.append(fun["key"])
-                    dssat_out.writerow(line)
-                else:
-                    for fun in funs:
-                        line.append(
-                            fun["fun"](
-                                [
-                                    line[col_indexes[arg_columns.index(x[1::].upper())]]
-                                    for x in fun["args"]
-                                ]
-                            )
-                        )
-                    dssat_out.writerow(line)
-            out_files.append(out_file)
-    return out_files
+	analytics_config = config.get("analytics_setup", {})
+	calculations = analytics_config.get("calculatedColumns", [])
+	funs = pythia.analytic_functions.generate_funs(calculations)
+	arg_columns = []
+	for fun in funs:
+		for a in fun["args"]:
+			if a.startswith("$"):
+				if a.upper() not in arg_columns:
+					arg_columns.append(a[1::].upper())
+	out_files = []
+	out_dir = os.path.join(config.get("workDir", "."), "scratch")
+	if not os.path.exists(out_dir):
+		os.makedirs(out_dir)
+	for current_file in outputs:
+		col_indexes = []
+		out_file = os.path.join(out_dir, "calculated_{}".format(os.path.basename(current_file)))
+		with open(current_file) as source, open(out_file, "w") as dest:
+			dssat_in = csv.reader(source)
+			dssat_out = csv.writer(dest)
+			num_cols = 0
+			try:
+			  for line in dssat_in:
+				  if dssat_in.line_num != 1:
+					  if num_cols == 0:
+						  print("we have a problem")
+					  else:
+						  line = line[0:num_cols]
+				  if dssat_in.line_num == 1:
+					  num_cols = len(line)
+					  col_indexes = [line.index(x) for x in arg_columns]
+					  for fun in funs:
+						  line.append(fun["key"])
+					  dssat_out.writerow(line)
+				  else:
+					  for fun in funs:
+						  line.append(
+							  fun["fun"](
+								  [
+									  line[col_indexes[arg_columns.index(x[1::].upper())]]
+									  for x in fun["args"]
+								  ]
+							  )
+						  )
+					  dssat_out.writerow(line)
+			except csv.Error as e:
+				logging.error("CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e)
+			out_files.append(out_file)
+	return out_files
 
 
 def combine_outputs(config, outputs):
-    analytics_config = config.get("analytics_setup", {})
-    combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
-    out_dir = config.get("workDir", ".")
-    collected_first_line = False
-    for current_file in outputs:
-        if os.path.exists(current_file):
-            if collected_first_line:
-                mode = "a"
-            else:
-                mode = "w"
-            with open(current_file) as source, open(
-                os.path.join(out_dir, combined_file_name), mode
-            ) as dest:
-                for i, line in enumerate(source):
-                    if i == 0:
-                        if not collected_first_line:
-                            dest.write(line)
-                            collected_first_line = True
-                    else:
-                        dest.write(line)
+	analytics_config = config.get("analytics_setup", {})
+	combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
+	out_dir = config.get("workDir", ".")
+	collected_first_line = False
+	for current_file in outputs:
+		if os.path.exists(current_file):
+			if collected_first_line:
+				mode = "a"
+			else:
+				mode = "w"
+			with open(current_file) as source, open(
+				os.path.join(out_dir, combined_file_name), mode
+			) as dest:
+				for i, line in enumerate(source):
+					if i == 0:
+						if not collected_first_line:
+							dest.write(line)
+							collected_first_line = True
+					else:
+						dest.write(line)
 
 
 def collate_outputs(config, run):
-    analytics_config = config.get("analytics_setup", {})
-    per_pixel_file_name = "{}_{}.csv".format(
-        analytics_config.get("per_pixel_prefix", "pp"), run["name"]
-    )
-    work_dir = get_run_basedir(config, run)
-    out_dir = os.path.join(config.get("workDir", "."), "scratch")
-    if not os.path.exists(out_dir):
-        os.makedirs(out_dir)
-    out_file = os.path.join(out_dir, per_pixel_file_name)
-    harea_info = run.get("harvestArea", None)
-    collected_first_line = False
-    for current_dir in _generated_run_files(work_dir, "summary.csv"):
-        lat, lng = extract_ll(current_dir)
-        if collected_first_line:
-            mode = "a"
-        else:
-            mode = "w"
-        with open(os.path.join(current_dir, "summary.csv")) as source, open(out_file, mode) as dest:
-            additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
-            ds = None
-            band = None
-            if harea_info:
-                additional_headers = f'{additional_headers},HARVEST_AREA'
-                harea_tiff = harea_info.split("::")[1]
-                ds = rasterio.open(harea_tiff)
-                band = ds.read(1)
-            for i, line in enumerate(source):
-                if i == 0:
-                    if not collected_first_line:
-                        dest.write(
-                            "{},{}\n".format(
-                                additional_headers,
-                                line.strip()
-                            )
-                        )
-                        collected_first_line = True
-                else:
-                    to_write = (lat, lng, run.get("name", ""))
-                    if ds is not None and not ds.closed:
-                        harea = pythia.io.get_site_raster_value(
-                            ds, band, (float(lng), float(lat))
-                        )
-                        if harea is None:
-                            harea = 0
-                            logging.warning("%s, %s is giving an invalid harea, replacing with 0")
-                        harea_s = "{:0.2f}".format(harea)
-                        to_write = to_write + (harea_s,)
-                    to_write = to_write + (line.strip()+"\n",)
-                    dest.write(",".join(to_write))
-            if ds is not None:
-                ds.close()
-    return out_file
+	analytics_config = config.get("analytics_setup", {})
+	per_pixel_file_name = "{}_{}.csv".format(
+		analytics_config.get("per_pixel_prefix", "pp"), run["name"]
+	)
+	work_dir = get_run_basedir(config, run)
+	out_dir = os.path.join(config.get("workDir", "."), "scratch")
+	if not os.path.exists(out_dir):
+		os.makedirs(out_dir)
+	out_file = os.path.join(out_dir, per_pixel_file_name)
+	harea_info = run.get("harvestArea", None)
+	collected_first_line = False
+	for current_dir in _generated_run_files(work_dir, "summary.csv"):
+		lat, lng = extract_ll(current_dir)
+		if collected_first_line:
+			mode = "a"
+		else:
+			mode = "w"
+		with open(os.path.join(current_dir, "summary.csv")) as source, open(out_file, mode) as dest:
+			additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
+			ds = None
+			band = None
+			if harea_info:
+				additional_headers = f'{additional_headers},HARVEST_AREA'
+				harea_tiff = harea_info.split("::")[1]
+				ds = rasterio.open(harea_tiff)
+				band = ds.read(1)
+			for i, line in enumerate(source):
+				if i == 0:
+					if not collected_first_line:
+						dest.write(
+							"{},{}\n".format(
+								additional_headers,
+								line.strip()
+							)
+						)
+						collected_first_line = True
+				else:
+					to_write = (lat, lng, run.get("name", ""))
+					if ds is not None and not ds.closed:
+						harea = pythia.io.get_site_raster_value(
+							ds, band, (float(lng), float(lat))
+						)
+						if harea is None:
+							harea = 0
+							logging.warning("%s, %s is giving an invalid harea, replacing with 0")
+						harea_s = "{:0.2f}".format(harea)
+						to_write = to_write + (harea_s,)
+					to_write = to_write + (line.strip()+"\n",)
+					dest.write(",".join(to_write))
+			if ds is not None:
+				ds.close()
+	return out_file
 
 
 def execute(config, plugins):
-    runs = config.get("runs", [])
-    analytics_config = config.get("analytics_setup", None)
-    run_outputs = []
-    calculated = None
-    filtered = None
-    if not analytics_config:
-        return
-    if len(runs) == 0:
-        return
-    for run in runs:
-        run_outputs.append(collate_outputs(config, run))
-    # Apply all the filters first
-    if analytics_config.get("calculatedColumns", None):
-        calculated = calculate_columns(config, run_outputs)
-    if calculated is None:
-        calculated = run_outputs
-    if analytics_config.get("columns", None):
-        filtered = filter_columns(config, calculated)
-    if filtered is None:
-        filtered = calculated
-    if analytics_config.get("singleOutput", False):
-        combine_outputs(config, filtered)
-    else:
-        final_outputs(config, filtered)
+	runs = config.get("runs", [])
+	analytics_config = config.get("analytics_setup", None)
+	run_outputs = []
+	calculated = None
+	filtered = None
+	if not analytics_config:
+		return
+	if len(runs) == 0:
+		return
+	for run in runs:
+		run_outputs.append(collate_outputs(config, run))
+	# Apply all the filters first
+	if analytics_config.get("calculatedColumns", None):
+		calculated = calculate_columns(config, run_outputs)
+	if calculated is None:
+		calculated = run_outputs
+	if analytics_config.get("columns", None):
+		filtered = filter_columns(config, calculated)
+	if filtered is None:
+		filtered = calculated
+	if analytics_config.get("singleOutput", False):
+		combine_outputs(config, filtered)
+	else:
+		final_outputs(config, filtered)

From 65b39adc2f38822d93a0ef4e7199b8d2bc883118 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 26 Jul 2021 17:00:42 -0400
Subject: [PATCH 007/105] Add a no_rename param to sensitivity config

* Pass the entire plugin config block to the plugin now.
* Need to work on the way this works in the future

commit 1209c706fcf942f880b617a1bb7a506347865a9b
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Mon Jul 26 16:59:25 2021 -0400

    Fix issue with no_rename being embedded in the config

    * Will need to work on better ways to pass config

commit 2a1454b96b4f00f6e6b1b88326c12e573d072a0b
Author: Christopher Villalobos <cvillalobos@ufl.edu>
Date:   Mon Jul 26 16:10:19 2021 -0400

    Modify how plugin configuration is read

    * Pass the entire plugin config block for each plugin to the initializer.
    * Let the plugin handle any filtering or modifications and save what is required
      by the plugin during registration.
---
 .gitignore                                     |  1 +
 pythia/plugin.py                               |  2 +-
 pythia/plugins/sensitivity_plugin/__init__.py  | 18 ++++++++++++------
 .../weather_forecast_simple/__init__.py        | 15 ++++++++-------
 4 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/.gitignore b/.gitignore
index f671c910..4748a48d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,4 @@ docs/source/_build
 docs/build
 .venv
 dist
+*~
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 16fa0274..a49498d9 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -81,7 +81,7 @@ def load_plugins(config, plugins={}, module_prefix="pythia.plugins"):
         # TODO: Check to see if the plugin conforms to the correct signature (optional)
 
         # Call plugin initialization
-        _imported = _loaded.initialize(plugin.get("params", {}), _imported, config)
+        _imported = _loaded.initialize(plugin, _imported, config)
     return _imported
 
 
diff --git a/pythia/plugins/sensitivity_plugin/__init__.py b/pythia/plugins/sensitivity_plugin/__init__.py
index 43b4e979..91aa9268 100644
--- a/pythia/plugins/sensitivity_plugin/__init__.py
+++ b/pythia/plugins/sensitivity_plugin/__init__.py
@@ -20,6 +20,7 @@
             "values" : ["M0.25", "M1.0", "M1.25"]
         }
     },
+    "no_rename": true, (optional, defaults to false)
     "order": 1
 ]
 """
@@ -37,11 +38,13 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[Sensitivity Plugin] Initializing plugin")
-    plugins = register_plugin_function(PluginHook.post_config, generate_sensitivity_runs, config,
+    cfg = config["params"]
+    cfg["no_rename"] = config.get("no_rename", False) 
+    plugins = register_plugin_function(PluginHook.post_config, generate_sensitivity_runs, cfg,
                                        plugins)
-    plugins = register_plugin_function(PluginHook.post_build_context, post_build_context_apply_factors, config, plugins)
+    plugins = register_plugin_function(PluginHook.post_build_context, post_build_context_apply_factors, cfg, plugins)
     plugins = register_plugin_function(PluginHook.post_build_context,
-                                       post_build_context_apply_static_factors, config, plugins)
+                                       post_build_context_apply_static_factors, cfg, plugins)
     return plugins
 
 
@@ -71,6 +74,8 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
             "_sens_post_context_static": {}}
     # First we organize them
     for k in plugin_config.keys():
+        if k == "no_rename":
+            continue
         hook = plugin_config[k].get("hook", "post_config").casefold()
         static = plugin_config[k].get("static", False)
         context_string = None
@@ -94,9 +99,10 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         current_name = run["name"]
         current_workDir = run["workDir"]
         for factor in factors:
-            f = generate_factorial_name(factor)
-            run["name"] = current_name + "__" + f
-            run["workDir"] = current_workDir + "__" + f
+            if not plugin_config.get("no_rename", False):
+            	f = generate_factorial_name(factor)
+            	run["name"] = current_name + "__" + f
+            	run["workDir"] = current_workDir + "__" + f
             out_runs.append({**run, **{"_sens": factor}})
     out_runs = [apply_factors("_sens_pre_context", run) for run in out_runs]
     out_runs = [apply_factors("_sens_pre_context_static", run) for run in out_runs]
diff --git a/pythia/plugins/weather_forecast_simple/__init__.py b/pythia/plugins/weather_forecast_simple/__init__.py
index 5dc6f03a..a60091ad 100644
--- a/pythia/plugins/weather_forecast_simple/__init__.py
+++ b/pythia/plugins/weather_forecast_simple/__init__.py
@@ -18,15 +18,16 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[SIMPLE WEATHER FORECAST PLUGIN] Initializing plugin")
-    config["weatherDir"] = full_config["weatherDir"]
-    config["start_date"] = pythia.util.to_julian_date(
-        pythia.util.from_iso_date(config["start_date"])
+    cfg = config["params"]
+    cfg["weatherDir"] = full_config["weatherDir"]
+    cfg["start_date"] = pythia.util.to_julian_date(
+        pythia.util.from_iso_date(cfg["start_date"])
     )
-    config["end_date"] = pythia.util.to_julian_date(pythia.util.from_iso_date(config["end_date"]))
-    config["start_on"] = config["start_date"][2:5]
-    config["end_on"] = config["end_date"][2:5]
+    cfg["end_date"] = pythia.util.to_julian_date(pythia.util.from_iso_date(cfg["end_date"]))
+    cfg["start_on"] = cfg["start_date"][2:5]
+    cfg["end_on"] = cfg["end_date"][2:5]
     return register_plugin_function(
-        PluginHook.post_build_context, construct_pixel_forecast, config, plugins
+        PluginHook.post_build_context, construct_pixel_forecast, cfg, plugins
     )
 
 

From c32178075f3bb21b8369406dc5dc86dad25e3115 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 18 Oct 2021 12:20:34 -0400
Subject: [PATCH 008/105] Add project.org

* Simple project management for things that need to be done.
---
 project.org | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 project.org

diff --git a/project.org b/project.org
new file mode 100644
index 00000000..b897780a
--- /dev/null
+++ b/project.org
@@ -0,0 +1,11 @@
+#+TITLE: Pythia Project Notes
+
+* Task List
+** TODO Implement ~run_mode~ in the ~dssat~ configuration.
+- Default is ~A~
+- Used to support ~forecast mode~
+** TODO Add ~FODATE~ to template
+- Default is ~-99~
+** TODO Add ~append_column~ in the ~analytics_setup~ configuration
+- Will add a column ~x~ to the end of each line of output.
+** TODO Validate ~vector::~ function works to feed any fields.

From cccb3c4ffc54c0170c433471d738dce9bd183463 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 18 Oct 2021 12:21:25 -0400
Subject: [PATCH 009/105] Update project dependencies

---
 poetry.lock | 305 +++++++++++++++++++++++++++++-----------------------
 1 file changed, 172 insertions(+), 133 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a5b84ed9..0dfc4e33 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -9,14 +9,6 @@ python-versions = "*"
 [package.extras]
 test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
 
-[[package]]
-name = "appdirs"
-version = "1.4.4"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "atomicwrites"
 version = "1.4.0"
@@ -41,31 +33,35 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>
 
 [[package]]
 name = "black"
-version = "21.5b2"
+version = "21.9b0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
 python-versions = ">=3.6.2"
 
 [package.dependencies]
-appdirs = "*"
 click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.8.1,<1"
+pathspec = ">=0.9.0,<1"
+platformdirs = ">=2"
 regex = ">=2020.1.8"
-toml = ">=0.10.1"
+tomli = ">=0.2.6,<2.0.0"
 typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
-typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+typing-extensions = [
+    {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
+    {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
+]
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
 d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 python2 = ["typed-ast (>=1.4.2)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2021.5.30"
+version = "2021.10.8"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
@@ -73,7 +69,7 @@ python-versions = "*"
 
 [[package]]
 name = "click"
-version = "8.0.1"
+version = "8.0.3"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
@@ -158,7 +154,7 @@ pyflakes = ">=2.3.0,<2.4.0"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.4.0"
+version = "4.8.1"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -170,7 +166,8 @@ zipp = ">=0.5"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+perf = ["ipython"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "jinja2"
@@ -204,7 +201,7 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.8.0"
+version = "8.10.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
@@ -235,7 +232,7 @@ python-versions = "*"
 
 [[package]]
 name = "numpy"
-version = "1.20.3"
+version = "1.21.1"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -243,22 +240,34 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "packaging"
-version = "20.9"
+version = "21.0"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.6"
 
 [package.dependencies]
 pyparsing = ">=2.0.2"
 
 [[package]]
 name = "pathspec"
-version = "0.8.1"
+version = "0.9.0"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[[package]]
+name = "platformdirs"
+version = "2.4.0"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
+test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
 
 [[package]]
 name = "pluggy"
@@ -331,7 +340,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 
 [[package]]
 name = "rasterio"
-version = "1.2.4"
+version = "1.2.10"
 description = "Fast and direct raster I/O for use with Numpy and SciPy"
 category = "main"
 optional = false
@@ -348,7 +357,7 @@ numpy = "*"
 snuggs = ">=1.4.1"
 
 [package.extras]
-all = ["sphinx-rtd-theme", "boto3 (>=1.2.4)", "matplotlib", "pytest (>=2.8.2)", "numpydoc", "ghp-import", "ipython (>=2.0)", "hypothesis", "packaging", "sphinx", "pytest-cov (>=2.2.0)", "shapely"]
+all = ["numpydoc", "hypothesis", "matplotlib", "pytest-cov (>=2.2.0)", "sphinx", "ipython (>=2.0)", "boto3 (>=1.2.4)", "shapely", "pytest (>=2.8.2)", "packaging", "sphinx-rtd-theme", "ghp-import"]
 docs = ["ghp-import", "numpydoc", "sphinx", "sphinx-rtd-theme"]
 ipython = ["ipython (>=2.0)"]
 plot = ["matplotlib"]
@@ -357,7 +366,7 @@ test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "p
 
 [[package]]
 name = "regex"
-version = "2021.4.4"
+version = "2021.10.8"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
@@ -408,12 +417,12 @@ pyparsing = ">=2.1.6"
 test = ["pytest", "hypothesis"]
 
 [[package]]
-name = "toml"
-version = "0.10.2"
-description = "Python Library for Tom's Obvious, Minimal Language"
+name = "tomli"
+version = "1.2.1"
+description = "A lil' TOML parser"
 category = "dev"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "typed-ast"
@@ -425,7 +434,7 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.10.0.0"
+version = "3.10.0.2"
 description = "Backported and Experimental Type Hints for Python 3.5+"
 category = "main"
 optional = false
@@ -441,7 +450,7 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.4.1"
+version = "3.6.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
@@ -449,7 +458,7 @@ python-versions = ">=3.6"
 
 [package.extras]
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-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
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@@ -474,16 +479,16 @@ attrs = [
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-    {file = "zipp-3.4.1-py3-none-any.whl", hash = "sha256:51cb66cc54621609dd593d1787f286ee42a5c0adbb4b29abea5a63edc3e03098"},
-    {file = "zipp-3.4.1.tar.gz", hash = "sha256:3607921face881ba3e026887d8150cca609d517579abe052ac81fc5aeffdbd76"},
+    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
+    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
 ]

From 6424a950510447458bafc463abad76e6a2cc1b34 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 20 Oct 2021 11:18:56 -0400
Subject: [PATCH 010/105] Add DSSAT forecast mode support

* Implement FODATE and 4-digit year formatter
* Add default parameter to template formatting (default default is -99)
* Add support for 4-digit Julian format
* Implement run_mode configuration parameter
  - Specify the `run_mode` as a string which matches the DSSAT run modes.
  - Defaults the `run_mode` to `A`
---
 project.org        |  6 ++---
 pythia/dssat.py    |  7 ++++--
 pythia/template.py | 60 +++++++++++++++++++++++++++++-----------------
 pythia/util.py     |  7 ++++++
 4 files changed, 53 insertions(+), 27 deletions(-)

diff --git a/project.org b/project.org
index b897780a..4b2a6e02 100644
--- a/project.org
+++ b/project.org
@@ -1,11 +1,11 @@
 #+TITLE: Pythia Project Notes
 
 * Task List
-** TODO Implement ~run_mode~ in the ~dssat~ configuration.
+** DONE Implement ~run_mode~ in the ~dssat~ configuration.
 - Default is ~A~
 - Used to support ~forecast mode~
-** TODO Add ~FODATE~ to template
+** DONE Add ~FODATE~ to template
 - Default is ~-99~
 ** TODO Add ~append_column~ in the ~analytics_setup~ configuration
 - Will add a column ~x~ to the end of each line of output.
-** TODO Validate ~vector::~ function works to feed any fields.
+** DONE Validate ~vector::~ function works to feed any fields.
diff --git a/pythia/dssat.py b/pythia/dssat.py
index 222c1394..4752011c 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -7,8 +7,11 @@
 
 def _run_dssat(details, config):
     logging.debug("Current WD: {}".format(os.getcwd()))
-    command_string = "cd {} && {} A {}".format(
-        details["dir"], config["dssat"]["executable"], details["file"]
+    run_mode = "A"
+    if "run_mode" in config["dssat"]:
+        run_mode = config["dssat"]["run_mode"].upper()
+    command_string = "cd {} && {} {} {}".format(
+        details["dir"], config["dssat"]["executable"], run_mode, details["file"]
     )
     # print(".", end="", flush=True)
     dssat = subprocess.Popen(
diff --git a/pythia/template.py b/pythia/template.py
index 36f53dd9..54ce7f93 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -25,43 +25,59 @@
     "fhdur": {"length": 5},
     "irrig": {"length": 5},
     "erain": {"raw": "M{:>4}"},
-    "ph2ol": {"length": 5}
+    "ph2ol": {"length": 5},
+    "fodate": {"length": 7},
 }
 
-_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate"]
+_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate"]
+_t_date_fields_4 = ["fodate"]
 
 
 def init_engine(template_dir):
-    return Environment(loader=FileSystemLoader(template_dir), trim_blocks=True, lstrip_blocks=True)
+    return Environment(
+        loader=FileSystemLoader(template_dir), trim_blocks=True, lstrip_blocks=True
+    )
 
+def wrap_format(k, v):
+    fmt = ""
+    if k in _t_formats:
+        if "raw" in _t_formats[k]:
+            fmt = _t_formats[k]["raw"]
+        elif "fmt" in _t_formats[k]:
+            fmt = "{" + _t_formats[k]["fmt"] + "}"
+        else:
+            fmt_align = _t_formats[k].get("align", ":>")
+            fmt_pad = _t_formats[k].get("pad_with", "")
+            if isinstance(v, float):
+                fmt_len = "{}.1f".format(_t_formats[k]["length"])
+            elif isinstance(v, int):
+                fmt_len = "{}d".format(_t_formats[k]["length"])
+            else:
+                if "length" in _t_formats[k]:
+                    fmt_len = "{}".format(_t_formats[k]["length"])
+                else:
+                    fmt_len = ""
+            fmt = "{" + fmt_align + fmt_pad + fmt_len + "}"
+    else:
+        fmt = "{}"
+    return fmt.format(v)
 
 def auto_format_dict(d):
     if isinstance(d, str):
         return d
     clean = {}
+    for k,v in _t_formats:
+        if "default" in v:
+            clean[k] = wrap_format(k, v["default"])
+        else:
+            clean[k] = wrap_format(k,-99)
     for k, v in d.items():
         if k in _t_date_fields and "::" not in v:
             clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
+        elif k in _t_date_fields_4 and "::" not in v:
+            clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
         elif k in _t_formats:
-            fmt = ""
-            if "raw" in _t_formats[k]:
-                fmt = _t_formats[k]["raw"]
-            elif "fmt" in _t_formats[k]:
-                fmt = "{" + _t_formats[k]["fmt"] + "}"
-            else:
-                fmt_align = _t_formats[k].get("align", ":>")
-                fmt_pad = _t_formats[k].get("pad_with", "")
-                if isinstance(v, float):
-                    fmt_len = "{}.1f".format(_t_formats[k]["length"])
-                elif isinstance(v, int):
-                    fmt_len = "{}d".format(_t_formats[k]["length"])
-                else:
-                    if "length" in _t_formats[k]:
-                        fmt_len = "{}".format(_t_formats[k]["length"])
-                    else:
-                        fmt_len = ""
-                fmt = "{" + fmt_align + fmt_pad + fmt_len + "}"
-            clean[k] = fmt.format(v)
+            clean[k] = wrap_format(k, v)
         elif isinstance(v, dict):
             clean[k] = auto_format_dict(v)
         elif isinstance(v, list) and not isinstance(v, str):
diff --git a/pythia/util.py b/pythia/util.py
index 900cf8c1..ff445e02 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -11,6 +11,13 @@ def to_julian_date(d):
         logging.error("Unable to convert %s to a julian date", d)
         return None
 
+def to_julian_date_4(d):
+    try:
+        return d.strftime("%Y%j")
+    except ValueError:
+        logging.error("Unable to convert %s to a julian date", d)
+        return None
+
 
 def to_iso_date(d):
     try:

From 9eccbec1f14f158f0b617315bac9f4bdf347ae5e Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 20 Oct 2021 15:41:41 -0400
Subject: [PATCH 011/105] Fix extraction problem

---
 pythia/template.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pythia/template.py b/pythia/template.py
index 54ce7f93..254f27d5 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -26,7 +26,7 @@
     "irrig": {"length": 5},
     "erain": {"raw": "M{:>4}"},
     "ph2ol": {"length": 5},
-    "fodate": {"length": 7},
+    "fodate": {"length": 7}
 }
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate"]
@@ -66,7 +66,8 @@ def auto_format_dict(d):
     if isinstance(d, str):
         return d
     clean = {}
-    for k,v in _t_formats:
+    for k in _t_formats:
+        v = _t_formats[k]
         if "default" in v:
             clean[k] = wrap_format(k, v["default"])
         else:

From 5403186967a1453a7058dc273f3e434a32b4d230 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 19 Nov 2021 15:17:35 -0500
Subject: [PATCH 012/105] Add batch_mode support and population hack

* Add batch_mode support
  * Allow for current batch run modes to be marked as batch
  * Check for a default file (DssBatch.*) to mark as the batch file
  * Allow user to specify custom file name for batch as `batch_file`
  * Allow user to specify custom file name for regular as `filex`
* Add a population hack
  * Just hardcode the population for the moment.
  * The goal is to extend the output process to enable this to be
    easier. Unfortunately, we are under a time pressure and cannot
    implement this properly yet.
* Update dependencies
* Format code
* Update project goals
---
 .python-version                               |   1 -
 bin/pythia                                    |   0
 docs/json.rst                                 |  18 +-
 poetry.lock                                   | 717 +++++++++++++++---
 project.org                                   |  30 +-
 pyproject.toml                                |   6 +
 pythia/analytic_functions.py                  |  22 +-
 pythia/analytics.py                           | 413 +++++-----
 pythia/cache_manager.py                       |   2 +-
 pythia/cli.py                                 |  37 +-
 pythia/config.py                              |  30 +-
 pythia/dssat.py                               |  28 +-
 pythia/functions.py                           |   2 +-
 pythia/io.py                                  |  22 +-
 pythia/peerless.py                            |   8 +-
 pythia/plugin.py                              |  26 +-
 pythia/plugins/sensitivity_plugin/__init__.py |  83 +-
 pythia/plugins/test_plugin/__init__.py        |   4 +-
 .../weather_forecast_simple/__init__.py       |  12 +-
 pythia/soil_handler.py                        |   3 +-
 pythia/template.py                            |   6 +-
 pythia/tests/plugin_test.py                   |  49 +-
 pythia/util.py                                |   1 +
 sample.json                                   |   6 +-
 tox.ini                                       |   4 +-
 25 files changed, 1146 insertions(+), 384 deletions(-)
 delete mode 100644 .python-version
 mode change 100755 => 100644 bin/pythia

diff --git a/.python-version b/.python-version
deleted file mode 100644
index f06fb9e9..00000000
--- a/.python-version
+++ /dev/null
@@ -1 +0,0 @@
-3.7.10
diff --git a/bin/pythia b/bin/pythia
old mode 100755
new mode 100644
diff --git a/docs/json.rst b/docs/json.rst
index 34ffc4af..a50533fa 100644
--- a/docs/json.rst
+++ b/docs/json.rst
@@ -8,13 +8,13 @@ General
 This is the root of the JSON object. All values in this section are considered to be globally available.
 
 name
-   :Type: no whitespace string 
+   :Type: no whitespace string
    :Required: true
    :Description: The name of this configuration.
-   
+
 
 workDir
-   :Type: directory string 
+   :Type: directory string
    :Required: true
    :Description: The root output directory of this run. All DSSAT files will generated under this directory.
 
@@ -32,13 +32,13 @@ cores
    :Type: positive integer
    :Default value: number of logical CPUs available.
    :Description: The number of cores to be used by pythia. Cores are used to execute the model.
-   
+
 
 threads
    :Type: positive integer
    :Default value: number of cores available / 2
-   :Description: The number of threads to be used by pythia. This is used for I/O work. 
-   
+   :Description: The number of threads to be used by pythia. This is used for I/O work.
+
 sample
    :Type: positive integer
    :Description: Used to subset the data. Applies the configuration the first *x* number of valid simulations. This may be different between runs.
@@ -72,8 +72,6 @@ sites
 
       {"sites": [[29.6340239,-82.3631502]]}
 
-               
-
 startYear
    :Type: 4-digit year
    :Required: true
@@ -107,7 +105,7 @@ DSSAT Structures
 ~~~~~~~~~~~~~~~~
 
 ic_layers
-   :Type: Array of initial condition layer objects 
+   :Type: Array of initial condition layer objects
    :Shape: ``[{"icbl": <value>, "sh2o": <value>, "shn4": <value>, "sno3": <value>},...]``
    :Helper function: ``generate_ic_layers``
 
@@ -121,4 +119,4 @@ Arbitrary Variables
 
 
 Useful Functions
-~~~~~~~~~~~~~~~~
\ No newline at end of file
+~~~~~~~~~~~~~~~~
diff --git a/poetry.lock b/poetry.lock
index 0dfc4e33..9ce53c74 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -9,6 +9,20 @@ python-versions = "*"
 [package.extras]
 test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
 
+[[package]]
+name = "astroid"
+version = "2.6.6"
+description = "An abstract syntax tree for Python with inference support."
+category = "dev"
+optional = false
+python-versions = "~=3.6"
+
+[package.dependencies]
+lazy-object-proxy = ">=1.4.0"
+typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
+typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+wrapt = ">=1.11,<1.13"
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.0"
@@ -31,9 +45,21 @@ docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
 tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
 tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
 
+[[package]]
+name = "autopep8"
+version = "1.5.7"
+description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pycodestyle = ">=2.7.0"
+toml = "*"
+
 [[package]]
 name = "black"
-version = "21.9b0"
+version = "21.10b0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
@@ -54,9 +80,9 @@ typing-extensions = [
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"]
+d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
-python2 = ["typed-ast (>=1.4.2)"]
+python2 = ["typed-ast (>=1.4.3)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
@@ -152,6 +178,17 @@ mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
 
+[[package]]
+name = "greenlet"
+version = "1.1.2"
+description = "Lightweight in-process concurrent programming"
+category = "dev"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+
+[package.extras]
+docs = ["sphinx"]
+
 [[package]]
 name = "importlib-metadata"
 version = "4.8.1"
@@ -169,6 +206,35 @@ docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
 testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
+[[package]]
+name = "isort"
+version = "5.10.0"
+description = "A Python utility / library to sort Python imports."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1,<4.0"
+
+[package.extras]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
+requirements_deprecated_finder = ["pipreqs", "pip-api"]
+colors = ["colorama (>=0.4.3,<0.5.0)"]
+plugins = ["setuptools"]
+
+[[package]]
+name = "jedi"
+version = "0.18.0"
+description = "An autocompletion tool for Python that can be used for text editors."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+parso = ">=0.8.0,<0.9.0"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
+
 [[package]]
 name = "jinja2"
 version = "2.11.3"
@@ -183,6 +249,14 @@ MarkupSafe = ">=0.23"
 [package.extras]
 i18n = ["Babel (>=0.8)"]
 
+[[package]]
+name = "lazy-object-proxy"
+version = "1.6.0"
+description = "A fast and thorough lazy object proxy."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+
 [[package]]
 name = "markupsafe"
 version = "2.0.1"
@@ -207,6 +281,14 @@ category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "msgpack"
+version = "1.0.2"
+description = "MessagePack (de)serializer."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "munch"
 version = "2.5.0"
@@ -230,6 +312,17 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "neovim"
+version = "0.3.1"
+description = "Transition packgage for pynvim"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pynvim = ">=0.3.1"
+
 [[package]]
 name = "numpy"
 version = "1.21.1"
@@ -240,14 +333,26 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "packaging"
-version = "21.0"
+version = "21.2"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-pyparsing = ">=2.0.2"
+pyparsing = ">=2.0.2,<3"
+
+[[package]]
+name = "parso"
+version = "0.8.2"
+description = "A Python Parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "pathspec"
@@ -285,11 +390,11 @@ dev = ["pre-commit", "tox"]
 
 [[package]]
 name = "py"
-version = "1.10.0"
+version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "pycodestyle"
@@ -299,6 +404,20 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pydocstyle"
+version = "6.1.1"
+description = "Python docstring style checker"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+snowballstemmer = "*"
+
+[package.extras]
+toml = ["toml"]
+
 [[package]]
 name = "pyflakes"
 version = "2.3.1"
@@ -307,6 +426,78 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pylint"
+version = "2.9.6"
+description = "python code static checker"
+category = "dev"
+optional = false
+python-versions = "~=3.6"
+
+[package.dependencies]
+astroid = ">=2.6.5,<2.7"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+isort = ">=4.2.5,<6"
+mccabe = ">=0.6,<0.7"
+toml = ">=0.7.1"
+
+[[package]]
+name = "pyls-flake8"
+version = "0.4.0"
+description = "A Flake8 plugin for the Python Language Server"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+flake8 = ">=3.6.0"
+python-lsp-server = "*"
+
+[[package]]
+name = "pyls-isort"
+version = "0.2.2"
+description = "Isort plugin for python-lsp-server"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+isort = "*"
+python-lsp-server = "*"
+
+[[package]]
+name = "pylsp-rope"
+version = "0.1.7"
+description = "Extended refactoring capabilities for Python LSP Server using Rope."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+python-lsp-server = "*"
+rope = ">=0.21.0"
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+
+[package.extras]
+dev = ["build", "pytest", "twine"]
+test = ["pytest"]
+
+[[package]]
+name = "pynvim"
+version = "0.4.3"
+description = "Python client to neovim"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+greenlet = "*"
+msgpack = ">=0.5.0"
+
+[package.extras]
+pyuv = ["pyuv (>=1.0.0)"]
+test = ["pytest (>=3.4.0)"]
+
 [[package]]
 name = "pyparsing"
 version = "2.4.7"
@@ -338,6 +529,72 @@ wcwidth = "*"
 checkqa-mypy = ["mypy (==v0.761)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
+[[package]]
+name = "python-lsp-black"
+version = "1.0.0"
+description = "Black plugin for the Python LSP Server"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+black = ">=19.3b0"
+python-lsp-server = "*"
+toml = "*"
+
+[package.extras]
+dev = ["isort (>=5.0)", "flake8", "pytest", "mypy"]
+
+[[package]]
+name = "python-lsp-jsonrpc"
+version = "1.0.0"
+description = "JSON RPC 2.0 server library"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+ujson = ">=3.0.0"
+
+[package.extras]
+test = ["pylint", "pycodestyle", "pyflakes", "pytest", "pytest-cov", "coverage"]
+
+[[package]]
+name = "python-lsp-server"
+version = "1.2.4"
+description = "Python Language Server for the Language Server Protocol"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
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+jedi = ">=0.17.2,<0.19.0"
+mccabe = {version = ">=0.6.0,<0.7.0", optional = true, markers = "extra == \"all\""}
+pluggy = "*"
+pycodestyle = {version = ">=2.7.0", optional = true, markers = "extra == \"all\""}
+pydocstyle = {version = ">=2.0.0", optional = true, markers = "extra == \"all\""}
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+pylint = {version = ">=2.5.0,<2.10.0", optional = true, markers = "extra == \"all\""}
+python-lsp-jsonrpc = ">=1.0.0"
+rope = {version = ">=0.10.5", optional = true, markers = "extra == \"all\""}
+ujson = ">=3.0.0"
+yapf = {version = "*", optional = true, markers = "extra == \"all\""}
+
+[package.extras]
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+autopep8 = ["autopep8"]
+flake8 = ["flake8 (>=3.8.0,<4.0.0)"]
+mccabe = ["mccabe (>=0.6.0,<0.7.0)"]
+pycodestyle = ["pycodestyle (>=2.7.0)"]
+pydocstyle = ["pydocstyle (>=2.0.0)"]
+pyflakes = ["pyflakes (>=2.3.0,<2.4.0)"]
+pylint = ["pylint (>=2.5.0,<2.10.0)"]
+rope = ["rope (>0.10.5)"]
+test = ["pylint (>=2.5.0,<2.10.0)", "pytest", "pytest-cov", "coverage", "numpy", "pandas", "matplotlib", "pyqt5", "flaky"]
+yapf = ["yapf"]
+
 [[package]]
 name = "rasterio"
 version = "1.2.10"
@@ -366,12 +623,23 @@ test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "p
 
 [[package]]
 name = "regex"
-version = "2021.10.8"
+version = "2021.11.2"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "rope"
+version = "0.21.0"
+description = "a python refactoring library..."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+dev = ["pytest", "pytest-timeout"]
+
 [[package]]
 name = "rtree"
 version = "0.8.3"
@@ -382,14 +650,14 @@ python-versions = "*"
 
 [[package]]
 name = "shapely"
-version = "1.7.1"
+version = "1.8.0"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [package.extras]
-all = ["numpy", "pytest", "pytest-cov"]
+all = ["pytest", "pytest-cov", "numpy"]
 test = ["pytest", "pytest-cov"]
 vectorized = ["numpy"]
 
@@ -401,6 +669,14 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "snowballstemmer"
+version = "2.1.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "snuggs"
 version = "1.4.7"
@@ -416,9 +692,17 @@ pyparsing = ">=2.1.6"
 [package.extras]
 test = ["pytest", "hypothesis"]
 
+[[package]]
+name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+
 [[package]]
 name = "tomli"
-version = "1.2.1"
+version = "1.2.2"
 description = "A lil' TOML parser"
 category = "dev"
 optional = false
@@ -440,6 +724,14 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "ujson"
+version = "4.2.0"
+description = "Ultra fast JSON encoder and decoder for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "wcwidth"
 version = "0.2.5"
@@ -448,6 +740,22 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "wrapt"
+version = "1.12.1"
+description = "Module for decorators, wrappers and monkey patching."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "yapf"
+version = "0.31.0"
+description = "A formatter for Python code."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "zipp"
 version = "3.6.0"
@@ -463,13 +771,17 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytes
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7"
-content-hash = "765c40c0da71552294c3d49408c9cddce3e514a157c5422f9eb1d00f1e371b28"
+content-hash = "f55eee3ae0ca41608fea98081bf32dbcf104db9105be41571dd3cd57dd449ef7"
 
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+    {file = "black-21.10b0-py3-none-any.whl", hash = "sha256:6eb7448da9143ee65b856a5f3676b7dda98ad9abe0f87fce8c59291f15e82a5b"},
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+    {file = "ujson-4.2.0-cp37-cp37m-win_amd64.whl", hash = "sha256:50f413177206373b3568dff28c091b2d8c9145e5e54b0a524d3823293d7a29b8"},
+    {file = "ujson-4.2.0-cp38-cp38-macosx_10_14_x86_64.whl", hash = "sha256:944dfdfae0cb4e4274a23e5070be913f7ff8f05666d8d143f2356cf873f9a77a"},
+    {file = "ujson-4.2.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:50ddff58727cc4f90ade4c818884c4f0fbeeb1f78f764ab2b2bc89cf1f4db126"},
+    {file = "ujson-4.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:78f8da27231b20d589319f743bd65011862691c102922be85c9f27e40656a0f7"},
+    {file = "ujson-4.2.0-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:99322e08e53580867c9909637747343354b7028a8208dc5df3d09233c8f52c30"},
+    {file = "ujson-4.2.0-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:5f863b12d27867b733d380a9878fc8c3ad11d3aea8a3650c33e7a8c2a888e1eb"},
+    {file = "ujson-4.2.0-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:c53653a12f6ce67b12e7806c190cce1db09c75de31212a5a9adbdbd7a2aba116"},
+    {file = "ujson-4.2.0-cp38-cp38-win32.whl", hash = "sha256:c9723a5e2743ded9bc6106cb04f86244dd779ad847d8ac189cfe808ab16946c1"},
+    {file = "ujson-4.2.0-cp38-cp38-win_amd64.whl", hash = "sha256:fae1e251d9f9362ebc4adbbb252d0f4a023f66f180390624826fcb1812b808e9"},
+    {file = "ujson-4.2.0-cp39-cp39-macosx_10_14_x86_64.whl", hash = "sha256:ab70a29914fc202f7c8f6353bb0622b91f878e2892e57a4c7293b341d5a85133"},
+    {file = "ujson-4.2.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cf272e6302c62a42ed0125efcc1d891dd909bcfb3c6aa075d89de209b2b8e930"},
+    {file = "ujson-4.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6182898d7031d083017f9be47c6d57f9c2155d9f4391b77ed6c020cab8e5a471"},
+    {file = "ujson-4.2.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:5a885675252e041e19cb92ff76419251fdd1ab4c2ca9766cb3ecfa6ae07884d2"},
+    {file = "ujson-4.2.0-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:535f1e5b336f7a0573da59bd9352e9cc6a93185bf4b1d96fb3379e07b4fc619a"},
+    {file = "ujson-4.2.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:26e299caa9bfc2e532e16de38de2af48cde48258922cda5efc0dd447d42692fc"},
+    {file = "ujson-4.2.0-cp39-cp39-win32.whl", hash = "sha256:fa68b25c987b73fb1c83ece34e52856c2c6da3031384f72638696c56fa8baca9"},
+    {file = "ujson-4.2.0-cp39-cp39-win_amd64.whl", hash = "sha256:c7b2643b063f33e5e0d539cf2811793a7df9da525e63483f70c9262a343bd59d"},
+    {file = "ujson-4.2.0-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0d61ae7a505105a16220a4282dbd552bef76968203e5e4f5edfdbb03d3159e3a"},
+    {file = "ujson-4.2.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bff484c162bd77877bc9ae6333b0a684493037ce3c5d8b664e8339becf9ad139"},
+    {file = "ujson-4.2.0-pp37-pypy37_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:74961587e9c1682d3e04fe29e02b67ec9c88cb0c3406ad94cc617d04c6fa6db2"},
+    {file = "ujson-4.2.0.tar.gz", hash = "sha256:fffe509f556861c7343c6cba57ed05fe7bcf4b48a934a5b946ccb45428cf8883"},
+]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
     {file = "wcwidth-0.2.5.tar.gz", hash = "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"},
 ]
+wrapt = [
+    {file = "wrapt-1.12.1.tar.gz", hash = "sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"},
+]
+yapf = [
+    {file = "yapf-0.31.0-py2.py3-none-any.whl", hash = "sha256:e3a234ba8455fe201eaa649cdac872d590089a18b661e39bbac7020978dd9c2e"},
+    {file = "yapf-0.31.0.tar.gz", hash = "sha256:408fb9a2b254c302f49db83c59f9aa0b4b0fd0ec25be3a5c51181327922ff63d"},
+]
 zipp = [
     {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
     {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
diff --git a/project.org b/project.org
index 4b2a6e02..af6d90b5 100644
--- a/project.org
+++ b/project.org
@@ -6,6 +6,34 @@
 - Used to support ~forecast mode~
 ** DONE Add ~FODATE~ to template
 - Default is ~-99~
-** TODO Add ~append_column~ in the ~analytics_setup~ configuration
+** PENDING Add ~append_column~ in the ~analytics_setup~ configuration
 - Will add a column ~x~ to the end of each line of output.
+- "appendColumns": [{"HARVEST_AREA": "from_config::$harvestArea"}, {"VNAM": "subtract::out$cnam::out$gnam"}]
+- Have to make sure the from_config is specific to a run. This means the run needs to be persisted through to the ~calculate_outputs()~ function.
 ** DONE Validate ~vector::~ function works to feed any fields.
+** DONE Batch mode support
+- [X] Configuration option to specify batch file to use.
+- [X] Default the batch file to DSSBatch.v4x
+** TODO auto-include LAT/LNG if -99 in the DSSAT XFile
+** TODO Auto-generate DSSBatch.v4x when needed for batch mode.
+* Execution Notes
+** Batch file support
+In order to use batch file support modes (specified by ~CheckRunMode.f90~), you should use ~includes~ to copy the batch file to every run directory. This should be in your ~default_setup~ or ~runs~ blocks.
+*NOTE* Forecast mode (~"run_mode": "Y"~) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
+
+* Breaking Changes (v3.0)
+** Move analytics to output
+"output": [
+{
+"filename": "summary.csv",
+** Support for single output file
+"singleOutput": true,
+** Suppffort for adding columns
+"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
+** Support for filtering columns
+"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
+},
+"filename": "daily.csv",
+"singleOutput": true,
+"outputColumns": ["SOME", "VARIABLE"]
+]
diff --git a/pyproject.toml b/pyproject.toml
index a9df6fe1..dd8c4eda 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,12 @@ rtree = "^0.8"
 pytest = "^5.1"
 black = "^21.5b2"
 flake8 = "^3.9.2"
+neovim = "^0.3.1"
+python-lsp-server = {extras = ["all"], version = "^1.2.4"}
+pyls-isort = "^0.2.2"
+python-lsp-black = "^1.0.0"
+pylsp-rope = "^0.1.7"
+pyls-flake8 = "^0.4.0"
 
 [tool.poetry.scripts]
 pythia = "pythia.cli:main"
diff --git a/pythia/analytic_functions.py b/pythia/analytic_functions.py
index 44af1e90..7d55957f 100644
--- a/pythia/analytic_functions.py
+++ b/pythia/analytic_functions.py
@@ -1,12 +1,14 @@
-def generate_funs(config):
+def generate_funs(config, run):
     funcs = []
-    for key,funs in config.items():
+    for key, funs in config.items():
         fun = {}
         f, *args = funs.split("::")
-        if (f == "subtract"):
-            fun['fun'] = subtract
-        fun['key'] = key
-        fun['args'] = args
+        fun["key"] = key
+        fun["args"] = args
+        if f == "subtract":
+            fun["fun"] = subtract
+        if f == "from_config":
+            pass
         funcs.append(fun)
     return funcs
 
@@ -14,7 +16,7 @@ def generate_funs(config):
 def subtract(terms):
     a = _numberify_term(terms[0])
     b = _numberify_term(terms[1])
-    return a-b
+    return a - b
 
 
 def _numberify_term(term):
@@ -22,3 +24,9 @@ def _numberify_term(term):
         return float(term)
     else:
         return int(term)
+
+
+def from_config(terms):
+    lat = _numberify_term(terms[0])
+    lng = _numberify_term(terms[1])
+    return lat + lng
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 3ef4b53b..734ea898 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -2,221 +2,258 @@
 import logging
 import os
 import shutil
+from typing import Optional
 import rasterio
+from rasterio.io import DatasetReader
 import pythia.analytic_functions
 import pythia.io
 import pythia.util
+from contextlib import _GeneratorContextManager
 
 
 def get_run_basedir(config, run):
-	return os.path.join(config.get("workDir", "."), run.get("name", ""))
+    return os.path.join(config.get("workDir", "."), run.get("name", ""))
 
 
 def _generated_run_files(run_path, target_file):
-	for root, subdir, files in os.walk(run_path, topdown=False):
-		if target_file in files:
-			yield root
-	pass
+    for root, subdir, files in os.walk(run_path, topdown=False):
+        if target_file in files:
+            yield root
+    pass
 
 
 def extract_ll(path):
-	ll = path.split(os.path.sep)[-2:]
-	return tuple([pythia.util.translate_news_coords(coords) for coords in ll])
+    ll = path.split(os.path.sep)[-2:]
+    return tuple([pythia.util.translate_news_coords(coords) for coords in ll])
 
 
 # Always by default keep the per_pixel_per_management file, but create a place
 # for the single output or analytics, should we have a "final outputs"
 # directory.
 def final_outputs(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	out_files = []
-	out_dir = os.path.join(config.get("workDir", "."))
-	file_prefix = "{}_".format(analytics_config.get("per_pixel_prefix", "pp"))
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	for current_file in outputs:
-		 bn = os.path.basename(current_file)
-		 out_file = os.path.join(out_dir, bn[bn.find(file_prefix):])
-		 shutil.copyfile(current_file, out_file)
+    analytics_config = config.get("analytics_setup", {})
+    out_dir = os.path.join(config.get("workDir", "."))
+    file_prefix = "{}_".format(analytics_config.get("per_pixel_prefix", "pp"))
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    for current_file in outputs:
+        bn = os.path.basename(current_file)
+        out_file = os.path.join(out_dir, bn[bn.find(file_prefix) :])
+        shutil.copyfile(current_file, out_file)
+
 
 def filter_columns(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	columns = analytics_config.get("columns", [])
-	out_files = []
-	out_dir = os.path.join(config.get("workDir", "."), "scratch")
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	for current_file in outputs:
-		col_indexes = []
-		out_file = os.path.join(out_dir, "filtered_{}".format(os.path.basename(current_file)))
-		with open(current_file) as source, open(out_file, "w") as dest:
-			dssat_in = csv.reader(source)
-			dssat_out = csv.writer(dest)
-			try:
-				for line in dssat_in:
-					if dssat_in.line_num == 1:
-						for x, col in enumerate(line):
-							if col in columns:
-								col_indexes.append(x)
-					row = [line[idx] for idx in col_indexes]
-					dssat_out.writerow(row)
-			except csv.Error as e:
-				logging.error("CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e)
-		out_files.append(out_file)
-	return out_files
+    analytics_config = config.get("analytics_setup", {})
+    columns = analytics_config.get("columns", [])
+    out_files = []
+    out_dir = os.path.join(config.get("workDir", "."), "scratch")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    for current_file in outputs:
+        col_indexes = []
+        out_file = os.path.join(
+            out_dir, "filtered_{}".format(os.path.basename(current_file))
+        )
+        with open(current_file) as source, open(out_file, "w") as dest:
+            dssat_in = csv.reader(source)
+            dssat_out = csv.writer(dest)
+            try:
+                for line in dssat_in:
+                    if dssat_in.line_num == 1:
+                        for x, col in enumerate(line):
+                            if col in columns:
+                                col_indexes.append(x)
+                    row = [line[idx] for idx in col_indexes]
+                    dssat_out.writerow(row)
+            except csv.Error as e:
+                logging.error(
+                    "CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e
+                )
+        out_files.append(out_file)
+    return out_files
 
 
 def calculate_columns(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	calculations = analytics_config.get("calculatedColumns", [])
-	funs = pythia.analytic_functions.generate_funs(calculations)
-	arg_columns = []
-	for fun in funs:
-		for a in fun["args"]:
-			if a.startswith("$"):
-				if a.upper() not in arg_columns:
-					arg_columns.append(a[1::].upper())
-	out_files = []
-	out_dir = os.path.join(config.get("workDir", "."), "scratch")
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	for current_file in outputs:
-		col_indexes = []
-		out_file = os.path.join(out_dir, "calculated_{}".format(os.path.basename(current_file)))
-		with open(current_file) as source, open(out_file, "w") as dest:
-			dssat_in = csv.reader(source)
-			dssat_out = csv.writer(dest)
-			num_cols = 0
-			try:
-			  for line in dssat_in:
-				  if dssat_in.line_num != 1:
-					  if num_cols == 0:
-						  print("we have a problem")
-					  else:
-						  line = line[0:num_cols]
-				  if dssat_in.line_num == 1:
-					  num_cols = len(line)
-					  col_indexes = [line.index(x) for x in arg_columns]
-					  for fun in funs:
-						  line.append(fun["key"])
-					  dssat_out.writerow(line)
-				  else:
-					  for fun in funs:
-						  line.append(
-							  fun["fun"](
-								  [
-									  line[col_indexes[arg_columns.index(x[1::].upper())]]
-									  for x in fun["args"]
-								  ]
-							  )
-						  )
-					  dssat_out.writerow(line)
-			except csv.Error as e:
-				logging.error("CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e)
-			out_files.append(out_file)
-	return out_files
-
-
-def combine_outputs(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
-	out_dir = config.get("workDir", ".")
-	collected_first_line = False
-	for current_file in outputs:
-		if os.path.exists(current_file):
-			if collected_first_line:
-				mode = "a"
-			else:
-				mode = "w"
-			with open(current_file) as source, open(
-				os.path.join(out_dir, combined_file_name), mode
-			) as dest:
-				for i, line in enumerate(source):
-					if i == 0:
-						if not collected_first_line:
-							dest.write(line)
-							collected_first_line = True
-					else:
-						dest.write(line)
+    analytics_config = config.get("analytics_setup", {})
+    calculations = analytics_config.get("calculatedColumns", [])
+
+    out_files = []
+    out_dir = os.path.join(config.get("workDir", "."), "scratch")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    for current in outputs:
+        run, current_file = current
+        funs = pythia.analytic_functions.generate_funs(calculations, run)
+        arg_columns = []
+        for fun in funs:
+            for a in fun["args"]:
+                if a.upper() not in arg_columns:
+                    arg_columns.append(a[1::].upper())
+
+        col_indexes = []
+        out_file = os.path.join(
+            out_dir, "calculated_{}".format(os.path.basename(current_file))
+        )
+        with open(current_file) as source, open(out_file, "w") as dest:
+            dssat_in = csv.reader(source)
+            dssat_out = csv.writer(dest)
+            num_cols = 0
+            try:
+                for line in dssat_in:
+                    if dssat_in.line_num != 1:
+                        if num_cols == 0:
+                            print("we have a problem")
+                        else:
+                            line = line[0:num_cols]
+                    if dssat_in.line_num == 1:
+                        num_cols = len(line)
+                        col_indexes = [line.index(x) for x in arg_columns]
+                        for fun in funs:
+                            line.append(fun["key"])
+                        dssat_out.writerow(line)
+                    else:
+                        for fun in funs:
+                            line.append(
+                                fun["fun"](
+                                    [
+                                        line[
+                                            col_indexes[
+                                                arg_columns.index(x[1::].upper())
+                                            ]
+                                        ]
+                                        for x in fun["args"]
+                                    ]
+                                )
+                            )
+                        dssat_out.writerow(line)
+            except csv.Error as e:
+                logging.error(
+                    "CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e
+                )
+            out_files.append(out_file)
+    return out_files
+
+
+def combine_outputs(outputs, config, run):
+    analytics_config = config.get("analytics_setup", {})
+    combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
+    out_dir = config.get("workDir", ".")
+    collected_first_line = False
+    for current_file in outputs:
+        if os.path.exists(current_file):
+            if collected_first_line:
+                mode = "a"
+            else:
+                mode = "w"
+            with open(current_file) as source, open(
+                os.path.join(out_dir, combined_file_name), mode
+            ) as dest:
+                for i, line in enumerate(source):
+                    if i == 0:
+                        if not collected_first_line:
+                            dest.write(line)
+                            collected_first_line = True
+                    else:
+                        dest.write(line)
 
 
 def collate_outputs(config, run):
-	analytics_config = config.get("analytics_setup", {})
-	per_pixel_file_name = "{}_{}.csv".format(
-		analytics_config.get("per_pixel_prefix", "pp"), run["name"]
-	)
-	work_dir = get_run_basedir(config, run)
-	out_dir = os.path.join(config.get("workDir", "."), "scratch")
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	out_file = os.path.join(out_dir, per_pixel_file_name)
-	harea_info = run.get("harvestArea", None)
-	collected_first_line = False
-	for current_dir in _generated_run_files(work_dir, "summary.csv"):
-		lat, lng = extract_ll(current_dir)
-		if collected_first_line:
-			mode = "a"
-		else:
-			mode = "w"
-		with open(os.path.join(current_dir, "summary.csv")) as source, open(out_file, mode) as dest:
-			additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
-			ds = None
-			band = None
-			if harea_info:
-				additional_headers = f'{additional_headers},HARVEST_AREA'
-				harea_tiff = harea_info.split("::")[1]
-				ds = rasterio.open(harea_tiff)
-				band = ds.read(1)
-			for i, line in enumerate(source):
-				if i == 0:
-					if not collected_first_line:
-						dest.write(
-							"{},{}\n".format(
-								additional_headers,
-								line.strip()
-							)
-						)
-						collected_first_line = True
-				else:
-					to_write = (lat, lng, run.get("name", ""))
-					if ds is not None and not ds.closed:
-						harea = pythia.io.get_site_raster_value(
-							ds, band, (float(lng), float(lat))
-						)
-						if harea is None:
-							harea = 0
-							logging.warning("%s, %s is giving an invalid harea, replacing with 0")
-						harea_s = "{:0.2f}".format(harea)
-						to_write = to_write + (harea_s,)
-					to_write = to_write + (line.strip()+"\n",)
-					dest.write(",".join(to_write))
-			if ds is not None:
-				ds.close()
-	return out_file
+    analytics_config = config.get("analytics_setup", {})
+    per_pixel_file_name = "{}_{}.csv".format(
+        analytics_config.get("per_pixel_prefix", "pp"), run["name"]
+    )
+    work_dir = get_run_basedir(config, run)
+    out_dir = os.path.join(config.get("workDir", "."), "scratch")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    out_file = os.path.join(out_dir, per_pixel_file_name)
+    harea_info = run.get("harvestArea", None)
+    pop_info = run.get("population", None)
+    collected_first_line = False
+    for current_dir in _generated_run_files(work_dir, "summary.csv"):
+        lat, lng = extract_ll(current_dir)
+        if collected_first_line:
+            mode = "a"
+        else:
+            mode = "w"
+        with open(os.path.join(current_dir, "summary.csv")) as source, open(
+            out_file, mode
+        ) as dest:
+            additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
+            ds_harea: Optional[_GeneratorContextManager[DatasetReader]] = None
+            ds_pop: Optional[_GeneratorContextManager[DatasetReader]] = None
+            band_harea = None
+            band_pop = None
+            if harea_info:
+                additional_headers = f"{additional_headers},HARVEST_AREA"
+                harea_tiff = harea_info.split("::")[1]
+                ds_harea = rasterio.open(harea_tiff)
+                band_harea = ds_harea.read(1)
+            if pop_info:
+                additional_headers = f"{additional_headers},POPULATION"
+                pop_tiff = pop_info.split("::")[1]
+                ds_pop = rasterio.open(pop_tiff)
+                band_pop = ds_pop.read(1)
+            for i, line in enumerate(source):
+                if i == 0:
+                    if not collected_first_line:
+                        dest.write("{},{}\n".format(additional_headers, line.strip()))
+                        collected_first_line = True
+                else:
+                    to_write = (lat, lng, run.get("name", ""))
+                    if ds_harea is not None and not ds_harea.closed:
+                        harea = pythia.io.get_site_raster_value(
+                            ds_harea, band_harea, (float(lng), float(lat))
+                        )
+                        if harea is None:
+                            harea = 0
+                            logging.warning(
+                                "%s, %s is giving an invalid harea, replacing with 0"
+                            )
+                        harea_s = "{:0.2f}".format(harea)
+                        to_write = to_write + (harea_s,)
+                    if ds_pop is not None and not ds_pop.closed:
+                        pop = pythia.io.get_site_raster_value(
+                            ds_pop, band_pop, (float(lng), float(lat))
+                        )
+                        if pop is None:
+                            pop = 0
+                            logging.warning(
+                                "%s, %s is giving an invalid population, replacing with 0"
+                            )
+                            pop_s = "{:0.2f}".format(pop)
+                            to_write = to_write + (pop_s,)
+                    to_write = to_write + (line.strip() + "\n",)
+                    dest.write(",".join(to_write))
+            if ds_harea is not None:
+                ds_harea.close()
+            if ds_pop is not None:
+                ds_pop.close()
+    return (run, out_file)
 
 
 def execute(config, plugins):
-	runs = config.get("runs", [])
-	analytics_config = config.get("analytics_setup", None)
-	run_outputs = []
-	calculated = None
-	filtered = None
-	if not analytics_config:
-		return
-	if len(runs) == 0:
-		return
-	for run in runs:
-		run_outputs.append(collate_outputs(config, run))
-	# Apply all the filters first
-	if analytics_config.get("calculatedColumns", None):
-		calculated = calculate_columns(config, run_outputs)
-	if calculated is None:
-		calculated = run_outputs
-	if analytics_config.get("columns", None):
-		filtered = filter_columns(config, calculated)
-	if filtered is None:
-		filtered = calculated
-	if analytics_config.get("singleOutput", False):
-		combine_outputs(config, filtered)
-	else:
-		final_outputs(config, filtered)
+    runs = config.get("runs", [])
+    analytics_config = config.get("analytics_setup", None)
+    run_outputs = []
+    calculated = None
+    filtered = None
+    if not analytics_config:
+        return
+    if len(runs) == 0:
+        return
+    for run in runs:
+        run_outputs.append(collate_outputs(config, run))
+    # Apply all the filters first
+    if analytics_config.get("calculatedColumns", None):
+        calculated = calculate_columns(config, run_outputs)
+    if calculated is None:
+        calculated = run_outputs
+    if analytics_config.get("columns", None):
+        filtered = filter_columns(config, calculated)
+    if filtered is None:
+        filtered = calculated
+    if analytics_config.get("singleOutput", False):
+        combine_outputs(config, filtered)
+    else:
+        final_outputs(config, filtered)
diff --git a/pythia/cache_manager.py b/pythia/cache_manager.py
index a4d06b03..039e6af9 100644
--- a/pythia/cache_manager.py
+++ b/pythia/cache_manager.py
@@ -1 +1 @@
-cache = {}
\ No newline at end of file
+cache = {}
diff --git a/pythia/cli.py b/pythia/cli.py
index 1f0f94f7..f1be2007 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -14,22 +14,33 @@
 def main():
     parser = argparse.ArgumentParser(prog="pythia")
     parser.add_argument("config", help="JSON configuration file to run")
-    parser.add_argument("--all", action="store_true", help="Run all the steps in pythia")
+    parser.add_argument(
+        "--all", action="store_true", help="Run all the steps in pythia"
+    )
     parser.add_argument(
         "--export-runlist",
         action="store_true",
         help="Export a list of all the directories to be run",
     )
-    parser.add_argument("--setup", action="store_true", help="Setup DSSAT run structure and files")
-    parser.add_argument("--run-dssat", action="store_true", help="Run DSSAT over the run structure")
+    parser.add_argument(
+        "--setup", action="store_true", help="Setup DSSAT run structure and files"
+    )
+    parser.add_argument(
+        "--run-dssat", action="store_true", help="Run DSSAT over the run structure"
+    )
     parser.add_argument(
         "--analyze", action="store_true", help="Run the analysis for the DSSAT runs"
     )
     parser.add_argument(
-        "--clean-work-dir", action="store_true", help="Clean the work directory prior to run"
+        "--clean-work-dir",
+        action="store_true",
+        help="Clean the work directory prior to run",
     )
     parser.add_argument(
-            "--logfile-prefix", default="pythia", help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log")
+        "--logfile-prefix",
+        default="pythia",
+        help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log",
+    )
     args = parser.parse_args()
 
     if not args.config:
@@ -37,12 +48,19 @@ def main():
     else:
         now = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
         logging.getLogger("pythia_app")
-        logging.basicConfig(level=logging.INFO, filename="{}-{}.log".format(args.logfile_prefix, now), filemode="w")
+        logging.basicConfig(
+            level=logging.INFO,
+            filename="{}-{}.log".format(args.logfile_prefix, now),
+            filemode="w",
+        )
         config = pythia.config.load_config(args.config)
         if args is None or not config:
             print("Invalid configuration file")
         else:
-            logging.info("Pythia started: %s", datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
+            logging.info(
+                "Pythia started: %s",
+                datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
+            )
             if args.clean_work_dir:
                 print("Cleaning the work directory")
                 if os.path.exists(config["workDir"]):
@@ -64,4 +82,7 @@ def main():
             if args.all or args.analyze:
                 print("Running simple analytics over DSSAT directory structure")
                 pythia.analytics.execute(config, plugins)
-            logging.info("Pythia completed: %s", datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
+            logging.info(
+                "Pythia completed: %s",
+                datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
+            )
diff --git a/pythia/config.py b/pythia/config.py
index d3c8cbcd..d4a66029 100644
--- a/pythia/config.py
+++ b/pythia/config.py
@@ -13,8 +13,7 @@ def load_config(config_file, validate=True, merge=True):
         with open(config_file) as f:
             config = json.load(f)
     except OSError:
-        logging.error(
-            "Error opening configuration file: {}".format(config_file))
+        logging.error("Error opening configuration file: {}".format(config_file))
     else:
         if validate:
             if not _validate_config(config):
@@ -27,11 +26,14 @@ def load_config(config_file, validate=True, merge=True):
 def _check_raster_profile(raster_file, cached_crs):
     logging.debug("Checking file {}".format(raster_file))
     try:
-        current_crs = pythia.io.get_rio_profile(raster_file)['crs'].data
+        current_crs = pythia.io.get_rio_profile(raster_file)["crs"].data
         if cached_crs:
             if cached_crs != current_crs:
-                logging.error("CRS mismatch for file {}. {} -> {}. Please reconcile.".format(
-                    raster_file, cached_crs['init'], current_crs['init']))
+                logging.error(
+                    "CRS mismatch for file {}. {} -> {}. Please reconcile.".format(
+                        raster_file, cached_crs["init"], current_crs["init"]
+                    )
+                )
             return cached_crs == current_crs, cached_crs
         else:
             return True, current_crs
@@ -44,9 +46,17 @@ def _validate_config(config):
     valid = True
     # Raster check pass 1 - all files are available and of the same projections
     values_iter = itertools.chain.from_iterable(
-        [list(config["default_setup"].values())] + [list(r.values()) for r in config["runs"]])
-    rasters = list(set([pythia.functions.extract_raster(raster) for raster in
-                        list(filter(lambda x: "raster::" in str(x), values_iter))]))
+        [list(config["default_setup"].values())]
+        + [list(r.values()) for r in config["runs"]]
+    )
+    rasters = list(
+        set(
+            [
+                pythia.functions.extract_raster(raster)
+                for raster in list(filter(lambda x: "raster::" in str(x), values_iter))
+            ]
+        )
+    )
     cached_crs = None
     for r in rasters:
         current_return, cached_crs = _check_raster_profile(r, cached_crs)
@@ -75,5 +85,7 @@ def _set_run_workdir(run, root, idx):
 
 def _merge_runs(config):
     runs = [_merge_default(config["default_setup"], r) for r in config["runs"]]
-    runs = [_set_run_workdir(r, config.get("workDir", "."), i) for (i, r) in enumerate(runs)]
+    runs = [
+        _set_run_workdir(r, config.get("workDir", "."), i) for (i, r) in enumerate(runs)
+    ]
     return runs
diff --git a/pythia/dssat.py b/pythia/dssat.py
index 4752011c..9130e424 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -25,9 +25,33 @@ def _run_dssat(details, config):
 def _generate_run_list(config):
     runlist = []
     for root, _, files in os.walk(config.get("workDir", "."), topdown=False):
+        batch_mode = config["dssat"].get("run_mode", "A") in {
+            "B",
+            "E",
+            "F",
+            "L",
+            "N",
+            "Q",
+            "S",
+            "T",
+            "Y",
+        }
+        target = None
+        if batch_mode:
+            target = config["dssat"].get("batch_file", None)
+        else:
+            target = config["dssat"].get("filex", None)
         for name in files:
-            if name.upper().endswith("X"):
-                runlist.append({"dir": root, "file": name})
+            if target is not None:
+                if name == target:
+                    runlist.append({"dir": root, "file": name})
+            else:
+                if batch_mode:
+                    if name.upper().startswith("DSSBATCH"):
+                        runlist.append({"dir": root, "file": name})
+                else:
+                    if name.upper().endswith("X"):
+                        runlist.append({"dir": root, "file": name})
     return runlist
 
 
diff --git a/pythia/functions.py b/pythia/functions.py
index 87db4fe3..cee5fb86 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -164,7 +164,7 @@ def split_fert_dap_percent(k, run, context, _):
 def assign_by_raster_value(k, run, context, _):
     init_args = run[k].split("::")[1:]
     if "raster" in init_args:
-        args = init_args[init_args.index("raster") + 2:]
+        args = init_args[init_args.index("raster") + 2 :]
     else:
         logging.error("Need to specify a raster for %s:assign_by_value", k)
         return None
diff --git a/pythia/io.py b/pythia/io.py
index 4af2658f..e4f35fab 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -18,7 +18,7 @@ def get_site_raster_value(dataset, band, site):
     data = []
     try:
         data = band[row, col]
-        if (data is ma.masked):
+        if data is ma.masked:
             data = None
     except IndexError:
         data = None
@@ -78,7 +78,7 @@ def get_shp_profile(f):
 
 def extract_vector_coords(f):
     points = []
-    with fiona.open(f, 'r') as source:
+    with fiona.open(f, "r") as source:
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
                 points.append(feature["geometry"]["coordinates"][0])
@@ -89,7 +89,7 @@ def extract_vector_coords(f):
 
 def find_vector_coords(f, lng, lat, a):
     coords = (lng, lat)
-    with fiona.open(f, 'r') as source:
+    with fiona.open(f, "r") as source:
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
                 if coords in feature["geometry"]["coordinates"]:
@@ -103,15 +103,21 @@ def find_closest_vector_coords(f, lng, lat, a):
     coords = Point(lng, lat)
     points = []
     ids = []
-    with fiona.open(f, 'r') as source:
+    with fiona.open(f, "r") as source:
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
-                points.extend([Point(p[0], p[1]) for p in feature["geometry"]["coordinates"]])
-                ids.extend([feature["properties"][a]] * len(feature["geometry"]["coordinates"]))
+                points.extend(
+                    [Point(p[0], p[1]) for p in feature["geometry"]["coordinates"]]
+                )
+                ids.extend(
+                    [feature["properties"][a]] * len(feature["geometry"]["coordinates"])
+                )
             if feature["geometry"]["type"] == "Point":
                 points.append(
-                    Point(feature["geometry"]["coordinates"][0],
-                          feature["geometry"]["coordinates"][1])
+                    Point(
+                        feature["geometry"]["coordinates"][0],
+                        feature["geometry"]["coordinates"][1],
+                    )
                 )
                 ids.append(feature["properties"][a])
     mp = MultiPoint(points)
diff --git a/pythia/peerless.py b/pythia/peerless.py
index 7a05d696..72459e14 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -52,7 +52,9 @@ def symlink_wth_soil(output_dir, config, context):
     for soil in context["soilFiles"]:
         soil_file = os.path.join(output_dir, os.path.basename(soil))
         if not os.path.exists(soil_file):
-            os.symlink(os.path.abspath(soil), os.path.join(output_dir, os.path.basename(soil)))
+            os.symlink(
+                os.path.abspath(soil), os.path.join(output_dir, os.path.basename(soil))
+            )
 
 
 def compose_peerless(context, config, env):
@@ -85,7 +87,9 @@ def execute(config, plugins):
                 # Post context hook
                 logging.debug("[PEERLESS] Running post_build_context plugins")
                 context = pythia.plugin.run_plugin_functions(
-                    pythia.plugin.PluginHook.post_build_context, plugins, context=context
+                    pythia.plugin.PluginHook.post_build_context,
+                    plugins,
+                    context=context,
                 )
                 runlist.append(os.path.abspath(compose_peerless(context, config, env)))
             else:
diff --git a/pythia/plugin.py b/pythia/plugin.py
index a49498d9..9740aadf 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -20,18 +20,24 @@ class PluginHook(Enum):
 def register_plugin_function(hook, fun, config, plugins):
     # Check to see if the hook is a PluginHook
     if not isinstance(hook, PluginHook):
-        logging.warning("[PLUGIN] Ignoring {} because {} is not a PluginHook".format(fun, hook))
+        logging.warning(
+            "[PLUGIN] Ignoring {} because {} is not a PluginHook".format(fun, hook)
+        )
         return plugins
 
     # Check to see if the function is a function.
     if not callable(fun):
-        logging.warning("[PLUGIN] Ignoring {} because {} is not a function.".format(fun, fun))
+        logging.warning(
+            "[PLUGIN] Ignoring {} because {} is not a function.".format(fun, fun)
+        )
         return plugins
 
     # Check to see if the config is an object.
     if not isinstance(config, dict):
         logging.warning(
-            "[PLUGIN] Ignoring {} because {} is not a valid configuration".format(fun, config)
+            "[PLUGIN] Ignoring {} because {} is not a valid configuration".format(
+                fun, config
+            )
         )
         return plugins
 
@@ -76,7 +82,9 @@ def load_plugins(config, plugins={}, module_prefix="pythia.plugins"):
         if spec is None:
             logging.warning("[PLUGIN] Cannot find plugin: {}".format(plugin["plugin"]))
             continue
-        _loaded = importlib.import_module("{}.{}".format(module_prefix, plugin["plugin"]))
+        _loaded = importlib.import_module(
+            "{}.{}".format(module_prefix, plugin["plugin"])
+        )
         # TODO: Check to see if the config works for the plugin
         # TODO: Check to see if the plugin conforms to the correct signature (optional)
 
@@ -94,7 +102,13 @@ def run_plugin_functions(hook, plugins, **kwargs):
     if hook in plugins:
         for plugin_fun in plugins[hook]:
             if hook == PluginHook.post_config:
-                _return = {**_return, **plugin_fun["fun"](plugin_fun.get("config", {}), _return)}
+                _return = {
+                    **_return,
+                    **plugin_fun["fun"](plugin_fun.get("config", {}), _return),
+                }
             elif hook == PluginHook.post_build_context:
-                _return = {**_return, **plugin_fun["fun"](plugin_fun.get("config", {}), _return)}
+                _return = {
+                    **_return,
+                    **plugin_fun["fun"](plugin_fun.get("config", {}), _return),
+                }
     return _return
diff --git a/pythia/plugins/sensitivity_plugin/__init__.py b/pythia/plugins/sensitivity_plugin/__init__.py
index 91aa9268..1694ba1c 100644
--- a/pythia/plugins/sensitivity_plugin/__init__.py
+++ b/pythia/plugins/sensitivity_plugin/__init__.py
@@ -39,28 +39,43 @@
 def initialize(config, plugins, full_config):
     logging.info("[Sensitivity Plugin] Initializing plugin")
     cfg = config["params"]
-    cfg["no_rename"] = config.get("no_rename", False) 
-    plugins = register_plugin_function(PluginHook.post_config, generate_sensitivity_runs, cfg,
-                                       plugins)
-    plugins = register_plugin_function(PluginHook.post_build_context, post_build_context_apply_factors, cfg, plugins)
-    plugins = register_plugin_function(PluginHook.post_build_context,
-                                       post_build_context_apply_static_factors, cfg, plugins)
+    cfg["no_rename"] = config.get("no_rename", False)
+    plugins = register_plugin_function(
+        PluginHook.post_config, generate_sensitivity_runs, cfg, plugins
+    )
+    plugins = register_plugin_function(
+        PluginHook.post_build_context, post_build_context_apply_factors, cfg, plugins
+    )
+    plugins = register_plugin_function(
+        PluginHook.post_build_context,
+        post_build_context_apply_static_factors,
+        cfg,
+        plugins,
+    )
     return plugins
 
 
 def _assign_static(sens, hook, key, plugin_config):
     if key not in sens[hook]:
         sens[hook][key] = []
-    sens[hook][key].append({"var": key, "method": plugin_config[key]["method"],
-                            "val": plugin_config[key]["value"], "hook": hook,
-                            "from": plugin_config[key].get("from", key)})
+    sens[hook][key].append(
+        {
+            "var": key,
+            "method": plugin_config[key]["method"],
+            "val": plugin_config[key]["value"],
+            "hook": hook,
+            "from": plugin_config[key].get("from", key),
+        }
+    )
 
 
 def _assign_factorial(sens, hook, key, plugin_config):
     if key not in sens[hook]:
         sens[hook][key] = []
     for v in plugin_config[key]["values"]:
-        sens[hook][key].append({"var": key, "method": plugin_config[key]["method"], "val": v, "hook": hook})
+        sens[hook][key].append(
+            {"var": key, "method": plugin_config[key]["method"], "val": v, "hook": hook}
+        )
 
 
 def merge_static(statics, factor):
@@ -68,10 +83,12 @@ def merge_static(statics, factor):
 
 
 def generate_sensitivity_runs(plugin_config={}, full_config={}):
-    sens = {"_sens_pre_context": {},
-            "_sens_pre_context_static": {},
-            "_sens_post_context": {},
-            "_sens_post_context_static": {}}
+    sens = {
+        "_sens_pre_context": {},
+        "_sens_pre_context_static": {},
+        "_sens_post_context": {},
+        "_sens_post_context_static": {},
+    }
     # First we organize them
     for k in plugin_config.keys():
         if k == "no_rename":
@@ -84,13 +101,23 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         elif hook == "post_build_context":
             context_string = "_sens_post_context"
         if static:
-            _assign_static(sens, context_string+"_static", k, plugin_config)
+            _assign_static(sens, context_string + "_static", k, plugin_config)
         else:
             _assign_factorial(sens, context_string, k, plugin_config)
 
-    factorial = list(itertools.product(*[*sens["_sens_pre_context"].values(), *sens["_sens_post_context"].values()]))
-    statics = list(itertools.chain.from_iterable(
-        [*sens["_sens_pre_context_static"].values(), *sens["_sens_post_context_static"].values()]))
+    factorial = list(
+        itertools.product(
+            *[*sens["_sens_pre_context"].values(), *sens["_sens_post_context"].values()]
+        )
+    )
+    statics = list(
+        itertools.chain.from_iterable(
+            [
+                *sens["_sens_pre_context_static"].values(),
+                *sens["_sens_post_context_static"].values(),
+            ]
+        )
+    )
     factors = [merge_static(statics, f) for f in factorial]
     # Next we generate the new runs for each analysis
     runs = full_config.get("runs", [])
@@ -100,9 +127,9 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         current_workDir = run["workDir"]
         for factor in factors:
             if not plugin_config.get("no_rename", False):
-            	f = generate_factorial_name(factor)
-            	run["name"] = current_name + "__" + f
-            	run["workDir"] = current_workDir + "__" + f
+                f = generate_factorial_name(factor)
+                run["name"] = current_name + "__" + f
+                run["workDir"] = current_workDir + "__" + f
             out_runs.append({**run, **{"_sens": factor}})
     out_runs = [apply_factors("_sens_pre_context", run) for run in out_runs]
     out_runs = [apply_factors("_sens_pre_context_static", run) for run in out_runs]
@@ -111,7 +138,13 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
 
 
 def generate_factorial_name(factors):
-    return "__".join([factor["var"]+str(factor["val"]) for factor in factors if factor["hook"].endswith("context")])
+    return "__".join(
+        [
+            factor["var"] + str(factor["val"])
+            for factor in factors
+            if factor["hook"].endswith("context")
+        ]
+    )
 
 
 def post_build_context_apply_factors(config={}, context={}):
@@ -125,9 +158,7 @@ def post_build_context_apply_static_factors(config={}, context={}):
 def apply_factors(hook, current_context):
     if current_context is None:
         return
-    call_list = {"date_offset": date_offset,
-                 "offset": offset,
-                 "env_mod": env_mod}
+    call_list = {"date_offset": date_offset, "offset": offset, "env_mod": env_mod}
     current_factors = [f for f in current_context["_sens"] if f["hook"] == hook]
     for cf in current_factors:
         cval = None
@@ -154,7 +185,7 @@ def date_offset(d, offset):
 
 
 def offset(v, offset):
-    return v+offset
+    return v + offset
 
 
 def env_mod(v, value):
diff --git a/pythia/plugins/test_plugin/__init__.py b/pythia/plugins/test_plugin/__init__.py
index 56c44b82..b4a1e4ac 100644
--- a/pythia/plugins/test_plugin/__init__.py
+++ b/pythia/plugins/test_plugin/__init__.py
@@ -4,7 +4,9 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[TEST PLUGIN] Initializing plugin")
-    plugins = register_plugin_function(PluginHook.post_config, sample_function, config, plugins)
+    plugins = register_plugin_function(
+        PluginHook.post_config, sample_function, config, plugins
+    )
     plugins = register_plugin_function(
         PluginHook.post_build_context, contexted_function, config, plugins
     )
diff --git a/pythia/plugins/weather_forecast_simple/__init__.py b/pythia/plugins/weather_forecast_simple/__init__.py
index a60091ad..30071fb3 100644
--- a/pythia/plugins/weather_forecast_simple/__init__.py
+++ b/pythia/plugins/weather_forecast_simple/__init__.py
@@ -23,7 +23,9 @@ def initialize(config, plugins, full_config):
     cfg["start_date"] = pythia.util.to_julian_date(
         pythia.util.from_iso_date(cfg["start_date"])
     )
-    cfg["end_date"] = pythia.util.to_julian_date(pythia.util.from_iso_date(cfg["end_date"]))
+    cfg["end_date"] = pythia.util.to_julian_date(
+        pythia.util.from_iso_date(cfg["end_date"])
+    )
     cfg["start_on"] = cfg["start_date"][2:5]
     cfg["end_on"] = cfg["end_date"][2:5]
     return register_plugin_function(
@@ -33,14 +35,16 @@ def initialize(config, plugins, full_config):
 
 def construct_pixel_forecast(config={}, context={}):
     """NOTE: This function is NOT side-effect free. It does I/O to create a new file in the
-       context["contextWorkDir"]. But this side-effect also is intentional to interrupt the
-       creation of the symlinks further along the process."""
+    context["contextWorkDir"]. But this side-effect also is intentional to interrupt the
+    creation of the symlinks further along the process."""
 
     """TODO: Fix the wrap around case for leap years"""
 
     logging.debug("[SIMPLE WEATHER FORECAST PLUGIN] Running construct_pixel_forecast()")
     source_weather = os.path.join(config["weatherDir"], context["wthFile"])
-    dest_weather = os.path.join(context["contextWorkDir"], "{}.WTH".format(config["wsta"]))
+    dest_weather = os.path.join(
+        context["contextWorkDir"], "{}.WTH".format(config["wsta"])
+    )
     target_lines = []
     with open(source_weather) as source:
         scraping_lines = False
diff --git a/pythia/soil_handler.py b/pythia/soil_handler.py
index 63589393..65231d47 100644
--- a/pythia/soil_handler.py
+++ b/pythia/soil_handler.py
@@ -157,4 +157,5 @@ def calculateICLayerData(soilData, run):
             calculateH2O(run["icsw%"], slll, sdul),
             [icnd * 0.1 for icnd in icndist],
             [icnd * 0.9 for icnd in icndist],
-        ])
+        ]
+    )
diff --git a/pythia/template.py b/pythia/template.py
index 254f27d5..e7abf8bb 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -26,7 +26,7 @@
     "irrig": {"length": 5},
     "erain": {"raw": "M{:>4}"},
     "ph2ol": {"length": 5},
-    "fodate": {"length": 7}
+    "fodate": {"length": 7},
 }
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate"]
@@ -38,6 +38,7 @@ def init_engine(template_dir):
         loader=FileSystemLoader(template_dir), trim_blocks=True, lstrip_blocks=True
     )
 
+
 def wrap_format(k, v):
     fmt = ""
     if k in _t_formats:
@@ -62,6 +63,7 @@ def wrap_format(k, v):
         fmt = "{}"
     return fmt.format(v)
 
+
 def auto_format_dict(d):
     if isinstance(d, str):
         return d
@@ -71,7 +73,7 @@ def auto_format_dict(d):
         if "default" in v:
             clean[k] = wrap_format(k, v["default"])
         else:
-            clean[k] = wrap_format(k,-99)
+            clean[k] = wrap_format(k, -99)
     for k, v in d.items():
         if k in _t_date_fields and "::" not in v:
             clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
diff --git a/pythia/tests/plugin_test.py b/pythia/tests/plugin_test.py
index b577c830..345fee77 100644
--- a/pythia/tests/plugin_test.py
+++ b/pythia/tests/plugin_test.py
@@ -1,4 +1,9 @@
-from pythia.plugin import PluginHook, register_plugin_function, load_plugins, run_plugin_functions
+from pythia.plugin import (
+    PluginHook,
+    register_plugin_function,
+    load_plugins,
+    run_plugin_functions,
+)
 
 
 def test_register_with_invalid_hook():
@@ -9,13 +14,17 @@ def test_register_with_invalid_hook():
 
 def test_register_with_invalid_fun():
     plugins = {}
-    plugins1 = register_plugin_function(PluginHook.analyze_file, "not a function", "", plugins)
+    plugins1 = register_plugin_function(
+        PluginHook.analyze_file, "not a function", "", plugins
+    )
     assert plugins1 == {}
 
 
 def test_register_with_invalid_config():
     plugins = {}
-    plugins1 = register_plugin_function(PluginHook.post_analysis, sample_function, "", plugins)
+    plugins1 = register_plugin_function(
+        PluginHook.post_analysis, sample_function, "", plugins
+    )
     assert plugins1 == {}
 
 
@@ -23,19 +32,27 @@ def test_register_twice():
     plugins = {}
     plugins1 = {}
     plugins2 = {}
-    plugins1 = register_plugin_function(PluginHook.analyze_file, sample_function, {}, plugins)
+    plugins1 = register_plugin_function(
+        PluginHook.analyze_file, sample_function, {}, plugins
+    )
     plugins2 = register_plugin_function(
         PluginHook.analyze_file, sample_function, {"a": 1}, plugins1
     )
-    assert plugins1 == {PluginHook.analyze_file: [{"fun": sample_function, "config": {}}]}
+    assert plugins1 == {
+        PluginHook.analyze_file: [{"fun": sample_function, "config": {}}]
+    }
     assert plugins1 == plugins2
 
 
 def test_register_properly():
     plugins = {}
     plugins1 = {}
-    plugins1 = register_plugin_function(PluginHook.post_build_context, sample_function, {}, plugins)
-    assert plugins1 == {PluginHook.post_build_context: [{"fun": sample_function, "config": {}}]}
+    plugins1 = register_plugin_function(
+        PluginHook.post_build_context, sample_function, {}, plugins
+    )
+    assert plugins1 == {
+        PluginHook.post_build_context: [{"fun": sample_function, "config": {}}]
+    }
 
 
 def sample_function(config, context):
@@ -53,7 +70,9 @@ def test_load_plugin():
     assert plugins1[PluginHook.post_config] == [
         {"fun": pythia.plugins.test_plugin.sample_function, "config": {}}
     ]
-    assert plugins1 != {PluginHook.post_config: [{"fun": sample_function, "config": {}}]}
+    assert plugins1 != {
+        PluginHook.post_config: [{"fun": sample_function, "config": {}}]
+    }
 
 
 def test_plugin_manual_execution():
@@ -72,7 +91,9 @@ def test_plugin_auto_execution():
     plugins1 = {}
     plugins1 = load_plugins(config, plugins)
     context = {"context_value": 7}
-    context1 = run_plugin_functions(PluginHook.post_build_context, plugins1, context=context)
+    context1 = run_plugin_functions(
+        PluginHook.post_build_context, plugins1, context=context
+    )
     context2 = run_plugin_functions(PluginHook.post_build_context, plugins1)
     assert context1 != context
     assert context1["context_value"] == 8
@@ -84,8 +105,12 @@ def test_no_plugin_does_not_change_context():
     plugins = {}
     plugins1 = load_plugins(config, plugins)
     context = {"hello": "there"}
-    context1 = run_plugin_functions(PluginHook.post_build_context, plugins, context=context)
+    context1 = run_plugin_functions(
+        PluginHook.post_build_context, plugins, context=context
+    )
     assert context == context1
-    context2 = run_plugin_functions(PluginHook.post_build_context, plugins1, context=context)
+    context2 = run_plugin_functions(
+        PluginHook.post_build_context, plugins1, context=context
+    )
     assert context1 != context2
-    assert(context2 == {**context, **{"context_value": 3}})
+    assert context2 == {**context, **{"context_value": 3}}
diff --git a/pythia/util.py b/pythia/util.py
index ff445e02..4129ee24 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -11,6 +11,7 @@ def to_julian_date(d):
         logging.error("Unable to convert %s to a julian date", d)
         return None
 
+
 def to_julian_date_4(d):
     try:
         return d.strftime("%Y%j")
diff --git a/sample.json b/sample.json
index 03227d3e..da7ca445 100644
--- a/sample.json
+++ b/sample.json
@@ -37,7 +37,8 @@
         "ic_layers": "generate_ic_layers::$id_soil",
         "ramt": 0,
         "fen_tot": 100.0,
-        "fertilizers": "split_fert_dap_percent::$fe"
+        "fertilizers": "split_fert_dap_percent::$fe",
+        "population": "raster::data/rasters/population.tif"
     },
     "dssat": {
         "executable": "/usr/local/dssat47/dscsm047"
@@ -53,6 +54,7 @@
             "LATITUDE",
             "LONGITUDE",
             "HARVEST_AREA",
+            "POPULATION",
             "RUN_NAME",
             "CR",
             "PDAT",
@@ -72,4 +74,4 @@
             "harvestArea": "raster::data/rasters/unity_spam_harvest_sorghum.tif"
         }
     ]
-}
\ No newline at end of file
+}
diff --git a/tox.ini b/tox.ini
index 6deafc26..68151ede 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,2 +1,4 @@
 [flake8]
-max-line-length = 120
+max-line-length = 160
+[pycodestyle]
+max-line-length = 160

From d84cf041cc9c57471042561a7913492e471ac2fd Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 19 Nov 2021 15:44:59 -0500
Subject: [PATCH 013/105] Removed tuple from `collate_outputs` function

Signed-off-by: Christopher Villalobos <cvillalobos@ufl.edu>
---
 pythia/analytics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 734ea898..7900212d 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -229,7 +229,7 @@ def collate_outputs(config, run):
                 ds_harea.close()
             if ds_pop is not None:
                 ds_pop.close()
-    return (run, out_file)
+    return out_file
 
 
 def execute(config, plugins):

From 1ef040ab04674cc263b17349e71af3982350fd60 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 19 Nov 2021 16:00:22 -0500
Subject: [PATCH 014/105] Fix population only writing on no value

---
 pythia/analytics.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 7900212d..bbcbfa2b 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -221,8 +221,8 @@ def collate_outputs(config, run):
                             logging.warning(
                                 "%s, %s is giving an invalid population, replacing with 0"
                             )
-                            pop_s = "{:0.2f}".format(pop)
-                            to_write = to_write + (pop_s,)
+                        pop_s = "{:0.2f}".format(pop)
+                        to_write = to_write + (pop_s,)
                     to_write = to_write + (line.strip() + "\n",)
                     dest.write(",".join(to_write))
             if ds_harea is not None:

From 60d0421c7f905272515a6481ef39d8951d831026 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 24 Nov 2021 13:21:06 -0500
Subject: [PATCH 015/105] Revert breaking changes in analytics

* Remove run from `generate_funs()`
---
 pythia/analytic_functions.py | 2 +-
 pythia/analytics.py          | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/pythia/analytic_functions.py b/pythia/analytic_functions.py
index 7d55957f..1e6e8fe5 100644
--- a/pythia/analytic_functions.py
+++ b/pythia/analytic_functions.py
@@ -1,4 +1,4 @@
-def generate_funs(config, run):
+def generate_funs(config):
     funcs = []
     for key, funs in config.items():
         fun = {}
diff --git a/pythia/analytics.py b/pythia/analytics.py
index bbcbfa2b..c3757708 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -81,9 +81,8 @@ def calculate_columns(config, outputs):
     out_dir = os.path.join(config.get("workDir", "."), "scratch")
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
-    for current in outputs:
-        run, current_file = current
-        funs = pythia.analytic_functions.generate_funs(calculations, run)
+    for current_file in outputs:
+        funs = pythia.analytic_functions.generate_funs(calculations)
         arg_columns = []
         for fun in funs:
             for a in fun["args"]:

From 5fb84c3a759c6bba09affa9eb394c1de0259343f Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 24 Nov 2021 14:17:12 -0500
Subject: [PATCH 016/105] Remove run from `combine_outputs()`

---
 project.org         | 2 ++
 pythia/analytics.py | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/project.org b/project.org
index af6d90b5..61816f32 100644
--- a/project.org
+++ b/project.org
@@ -37,3 +37,5 @@ In order to use batch file support modes (specified by ~CheckRunMode.f90~), you
 "singleOutput": true,
 "outputColumns": ["SOME", "VARIABLE"]
 ]
+* Windows-specific issues?
+** 
diff --git a/pythia/analytics.py b/pythia/analytics.py
index c3757708..00d075a7 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -133,7 +133,7 @@ def calculate_columns(config, outputs):
     return out_files
 
 
-def combine_outputs(outputs, config, run):
+def combine_outputs(outputs, config):
     analytics_config = config.get("analytics_setup", {})
     combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
     out_dir = config.get("workDir", ".")

From 33a6907816720918b8e4a2923f01fbe074f8b6dc Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 30 Nov 2021 15:09:57 -0500
Subject: [PATCH 017/105] Add support for more date variables

* Harvest Date (hdate)
* Planting Date (pdate)
* Planting Window (pfrst, plast)
---
 pythia/template.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pythia/template.py b/pythia/template.py
index e7abf8bb..f03a9db1 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -27,9 +27,13 @@
     "erain": {"raw": "M{:>4}"},
     "ph2ol": {"length": 5},
     "fodate": {"length": 7},
+    "pdate": {"length": 5},
+    "pfrst": {"length": 5},
+    "plast": {"length": 5},
+    "hdate": {"length": 5}
 }
 
-_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate"]
+_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate", "hdate"]
 _t_date_fields_4 = ["fodate"]
 
 

From 1f273755e324cd45de5a1dbf6a07b44ed096ac98 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 30 Nov 2021 15:12:21 -0500
Subject: [PATCH 018/105] Fix issue-36

* Remove run from `combine_outputs()`
* Remove run from `generate_funs()`
* Fix population only writing on no value
* Removed tuple from `collate_outputs` function
---
 project.org                  |  2 ++
 pythia/analytic_functions.py |  2 +-
 pythia/analytics.py          | 13 ++++++-------
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/project.org b/project.org
index af6d90b5..61816f32 100644
--- a/project.org
+++ b/project.org
@@ -37,3 +37,5 @@ In order to use batch file support modes (specified by ~CheckRunMode.f90~), you
 "singleOutput": true,
 "outputColumns": ["SOME", "VARIABLE"]
 ]
+* Windows-specific issues?
+** 
diff --git a/pythia/analytic_functions.py b/pythia/analytic_functions.py
index 7d55957f..1e6e8fe5 100644
--- a/pythia/analytic_functions.py
+++ b/pythia/analytic_functions.py
@@ -1,4 +1,4 @@
-def generate_funs(config, run):
+def generate_funs(config):
     funcs = []
     for key, funs in config.items():
         fun = {}
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 734ea898..00d075a7 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -81,9 +81,8 @@ def calculate_columns(config, outputs):
     out_dir = os.path.join(config.get("workDir", "."), "scratch")
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
-    for current in outputs:
-        run, current_file = current
-        funs = pythia.analytic_functions.generate_funs(calculations, run)
+    for current_file in outputs:
+        funs = pythia.analytic_functions.generate_funs(calculations)
         arg_columns = []
         for fun in funs:
             for a in fun["args"]:
@@ -134,7 +133,7 @@ def calculate_columns(config, outputs):
     return out_files
 
 
-def combine_outputs(outputs, config, run):
+def combine_outputs(outputs, config):
     analytics_config = config.get("analytics_setup", {})
     combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
     out_dir = config.get("workDir", ".")
@@ -221,15 +220,15 @@ def collate_outputs(config, run):
                             logging.warning(
                                 "%s, %s is giving an invalid population, replacing with 0"
                             )
-                            pop_s = "{:0.2f}".format(pop)
-                            to_write = to_write + (pop_s,)
+                        pop_s = "{:0.2f}".format(pop)
+                        to_write = to_write + (pop_s,)
                     to_write = to_write + (line.strip() + "\n",)
                     dest.write(",".join(to_write))
             if ds_harea is not None:
                 ds_harea.close()
             if ds_pop is not None:
                 ds_pop.close()
-    return (run, out_file)
+    return out_file
 
 
 def execute(config, plugins):

From 1669a7a9e207a1d26364fafb637ebdf29f847f81 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 1 Dec 2021 10:19:03 -0500
Subject: [PATCH 019/105] Fix order of arguments for combine_outputs()

---
 pythia/analytics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 00d075a7..751a55af 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -133,7 +133,7 @@ def calculate_columns(config, outputs):
     return out_files
 
 
-def combine_outputs(outputs, config):
+def combine_outputs(config, outputs):
     analytics_config = config.get("analytics_setup", {})
     combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
     out_dir = config.get("workDir", ".")

From 6c364d4b7d65586221554428b173dfe28fed34d9 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 1 Dec 2021 10:49:48 -0500
Subject: [PATCH 020/105] Finalize issue-36 fix

---
 pythia/analytics.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 47699046..751a55af 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -133,11 +133,7 @@ def calculate_columns(config, outputs):
     return out_files
 
 
-<<<<<<< HEAD
-def combine_outputs(outputs, config):
-=======
 def combine_outputs(config, outputs):
->>>>>>> frostbytten/issue-36
     analytics_config = config.get("analytics_setup", {})
     combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
     out_dir = config.get("workDir", ".")

From 602e9d299997af0ce2b7786b3d436317603c8067 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 11:40:15 -0500
Subject: [PATCH 021/105] Change formatting for IC variables

* sh2o is now ":>6.3f"
* snh4 and sno3 is now ":>6.2f"
---
 pythia/template.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pythia/template.py b/pythia/template.py
index f03a9db1..dd2361fd 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -12,9 +12,9 @@
     "icres": {"length": 6},
     "icren": {"length": 6},
     "icbl": {"length": 6},
-    "sh2o": {"length": 6},
-    "snh4": {"length": 6},
-    "sno3": {"length": 6},
+    "sh2o": {"fmt": ":>6.3f"},
+    "snh4": {"fmt": ":>6.2f"},
+    "sno3": {"fmt": ":>6.2f"},
     "fdate": {"length": 5},
     "fdap": {"length": 5},
     "famn": {"length": 5},

From c5d5136dd8e0c50340a6a1430ba178a2ecb026ed Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 15:36:41 -0500
Subject: [PATCH 022/105] Release version 2.1.0

* Support for DSSAT 4.8+
* Support for 4-digit years (fodate)
* Support DSSAT Run modes
* Support DSSAT Batch files (simple)
* Support DSSAT Forecast Mode (replaces simple_forecast plugin)
  The simple_forecast plugin is still in-place for DSSAT <4.8
* Fix #36
* Fix #37
* Fix #38
* Add HDATE, PDATE, PFRST, and PLAST as complete date variables
* Add hardwired population values
---
 .gitignore                                    |   1 +
 .python-version                               |   1 -
 bin/pythia                                    |   0
 docs/json.rst                                 |  18 +-
 poetry.lock                                   | 884 +++++++++++++++---
 project.org                                   |  41 +
 pyproject.toml                                |   8 +-
 pythia/analytic_functions.py                  |  20 +-
 pythia/analytics.py                           | 406 ++++----
 pythia/cache_manager.py                       |   2 +-
 pythia/cli.py                                 |  37 +-
 pythia/config.py                              |  30 +-
 pythia/dssat.py                               |  35 +-
 pythia/functions.py                           |   2 +-
 pythia/io.py                                  |  22 +-
 pythia/peerless.py                            |   8 +-
 pythia/plugin.py                              |  28 +-
 pythia/plugins/sensitivity_plugin/__init__.py |  87 +-
 pythia/plugins/test_plugin/__init__.py        |   4 +-
 .../weather_forecast_simple/__init__.py       |  25 +-
 pythia/soil_handler.py                        |   3 +-
 pythia/template.py                            |  73 +-
 pythia/tests/plugin_test.py                   |  49 +-
 pythia/util.py                                |   8 +
 sample.json                                   |   6 +-
 tox.ini                                       |   4 +-
 26 files changed, 1327 insertions(+), 475 deletions(-)
 delete mode 100644 .python-version
 mode change 100755 => 100644 bin/pythia
 create mode 100644 project.org

diff --git a/.gitignore b/.gitignore
index f671c910..4748a48d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,4 @@ docs/source/_build
 docs/build
 .venv
 dist
+*~
diff --git a/.python-version b/.python-version
deleted file mode 100644
index f06fb9e9..00000000
--- a/.python-version
+++ /dev/null
@@ -1 +0,0 @@
-3.7.10
diff --git a/bin/pythia b/bin/pythia
old mode 100755
new mode 100644
diff --git a/docs/json.rst b/docs/json.rst
index 34ffc4af..a50533fa 100644
--- a/docs/json.rst
+++ b/docs/json.rst
@@ -8,13 +8,13 @@ General
 This is the root of the JSON object. All values in this section are considered to be globally available.
 
 name
-   :Type: no whitespace string 
+   :Type: no whitespace string
    :Required: true
    :Description: The name of this configuration.
-   
+
 
 workDir
-   :Type: directory string 
+   :Type: directory string
    :Required: true
    :Description: The root output directory of this run. All DSSAT files will generated under this directory.
 
@@ -32,13 +32,13 @@ cores
    :Type: positive integer
    :Default value: number of logical CPUs available.
    :Description: The number of cores to be used by pythia. Cores are used to execute the model.
-   
+
 
 threads
    :Type: positive integer
    :Default value: number of cores available / 2
-   :Description: The number of threads to be used by pythia. This is used for I/O work. 
-   
+   :Description: The number of threads to be used by pythia. This is used for I/O work.
+
 sample
    :Type: positive integer
    :Description: Used to subset the data. Applies the configuration the first *x* number of valid simulations. This may be different between runs.
@@ -72,8 +72,6 @@ sites
 
       {"sites": [[29.6340239,-82.3631502]]}
 
-               
-
 startYear
    :Type: 4-digit year
    :Required: true
@@ -107,7 +105,7 @@ DSSAT Structures
 ~~~~~~~~~~~~~~~~
 
 ic_layers
-   :Type: Array of initial condition layer objects 
+   :Type: Array of initial condition layer objects
    :Shape: ``[{"icbl": <value>, "sh2o": <value>, "shn4": <value>, "sno3": <value>},...]``
    :Helper function: ``generate_ic_layers``
 
@@ -121,4 +119,4 @@ Arbitrary Variables
 
 
 Useful Functions
-~~~~~~~~~~~~~~~~
\ No newline at end of file
+~~~~~~~~~~~~~~~~
diff --git a/poetry.lock b/poetry.lock
index a5b84ed9..9ce53c74 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -10,12 +10,18 @@ python-versions = "*"
 test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
 
 [[package]]
-name = "appdirs"
-version = "1.4.4"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+name = "astroid"
+version = "2.6.6"
+description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = "~=3.6"
+
+[package.dependencies]
+lazy-object-proxy = ">=1.4.0"
+typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
+typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+wrapt = ">=1.11,<1.13"
 
 [[package]]
 name = "atomicwrites"
@@ -39,33 +45,49 @@ docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
 tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
 tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
 
+[[package]]
+name = "autopep8"
+version = "1.5.7"
+description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pycodestyle = ">=2.7.0"
+toml = "*"
+
 [[package]]
 name = "black"
-version = "21.5b2"
+version = "21.10b0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
 python-versions = ">=3.6.2"
 
 [package.dependencies]
-appdirs = "*"
 click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.8.1,<1"
+pathspec = ">=0.9.0,<1"
+platformdirs = ">=2"
 regex = ">=2020.1.8"
-toml = ">=0.10.1"
+tomli = ">=0.2.6,<2.0.0"
 typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
-typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+typing-extensions = [
+    {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
+    {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
+]
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"]
-python2 = ["typed-ast (>=1.4.2)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+python2 = ["typed-ast (>=1.4.3)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2021.5.30"
+version = "2021.10.8"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
@@ -73,7 +95,7 @@ python-versions = "*"
 
 [[package]]
 name = "click"
-version = "8.0.1"
+version = "8.0.3"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
@@ -156,9 +178,20 @@ mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
 
+[[package]]
+name = "greenlet"
+version = "1.1.2"
+description = "Lightweight in-process concurrent programming"
+category = "dev"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+
+[package.extras]
+docs = ["sphinx"]
+
 [[package]]
 name = "importlib-metadata"
-version = "4.4.0"
+version = "4.8.1"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -170,7 +203,37 @@ zipp = ">=0.5"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+perf = ["ipython"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+
+[[package]]
+name = "isort"
+version = "5.10.0"
+description = "A Python utility / library to sort Python imports."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1,<4.0"
+
+[package.extras]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
+requirements_deprecated_finder = ["pipreqs", "pip-api"]
+colors = ["colorama (>=0.4.3,<0.5.0)"]
+plugins = ["setuptools"]
+
+[[package]]
+name = "jedi"
+version = "0.18.0"
+description = "An autocompletion tool for Python that can be used for text editors."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+parso = ">=0.8.0,<0.9.0"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -186,6 +249,14 @@ MarkupSafe = ">=0.23"
 [package.extras]
 i18n = ["Babel (>=0.8)"]
 
+[[package]]
+name = "lazy-object-proxy"
+version = "1.6.0"
+description = "A fast and thorough lazy object proxy."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+
 [[package]]
 name = "markupsafe"
 version = "2.0.1"
@@ -204,12 +275,20 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.8.0"
+version = "8.10.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "msgpack"
+version = "1.0.2"
+description = "MessagePack (de)serializer."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "munch"
 version = "2.5.0"
@@ -233,9 +312,20 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "neovim"
+version = "0.3.1"
+description = "Transition packgage for pynvim"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pynvim = ">=0.3.1"
+
 [[package]]
 name = "numpy"
-version = "1.20.3"
+version = "1.21.1"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -243,22 +333,46 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "packaging"
-version = "20.9"
+version = "21.2"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.6"
 
 [package.dependencies]
-pyparsing = ">=2.0.2"
+pyparsing = ">=2.0.2,<3"
+
+[[package]]
+name = "parso"
+version = "0.8.2"
+description = "A Python Parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "pathspec"
-version = "0.8.1"
+version = "0.9.0"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[[package]]
+name = "platformdirs"
+version = "2.4.0"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
+test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
 
 [[package]]
 name = "pluggy"
@@ -276,11 +390,11 @@ dev = ["pre-commit", "tox"]
 
 [[package]]
 name = "py"
-version = "1.10.0"
+version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "pycodestyle"
@@ -290,6 +404,20 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pydocstyle"
+version = "6.1.1"
+description = "Python docstring style checker"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+snowballstemmer = "*"
+
+[package.extras]
+toml = ["toml"]
+
 [[package]]
 name = "pyflakes"
 version = "2.3.1"
@@ -298,6 +426,78 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pylint"
+version = "2.9.6"
+description = "python code static checker"
+category = "dev"
+optional = false
+python-versions = "~=3.6"
+
+[package.dependencies]
+astroid = ">=2.6.5,<2.7"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+isort = ">=4.2.5,<6"
+mccabe = ">=0.6,<0.7"
+toml = ">=0.7.1"
+
+[[package]]
+name = "pyls-flake8"
+version = "0.4.0"
+description = "A Flake8 plugin for the Python Language Server"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+flake8 = ">=3.6.0"
+python-lsp-server = "*"
+
+[[package]]
+name = "pyls-isort"
+version = "0.2.2"
+description = "Isort plugin for python-lsp-server"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+isort = "*"
+python-lsp-server = "*"
+
+[[package]]
+name = "pylsp-rope"
+version = "0.1.7"
+description = "Extended refactoring capabilities for Python LSP Server using Rope."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+python-lsp-server = "*"
+rope = ">=0.21.0"
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+
+[package.extras]
+dev = ["build", "pytest", "twine"]
+test = ["pytest"]
+
+[[package]]
+name = "pynvim"
+version = "0.4.3"
+description = "Python client to neovim"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+greenlet = "*"
+msgpack = ">=0.5.0"
+
+[package.extras]
+pyuv = ["pyuv (>=1.0.0)"]
+test = ["pytest (>=3.4.0)"]
+
 [[package]]
 name = "pyparsing"
 version = "2.4.7"
@@ -330,8 +530,74 @@ checkqa-mypy = ["mypy (==v0.761)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
-name = "rasterio"
+name = "python-lsp-black"
+version = "1.0.0"
+description = "Black plugin for the Python LSP Server"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+black = ">=19.3b0"
+python-lsp-server = "*"
+toml = "*"
+
+[package.extras]
+dev = ["isort (>=5.0)", "flake8", "pytest", "mypy"]
+
+[[package]]
+name = "python-lsp-jsonrpc"
+version = "1.0.0"
+description = "JSON RPC 2.0 server library"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+ujson = ">=3.0.0"
+
+[package.extras]
+test = ["pylint", "pycodestyle", "pyflakes", "pytest", "pytest-cov", "coverage"]
+
+[[package]]
+name = "python-lsp-server"
 version = "1.2.4"
+description = "Python Language Server for the Language Server Protocol"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+autopep8 = {version = "*", optional = true, markers = "extra == \"all\""}
+flake8 = {version = ">=3.8.0,<4.0.0", optional = true, markers = "extra == \"all\""}
+jedi = ">=0.17.2,<0.19.0"
+mccabe = {version = ">=0.6.0,<0.7.0", optional = true, markers = "extra == \"all\""}
+pluggy = "*"
+pycodestyle = {version = ">=2.7.0", optional = true, markers = "extra == \"all\""}
+pydocstyle = {version = ">=2.0.0", optional = true, markers = "extra == \"all\""}
+pyflakes = {version = ">=2.3.0,<2.4.0", optional = true, markers = "extra == \"all\""}
+pylint = {version = ">=2.5.0,<2.10.0", optional = true, markers = "extra == \"all\""}
+python-lsp-jsonrpc = ">=1.0.0"
+rope = {version = ">=0.10.5", optional = true, markers = "extra == \"all\""}
+ujson = ">=3.0.0"
+yapf = {version = "*", optional = true, markers = "extra == \"all\""}
+
+[package.extras]
+all = ["autopep8", "flake8 (>=3.8.0,<4.0.0)", "mccabe (>=0.6.0,<0.7.0)", "pycodestyle (>=2.7.0)", "pydocstyle (>=2.0.0)", "pyflakes (>=2.3.0,<2.4.0)", "pylint (>=2.5.0,<2.10.0)", "rope (>=0.10.5)", "yapf"]
+autopep8 = ["autopep8"]
+flake8 = ["flake8 (>=3.8.0,<4.0.0)"]
+mccabe = ["mccabe (>=0.6.0,<0.7.0)"]
+pycodestyle = ["pycodestyle (>=2.7.0)"]
+pydocstyle = ["pydocstyle (>=2.0.0)"]
+pyflakes = ["pyflakes (>=2.3.0,<2.4.0)"]
+pylint = ["pylint (>=2.5.0,<2.10.0)"]
+rope = ["rope (>0.10.5)"]
+test = ["pylint (>=2.5.0,<2.10.0)", "pytest", "pytest-cov", "coverage", "numpy", "pandas", "matplotlib", "pyqt5", "flaky"]
+yapf = ["yapf"]
+
+[[package]]
+name = "rasterio"
+version = "1.2.10"
 description = "Fast and direct raster I/O for use with Numpy and SciPy"
 category = "main"
 optional = false
@@ -348,7 +614,7 @@ numpy = "*"
 snuggs = ">=1.4.1"
 
 [package.extras]
-all = ["sphinx-rtd-theme", "boto3 (>=1.2.4)", "matplotlib", "pytest (>=2.8.2)", "numpydoc", "ghp-import", "ipython (>=2.0)", "hypothesis", "packaging", "sphinx", "pytest-cov (>=2.2.0)", "shapely"]
+all = ["numpydoc", "hypothesis", "matplotlib", "pytest-cov (>=2.2.0)", "sphinx", "ipython (>=2.0)", "boto3 (>=1.2.4)", "shapely", "pytest (>=2.8.2)", "packaging", "sphinx-rtd-theme", "ghp-import"]
 docs = ["ghp-import", "numpydoc", "sphinx", "sphinx-rtd-theme"]
 ipython = ["ipython (>=2.0)"]
 plot = ["matplotlib"]
@@ -357,12 +623,23 @@ test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "p
 
 [[package]]
 name = "regex"
-version = "2021.4.4"
+version = "2021.11.2"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "rope"
+version = "0.21.0"
+description = "a python refactoring library..."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+dev = ["pytest", "pytest-timeout"]
+
 [[package]]
 name = "rtree"
 version = "0.8.3"
@@ -373,14 +650,14 @@ python-versions = "*"
 
 [[package]]
 name = "shapely"
-version = "1.7.1"
+version = "1.8.0"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [package.extras]
-all = ["numpy", "pytest", "pytest-cov"]
+all = ["pytest", "pytest-cov", "numpy"]
 test = ["pytest", "pytest-cov"]
 vectorized = ["numpy"]
 
@@ -392,6 +669,14 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "snowballstemmer"
+version = "2.1.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "snuggs"
 version = "1.4.7"
@@ -415,6 +700,14 @@ category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "tomli"
+version = "1.2.2"
+description = "A lil' TOML parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "typed-ast"
 version = "1.4.3"
@@ -425,12 +718,20 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.10.0.0"
+version = "3.10.0.2"
 description = "Backported and Experimental Type Hints for Python 3.5+"
 category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "ujson"
+version = "4.2.0"
+description = "Ultra fast JSON encoder and decoder for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "wcwidth"
 version = "0.2.5"
@@ -439,9 +740,25 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "wrapt"
+version = "1.12.1"
+description = "Module for decorators, wrappers and monkey patching."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "yapf"
+version = "0.31.0"
+description = "A formatter for Python code."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "zipp"
-version = "3.4.1"
+version = "3.6.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
@@ -449,21 +766,21 @@ python-versions = ">=3.6"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
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 python-versions = "^3.7"
-content-hash = "765c40c0da71552294c3d49408c9cddce3e514a157c5422f9eb1d00f1e371b28"
+content-hash = "f55eee3ae0ca41608fea98081bf32dbcf104db9105be41571dd3cd57dd449ef7"
 
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+    {file = "ujson-4.2.0.tar.gz", hash = "sha256:fffe509f556861c7343c6cba57ed05fe7bcf4b48a934a5b946ccb45428cf8883"},
 ]
 wcwidth = [
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 ]
+wrapt = [
+    {file = "wrapt-1.12.1.tar.gz", hash = "sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"},
+]
+yapf = [
+    {file = "yapf-0.31.0-py2.py3-none-any.whl", hash = "sha256:e3a234ba8455fe201eaa649cdac872d590089a18b661e39bbac7020978dd9c2e"},
+    {file = "yapf-0.31.0.tar.gz", hash = "sha256:408fb9a2b254c302f49db83c59f9aa0b4b0fd0ec25be3a5c51181327922ff63d"},
+]
 zipp = [
-    {file = "zipp-3.4.1-py3-none-any.whl", hash = "sha256:51cb66cc54621609dd593d1787f286ee42a5c0adbb4b29abea5a63edc3e03098"},
-    {file = "zipp-3.4.1.tar.gz", hash = "sha256:3607921face881ba3e026887d8150cca609d517579abe052ac81fc5aeffdbd76"},
+    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
+    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
 ]
diff --git a/project.org b/project.org
new file mode 100644
index 00000000..61816f32
--- /dev/null
+++ b/project.org
@@ -0,0 +1,41 @@
+#+TITLE: Pythia Project Notes
+
+* Task List
+** DONE Implement ~run_mode~ in the ~dssat~ configuration.
+- Default is ~A~
+- Used to support ~forecast mode~
+** DONE Add ~FODATE~ to template
+- Default is ~-99~
+** PENDING Add ~append_column~ in the ~analytics_setup~ configuration
+- Will add a column ~x~ to the end of each line of output.
+- "appendColumns": [{"HARVEST_AREA": "from_config::$harvestArea"}, {"VNAM": "subtract::out$cnam::out$gnam"}]
+- Have to make sure the from_config is specific to a run. This means the run needs to be persisted through to the ~calculate_outputs()~ function.
+** DONE Validate ~vector::~ function works to feed any fields.
+** DONE Batch mode support
+- [X] Configuration option to specify batch file to use.
+- [X] Default the batch file to DSSBatch.v4x
+** TODO auto-include LAT/LNG if -99 in the DSSAT XFile
+** TODO Auto-generate DSSBatch.v4x when needed for batch mode.
+* Execution Notes
+** Batch file support
+In order to use batch file support modes (specified by ~CheckRunMode.f90~), you should use ~includes~ to copy the batch file to every run directory. This should be in your ~default_setup~ or ~runs~ blocks.
+*NOTE* Forecast mode (~"run_mode": "Y"~) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
+
+* Breaking Changes (v3.0)
+** Move analytics to output
+"output": [
+{
+"filename": "summary.csv",
+** Support for single output file
+"singleOutput": true,
+** Suppffort for adding columns
+"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
+** Support for filtering columns
+"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
+},
+"filename": "daily.csv",
+"singleOutput": true,
+"outputColumns": ["SOME", "VARIABLE"]
+]
+* Windows-specific issues?
+** 
diff --git a/pyproject.toml b/pyproject.toml
index a9df6fe1..2b75f69e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.0.0-beta.0"
+version = "2.1.0"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"
@@ -18,6 +18,12 @@ rtree = "^0.8"
 pytest = "^5.1"
 black = "^21.5b2"
 flake8 = "^3.9.2"
+neovim = "^0.3.1"
+python-lsp-server = {extras = ["all"], version = "^1.2.4"}
+pyls-isort = "^0.2.2"
+python-lsp-black = "^1.0.0"
+pylsp-rope = "^0.1.7"
+pyls-flake8 = "^0.4.0"
 
 [tool.poetry.scripts]
 pythia = "pythia.cli:main"
diff --git a/pythia/analytic_functions.py b/pythia/analytic_functions.py
index 44af1e90..1e6e8fe5 100644
--- a/pythia/analytic_functions.py
+++ b/pythia/analytic_functions.py
@@ -1,12 +1,14 @@
 def generate_funs(config):
     funcs = []
-    for key,funs in config.items():
+    for key, funs in config.items():
         fun = {}
         f, *args = funs.split("::")
-        if (f == "subtract"):
-            fun['fun'] = subtract
-        fun['key'] = key
-        fun['args'] = args
+        fun["key"] = key
+        fun["args"] = args
+        if f == "subtract":
+            fun["fun"] = subtract
+        if f == "from_config":
+            pass
         funcs.append(fun)
     return funcs
 
@@ -14,7 +16,7 @@ def generate_funs(config):
 def subtract(terms):
     a = _numberify_term(terms[0])
     b = _numberify_term(terms[1])
-    return a-b
+    return a - b
 
 
 def _numberify_term(term):
@@ -22,3 +24,9 @@ def _numberify_term(term):
         return float(term)
     else:
         return int(term)
+
+
+def from_config(terms):
+    lat = _numberify_term(terms[0])
+    lng = _numberify_term(terms[1])
+    return lat + lng
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 3ef4b53b..751a55af 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -2,221 +2,257 @@
 import logging
 import os
 import shutil
+from typing import Optional
 import rasterio
+from rasterio.io import DatasetReader
 import pythia.analytic_functions
 import pythia.io
 import pythia.util
+from contextlib import _GeneratorContextManager
 
 
 def get_run_basedir(config, run):
-	return os.path.join(config.get("workDir", "."), run.get("name", ""))
+    return os.path.join(config.get("workDir", "."), run.get("name", ""))
 
 
 def _generated_run_files(run_path, target_file):
-	for root, subdir, files in os.walk(run_path, topdown=False):
-		if target_file in files:
-			yield root
-	pass
+    for root, subdir, files in os.walk(run_path, topdown=False):
+        if target_file in files:
+            yield root
+    pass
 
 
 def extract_ll(path):
-	ll = path.split(os.path.sep)[-2:]
-	return tuple([pythia.util.translate_news_coords(coords) for coords in ll])
+    ll = path.split(os.path.sep)[-2:]
+    return tuple([pythia.util.translate_news_coords(coords) for coords in ll])
 
 
 # Always by default keep the per_pixel_per_management file, but create a place
 # for the single output or analytics, should we have a "final outputs"
 # directory.
 def final_outputs(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	out_files = []
-	out_dir = os.path.join(config.get("workDir", "."))
-	file_prefix = "{}_".format(analytics_config.get("per_pixel_prefix", "pp"))
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	for current_file in outputs:
-		 bn = os.path.basename(current_file)
-		 out_file = os.path.join(out_dir, bn[bn.find(file_prefix):])
-		 shutil.copyfile(current_file, out_file)
+    analytics_config = config.get("analytics_setup", {})
+    out_dir = os.path.join(config.get("workDir", "."))
+    file_prefix = "{}_".format(analytics_config.get("per_pixel_prefix", "pp"))
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    for current_file in outputs:
+        bn = os.path.basename(current_file)
+        out_file = os.path.join(out_dir, bn[bn.find(file_prefix) :])
+        shutil.copyfile(current_file, out_file)
+
 
 def filter_columns(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	columns = analytics_config.get("columns", [])
-	out_files = []
-	out_dir = os.path.join(config.get("workDir", "."), "scratch")
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	for current_file in outputs:
-		col_indexes = []
-		out_file = os.path.join(out_dir, "filtered_{}".format(os.path.basename(current_file)))
-		with open(current_file) as source, open(out_file, "w") as dest:
-			dssat_in = csv.reader(source)
-			dssat_out = csv.writer(dest)
-			try:
-				for line in dssat_in:
-					if dssat_in.line_num == 1:
-						for x, col in enumerate(line):
-							if col in columns:
-								col_indexes.append(x)
-					row = [line[idx] for idx in col_indexes]
-					dssat_out.writerow(row)
-			except csv.Error as e:
-				logging.error("CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e)
-		out_files.append(out_file)
-	return out_files
+    analytics_config = config.get("analytics_setup", {})
+    columns = analytics_config.get("columns", [])
+    out_files = []
+    out_dir = os.path.join(config.get("workDir", "."), "scratch")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    for current_file in outputs:
+        col_indexes = []
+        out_file = os.path.join(
+            out_dir, "filtered_{}".format(os.path.basename(current_file))
+        )
+        with open(current_file) as source, open(out_file, "w") as dest:
+            dssat_in = csv.reader(source)
+            dssat_out = csv.writer(dest)
+            try:
+                for line in dssat_in:
+                    if dssat_in.line_num == 1:
+                        for x, col in enumerate(line):
+                            if col in columns:
+                                col_indexes.append(x)
+                    row = [line[idx] for idx in col_indexes]
+                    dssat_out.writerow(row)
+            except csv.Error as e:
+                logging.error(
+                    "CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e
+                )
+        out_files.append(out_file)
+    return out_files
 
 
 def calculate_columns(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	calculations = analytics_config.get("calculatedColumns", [])
-	funs = pythia.analytic_functions.generate_funs(calculations)
-	arg_columns = []
-	for fun in funs:
-		for a in fun["args"]:
-			if a.startswith("$"):
-				if a.upper() not in arg_columns:
-					arg_columns.append(a[1::].upper())
-	out_files = []
-	out_dir = os.path.join(config.get("workDir", "."), "scratch")
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	for current_file in outputs:
-		col_indexes = []
-		out_file = os.path.join(out_dir, "calculated_{}".format(os.path.basename(current_file)))
-		with open(current_file) as source, open(out_file, "w") as dest:
-			dssat_in = csv.reader(source)
-			dssat_out = csv.writer(dest)
-			num_cols = 0
-			try:
-			  for line in dssat_in:
-				  if dssat_in.line_num != 1:
-					  if num_cols == 0:
-						  print("we have a problem")
-					  else:
-						  line = line[0:num_cols]
-				  if dssat_in.line_num == 1:
-					  num_cols = len(line)
-					  col_indexes = [line.index(x) for x in arg_columns]
-					  for fun in funs:
-						  line.append(fun["key"])
-					  dssat_out.writerow(line)
-				  else:
-					  for fun in funs:
-						  line.append(
-							  fun["fun"](
-								  [
-									  line[col_indexes[arg_columns.index(x[1::].upper())]]
-									  for x in fun["args"]
-								  ]
-							  )
-						  )
-					  dssat_out.writerow(line)
-			except csv.Error as e:
-				logging.error("CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e)
-			out_files.append(out_file)
-	return out_files
+    analytics_config = config.get("analytics_setup", {})
+    calculations = analytics_config.get("calculatedColumns", [])
+
+    out_files = []
+    out_dir = os.path.join(config.get("workDir", "."), "scratch")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    for current_file in outputs:
+        funs = pythia.analytic_functions.generate_funs(calculations)
+        arg_columns = []
+        for fun in funs:
+            for a in fun["args"]:
+                if a.upper() not in arg_columns:
+                    arg_columns.append(a[1::].upper())
+
+        col_indexes = []
+        out_file = os.path.join(
+            out_dir, "calculated_{}".format(os.path.basename(current_file))
+        )
+        with open(current_file) as source, open(out_file, "w") as dest:
+            dssat_in = csv.reader(source)
+            dssat_out = csv.writer(dest)
+            num_cols = 0
+            try:
+                for line in dssat_in:
+                    if dssat_in.line_num != 1:
+                        if num_cols == 0:
+                            print("we have a problem")
+                        else:
+                            line = line[0:num_cols]
+                    if dssat_in.line_num == 1:
+                        num_cols = len(line)
+                        col_indexes = [line.index(x) for x in arg_columns]
+                        for fun in funs:
+                            line.append(fun["key"])
+                        dssat_out.writerow(line)
+                    else:
+                        for fun in funs:
+                            line.append(
+                                fun["fun"](
+                                    [
+                                        line[
+                                            col_indexes[
+                                                arg_columns.index(x[1::].upper())
+                                            ]
+                                        ]
+                                        for x in fun["args"]
+                                    ]
+                                )
+                            )
+                        dssat_out.writerow(line)
+            except csv.Error as e:
+                logging.error(
+                    "CSV error in %s on line %d: %s", current_file, dssat_in.line_num, e
+                )
+            out_files.append(out_file)
+    return out_files
 
 
 def combine_outputs(config, outputs):
-	analytics_config = config.get("analytics_setup", {})
-	combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
-	out_dir = config.get("workDir", ".")
-	collected_first_line = False
-	for current_file in outputs:
-		if os.path.exists(current_file):
-			if collected_first_line:
-				mode = "a"
-			else:
-				mode = "w"
-			with open(current_file) as source, open(
-				os.path.join(out_dir, combined_file_name), mode
-			) as dest:
-				for i, line in enumerate(source):
-					if i == 0:
-						if not collected_first_line:
-							dest.write(line)
-							collected_first_line = True
-					else:
-						dest.write(line)
+    analytics_config = config.get("analytics_setup", {})
+    combined_file_name = "{}.csv".format(analytics_config.get("per_pixel_prefix", "pp"))
+    out_dir = config.get("workDir", ".")
+    collected_first_line = False
+    for current_file in outputs:
+        if os.path.exists(current_file):
+            if collected_first_line:
+                mode = "a"
+            else:
+                mode = "w"
+            with open(current_file) as source, open(
+                os.path.join(out_dir, combined_file_name), mode
+            ) as dest:
+                for i, line in enumerate(source):
+                    if i == 0:
+                        if not collected_first_line:
+                            dest.write(line)
+                            collected_first_line = True
+                    else:
+                        dest.write(line)
 
 
 def collate_outputs(config, run):
-	analytics_config = config.get("analytics_setup", {})
-	per_pixel_file_name = "{}_{}.csv".format(
-		analytics_config.get("per_pixel_prefix", "pp"), run["name"]
-	)
-	work_dir = get_run_basedir(config, run)
-	out_dir = os.path.join(config.get("workDir", "."), "scratch")
-	if not os.path.exists(out_dir):
-		os.makedirs(out_dir)
-	out_file = os.path.join(out_dir, per_pixel_file_name)
-	harea_info = run.get("harvestArea", None)
-	collected_first_line = False
-	for current_dir in _generated_run_files(work_dir, "summary.csv"):
-		lat, lng = extract_ll(current_dir)
-		if collected_first_line:
-			mode = "a"
-		else:
-			mode = "w"
-		with open(os.path.join(current_dir, "summary.csv")) as source, open(out_file, mode) as dest:
-			additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
-			ds = None
-			band = None
-			if harea_info:
-				additional_headers = f'{additional_headers},HARVEST_AREA'
-				harea_tiff = harea_info.split("::")[1]
-				ds = rasterio.open(harea_tiff)
-				band = ds.read(1)
-			for i, line in enumerate(source):
-				if i == 0:
-					if not collected_first_line:
-						dest.write(
-							"{},{}\n".format(
-								additional_headers,
-								line.strip()
-							)
-						)
-						collected_first_line = True
-				else:
-					to_write = (lat, lng, run.get("name", ""))
-					if ds is not None and not ds.closed:
-						harea = pythia.io.get_site_raster_value(
-							ds, band, (float(lng), float(lat))
-						)
-						if harea is None:
-							harea = 0
-							logging.warning("%s, %s is giving an invalid harea, replacing with 0")
-						harea_s = "{:0.2f}".format(harea)
-						to_write = to_write + (harea_s,)
-					to_write = to_write + (line.strip()+"\n",)
-					dest.write(",".join(to_write))
-			if ds is not None:
-				ds.close()
-	return out_file
+    analytics_config = config.get("analytics_setup", {})
+    per_pixel_file_name = "{}_{}.csv".format(
+        analytics_config.get("per_pixel_prefix", "pp"), run["name"]
+    )
+    work_dir = get_run_basedir(config, run)
+    out_dir = os.path.join(config.get("workDir", "."), "scratch")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    out_file = os.path.join(out_dir, per_pixel_file_name)
+    harea_info = run.get("harvestArea", None)
+    pop_info = run.get("population", None)
+    collected_first_line = False
+    for current_dir in _generated_run_files(work_dir, "summary.csv"):
+        lat, lng = extract_ll(current_dir)
+        if collected_first_line:
+            mode = "a"
+        else:
+            mode = "w"
+        with open(os.path.join(current_dir, "summary.csv")) as source, open(
+            out_file, mode
+        ) as dest:
+            additional_headers = "LATITUDE,LONGITUDE,RUN_NAME"
+            ds_harea: Optional[_GeneratorContextManager[DatasetReader]] = None
+            ds_pop: Optional[_GeneratorContextManager[DatasetReader]] = None
+            band_harea = None
+            band_pop = None
+            if harea_info:
+                additional_headers = f"{additional_headers},HARVEST_AREA"
+                harea_tiff = harea_info.split("::")[1]
+                ds_harea = rasterio.open(harea_tiff)
+                band_harea = ds_harea.read(1)
+            if pop_info:
+                additional_headers = f"{additional_headers},POPULATION"
+                pop_tiff = pop_info.split("::")[1]
+                ds_pop = rasterio.open(pop_tiff)
+                band_pop = ds_pop.read(1)
+            for i, line in enumerate(source):
+                if i == 0:
+                    if not collected_first_line:
+                        dest.write("{},{}\n".format(additional_headers, line.strip()))
+                        collected_first_line = True
+                else:
+                    to_write = (lat, lng, run.get("name", ""))
+                    if ds_harea is not None and not ds_harea.closed:
+                        harea = pythia.io.get_site_raster_value(
+                            ds_harea, band_harea, (float(lng), float(lat))
+                        )
+                        if harea is None:
+                            harea = 0
+                            logging.warning(
+                                "%s, %s is giving an invalid harea, replacing with 0"
+                            )
+                        harea_s = "{:0.2f}".format(harea)
+                        to_write = to_write + (harea_s,)
+                    if ds_pop is not None and not ds_pop.closed:
+                        pop = pythia.io.get_site_raster_value(
+                            ds_pop, band_pop, (float(lng), float(lat))
+                        )
+                        if pop is None:
+                            pop = 0
+                            logging.warning(
+                                "%s, %s is giving an invalid population, replacing with 0"
+                            )
+                        pop_s = "{:0.2f}".format(pop)
+                        to_write = to_write + (pop_s,)
+                    to_write = to_write + (line.strip() + "\n",)
+                    dest.write(",".join(to_write))
+            if ds_harea is not None:
+                ds_harea.close()
+            if ds_pop is not None:
+                ds_pop.close()
+    return out_file
 
 
 def execute(config, plugins):
-	runs = config.get("runs", [])
-	analytics_config = config.get("analytics_setup", None)
-	run_outputs = []
-	calculated = None
-	filtered = None
-	if not analytics_config:
-		return
-	if len(runs) == 0:
-		return
-	for run in runs:
-		run_outputs.append(collate_outputs(config, run))
-	# Apply all the filters first
-	if analytics_config.get("calculatedColumns", None):
-		calculated = calculate_columns(config, run_outputs)
-	if calculated is None:
-		calculated = run_outputs
-	if analytics_config.get("columns", None):
-		filtered = filter_columns(config, calculated)
-	if filtered is None:
-		filtered = calculated
-	if analytics_config.get("singleOutput", False):
-		combine_outputs(config, filtered)
-	else:
-		final_outputs(config, filtered)
+    runs = config.get("runs", [])
+    analytics_config = config.get("analytics_setup", None)
+    run_outputs = []
+    calculated = None
+    filtered = None
+    if not analytics_config:
+        return
+    if len(runs) == 0:
+        return
+    for run in runs:
+        run_outputs.append(collate_outputs(config, run))
+    # Apply all the filters first
+    if analytics_config.get("calculatedColumns", None):
+        calculated = calculate_columns(config, run_outputs)
+    if calculated is None:
+        calculated = run_outputs
+    if analytics_config.get("columns", None):
+        filtered = filter_columns(config, calculated)
+    if filtered is None:
+        filtered = calculated
+    if analytics_config.get("singleOutput", False):
+        combine_outputs(config, filtered)
+    else:
+        final_outputs(config, filtered)
diff --git a/pythia/cache_manager.py b/pythia/cache_manager.py
index a4d06b03..039e6af9 100644
--- a/pythia/cache_manager.py
+++ b/pythia/cache_manager.py
@@ -1 +1 @@
-cache = {}
\ No newline at end of file
+cache = {}
diff --git a/pythia/cli.py b/pythia/cli.py
index 1f0f94f7..f1be2007 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -14,22 +14,33 @@
 def main():
     parser = argparse.ArgumentParser(prog="pythia")
     parser.add_argument("config", help="JSON configuration file to run")
-    parser.add_argument("--all", action="store_true", help="Run all the steps in pythia")
+    parser.add_argument(
+        "--all", action="store_true", help="Run all the steps in pythia"
+    )
     parser.add_argument(
         "--export-runlist",
         action="store_true",
         help="Export a list of all the directories to be run",
     )
-    parser.add_argument("--setup", action="store_true", help="Setup DSSAT run structure and files")
-    parser.add_argument("--run-dssat", action="store_true", help="Run DSSAT over the run structure")
+    parser.add_argument(
+        "--setup", action="store_true", help="Setup DSSAT run structure and files"
+    )
+    parser.add_argument(
+        "--run-dssat", action="store_true", help="Run DSSAT over the run structure"
+    )
     parser.add_argument(
         "--analyze", action="store_true", help="Run the analysis for the DSSAT runs"
     )
     parser.add_argument(
-        "--clean-work-dir", action="store_true", help="Clean the work directory prior to run"
+        "--clean-work-dir",
+        action="store_true",
+        help="Clean the work directory prior to run",
     )
     parser.add_argument(
-            "--logfile-prefix", default="pythia", help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log")
+        "--logfile-prefix",
+        default="pythia",
+        help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log",
+    )
     args = parser.parse_args()
 
     if not args.config:
@@ -37,12 +48,19 @@ def main():
     else:
         now = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
         logging.getLogger("pythia_app")
-        logging.basicConfig(level=logging.INFO, filename="{}-{}.log".format(args.logfile_prefix, now), filemode="w")
+        logging.basicConfig(
+            level=logging.INFO,
+            filename="{}-{}.log".format(args.logfile_prefix, now),
+            filemode="w",
+        )
         config = pythia.config.load_config(args.config)
         if args is None or not config:
             print("Invalid configuration file")
         else:
-            logging.info("Pythia started: %s", datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
+            logging.info(
+                "Pythia started: %s",
+                datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
+            )
             if args.clean_work_dir:
                 print("Cleaning the work directory")
                 if os.path.exists(config["workDir"]):
@@ -64,4 +82,7 @@ def main():
             if args.all or args.analyze:
                 print("Running simple analytics over DSSAT directory structure")
                 pythia.analytics.execute(config, plugins)
-            logging.info("Pythia completed: %s", datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
+            logging.info(
+                "Pythia completed: %s",
+                datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
+            )
diff --git a/pythia/config.py b/pythia/config.py
index d3c8cbcd..d4a66029 100644
--- a/pythia/config.py
+++ b/pythia/config.py
@@ -13,8 +13,7 @@ def load_config(config_file, validate=True, merge=True):
         with open(config_file) as f:
             config = json.load(f)
     except OSError:
-        logging.error(
-            "Error opening configuration file: {}".format(config_file))
+        logging.error("Error opening configuration file: {}".format(config_file))
     else:
         if validate:
             if not _validate_config(config):
@@ -27,11 +26,14 @@ def load_config(config_file, validate=True, merge=True):
 def _check_raster_profile(raster_file, cached_crs):
     logging.debug("Checking file {}".format(raster_file))
     try:
-        current_crs = pythia.io.get_rio_profile(raster_file)['crs'].data
+        current_crs = pythia.io.get_rio_profile(raster_file)["crs"].data
         if cached_crs:
             if cached_crs != current_crs:
-                logging.error("CRS mismatch for file {}. {} -> {}. Please reconcile.".format(
-                    raster_file, cached_crs['init'], current_crs['init']))
+                logging.error(
+                    "CRS mismatch for file {}. {} -> {}. Please reconcile.".format(
+                        raster_file, cached_crs["init"], current_crs["init"]
+                    )
+                )
             return cached_crs == current_crs, cached_crs
         else:
             return True, current_crs
@@ -44,9 +46,17 @@ def _validate_config(config):
     valid = True
     # Raster check pass 1 - all files are available and of the same projections
     values_iter = itertools.chain.from_iterable(
-        [list(config["default_setup"].values())] + [list(r.values()) for r in config["runs"]])
-    rasters = list(set([pythia.functions.extract_raster(raster) for raster in
-                        list(filter(lambda x: "raster::" in str(x), values_iter))]))
+        [list(config["default_setup"].values())]
+        + [list(r.values()) for r in config["runs"]]
+    )
+    rasters = list(
+        set(
+            [
+                pythia.functions.extract_raster(raster)
+                for raster in list(filter(lambda x: "raster::" in str(x), values_iter))
+            ]
+        )
+    )
     cached_crs = None
     for r in rasters:
         current_return, cached_crs = _check_raster_profile(r, cached_crs)
@@ -75,5 +85,7 @@ def _set_run_workdir(run, root, idx):
 
 def _merge_runs(config):
     runs = [_merge_default(config["default_setup"], r) for r in config["runs"]]
-    runs = [_set_run_workdir(r, config.get("workDir", "."), i) for (i, r) in enumerate(runs)]
+    runs = [
+        _set_run_workdir(r, config.get("workDir", "."), i) for (i, r) in enumerate(runs)
+    ]
     return runs
diff --git a/pythia/dssat.py b/pythia/dssat.py
index 222c1394..9130e424 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -7,8 +7,11 @@
 
 def _run_dssat(details, config):
     logging.debug("Current WD: {}".format(os.getcwd()))
-    command_string = "cd {} && {} A {}".format(
-        details["dir"], config["dssat"]["executable"], details["file"]
+    run_mode = "A"
+    if "run_mode" in config["dssat"]:
+        run_mode = config["dssat"]["run_mode"].upper()
+    command_string = "cd {} && {} {} {}".format(
+        details["dir"], config["dssat"]["executable"], run_mode, details["file"]
     )
     # print(".", end="", flush=True)
     dssat = subprocess.Popen(
@@ -22,9 +25,33 @@ def _run_dssat(details, config):
 def _generate_run_list(config):
     runlist = []
     for root, _, files in os.walk(config.get("workDir", "."), topdown=False):
+        batch_mode = config["dssat"].get("run_mode", "A") in {
+            "B",
+            "E",
+            "F",
+            "L",
+            "N",
+            "Q",
+            "S",
+            "T",
+            "Y",
+        }
+        target = None
+        if batch_mode:
+            target = config["dssat"].get("batch_file", None)
+        else:
+            target = config["dssat"].get("filex", None)
         for name in files:
-            if name.upper().endswith("X"):
-                runlist.append({"dir": root, "file": name})
+            if target is not None:
+                if name == target:
+                    runlist.append({"dir": root, "file": name})
+            else:
+                if batch_mode:
+                    if name.upper().startswith("DSSBATCH"):
+                        runlist.append({"dir": root, "file": name})
+                else:
+                    if name.upper().endswith("X"):
+                        runlist.append({"dir": root, "file": name})
     return runlist
 
 
diff --git a/pythia/functions.py b/pythia/functions.py
index 87db4fe3..cee5fb86 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -164,7 +164,7 @@ def split_fert_dap_percent(k, run, context, _):
 def assign_by_raster_value(k, run, context, _):
     init_args = run[k].split("::")[1:]
     if "raster" in init_args:
-        args = init_args[init_args.index("raster") + 2:]
+        args = init_args[init_args.index("raster") + 2 :]
     else:
         logging.error("Need to specify a raster for %s:assign_by_value", k)
         return None
diff --git a/pythia/io.py b/pythia/io.py
index 4af2658f..e4f35fab 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -18,7 +18,7 @@ def get_site_raster_value(dataset, band, site):
     data = []
     try:
         data = band[row, col]
-        if (data is ma.masked):
+        if data is ma.masked:
             data = None
     except IndexError:
         data = None
@@ -78,7 +78,7 @@ def get_shp_profile(f):
 
 def extract_vector_coords(f):
     points = []
-    with fiona.open(f, 'r') as source:
+    with fiona.open(f, "r") as source:
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
                 points.append(feature["geometry"]["coordinates"][0])
@@ -89,7 +89,7 @@ def extract_vector_coords(f):
 
 def find_vector_coords(f, lng, lat, a):
     coords = (lng, lat)
-    with fiona.open(f, 'r') as source:
+    with fiona.open(f, "r") as source:
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
                 if coords in feature["geometry"]["coordinates"]:
@@ -103,15 +103,21 @@ def find_closest_vector_coords(f, lng, lat, a):
     coords = Point(lng, lat)
     points = []
     ids = []
-    with fiona.open(f, 'r') as source:
+    with fiona.open(f, "r") as source:
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
-                points.extend([Point(p[0], p[1]) for p in feature["geometry"]["coordinates"]])
-                ids.extend([feature["properties"][a]] * len(feature["geometry"]["coordinates"]))
+                points.extend(
+                    [Point(p[0], p[1]) for p in feature["geometry"]["coordinates"]]
+                )
+                ids.extend(
+                    [feature["properties"][a]] * len(feature["geometry"]["coordinates"])
+                )
             if feature["geometry"]["type"] == "Point":
                 points.append(
-                    Point(feature["geometry"]["coordinates"][0],
-                          feature["geometry"]["coordinates"][1])
+                    Point(
+                        feature["geometry"]["coordinates"][0],
+                        feature["geometry"]["coordinates"][1],
+                    )
                 )
                 ids.append(feature["properties"][a])
     mp = MultiPoint(points)
diff --git a/pythia/peerless.py b/pythia/peerless.py
index 7a05d696..72459e14 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -52,7 +52,9 @@ def symlink_wth_soil(output_dir, config, context):
     for soil in context["soilFiles"]:
         soil_file = os.path.join(output_dir, os.path.basename(soil))
         if not os.path.exists(soil_file):
-            os.symlink(os.path.abspath(soil), os.path.join(output_dir, os.path.basename(soil)))
+            os.symlink(
+                os.path.abspath(soil), os.path.join(output_dir, os.path.basename(soil))
+            )
 
 
 def compose_peerless(context, config, env):
@@ -85,7 +87,9 @@ def execute(config, plugins):
                 # Post context hook
                 logging.debug("[PEERLESS] Running post_build_context plugins")
                 context = pythia.plugin.run_plugin_functions(
-                    pythia.plugin.PluginHook.post_build_context, plugins, context=context
+                    pythia.plugin.PluginHook.post_build_context,
+                    plugins,
+                    context=context,
                 )
                 runlist.append(os.path.abspath(compose_peerless(context, config, env)))
             else:
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 16fa0274..9740aadf 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -20,18 +20,24 @@ class PluginHook(Enum):
 def register_plugin_function(hook, fun, config, plugins):
     # Check to see if the hook is a PluginHook
     if not isinstance(hook, PluginHook):
-        logging.warning("[PLUGIN] Ignoring {} because {} is not a PluginHook".format(fun, hook))
+        logging.warning(
+            "[PLUGIN] Ignoring {} because {} is not a PluginHook".format(fun, hook)
+        )
         return plugins
 
     # Check to see if the function is a function.
     if not callable(fun):
-        logging.warning("[PLUGIN] Ignoring {} because {} is not a function.".format(fun, fun))
+        logging.warning(
+            "[PLUGIN] Ignoring {} because {} is not a function.".format(fun, fun)
+        )
         return plugins
 
     # Check to see if the config is an object.
     if not isinstance(config, dict):
         logging.warning(
-            "[PLUGIN] Ignoring {} because {} is not a valid configuration".format(fun, config)
+            "[PLUGIN] Ignoring {} because {} is not a valid configuration".format(
+                fun, config
+            )
         )
         return plugins
 
@@ -76,12 +82,14 @@ def load_plugins(config, plugins={}, module_prefix="pythia.plugins"):
         if spec is None:
             logging.warning("[PLUGIN] Cannot find plugin: {}".format(plugin["plugin"]))
             continue
-        _loaded = importlib.import_module("{}.{}".format(module_prefix, plugin["plugin"]))
+        _loaded = importlib.import_module(
+            "{}.{}".format(module_prefix, plugin["plugin"])
+        )
         # TODO: Check to see if the config works for the plugin
         # TODO: Check to see if the plugin conforms to the correct signature (optional)
 
         # Call plugin initialization
-        _imported = _loaded.initialize(plugin.get("params", {}), _imported, config)
+        _imported = _loaded.initialize(plugin, _imported, config)
     return _imported
 
 
@@ -94,7 +102,13 @@ def run_plugin_functions(hook, plugins, **kwargs):
     if hook in plugins:
         for plugin_fun in plugins[hook]:
             if hook == PluginHook.post_config:
-                _return = {**_return, **plugin_fun["fun"](plugin_fun.get("config", {}), _return)}
+                _return = {
+                    **_return,
+                    **plugin_fun["fun"](plugin_fun.get("config", {}), _return),
+                }
             elif hook == PluginHook.post_build_context:
-                _return = {**_return, **plugin_fun["fun"](plugin_fun.get("config", {}), _return)}
+                _return = {
+                    **_return,
+                    **plugin_fun["fun"](plugin_fun.get("config", {}), _return),
+                }
     return _return
diff --git a/pythia/plugins/sensitivity_plugin/__init__.py b/pythia/plugins/sensitivity_plugin/__init__.py
index 43b4e979..1694ba1c 100644
--- a/pythia/plugins/sensitivity_plugin/__init__.py
+++ b/pythia/plugins/sensitivity_plugin/__init__.py
@@ -20,6 +20,7 @@
             "values" : ["M0.25", "M1.0", "M1.25"]
         }
     },
+    "no_rename": true, (optional, defaults to false)
     "order": 1
 ]
 """
@@ -37,27 +38,44 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[Sensitivity Plugin] Initializing plugin")
-    plugins = register_plugin_function(PluginHook.post_config, generate_sensitivity_runs, config,
-                                       plugins)
-    plugins = register_plugin_function(PluginHook.post_build_context, post_build_context_apply_factors, config, plugins)
-    plugins = register_plugin_function(PluginHook.post_build_context,
-                                       post_build_context_apply_static_factors, config, plugins)
+    cfg = config["params"]
+    cfg["no_rename"] = config.get("no_rename", False)
+    plugins = register_plugin_function(
+        PluginHook.post_config, generate_sensitivity_runs, cfg, plugins
+    )
+    plugins = register_plugin_function(
+        PluginHook.post_build_context, post_build_context_apply_factors, cfg, plugins
+    )
+    plugins = register_plugin_function(
+        PluginHook.post_build_context,
+        post_build_context_apply_static_factors,
+        cfg,
+        plugins,
+    )
     return plugins
 
 
 def _assign_static(sens, hook, key, plugin_config):
     if key not in sens[hook]:
         sens[hook][key] = []
-    sens[hook][key].append({"var": key, "method": plugin_config[key]["method"],
-                            "val": plugin_config[key]["value"], "hook": hook,
-                            "from": plugin_config[key].get("from", key)})
+    sens[hook][key].append(
+        {
+            "var": key,
+            "method": plugin_config[key]["method"],
+            "val": plugin_config[key]["value"],
+            "hook": hook,
+            "from": plugin_config[key].get("from", key),
+        }
+    )
 
 
 def _assign_factorial(sens, hook, key, plugin_config):
     if key not in sens[hook]:
         sens[hook][key] = []
     for v in plugin_config[key]["values"]:
-        sens[hook][key].append({"var": key, "method": plugin_config[key]["method"], "val": v, "hook": hook})
+        sens[hook][key].append(
+            {"var": key, "method": plugin_config[key]["method"], "val": v, "hook": hook}
+        )
 
 
 def merge_static(statics, factor):
@@ -65,12 +83,16 @@ def merge_static(statics, factor):
 
 
 def generate_sensitivity_runs(plugin_config={}, full_config={}):
-    sens = {"_sens_pre_context": {},
-            "_sens_pre_context_static": {},
-            "_sens_post_context": {},
-            "_sens_post_context_static": {}}
+    sens = {
+        "_sens_pre_context": {},
+        "_sens_pre_context_static": {},
+        "_sens_post_context": {},
+        "_sens_post_context_static": {},
+    }
     # First we organize them
     for k in plugin_config.keys():
+        if k == "no_rename":
+            continue
         hook = plugin_config[k].get("hook", "post_config").casefold()
         static = plugin_config[k].get("static", False)
         context_string = None
@@ -79,13 +101,23 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         elif hook == "post_build_context":
             context_string = "_sens_post_context"
         if static:
-            _assign_static(sens, context_string+"_static", k, plugin_config)
+            _assign_static(sens, context_string + "_static", k, plugin_config)
         else:
             _assign_factorial(sens, context_string, k, plugin_config)
 
-    factorial = list(itertools.product(*[*sens["_sens_pre_context"].values(), *sens["_sens_post_context"].values()]))
-    statics = list(itertools.chain.from_iterable(
-        [*sens["_sens_pre_context_static"].values(), *sens["_sens_post_context_static"].values()]))
+    factorial = list(
+        itertools.product(
+            *[*sens["_sens_pre_context"].values(), *sens["_sens_post_context"].values()]
+        )
+    )
+    statics = list(
+        itertools.chain.from_iterable(
+            [
+                *sens["_sens_pre_context_static"].values(),
+                *sens["_sens_post_context_static"].values(),
+            ]
+        )
+    )
     factors = [merge_static(statics, f) for f in factorial]
     # Next we generate the new runs for each analysis
     runs = full_config.get("runs", [])
@@ -94,9 +126,10 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         current_name = run["name"]
         current_workDir = run["workDir"]
         for factor in factors:
-            f = generate_factorial_name(factor)
-            run["name"] = current_name + "__" + f
-            run["workDir"] = current_workDir + "__" + f
+            if not plugin_config.get("no_rename", False):
+                f = generate_factorial_name(factor)
+                run["name"] = current_name + "__" + f
+                run["workDir"] = current_workDir + "__" + f
             out_runs.append({**run, **{"_sens": factor}})
     out_runs = [apply_factors("_sens_pre_context", run) for run in out_runs]
     out_runs = [apply_factors("_sens_pre_context_static", run) for run in out_runs]
@@ -105,7 +138,13 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
 
 
 def generate_factorial_name(factors):
-    return "__".join([factor["var"]+str(factor["val"]) for factor in factors if factor["hook"].endswith("context")])
+    return "__".join(
+        [
+            factor["var"] + str(factor["val"])
+            for factor in factors
+            if factor["hook"].endswith("context")
+        ]
+    )
 
 
 def post_build_context_apply_factors(config={}, context={}):
@@ -119,9 +158,7 @@ def post_build_context_apply_static_factors(config={}, context={}):
 def apply_factors(hook, current_context):
     if current_context is None:
         return
-    call_list = {"date_offset": date_offset,
-                 "offset": offset,
-                 "env_mod": env_mod}
+    call_list = {"date_offset": date_offset, "offset": offset, "env_mod": env_mod}
     current_factors = [f for f in current_context["_sens"] if f["hook"] == hook]
     for cf in current_factors:
         cval = None
@@ -148,7 +185,7 @@ def date_offset(d, offset):
 
 
 def offset(v, offset):
-    return v+offset
+    return v + offset
 
 
 def env_mod(v, value):
diff --git a/pythia/plugins/test_plugin/__init__.py b/pythia/plugins/test_plugin/__init__.py
index 56c44b82..b4a1e4ac 100644
--- a/pythia/plugins/test_plugin/__init__.py
+++ b/pythia/plugins/test_plugin/__init__.py
@@ -4,7 +4,9 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[TEST PLUGIN] Initializing plugin")
-    plugins = register_plugin_function(PluginHook.post_config, sample_function, config, plugins)
+    plugins = register_plugin_function(
+        PluginHook.post_config, sample_function, config, plugins
+    )
     plugins = register_plugin_function(
         PluginHook.post_build_context, contexted_function, config, plugins
     )
diff --git a/pythia/plugins/weather_forecast_simple/__init__.py b/pythia/plugins/weather_forecast_simple/__init__.py
index 5dc6f03a..30071fb3 100644
--- a/pythia/plugins/weather_forecast_simple/__init__.py
+++ b/pythia/plugins/weather_forecast_simple/__init__.py
@@ -18,28 +18,33 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[SIMPLE WEATHER FORECAST PLUGIN] Initializing plugin")
-    config["weatherDir"] = full_config["weatherDir"]
-    config["start_date"] = pythia.util.to_julian_date(
-        pythia.util.from_iso_date(config["start_date"])
+    cfg = config["params"]
+    cfg["weatherDir"] = full_config["weatherDir"]
+    cfg["start_date"] = pythia.util.to_julian_date(
+        pythia.util.from_iso_date(cfg["start_date"])
     )
-    config["end_date"] = pythia.util.to_julian_date(pythia.util.from_iso_date(config["end_date"]))
-    config["start_on"] = config["start_date"][2:5]
-    config["end_on"] = config["end_date"][2:5]
+    cfg["end_date"] = pythia.util.to_julian_date(
+        pythia.util.from_iso_date(cfg["end_date"])
+    )
+    cfg["start_on"] = cfg["start_date"][2:5]
+    cfg["end_on"] = cfg["end_date"][2:5]
     return register_plugin_function(
-        PluginHook.post_build_context, construct_pixel_forecast, config, plugins
+        PluginHook.post_build_context, construct_pixel_forecast, cfg, plugins
     )
 
 
 def construct_pixel_forecast(config={}, context={}):
     """NOTE: This function is NOT side-effect free. It does I/O to create a new file in the
-       context["contextWorkDir"]. But this side-effect also is intentional to interrupt the
-       creation of the symlinks further along the process."""
+    context["contextWorkDir"]. But this side-effect also is intentional to interrupt the
+    creation of the symlinks further along the process."""
 
     """TODO: Fix the wrap around case for leap years"""
 
     logging.debug("[SIMPLE WEATHER FORECAST PLUGIN] Running construct_pixel_forecast()")
     source_weather = os.path.join(config["weatherDir"], context["wthFile"])
-    dest_weather = os.path.join(context["contextWorkDir"], "{}.WTH".format(config["wsta"]))
+    dest_weather = os.path.join(
+        context["contextWorkDir"], "{}.WTH".format(config["wsta"])
+    )
     target_lines = []
     with open(source_weather) as source:
         scraping_lines = False
diff --git a/pythia/soil_handler.py b/pythia/soil_handler.py
index 63589393..65231d47 100644
--- a/pythia/soil_handler.py
+++ b/pythia/soil_handler.py
@@ -157,4 +157,5 @@ def calculateICLayerData(soilData, run):
             calculateH2O(run["icsw%"], slll, sdul),
             [icnd * 0.1 for icnd in icndist],
             [icnd * 0.9 for icnd in icndist],
-        ])
+        ]
+    )
diff --git a/pythia/template.py b/pythia/template.py
index 36f53dd9..dd2361fd 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -12,9 +12,9 @@
     "icres": {"length": 6},
     "icren": {"length": 6},
     "icbl": {"length": 6},
-    "sh2o": {"length": 6},
-    "snh4": {"length": 6},
-    "sno3": {"length": 6},
+    "sh2o": {"fmt": ":>6.3f"},
+    "snh4": {"fmt": ":>6.2f"},
+    "sno3": {"fmt": ":>6.2f"},
     "fdate": {"length": 5},
     "fdap": {"length": 5},
     "famn": {"length": 5},
@@ -25,43 +25,66 @@
     "fhdur": {"length": 5},
     "irrig": {"length": 5},
     "erain": {"raw": "M{:>4}"},
-    "ph2ol": {"length": 5}
+    "ph2ol": {"length": 5},
+    "fodate": {"length": 7},
+    "pdate": {"length": 5},
+    "pfrst": {"length": 5},
+    "plast": {"length": 5},
+    "hdate": {"length": 5}
 }
 
-_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate"]
+_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate", "hdate"]
+_t_date_fields_4 = ["fodate"]
 
 
 def init_engine(template_dir):
-    return Environment(loader=FileSystemLoader(template_dir), trim_blocks=True, lstrip_blocks=True)
+    return Environment(
+        loader=FileSystemLoader(template_dir), trim_blocks=True, lstrip_blocks=True
+    )
+
+
+def wrap_format(k, v):
+    fmt = ""
+    if k in _t_formats:
+        if "raw" in _t_formats[k]:
+            fmt = _t_formats[k]["raw"]
+        elif "fmt" in _t_formats[k]:
+            fmt = "{" + _t_formats[k]["fmt"] + "}"
+        else:
+            fmt_align = _t_formats[k].get("align", ":>")
+            fmt_pad = _t_formats[k].get("pad_with", "")
+            if isinstance(v, float):
+                fmt_len = "{}.1f".format(_t_formats[k]["length"])
+            elif isinstance(v, int):
+                fmt_len = "{}d".format(_t_formats[k]["length"])
+            else:
+                if "length" in _t_formats[k]:
+                    fmt_len = "{}".format(_t_formats[k]["length"])
+                else:
+                    fmt_len = ""
+            fmt = "{" + fmt_align + fmt_pad + fmt_len + "}"
+    else:
+        fmt = "{}"
+    return fmt.format(v)
 
 
 def auto_format_dict(d):
     if isinstance(d, str):
         return d
     clean = {}
+    for k in _t_formats:
+        v = _t_formats[k]
+        if "default" in v:
+            clean[k] = wrap_format(k, v["default"])
+        else:
+            clean[k] = wrap_format(k, -99)
     for k, v in d.items():
         if k in _t_date_fields and "::" not in v:
             clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
+        elif k in _t_date_fields_4 and "::" not in v:
+            clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
         elif k in _t_formats:
-            fmt = ""
-            if "raw" in _t_formats[k]:
-                fmt = _t_formats[k]["raw"]
-            elif "fmt" in _t_formats[k]:
-                fmt = "{" + _t_formats[k]["fmt"] + "}"
-            else:
-                fmt_align = _t_formats[k].get("align", ":>")
-                fmt_pad = _t_formats[k].get("pad_with", "")
-                if isinstance(v, float):
-                    fmt_len = "{}.1f".format(_t_formats[k]["length"])
-                elif isinstance(v, int):
-                    fmt_len = "{}d".format(_t_formats[k]["length"])
-                else:
-                    if "length" in _t_formats[k]:
-                        fmt_len = "{}".format(_t_formats[k]["length"])
-                    else:
-                        fmt_len = ""
-                fmt = "{" + fmt_align + fmt_pad + fmt_len + "}"
-            clean[k] = fmt.format(v)
+            clean[k] = wrap_format(k, v)
         elif isinstance(v, dict):
             clean[k] = auto_format_dict(v)
         elif isinstance(v, list) and not isinstance(v, str):
diff --git a/pythia/tests/plugin_test.py b/pythia/tests/plugin_test.py
index b577c830..345fee77 100644
--- a/pythia/tests/plugin_test.py
+++ b/pythia/tests/plugin_test.py
@@ -1,4 +1,9 @@
-from pythia.plugin import PluginHook, register_plugin_function, load_plugins, run_plugin_functions
+from pythia.plugin import (
+    PluginHook,
+    register_plugin_function,
+    load_plugins,
+    run_plugin_functions,
+)
 
 
 def test_register_with_invalid_hook():
@@ -9,13 +14,17 @@ def test_register_with_invalid_hook():
 
 def test_register_with_invalid_fun():
     plugins = {}
-    plugins1 = register_plugin_function(PluginHook.analyze_file, "not a function", "", plugins)
+    plugins1 = register_plugin_function(
+        PluginHook.analyze_file, "not a function", "", plugins
+    )
     assert plugins1 == {}
 
 
 def test_register_with_invalid_config():
     plugins = {}
-    plugins1 = register_plugin_function(PluginHook.post_analysis, sample_function, "", plugins)
+    plugins1 = register_plugin_function(
+        PluginHook.post_analysis, sample_function, "", plugins
+    )
     assert plugins1 == {}
 
 
@@ -23,19 +32,27 @@ def test_register_twice():
     plugins = {}
     plugins1 = {}
     plugins2 = {}
-    plugins1 = register_plugin_function(PluginHook.analyze_file, sample_function, {}, plugins)
+    plugins1 = register_plugin_function(
+        PluginHook.analyze_file, sample_function, {}, plugins
+    )
     plugins2 = register_plugin_function(
         PluginHook.analyze_file, sample_function, {"a": 1}, plugins1
     )
-    assert plugins1 == {PluginHook.analyze_file: [{"fun": sample_function, "config": {}}]}
+    assert plugins1 == {
+        PluginHook.analyze_file: [{"fun": sample_function, "config": {}}]
+    }
     assert plugins1 == plugins2
 
 
 def test_register_properly():
     plugins = {}
     plugins1 = {}
-    plugins1 = register_plugin_function(PluginHook.post_build_context, sample_function, {}, plugins)
-    assert plugins1 == {PluginHook.post_build_context: [{"fun": sample_function, "config": {}}]}
+    plugins1 = register_plugin_function(
+        PluginHook.post_build_context, sample_function, {}, plugins
+    )
+    assert plugins1 == {
+        PluginHook.post_build_context: [{"fun": sample_function, "config": {}}]
+    }
 
 
 def sample_function(config, context):
@@ -53,7 +70,9 @@ def test_load_plugin():
     assert plugins1[PluginHook.post_config] == [
         {"fun": pythia.plugins.test_plugin.sample_function, "config": {}}
     ]
-    assert plugins1 != {PluginHook.post_config: [{"fun": sample_function, "config": {}}]}
+    assert plugins1 != {
+        PluginHook.post_config: [{"fun": sample_function, "config": {}}]
+    }
 
 
 def test_plugin_manual_execution():
@@ -72,7 +91,9 @@ def test_plugin_auto_execution():
     plugins1 = {}
     plugins1 = load_plugins(config, plugins)
     context = {"context_value": 7}
-    context1 = run_plugin_functions(PluginHook.post_build_context, plugins1, context=context)
+    context1 = run_plugin_functions(
+        PluginHook.post_build_context, plugins1, context=context
+    )
     context2 = run_plugin_functions(PluginHook.post_build_context, plugins1)
     assert context1 != context
     assert context1["context_value"] == 8
@@ -84,8 +105,12 @@ def test_no_plugin_does_not_change_context():
     plugins = {}
     plugins1 = load_plugins(config, plugins)
     context = {"hello": "there"}
-    context1 = run_plugin_functions(PluginHook.post_build_context, plugins, context=context)
+    context1 = run_plugin_functions(
+        PluginHook.post_build_context, plugins, context=context
+    )
     assert context == context1
-    context2 = run_plugin_functions(PluginHook.post_build_context, plugins1, context=context)
+    context2 = run_plugin_functions(
+        PluginHook.post_build_context, plugins1, context=context
+    )
     assert context1 != context2
-    assert(context2 == {**context, **{"context_value": 3}})
+    assert context2 == {**context, **{"context_value": 3}}
diff --git a/pythia/util.py b/pythia/util.py
index 900cf8c1..4129ee24 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -12,6 +12,14 @@ def to_julian_date(d):
         return None
 
 
+def to_julian_date_4(d):
+    try:
+        return d.strftime("%Y%j")
+    except ValueError:
+        logging.error("Unable to convert %s to a julian date", d)
+        return None
+
+
 def to_iso_date(d):
     try:
         return d.strftime("%Y-%m-%d")
diff --git a/sample.json b/sample.json
index 03227d3e..da7ca445 100644
--- a/sample.json
+++ b/sample.json
@@ -37,7 +37,8 @@
         "ic_layers": "generate_ic_layers::$id_soil",
         "ramt": 0,
         "fen_tot": 100.0,
-        "fertilizers": "split_fert_dap_percent::$fe"
+        "fertilizers": "split_fert_dap_percent::$fe",
+        "population": "raster::data/rasters/population.tif"
     },
     "dssat": {
         "executable": "/usr/local/dssat47/dscsm047"
@@ -53,6 +54,7 @@
             "LATITUDE",
             "LONGITUDE",
             "HARVEST_AREA",
+            "POPULATION",
             "RUN_NAME",
             "CR",
             "PDAT",
@@ -72,4 +74,4 @@
             "harvestArea": "raster::data/rasters/unity_spam_harvest_sorghum.tif"
         }
     ]
-}
\ No newline at end of file
+}
diff --git a/tox.ini b/tox.ini
index 6deafc26..68151ede 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,2 +1,4 @@
 [flake8]
-max-line-length = 120
+max-line-length = 160
+[pycodestyle]
+max-line-length = 160

From 12071e504f76243865096bacca141b5e4ec51834 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 15:50:02 -0500
Subject: [PATCH 023/105] Updating develop to 2.1.0-main

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dd8c4eda..2b75f69e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.0.0-beta.0"
+version = "2.1.0"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 5d91556d351d66d11534400917782f924beb758c Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 16:06:33 -0500
Subject: [PATCH 024/105] Fix #39

* Hardwire season as string
---
 project.org         | 9 +++------
 pythia/analytics.py | 5 +++++
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/project.org b/project.org
index 61816f32..6eee866e 100644
--- a/project.org
+++ b/project.org
@@ -6,16 +6,13 @@
 - Used to support ~forecast mode~
 ** DONE Add ~FODATE~ to template
 - Default is ~-99~
-** PENDING Add ~append_column~ in the ~analytics_setup~ configuration
-- Will add a column ~x~ to the end of each line of output.
-- "appendColumns": [{"HARVEST_AREA": "from_config::$harvestArea"}, {"VNAM": "subtract::out$cnam::out$gnam"}]
-- Have to make sure the from_config is specific to a run. This means the run needs to be persisted through to the ~calculate_outputs()~ function.
 ** DONE Validate ~vector::~ function works to feed any fields.
 ** DONE Batch mode support
 - [X] Configuration option to specify batch file to use.
 - [X] Default the batch file to DSSBatch.v4x
 ** TODO auto-include LAT/LNG if -99 in the DSSAT XFile
 ** TODO Auto-generate DSSBatch.v4x when needed for batch mode.
+** DONE Hardwire "season" variable in output
 * Execution Notes
 ** Batch file support
 In order to use batch file support modes (specified by ~CheckRunMode.f90~), you should use ~includes~ to copy the batch file to every run directory. This should be in your ~default_setup~ or ~runs~ blocks.
@@ -31,11 +28,11 @@ In order to use batch file support modes (specified by ~CheckRunMode.f90~), you
 ** Suppffort for adding columns
 "outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
 ** Support for filtering columns
+** All these hardwired variables will be removed in 3.0
 "outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
 },
 "filename": "daily.csv",
 "singleOutput": true,
 "outputColumns": ["SOME", "VARIABLE"]
 ]
-* Windows-specific issues?
-** 
+
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 751a55af..9a7377c6 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -168,6 +168,7 @@ def collate_outputs(config, run):
     out_file = os.path.join(out_dir, per_pixel_file_name)
     harea_info = run.get("harvestArea", None)
     pop_info = run.get("population", None)
+    season_info = run.get("season", None)
     collected_first_line = False
     for current_dir in _generated_run_files(work_dir, "summary.csv"):
         lat, lng = extract_ll(current_dir)
@@ -183,6 +184,8 @@ def collate_outputs(config, run):
             ds_pop: Optional[_GeneratorContextManager[DatasetReader]] = None
             band_harea = None
             band_pop = None
+            if season_info:
+                additional_headers = f"{additional_headers},SEASON"
             if harea_info:
                 additional_headers = f"{additional_headers},HARVEST_AREA"
                 harea_tiff = harea_info.split("::")[1]
@@ -200,6 +203,8 @@ def collate_outputs(config, run):
                         collected_first_line = True
                 else:
                     to_write = (lat, lng, run.get("name", ""))
+                    if season_info is not None:
+                        to_write = to_write + (season_info,)
                     if ds_harea is not None and not ds_harea.closed:
                         harea = pythia.io.get_site_raster_value(
                             ds_harea, band_harea, (float(lng), float(lat))

From 0a981ebc1aa96c55606903d3496ab43e8ac0c8d8 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 16:12:44 -0500
Subject: [PATCH 025/105] Release 2.1.1

* Fix #39
---
 project.org         | 8 ++------
 pythia/analytics.py | 5 +++++
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/project.org b/project.org
index 61816f32..c203f399 100644
--- a/project.org
+++ b/project.org
@@ -6,16 +6,13 @@
 - Used to support ~forecast mode~
 ** DONE Add ~FODATE~ to template
 - Default is ~-99~
-** PENDING Add ~append_column~ in the ~analytics_setup~ configuration
-- Will add a column ~x~ to the end of each line of output.
-- "appendColumns": [{"HARVEST_AREA": "from_config::$harvestArea"}, {"VNAM": "subtract::out$cnam::out$gnam"}]
-- Have to make sure the from_config is specific to a run. This means the run needs to be persisted through to the ~calculate_outputs()~ function.
 ** DONE Validate ~vector::~ function works to feed any fields.
 ** DONE Batch mode support
 - [X] Configuration option to specify batch file to use.
 - [X] Default the batch file to DSSBatch.v4x
 ** TODO auto-include LAT/LNG if -99 in the DSSAT XFile
 ** TODO Auto-generate DSSBatch.v4x when needed for batch mode.
+** DONE Hardwire "season" variable in output
 * Execution Notes
 ** Batch file support
 In order to use batch file support modes (specified by ~CheckRunMode.f90~), you should use ~includes~ to copy the batch file to every run directory. This should be in your ~default_setup~ or ~runs~ blocks.
@@ -31,11 +28,10 @@ In order to use batch file support modes (specified by ~CheckRunMode.f90~), you
 ** Suppffort for adding columns
 "outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
 ** Support for filtering columns
+** All these hardwired variables will be removed in 3.0
 "outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
 },
 "filename": "daily.csv",
 "singleOutput": true,
 "outputColumns": ["SOME", "VARIABLE"]
 ]
-* Windows-specific issues?
-** 
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 751a55af..9a7377c6 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -168,6 +168,7 @@ def collate_outputs(config, run):
     out_file = os.path.join(out_dir, per_pixel_file_name)
     harea_info = run.get("harvestArea", None)
     pop_info = run.get("population", None)
+    season_info = run.get("season", None)
     collected_first_line = False
     for current_dir in _generated_run_files(work_dir, "summary.csv"):
         lat, lng = extract_ll(current_dir)
@@ -183,6 +184,8 @@ def collate_outputs(config, run):
             ds_pop: Optional[_GeneratorContextManager[DatasetReader]] = None
             band_harea = None
             band_pop = None
+            if season_info:
+                additional_headers = f"{additional_headers},SEASON"
             if harea_info:
                 additional_headers = f"{additional_headers},HARVEST_AREA"
                 harea_tiff = harea_info.split("::")[1]
@@ -200,6 +203,8 @@ def collate_outputs(config, run):
                         collected_first_line = True
                 else:
                     to_write = (lat, lng, run.get("name", ""))
+                    if season_info is not None:
+                        to_write = to_write + (season_info,)
                     if ds_harea is not None and not ds_harea.closed:
                         harea = pythia.io.get_site_raster_value(
                             ds_harea, band_harea, (float(lng), float(lat))

From 64fe8d658c0380bd312185e9cddca090c99286a6 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 16:15:04 -0500
Subject: [PATCH 026/105] * Merge in 2.1.1 release

---
 project.org | 1 -
 1 file changed, 1 deletion(-)

diff --git a/project.org b/project.org
index 6eee866e..c203f399 100644
--- a/project.org
+++ b/project.org
@@ -35,4 +35,3 @@ In order to use batch file support modes (specified by ~CheckRunMode.f90~), you
 "singleOutput": true,
 "outputColumns": ["SOME", "VARIABLE"]
 ]
-

From 4fd88dfb5fb67010a50f06c4c92c9cdef9bed851 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 16:19:50 -0500
Subject: [PATCH 027/105] Bump version in pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b75f69e..60257e36 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.0"
+version = "2.1.1"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 5aa57c3c03b90c2e81ea5851cf4f80d642b919b1 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 16:21:16 -0500
Subject: [PATCH 028/105] Bump version to 2.1-devel

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b75f69e..ad43ff5b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.0"
+version = "2.1-devel"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From f3931c54dde210b2a018741511b67dc25552e491 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 16:24:38 -0500
Subject: [PATCH 029/105] Fix version numbering for development

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ad43ff5b..87613580 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1-devel"
+version = "2.1.devel"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 2401f615d6826301bc595e6da14f75bf845717f3 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 6 Dec 2021 17:10:29 -0500
Subject: [PATCH 030/105] Fix version numbering to match PEP-440

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 87613580..92ff8296 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.devel"
+version = "2.1.dev2"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From dab353f31790a5101acc32879c46682d1de1a93b Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 17 Dec 2021 10:44:37 -0500
Subject: [PATCH 031/105] Fix #40

Remove fodate from _t_date_fields
---
 pythia/template.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/template.py b/pythia/template.py
index dd2361fd..e8f1714e 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -33,7 +33,7 @@
     "hdate": {"length": 5}
 }
 
-_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate", "hdate"]
+_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]
 _t_date_fields_4 = ["fodate"]
 
 

From e5ee4c15421066a1d664eb1753183889c8795ed6 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 17 Dec 2021 10:48:25 -0500
Subject: [PATCH 032/105] Release 2.1.2

Fix #40
* Remove fodate from _t_date_fields
---
 pyproject.toml     | 2 +-
 pythia/template.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 60257e36..3aa44d1e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.1"
+version = "2.1.2"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"
diff --git a/pythia/template.py b/pythia/template.py
index dd2361fd..e8f1714e 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -33,7 +33,7 @@
     "hdate": {"length": 5}
 }
 
-_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "fodate", "hdate"]
+_t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]
 _t_date_fields_4 = ["fodate"]
 
 

From fc2e330afcaab5e35c25c2b2ece564449c393c57 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 17 Dec 2021 10:50:08 -0500
Subject: [PATCH 033/105] Bump to next development version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 92ff8296..a21f8646 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.dev2"
+version = "2.1.dev3"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From dd2e3fb56cee280dced30586a44d459b7af636bc Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 15 Feb 2022 09:42:21 -0500
Subject: [PATCH 034/105] Add management as a passthru key

* Management outputs as MGMT in the outputs
* Pixel directories have increase precision
---
 pythia/analytics.py | 5 +++++
 pythia/util.py      | 8 ++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 9a7377c6..07134756 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -169,6 +169,7 @@ def collate_outputs(config, run):
     harea_info = run.get("harvestArea", None)
     pop_info = run.get("population", None)
     season_info = run.get("season", None)
+    mgmt_info = run.get("management", None)
     collected_first_line = False
     for current_dir in _generated_run_files(work_dir, "summary.csv"):
         lat, lng = extract_ll(current_dir)
@@ -186,6 +187,8 @@ def collate_outputs(config, run):
             band_pop = None
             if season_info:
                 additional_headers = f"{additional_headers},SEASON"
+            if mgmt_info:
+                additional_headers = f"{additional_headers},MGMT"
             if harea_info:
                 additional_headers = f"{additional_headers},HARVEST_AREA"
                 harea_tiff = harea_info.split("::")[1]
@@ -205,6 +208,8 @@ def collate_outputs(config, run):
                     to_write = (lat, lng, run.get("name", ""))
                     if season_info is not None:
                         to_write = to_write + (season_info,)
+                    if mgmt_info is not None:
+                        to_write = to_write + (mgmt_info,)
                     if ds_harea is not None and not ds_harea.closed:
                         harea = pythia.io.get_site_raster_value(
                             ds_harea, band_harea, (float(lng), float(lat))
diff --git a/pythia/util.py b/pythia/util.py
index 4129ee24..f7a69e87 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -69,13 +69,13 @@ def get_rasters_dict(iterator):
 
 def translate_coords_news(lat, lng):
     if lat >= 0:
-        y = "{:.3f}N".format(lat).replace(".", "_")
+        y = "{:.4f}N".format(lat).replace(".", "_")
     else:
-        y = "{:.3f}S".format(abs(lat)).replace(".", "_")
+        y = "{:.4f}S".format(abs(lat)).replace(".", "_")
     if lng >= 0:
-        x = "{:.3f}E".format(lng).replace(".", "_")
+        x = "{:.4f}E".format(lng).replace(".", "_")
     else:
-        x = "{:.3f}W".format(abs(lng)).replace(".", "_")
+        x = "{:.4f}W".format(abs(lng)).replace(".", "_")
     return y, x
 
 

From c8204b1c433969a60fe6c0a193ea41d2a7521ff8 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 15 Feb 2022 11:13:51 -0500
Subject: [PATCH 035/105] Change documenation to AsciiDoc

---
 project.adoc | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 project.org  | 37 -----------------------------------
 2 files changed, 54 insertions(+), 37 deletions(-)
 create mode 100644 project.adoc
 delete mode 100644 project.org

diff --git a/project.adoc b/project.adoc
new file mode 100644
index 00000000..d6e9a1a2
--- /dev/null
+++ b/project.adoc
@@ -0,0 +1,54 @@
+= Pythia Project Notes
+Christopher Villalobos <cvillalobos@ufl.edu>
+:toc:
+
+== Task List
+* [x] Implement `run_mode` in the `dssat` configuration.
+** Default is `A`
+** Used to support `forecast mode`
+* [x] Add `FODATE` to template
+** Default is `-99`
+* [x] Validate `vector::` function works to feed any fields.
+* [x] Batch mode support
+** [x] Configuration option to specify batch file to use.
+** [x] Default the batch file to DSSBatch.v4x
+* [ ] Auto-include LAT/LNG if -99 in the DSSAT XFile
+* [ ] Auto-generate DSSBatch.v4x when needed for batch mode.
+* [x] Hardwire "season" variable in output
+* [x] Hardwire "management" variable in output
+
+== Execution Notes
+=== Batch file support
+In order to use batch file support modes (specified by `CheckRunMode.f90`), you should use `includes` to copy the batch file to every run directory. This should be in your `default_setup` or `runs` blocks.
+NOTE: Forecast mode (`"run_mode": "Y"`) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
+
+= Breaking Changes (v3.0)
+== Move analytics to output
+--
+"output": [
+{
+"filename": "summary.csv",
+--
+
+* Support for single output file
+--
+"singleOutput": true,
+--
+
+* Support for adding columns
+--
+"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
+--
+
+* Support for filtering columns
+
+NOTE: All hardwired variables will be removed in 3.0
+
+--
+"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
+},
+"filename": "daily.csv",
+"singleOutput": true,
+"outputColumns": ["SOME", "VARIABLE"]
+]
+--
diff --git a/project.org b/project.org
deleted file mode 100644
index c203f399..00000000
--- a/project.org
+++ /dev/null
@@ -1,37 +0,0 @@
-#+TITLE: Pythia Project Notes
-
-* Task List
-** DONE Implement ~run_mode~ in the ~dssat~ configuration.
-- Default is ~A~
-- Used to support ~forecast mode~
-** DONE Add ~FODATE~ to template
-- Default is ~-99~
-** DONE Validate ~vector::~ function works to feed any fields.
-** DONE Batch mode support
-- [X] Configuration option to specify batch file to use.
-- [X] Default the batch file to DSSBatch.v4x
-** TODO auto-include LAT/LNG if -99 in the DSSAT XFile
-** TODO Auto-generate DSSBatch.v4x when needed for batch mode.
-** DONE Hardwire "season" variable in output
-* Execution Notes
-** Batch file support
-In order to use batch file support modes (specified by ~CheckRunMode.f90~), you should use ~includes~ to copy the batch file to every run directory. This should be in your ~default_setup~ or ~runs~ blocks.
-*NOTE* Forecast mode (~"run_mode": "Y"~) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
-
-* Breaking Changes (v3.0)
-** Move analytics to output
-"output": [
-{
-"filename": "summary.csv",
-** Support for single output file
-"singleOutput": true,
-** Suppffort for adding columns
-"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
-** Support for filtering columns
-** All these hardwired variables will be removed in 3.0
-"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
-},
-"filename": "daily.csv",
-"singleOutput": true,
-"outputColumns": ["SOME", "VARIABLE"]
-]

From 8f664100048d1515c3f85a10acbb9055c3d99239 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 15 Feb 2022 11:18:25 -0500
Subject: [PATCH 036/105] Fix codeblocks in project.adoc

---
 project.adoc | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/project.adoc b/project.adoc
index d6e9a1a2..87c82390 100644
--- a/project.adoc
+++ b/project.adoc
@@ -24,31 +24,31 @@ NOTE: Forecast mode (`"run_mode": "Y"`) only works with DSSAT v4.8 and higher. T
 
 = Breaking Changes (v3.0)
 == Move analytics to output
---
+----
 "output": [
 {
 "filename": "summary.csv",
---
+----
 
 * Support for single output file
---
+----
 "singleOutput": true,
---
+----
 
 * Support for adding columns
---
+----
 "outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
---
+----
 
 * Support for filtering columns
 
 NOTE: All hardwired variables will be removed in 3.0
 
---
+----
 "outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
 },
 "filename": "daily.csv",
 "singleOutput": true,
 "outputColumns": ["SOME", "VARIABLE"]
 ]
---
+----

From a8e89fccf8dc7d8c26ff1df81385411b2f8bddf4 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 15 Feb 2022 13:36:28 -0500
Subject: [PATCH 037/105] Release v2.1.3

* Add management (MGMT) to hardwired outputs
* Convert from Org to AsciiDoc documentation for project status
* Move from `master` to `main` as publishing branch
---
 project.adoc        | 54 +++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml      |  2 +-
 pythia/analytics.py |  5 +++++
 pythia/util.py      |  8 +++----
 4 files changed, 64 insertions(+), 5 deletions(-)
 create mode 100644 project.adoc

diff --git a/project.adoc b/project.adoc
new file mode 100644
index 00000000..87c82390
--- /dev/null
+++ b/project.adoc
@@ -0,0 +1,54 @@
+= Pythia Project Notes
+Christopher Villalobos <cvillalobos@ufl.edu>
+:toc:
+
+== Task List
+* [x] Implement `run_mode` in the `dssat` configuration.
+** Default is `A`
+** Used to support `forecast mode`
+* [x] Add `FODATE` to template
+** Default is `-99`
+* [x] Validate `vector::` function works to feed any fields.
+* [x] Batch mode support
+** [x] Configuration option to specify batch file to use.
+** [x] Default the batch file to DSSBatch.v4x
+* [ ] Auto-include LAT/LNG if -99 in the DSSAT XFile
+* [ ] Auto-generate DSSBatch.v4x when needed for batch mode.
+* [x] Hardwire "season" variable in output
+* [x] Hardwire "management" variable in output
+
+== Execution Notes
+=== Batch file support
+In order to use batch file support modes (specified by `CheckRunMode.f90`), you should use `includes` to copy the batch file to every run directory. This should be in your `default_setup` or `runs` blocks.
+NOTE: Forecast mode (`"run_mode": "Y"`) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
+
+= Breaking Changes (v3.0)
+== Move analytics to output
+----
+"output": [
+{
+"filename": "summary.csv",
+----
+
+* Support for single output file
+----
+"singleOutput": true,
+----
+
+* Support for adding columns
+----
+"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
+----
+
+* Support for filtering columns
+
+NOTE: All hardwired variables will be removed in 3.0
+
+----
+"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
+},
+"filename": "daily.csv",
+"singleOutput": true,
+"outputColumns": ["SOME", "VARIABLE"]
+]
+----
diff --git a/pyproject.toml b/pyproject.toml
index 3aa44d1e..cfa30ce3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.2"
+version = "2.1.3"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 9a7377c6..07134756 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -169,6 +169,7 @@ def collate_outputs(config, run):
     harea_info = run.get("harvestArea", None)
     pop_info = run.get("population", None)
     season_info = run.get("season", None)
+    mgmt_info = run.get("management", None)
     collected_first_line = False
     for current_dir in _generated_run_files(work_dir, "summary.csv"):
         lat, lng = extract_ll(current_dir)
@@ -186,6 +187,8 @@ def collate_outputs(config, run):
             band_pop = None
             if season_info:
                 additional_headers = f"{additional_headers},SEASON"
+            if mgmt_info:
+                additional_headers = f"{additional_headers},MGMT"
             if harea_info:
                 additional_headers = f"{additional_headers},HARVEST_AREA"
                 harea_tiff = harea_info.split("::")[1]
@@ -205,6 +208,8 @@ def collate_outputs(config, run):
                     to_write = (lat, lng, run.get("name", ""))
                     if season_info is not None:
                         to_write = to_write + (season_info,)
+                    if mgmt_info is not None:
+                        to_write = to_write + (mgmt_info,)
                     if ds_harea is not None and not ds_harea.closed:
                         harea = pythia.io.get_site_raster_value(
                             ds_harea, band_harea, (float(lng), float(lat))
diff --git a/pythia/util.py b/pythia/util.py
index 4129ee24..f7a69e87 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -69,13 +69,13 @@ def get_rasters_dict(iterator):
 
 def translate_coords_news(lat, lng):
     if lat >= 0:
-        y = "{:.3f}N".format(lat).replace(".", "_")
+        y = "{:.4f}N".format(lat).replace(".", "_")
     else:
-        y = "{:.3f}S".format(abs(lat)).replace(".", "_")
+        y = "{:.4f}S".format(abs(lat)).replace(".", "_")
     if lng >= 0:
-        x = "{:.3f}E".format(lng).replace(".", "_")
+        x = "{:.4f}E".format(lng).replace(".", "_")
     else:
-        x = "{:.3f}W".format(abs(lng)).replace(".", "_")
+        x = "{:.4f}W".format(abs(lng)).replace(".", "_")
     return y, x
 
 

From eb62b3bf44481f2d4019854beae8b4549a912bd1 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 15 Feb 2022 13:39:56 -0500
Subject: [PATCH 038/105] Bump to next dev version (2.1.dev4)

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a21f8646..6e3a0e3c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.dev3"
+version = "2.1.dev4"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 57c596e875717cf52ba24aacf155bb2dc591cddd Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 16 Feb 2022 16:30:04 -0500
Subject: [PATCH 039/105] Fix #43

* Implement `lateSeason` in the JSON configuration.
* Only works if `season` is also specified in the JSON.
* If not used, `lateSeason` defaults to `False`.
* In output files as LATE_SEASON column.
---
 project.adoc        | 1 +
 pythia/analytics.py | 9 +++++++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/project.adoc b/project.adoc
index 87c82390..09e160c6 100644
--- a/project.adoc
+++ b/project.adoc
@@ -16,6 +16,7 @@ Christopher Villalobos <cvillalobos@ufl.edu>
 * [ ] Auto-generate DSSBatch.v4x when needed for batch mode.
 * [x] Hardwire "season" variable in output
 * [x] Hardwire "management" variable in output
+* [x] Hardwire "late_season" variable in output (binary)
 
 == Execution Notes
 === Batch file support
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 07134756..09fff1ef 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -170,6 +170,7 @@ def collate_outputs(config, run):
     pop_info = run.get("population", None)
     season_info = run.get("season", None)
     mgmt_info = run.get("management", None)
+    late_season_flag = run.get("lateSeason", False)
     collected_first_line = False
     for current_dir in _generated_run_files(work_dir, "summary.csv"):
         lat, lng = extract_ll(current_dir)
@@ -186,7 +187,7 @@ def collate_outputs(config, run):
             band_harea = None
             band_pop = None
             if season_info:
-                additional_headers = f"{additional_headers},SEASON"
+                additional_headers = f"{additional_headers},SEASON,LATE_SEASON"
             if mgmt_info:
                 additional_headers = f"{additional_headers},MGMT"
             if harea_info:
@@ -198,7 +199,7 @@ def collate_outputs(config, run):
                 additional_headers = f"{additional_headers},POPULATION"
                 pop_tiff = pop_info.split("::")[1]
                 ds_pop = rasterio.open(pop_tiff)
-                band_pop = ds_pop.read(1)
+                band_pop = ds_pop.read(1)                
             for i, line in enumerate(source):
                 if i == 0:
                     if not collected_first_line:
@@ -208,6 +209,10 @@ def collate_outputs(config, run):
                     to_write = (lat, lng, run.get("name", ""))
                     if season_info is not None:
                         to_write = to_write + (season_info,)
+                        if late_season_flag:
+                            to_write = to_write + (str(True),)
+                        else:
+                            to_write = to_write + (str(False),)
                     if mgmt_info is not None:
                         to_write = to_write + (mgmt_info,)
                     if ds_harea is not None and not ds_harea.closed:

From 7ea730da1ed3895f5e0458dda3117b72d1d1cf59 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 16 Feb 2022 16:37:06 -0500
Subject: [PATCH 040/105] Bump to next dev version (2.1.5dev)

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6e3a0e3c..529a2723 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.dev4"
+version = "2.1.dev5"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 503980fc68bf9c22702f95906b194b30d43d08c1 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 2 Mar 2022 08:30:28 -0500
Subject: [PATCH 041/105] Fix #44

* Upgrade ujson
* Upgrade dev dependencies
---
 poetry.lock | 612 +++++++++++++++++++++++++---------------------------
 1 file changed, 290 insertions(+), 322 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9ce53c74..796ffae3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -33,17 +33,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "autopep8"
@@ -59,7 +59,7 @@ toml = "*"
 
 [[package]]
 name = "black"
-version = "21.10b0"
+version = "21.12b0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
@@ -70,9 +70,8 @@ click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
 pathspec = ">=0.9.0,<1"
 platformdirs = ">=2"
-regex = ">=2020.1.8"
 tomli = ">=0.2.6,<2.0.0"
-typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
 typing-extensions = [
     {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
     {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
@@ -95,7 +94,7 @@ python-versions = "*"
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.0.4"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
@@ -143,7 +142,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "fiona"
-version = "1.8.20"
+version = "1.8.21"
 description = "Fiona reads and writes spatial data files"
 category = "main"
 optional = false
@@ -159,7 +158,7 @@ munch = "*"
 six = ">=1.7"
 
 [package.extras]
-all = ["pytest (>=3)", "boto3 (>=1.2.4)", "pytest-cov", "shapely", "mock"]
+all = ["boto3 (>=1.2.4)", "pytest-cov", "shapely", "pytest (>=3)", "mock"]
 calc = ["shapely"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["pytest (>=3)", "pytest-cov", "boto3 (>=1.2.4)", "mock"]
@@ -191,24 +190,24 @@ docs = ["sphinx"]
 
 [[package]]
 name = "importlib-metadata"
-version = "4.8.1"
+version = "4.11.2"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "isort"
-version = "5.10.0"
+version = "5.10.1"
 description = "A Python utility / library to sort Python imports."
 category = "dev"
 optional = false
@@ -222,7 +221,7 @@ plugins = ["setuptools"]
 
 [[package]]
 name = "jedi"
-version = "0.18.0"
+version = "0.18.1"
 description = "An autocompletion tool for Python that can be used for text editors."
 category = "dev"
 optional = false
@@ -233,7 +232,7 @@ parso = ">=0.8.0,<0.9.0"
 
 [package.extras]
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -251,19 +250,19 @@ i18n = ["Babel (>=0.8)"]
 
 [[package]]
 name = "lazy-object-proxy"
-version = "1.6.0"
+version = "1.7.1"
 description = "A fast and thorough lazy object proxy."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "markupsafe"
-version = "2.0.1"
+version = "2.1.0"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "mccabe"
@@ -275,7 +274,7 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.10.0"
+version = "8.12.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
@@ -283,7 +282,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "msgpack"
-version = "1.0.2"
+version = "1.0.3"
 description = "MessagePack (de)serializer."
 category = "dev"
 optional = false
@@ -333,18 +332,18 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "packaging"
-version = "21.2"
+version = "21.3"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-pyparsing = ">=2.0.2,<3"
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "parso"
-version = "0.8.2"
+version = "0.8.3"
 description = "A Python Parser"
 category = "dev"
 optional = false
@@ -364,11 +363,11 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "platformdirs"
-version = "2.4.0"
+version = "2.5.1"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
@@ -467,7 +466,7 @@ python-lsp-server = "*"
 
 [[package]]
 name = "pylsp-rope"
-version = "0.1.7"
+version = "0.1.8"
 description = "Extended refactoring capabilities for Python LSP Server using Rope."
 category = "dev"
 optional = false
@@ -500,11 +499,14 @@ test = ["pytest (>=3.4.0)"]
 
 [[package]]
 name = "pyparsing"
-version = "2.4.7"
+version = "3.0.7"
 description = "Python parsing module"
 category = "main"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = ">=3.6"
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
@@ -531,7 +533,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 
 [[package]]
 name = "python-lsp-black"
-version = "1.0.0"
+version = "1.1.0"
 description = "Black plugin for the Python LSP Server"
 category = "dev"
 optional = false
@@ -543,7 +545,7 @@ python-lsp-server = "*"
 toml = "*"
 
 [package.extras]
-dev = ["isort (>=5.0)", "flake8", "pytest", "mypy"]
+dev = ["flake8", "isort (>=5.0)", "mypy", "pre-commit", "pytest", "types-pkg-resources", "types-setuptools", "types-toml"]
 
 [[package]]
 name = "python-lsp-jsonrpc"
@@ -621,24 +623,16 @@ plot = ["matplotlib"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "pytest (>=2.8.2)", "shapely"]
 
-[[package]]
-name = "regex"
-version = "2021.11.2"
-description = "Alternative regular expression module, to replace re."
-category = "dev"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "rope"
-version = "0.21.0"
+version = "0.23.0"
 description = "a python refactoring library..."
 category = "dev"
 optional = false
 python-versions = "*"
 
 [package.extras]
-dev = ["pytest", "pytest-timeout"]
+dev = ["build", "pytest", "pytest-timeout"]
 
 [[package]]
 name = "rtree"
@@ -650,7 +644,7 @@ python-versions = "*"
 
 [[package]]
 name = "shapely"
-version = "1.8.0"
+version = "1.8.1.post1"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
@@ -671,7 +665,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "snowballstemmer"
-version = "2.1.0"
+version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 category = "dev"
 optional = false
@@ -702,7 +696,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "tomli"
-version = "1.2.2"
+version = "1.2.3"
 description = "A lil' TOML parser"
 category = "dev"
 optional = false
@@ -718,19 +712,19 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.10.0.2"
-description = "Backported and Experimental Type Hints for Python 3.5+"
+version = "4.1.1"
+description = "Backported and Experimental Type Hints for Python 3.6+"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "ujson"
-version = "4.2.0"
+version = "5.1.0"
 description = "Ultra fast JSON encoder and decoder for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "wcwidth"
@@ -750,7 +744,7 @@ python-versions = "*"
 
 [[package]]
 name = "yapf"
-version = "0.31.0"
+version = "0.32.0"
 description = "A formatter for Python code."
 category = "dev"
 optional = false
@@ -758,15 +752,15 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.6.0"
+version = "3.7.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [metadata]
 lock-version = "1.1"
@@ -787,24 +781,24 @@ atomicwrites = [
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
 ]
 attrs = [
-    {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
-    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
+    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
+    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
 ]
 autopep8 = [
     {file = "autopep8-1.5.7-py2.py3-none-any.whl", hash = "sha256:aa213493c30dcdac99537249ee65b24af0b2c29f2e83cd8b3f68760441ed0db9"},
     {file = "autopep8-1.5.7.tar.gz", hash = "sha256:276ced7e9e3cb22e5d7c14748384a5cf5d9002257c0ed50c0e075b68011bb6d0"},
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 zipp = [
-    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
-    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
+    {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
+    {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
 ]

From 0a9624d75758f906e28f08a1bd1ddcc45eb98a2c Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 2 Mar 2022 12:05:16 -0500
Subject: [PATCH 042/105] Upgrade Jinja2

* Jinja2 had an old broken dependency which is now fixed.
* Upgrade to 3.8+ python
---
 poetry.lock    | 313 ++++++++++++++++++++++++++++++++++++-------------
 pyproject.toml |   5 +-
 2 files changed, 234 insertions(+), 84 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 796ffae3..9443d7b1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -9,6 +9,14 @@ python-versions = "*"
 [package.extras]
 test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
 
+[[package]]
+name = "appnope"
+version = "0.1.2"
+description = "Disable App Nap on macOS >= 10.9"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "astroid"
 version = "2.6.6"
@@ -19,10 +27,22 @@ python-versions = "~=3.6"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
-typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
-typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 wrapt = ">=1.11,<1.13"
 
+[[package]]
+name = "asttokens"
+version = "2.0.5"
+description = "Annotate AST trees with source code positions"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+six = "*"
+
+[package.extras]
+test = ["astroid", "pytest"]
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.0"
@@ -57,6 +77,14 @@ python-versions = "*"
 pycodestyle = ">=2.7.0"
 toml = "*"
 
+[[package]]
+name = "backcall"
+version = "0.2.0"
+description = "Specifications for callback functions passed in to an API"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "black"
 version = "21.12b0"
@@ -71,7 +99,6 @@ mypy-extensions = ">=0.4.3"
 pathspec = ">=0.9.0,<1"
 platformdirs = ">=2"
 tomli = ">=0.2.6,<2.0.0"
-typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
 typing-extensions = [
     {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
     {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
@@ -102,7 +129,6 @@ python-versions = ">=3.6"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [[package]]
 name = "click-plugins"
@@ -140,6 +166,22 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
+name = "executing"
+version = "0.8.3"
+description = "Get the currently executing AST node of a frame, and other information"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "fiona"
 version = "1.8.21"
@@ -172,7 +214,6 @@ optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [package.dependencies]
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
@@ -189,21 +230,39 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 docs = ["sphinx"]
 
 [[package]]
-name = "importlib-metadata"
-version = "4.11.2"
-description = "Read metadata from Python packages"
-category = "main"
+name = "ipython"
+version = "8.1.0"
+description = "IPython: Productive Interactive Computing"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
-zipp = ">=0.5"
+appnope = {version = "*", markers = "sys_platform == \"darwin\""}
+backcall = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+decorator = "*"
+jedi = ">=0.16"
+matplotlib-inline = "*"
+pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
+pickleshare = "*"
+prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
+pygments = ">=2.4.0"
+stack-data = "*"
+traitlets = ">=5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+all = ["black", "Sphinx (>=1.3)", "ipykernel", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.19)", "pandas", "pytest", "testpath", "trio", "pytest-asyncio"]
+black = ["black"]
+doc = ["Sphinx (>=1.3)"]
+kernel = ["ipykernel"]
+nbconvert = ["nbconvert"]
+nbformat = ["nbformat"]
+notebook = ["ipywidgets", "notebook"]
+parallel = ["ipyparallel"]
+qtconsole = ["qtconsole"]
+test = ["pytest", "pytest-asyncio", "testpath"]
+test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest", "testpath", "trio"]
 
 [[package]]
 name = "isort"
@@ -236,17 +295,17 @@ testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "2.11.3"
+version = "3.0.3"
 description = "A very fast and expressive template engine."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
 
 [package.dependencies]
-MarkupSafe = ">=0.23"
+MarkupSafe = ">=2.0"
 
 [package.extras]
-i18n = ["Babel (>=0.8)"]
+i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "lazy-object-proxy"
@@ -264,6 +323,17 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "matplotlib-inline"
+version = "0.1.3"
+description = "Inline Matplotlib backend for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+traitlets = "*"
+
 [[package]]
 name = "mccabe"
 version = "0.6.1"
@@ -361,6 +431,25 @@ category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
+[[package]]
+name = "pexpect"
+version = "4.8.0"
+description = "Pexpect allows easy control of interactive console applications."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+ptyprocess = ">=0.5"
+
+[[package]]
+name = "pickleshare"
+version = "0.7.5"
+description = "Tiny 'shelve'-like database with concurrency support"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "platformdirs"
 version = "2.5.1"
@@ -381,11 +470,38 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.extras]
+dev = ["pre-commit", "tox"]
+
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.28"
+description = "Library for building powerful interactive command lines in Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
 [package.dependencies]
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+wcwidth = "*"
+
+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "pure-eval"
+version = "0.2.2"
+description = "Safely evaluate AST nodes without side effects"
+category = "dev"
+optional = false
+python-versions = "*"
 
 [package.extras]
-dev = ["pre-commit", "tox"]
+tests = ["pytest"]
 
 [[package]]
 name = "py"
@@ -425,6 +541,14 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pygments"
+version = "2.11.2"
+description = "Pygments is a syntax highlighting package written in Python."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "pylint"
 version = "2.9.6"
@@ -475,7 +599,6 @@ python-versions = ">=3.6"
 [package.dependencies]
 python-lsp-server = "*"
 rope = ">=0.21.0"
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 dev = ["build", "pytest", "twine"]
@@ -520,7 +643,6 @@ python-versions = ">=3.5"
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=17.4.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 more-itertools = ">=4.0.0"
 packaging = "*"
 pluggy = ">=0.12,<1.0"
@@ -686,6 +808,22 @@ pyparsing = ">=2.1.6"
 [package.extras]
 test = ["pytest", "hypothesis"]
 
+[[package]]
+name = "stack-data"
+version = "0.2.0"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+asttokens = "*"
+executing = "*"
+pure-eval = "*"
+
+[package.extras]
+tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -703,18 +841,21 @@ optional = false
 python-versions = ">=3.6"
 
 [[package]]
-name = "typed-ast"
-version = "1.4.3"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
+name = "traitlets"
+version = "5.1.1"
+description = "Traitlets Python configuration system"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+
+[package.extras]
+test = ["pytest"]
 
 [[package]]
 name = "typing-extensions"
 version = "4.1.1"
 description = "Backported and Experimental Type Hints for Python 3.6+"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 
@@ -750,32 +891,28 @@ category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "zipp"
-version = "3.7.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
-
 [metadata]
 lock-version = "1.1"
-python-versions = "^3.7"
-content-hash = "f55eee3ae0ca41608fea98081bf32dbcf104db9105be41571dd3cd57dd449ef7"
+python-versions = "^3.8"
+content-hash = "f99cb43ca081505d52d25211f1dadde1a032af87a89732f01a768d2d7a4a9c50"
 
 [metadata.files]
 affine = [
     {file = "affine-2.3.0-py2.py3-none-any.whl", hash = "sha256:34b05b070d954c382e56f02c207a372d8a32621a87653cc30cdd31cd7f65799f"},
     {file = "affine-2.3.0.tar.gz", hash = "sha256:2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102"},
 ]
+appnope = [
+    {file = "appnope-0.1.2-py2.py3-none-any.whl", hash = "sha256:93aa393e9d6c54c5cd570ccadd8edad61ea0c4b9ea7a01409020c9aa019eb442"},
+    {file = "appnope-0.1.2.tar.gz", hash = "sha256:dd83cd4b5b460958838f6eb3000c660b1f9caf2a5b1de4264e941512f603258a"},
+]
 astroid = [
     {file = "astroid-2.6.6-py3-none-any.whl", hash = "sha256:ab7f36e8a78b8e54a62028ba6beef7561db4cdb6f2a5009ecc44a6f42b5697ef"},
     {file = "astroid-2.6.6.tar.gz", hash = "sha256:3975a0bd5373bdce166e60c851cfcbaf21ee96de80ec518c1f4cb3e94c3fb334"},
 ]
+asttokens = [
+    {file = "asttokens-2.0.5-py2.py3-none-any.whl", hash = "sha256:0844691e88552595a6f4a4281a9f7f79b8dd45ca4ccea82e5e05b4bbdb76705c"},
+    {file = "asttokens-2.0.5.tar.gz", hash = "sha256:9a54c114f02c7a9480d56550932546a3f1fe71d8a02f1bc7ccd0ee3ee35cf4d5"},
+]
 atomicwrites = [
     {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
@@ -788,6 +925,10 @@ autopep8 = [
     {file = "autopep8-1.5.7-py2.py3-none-any.whl", hash = "sha256:aa213493c30dcdac99537249ee65b24af0b2c29f2e83cd8b3f68760441ed0db9"},
     {file = "autopep8-1.5.7.tar.gz", hash = "sha256:276ced7e9e3cb22e5d7c14748384a5cf5d9002257c0ed50c0e075b68011bb6d0"},
 ]
+backcall = [
+    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
+    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
+]
 black = [
     {file = "black-21.12b0-py3-none-any.whl", hash = "sha256:a615e69ae185e08fdd73e4715e260e2479c861b5740057fde6e8b4e3b7dd589f"},
     {file = "black-21.12b0.tar.gz", hash = "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3"},
@@ -812,6 +953,14 @@ colorama = [
     {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
     {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
 ]
+decorator = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
+executing = [
+    {file = "executing-0.8.3-py2.py3-none-any.whl", hash = "sha256:d1eef132db1b83649a3905ca6dd8897f71ac6f8cac79a7e58a1a09cf137546c9"},
+    {file = "executing-0.8.3.tar.gz", hash = "sha256:c6554e21c6b060590a6d3be4b82fb78f8f0194d809de5ea7df1c093763311501"},
+]
 fiona = [
     {file = "Fiona-1.8.21-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:39c656421e25b4d0d73d0b6acdcbf9848e71f3d9b74f44c27d2d516d463409ae"},
     {file = "Fiona-1.8.21-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:43b1d2e45506e56cf3a9f59ba5d6f7981f3f75f4725d1e6cb9a33ba856371ebd"},
@@ -886,9 +1035,9 @@ greenlet = [
     {file = "greenlet-1.1.2-cp39-cp39-win_amd64.whl", hash = "sha256:013d61294b6cd8fe3242932c1c5e36e5d1db2c8afb58606c5a67efce62c1f5fd"},
     {file = "greenlet-1.1.2.tar.gz", hash = "sha256:e30f5ea4ae2346e62cedde8794a56858a67b878dd79f7df76a0767e356b1744a"},
 ]
-importlib-metadata = [
-    {file = "importlib_metadata-4.11.2-py3-none-any.whl", hash = "sha256:d16e8c1deb60de41b8e8ed21c1a7b947b0bc62fab7e1d470bcdf331cea2e6735"},
-    {file = "importlib_metadata-4.11.2.tar.gz", hash = "sha256:b36ffa925fe3139b2f6ff11d6925ffd4fa7bc47870165e3ac260ac7b4f91e6ac"},
+ipython = [
+    {file = "ipython-8.1.0-py3-none-any.whl", hash = "sha256:7bfeb6f298b2d7f3859c4f3e134082015cf34de90f89f5020e107a5a762ef6db"},
+    {file = "ipython-8.1.0.tar.gz", hash = "sha256:42c23e90b2deaae631266885de1656a517a1673d7e1db57e8eb3a4bb6cd5ce1b"},
 ]
 isort = [
     {file = "isort-5.10.1-py3-none-any.whl", hash = "sha256:6f62d78e2f89b4500b080fe3a81690850cd254227f27f75c3a0c491a1f351ba7"},
@@ -899,8 +1048,8 @@ jedi = [
     {file = "jedi-0.18.1.tar.gz", hash = "sha256:74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab"},
 ]
 jinja2 = [
-    {file = "Jinja2-2.11.3-py2.py3-none-any.whl", hash = "sha256:03e47ad063331dd6a3f04a43eddca8a966a26ba0c5b7207a9a9e4e08f1b29419"},
-    {file = "Jinja2-2.11.3.tar.gz", hash = "sha256:a6d58433de0ae800347cab1fa3043cebbabe8baa9d29e668f1c768cb87a333c6"},
+    {file = "Jinja2-3.0.3-py3-none-any.whl", hash = "sha256:077ce6014f7b40d03b47d1f1ca4b0fc8328a692bd284016f806ed0eaca390ad8"},
+    {file = "Jinja2-3.0.3.tar.gz", hash = "sha256:611bb273cd68f3b993fabdc4064fc858c5b47a973cb5aa7999ec1ba405c87cd7"},
 ]
 lazy-object-proxy = [
     {file = "lazy-object-proxy-1.7.1.tar.gz", hash = "sha256:d609c75b986def706743cdebe5e47553f4a5a1da9c5ff66d76013ef396b5a8a4"},
@@ -983,6 +1132,10 @@ markupsafe = [
     {file = "MarkupSafe-2.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:b8811d48078d1cf2a6863dafb896e68406c5f513048451cd2ded0473133473c7"},
     {file = "MarkupSafe-2.1.0.tar.gz", hash = "sha256:80beaf63ddfbc64a0452b841d8036ca0611e049650e20afcb882f5d3c266d65f"},
 ]
+matplotlib-inline = [
+    {file = "matplotlib-inline-0.1.3.tar.gz", hash = "sha256:a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee"},
+    {file = "matplotlib_inline-0.1.3-py3-none-any.whl", hash = "sha256:aed605ba3b72462d64d475a21a9296f400a19c4f74a31b59103d2a99ffd5aa5c"},
+]
 mccabe = [
     {file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
     {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
@@ -1080,6 +1233,14 @@ pathspec = [
     {file = "pathspec-0.9.0-py2.py3-none-any.whl", hash = "sha256:7d15c4ddb0b5c802d161efc417ec1a2558ea2653c2e8ad9c19098201dc1c993a"},
     {file = "pathspec-0.9.0.tar.gz", hash = "sha256:e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1"},
 ]
+pexpect = [
+    {file = "pexpect-4.8.0-py2.py3-none-any.whl", hash = "sha256:0b48a55dcb3c05f3329815901ea4fc1537514d6ba867a152b581d69ae3710937"},
+    {file = "pexpect-4.8.0.tar.gz", hash = "sha256:fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c"},
+]
+pickleshare = [
+    {file = "pickleshare-0.7.5-py2.py3-none-any.whl", hash = "sha256:9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56"},
+    {file = "pickleshare-0.7.5.tar.gz", hash = "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca"},
+]
 platformdirs = [
     {file = "platformdirs-2.5.1-py3-none-any.whl", hash = "sha256:bcae7cab893c2d310a711b70b24efb93334febe65f8de776ee320b517471e227"},
     {file = "platformdirs-2.5.1.tar.gz", hash = "sha256:7535e70dfa32e84d4b34996ea99c5e432fa29a708d0f4e394bbcb2a8faa4f16d"},
@@ -1088,6 +1249,18 @@ pluggy = [
     {file = "pluggy-0.13.1-py2.py3-none-any.whl", hash = "sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"},
     {file = "pluggy-0.13.1.tar.gz", hash = "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0"},
 ]
+prompt-toolkit = [
+    {file = "prompt_toolkit-3.0.28-py3-none-any.whl", hash = "sha256:30129d870dcb0b3b6a53efdc9d0a83ea96162ffd28ffe077e94215b233dc670c"},
+    {file = "prompt_toolkit-3.0.28.tar.gz", hash = "sha256:9f1cd16b1e86c2968f2519d7fb31dd9d669916f515612c269d14e9ed52b51650"},
+]
+ptyprocess = [
+    {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"},
+    {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
+]
+pure-eval = [
+    {file = "pure_eval-0.2.2-py3-none-any.whl", hash = "sha256:01eaab343580944bc56080ebe0a674b39ec44a945e6d09ba7db3cb8cec289350"},
+    {file = "pure_eval-0.2.2.tar.gz", hash = "sha256:2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3"},
+]
 py = [
     {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
     {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
@@ -1104,6 +1277,10 @@ pyflakes = [
     {file = "pyflakes-2.3.1-py2.py3-none-any.whl", hash = "sha256:7893783d01b8a89811dd72d7dfd4d84ff098e5eed95cfa8905b22bbffe52efc3"},
     {file = "pyflakes-2.3.1.tar.gz", hash = "sha256:f5bc8ecabc05bb9d291eb5203d6810b49040f6ff446a756326104746cc00c1db"},
 ]
+pygments = [
+    {file = "Pygments-2.11.2-py3-none-any.whl", hash = "sha256:44238f1b60a76d78fc8ca0528ee429702aae011c265fe6a8dd8b63049ae41c65"},
+    {file = "Pygments-2.11.2.tar.gz", hash = "sha256:4e426f72023d88d03b2fa258de560726ce890ff3b630f88c21cbb8b2503b8c6a"},
+]
 pylint = [
     {file = "pylint-2.9.6-py3-none-any.whl", hash = "sha256:2e1a0eb2e8ab41d6b5dbada87f066492bb1557b12b76c47c2ee8aa8a11186594"},
     {file = "pylint-2.9.6.tar.gz", hash = "sha256:8b838c8983ee1904b2de66cce9d0b96649a91901350e956d78f289c3bc87b48e"},
@@ -1202,6 +1379,10 @@ snuggs = [
     {file = "snuggs-1.4.7-py3-none-any.whl", hash = "sha256:988dde5d4db88e9d71c99457404773dabcc7a1c45971bfbe81900999942d9f07"},
     {file = "snuggs-1.4.7.tar.gz", hash = "sha256:501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b"},
 ]
+stack-data = [
+    {file = "stack_data-0.2.0-py3-none-any.whl", hash = "sha256:999762f9c3132308789affa03e9271bbbe947bf78311851f4d485d8402ed858e"},
+    {file = "stack_data-0.2.0.tar.gz", hash = "sha256:45692d41bd633a9503a5195552df22b583caf16f0b27c4e58c98d88c8b648e12"},
+]
 toml = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
@@ -1210,37 +1391,9 @@ tomli = [
     {file = "tomli-1.2.3-py3-none-any.whl", hash = "sha256:e3069e4be3ead9668e21cb9b074cd948f7b3113fd9c8bba083f48247aab8b11c"},
     {file = "tomli-1.2.3.tar.gz", hash = "sha256:05b6166bff487dc068d322585c7ea4ef78deed501cc124060e0f238e89a9231f"},
 ]
-typed-ast = [
-    {file = "typed_ast-1.4.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:2068531575a125b87a41802130fa7e29f26c09a2833fea68d9a40cf33902eba6"},
-    {file = "typed_ast-1.4.3-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:c907f561b1e83e93fad565bac5ba9c22d96a54e7ea0267c708bffe863cbe4075"},
-    {file = "typed_ast-1.4.3-cp35-cp35m-manylinux2014_aarch64.whl", hash = "sha256:1b3ead4a96c9101bef08f9f7d1217c096f31667617b58de957f690c92378b528"},
-    {file = "typed_ast-1.4.3-cp35-cp35m-win32.whl", hash = "sha256:dde816ca9dac1d9c01dd504ea5967821606f02e510438120091b84e852367428"},
-    {file = "typed_ast-1.4.3-cp35-cp35m-win_amd64.whl", hash = "sha256:777a26c84bea6cd934422ac2e3b78863a37017618b6e5c08f92ef69853e765d3"},
-    {file = "typed_ast-1.4.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:f8afcf15cc511ada719a88e013cec87c11aff7b91f019295eb4530f96fe5ef2f"},
-    {file = "typed_ast-1.4.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:52b1eb8c83f178ab787f3a4283f68258525f8d70f778a2f6dd54d3b5e5fb4341"},
-    {file = "typed_ast-1.4.3-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:01ae5f73431d21eead5015997ab41afa53aa1fbe252f9da060be5dad2c730ace"},
-    {file = "typed_ast-1.4.3-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:c190f0899e9f9f8b6b7863debfb739abcb21a5c054f911ca3596d12b8a4c4c7f"},
-    {file = "typed_ast-1.4.3-cp36-cp36m-win32.whl", hash = "sha256:398e44cd480f4d2b7ee8d98385ca104e35c81525dd98c519acff1b79bdaac363"},
-    {file = "typed_ast-1.4.3-cp36-cp36m-win_amd64.whl", hash = "sha256:bff6ad71c81b3bba8fa35f0f1921fb24ff4476235a6e94a26ada2e54370e6da7"},
-    {file = "typed_ast-1.4.3-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:0fb71b8c643187d7492c1f8352f2c15b4c4af3f6338f21681d3681b3dc31a266"},
-    {file = "typed_ast-1.4.3-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:760ad187b1041a154f0e4d0f6aae3e40fdb51d6de16e5c99aedadd9246450e9e"},
-    {file = "typed_ast-1.4.3-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:5feca99c17af94057417d744607b82dd0a664fd5e4ca98061480fd8b14b18d04"},
-    {file = "typed_ast-1.4.3-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:95431a26309a21874005845c21118c83991c63ea800dd44843e42a916aec5899"},
-    {file = "typed_ast-1.4.3-cp37-cp37m-win32.whl", hash = "sha256:aee0c1256be6c07bd3e1263ff920c325b59849dc95392a05f258bb9b259cf39c"},
-    {file = "typed_ast-1.4.3-cp37-cp37m-win_amd64.whl", hash = "sha256:9ad2c92ec681e02baf81fdfa056fe0d818645efa9af1f1cd5fd6f1bd2bdfd805"},
-    {file = "typed_ast-1.4.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:b36b4f3920103a25e1d5d024d155c504080959582b928e91cb608a65c3a49e1a"},
-    {file = "typed_ast-1.4.3-cp38-cp38-manylinux1_i686.whl", hash = "sha256:067a74454df670dcaa4e59349a2e5c81e567d8d65458d480a5b3dfecec08c5ff"},
-    {file = "typed_ast-1.4.3-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:7538e495704e2ccda9b234b82423a4038f324f3a10c43bc088a1636180f11a41"},
-    {file = "typed_ast-1.4.3-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:af3d4a73793725138d6b334d9d247ce7e5f084d96284ed23f22ee626a7b88e39"},
-    {file = "typed_ast-1.4.3-cp38-cp38-win32.whl", hash = "sha256:f2362f3cb0f3172c42938946dbc5b7843c2a28aec307c49100c8b38764eb6927"},
-    {file = "typed_ast-1.4.3-cp38-cp38-win_amd64.whl", hash = "sha256:dd4a21253f42b8d2b48410cb31fe501d32f8b9fbeb1f55063ad102fe9c425e40"},
-    {file = "typed_ast-1.4.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:f328adcfebed9f11301eaedfa48e15bdece9b519fb27e6a8c01aa52a17ec31b3"},
-    {file = "typed_ast-1.4.3-cp39-cp39-manylinux1_i686.whl", hash = "sha256:2c726c276d09fc5c414693a2de063f521052d9ea7c240ce553316f70656c84d4"},
-    {file = "typed_ast-1.4.3-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:cae53c389825d3b46fb37538441f75d6aecc4174f615d048321b716df2757fb0"},
-    {file = "typed_ast-1.4.3-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:b9574c6f03f685070d859e75c7f9eeca02d6933273b5e69572e5ff9d5e3931c3"},
-    {file = "typed_ast-1.4.3-cp39-cp39-win32.whl", hash = "sha256:209596a4ec71d990d71d5e0d312ac935d86930e6eecff6ccc7007fe54d703808"},
-    {file = "typed_ast-1.4.3-cp39-cp39-win_amd64.whl", hash = "sha256:9c6d1a54552b5330bc657b7ef0eae25d00ba7ffe85d9ea8ae6540d2197a3788c"},
-    {file = "typed_ast-1.4.3.tar.gz", hash = "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"},
+traitlets = [
+    {file = "traitlets-5.1.1-py3-none-any.whl", hash = "sha256:2d313cc50a42cd6c277e7d7dc8d4d7fedd06a2c215f78766ae7b1a66277e0033"},
+    {file = "traitlets-5.1.1.tar.gz", hash = "sha256:059f456c5a7c1c82b98c2e8c799f39c9b8128f6d0d46941ee118daace9eb70c7"},
 ]
 typing-extensions = [
     {file = "typing_extensions-4.1.1-py3-none-any.whl", hash = "sha256:21c85e0fe4b9a155d0799430b0ad741cdce7e359660ccbd8b530613e8df88ce2"},
@@ -1309,7 +1462,3 @@ yapf = [
     {file = "yapf-0.32.0-py2.py3-none-any.whl", hash = "sha256:8fea849025584e486fd06d6ba2bed717f396080fd3cc236ba10cb97c4c51cf32"},
     {file = "yapf-0.32.0.tar.gz", hash = "sha256:a3f5085d37ef7e3e004c4ba9f9b3e40c54ff1901cd111f05145ae313a7c67d1b"},
 ]
-zipp = [
-    {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
-    {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
-]
diff --git a/pyproject.toml b/pyproject.toml
index 529a2723..67f7402d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,9 +6,9 @@ authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"
 
 [tool.poetry.dependencies]
-python = "^3.7"
+python = "^3.8"
 fiona = "^1.8"
-jinja2 = "^2.10"
+jinja2 = "^3.0"
 numpy = "^1.16"
 rasterio = "^1.0"
 shapely = "^1.6"
@@ -24,6 +24,7 @@ pyls-isort = "^0.2.2"
 python-lsp-black = "^1.0.0"
 pylsp-rope = "^0.1.7"
 pyls-flake8 = "^0.4.0"
+ipython = "^8.1.0"
 
 [tool.poetry.scripts]
 pythia = "pythia.cli:main"

From 66ae9f11a85b1c4f006fb5461d37b1cc3f87f081 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 2 Mar 2022 08:30:28 -0500
Subject: [PATCH 043/105] Fix #44

* Upgrade ujson
* Upgrade dev dependencies
---
 poetry.lock | 612 +++++++++++++++++++++++++---------------------------
 1 file changed, 290 insertions(+), 322 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9ce53c74..796ffae3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -33,17 +33,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "autopep8"
@@ -59,7 +59,7 @@ toml = "*"
 
 [[package]]
 name = "black"
-version = "21.10b0"
+version = "21.12b0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
@@ -70,9 +70,8 @@ click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
 pathspec = ">=0.9.0,<1"
 platformdirs = ">=2"
-regex = ">=2020.1.8"
 tomli = ">=0.2.6,<2.0.0"
-typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
 typing-extensions = [
     {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
     {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
@@ -95,7 +94,7 @@ python-versions = "*"
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.0.4"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
@@ -143,7 +142,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "fiona"
-version = "1.8.20"
+version = "1.8.21"
 description = "Fiona reads and writes spatial data files"
 category = "main"
 optional = false
@@ -159,7 +158,7 @@ munch = "*"
 six = ">=1.7"
 
 [package.extras]
-all = ["pytest (>=3)", "boto3 (>=1.2.4)", "pytest-cov", "shapely", "mock"]
+all = ["boto3 (>=1.2.4)", "pytest-cov", "shapely", "pytest (>=3)", "mock"]
 calc = ["shapely"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["pytest (>=3)", "pytest-cov", "boto3 (>=1.2.4)", "mock"]
@@ -191,24 +190,24 @@ docs = ["sphinx"]
 
 [[package]]
 name = "importlib-metadata"
-version = "4.8.1"
+version = "4.11.2"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "isort"
-version = "5.10.0"
+version = "5.10.1"
 description = "A Python utility / library to sort Python imports."
 category = "dev"
 optional = false
@@ -222,7 +221,7 @@ plugins = ["setuptools"]
 
 [[package]]
 name = "jedi"
-version = "0.18.0"
+version = "0.18.1"
 description = "An autocompletion tool for Python that can be used for text editors."
 category = "dev"
 optional = false
@@ -233,7 +232,7 @@ parso = ">=0.8.0,<0.9.0"
 
 [package.extras]
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -251,19 +250,19 @@ i18n = ["Babel (>=0.8)"]
 
 [[package]]
 name = "lazy-object-proxy"
-version = "1.6.0"
+version = "1.7.1"
 description = "A fast and thorough lazy object proxy."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "markupsafe"
-version = "2.0.1"
+version = "2.1.0"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "mccabe"
@@ -275,7 +274,7 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.10.0"
+version = "8.12.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
@@ -283,7 +282,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "msgpack"
-version = "1.0.2"
+version = "1.0.3"
 description = "MessagePack (de)serializer."
 category = "dev"
 optional = false
@@ -333,18 +332,18 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "packaging"
-version = "21.2"
+version = "21.3"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-pyparsing = ">=2.0.2,<3"
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "parso"
-version = "0.8.2"
+version = "0.8.3"
 description = "A Python Parser"
 category = "dev"
 optional = false
@@ -364,11 +363,11 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "platformdirs"
-version = "2.4.0"
+version = "2.5.1"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
@@ -467,7 +466,7 @@ python-lsp-server = "*"
 
 [[package]]
 name = "pylsp-rope"
-version = "0.1.7"
+version = "0.1.8"
 description = "Extended refactoring capabilities for Python LSP Server using Rope."
 category = "dev"
 optional = false
@@ -500,11 +499,14 @@ test = ["pytest (>=3.4.0)"]
 
 [[package]]
 name = "pyparsing"
-version = "2.4.7"
+version = "3.0.7"
 description = "Python parsing module"
 category = "main"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = ">=3.6"
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
@@ -531,7 +533,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 
 [[package]]
 name = "python-lsp-black"
-version = "1.0.0"
+version = "1.1.0"
 description = "Black plugin for the Python LSP Server"
 category = "dev"
 optional = false
@@ -543,7 +545,7 @@ python-lsp-server = "*"
 toml = "*"
 
 [package.extras]
-dev = ["isort (>=5.0)", "flake8", "pytest", "mypy"]
+dev = ["flake8", "isort (>=5.0)", "mypy", "pre-commit", "pytest", "types-pkg-resources", "types-setuptools", "types-toml"]
 
 [[package]]
 name = "python-lsp-jsonrpc"
@@ -621,24 +623,16 @@ plot = ["matplotlib"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "pytest (>=2.8.2)", "shapely"]
 
-[[package]]
-name = "regex"
-version = "2021.11.2"
-description = "Alternative regular expression module, to replace re."
-category = "dev"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "rope"
-version = "0.21.0"
+version = "0.23.0"
 description = "a python refactoring library..."
 category = "dev"
 optional = false
 python-versions = "*"
 
 [package.extras]
-dev = ["pytest", "pytest-timeout"]
+dev = ["build", "pytest", "pytest-timeout"]
 
 [[package]]
 name = "rtree"
@@ -650,7 +644,7 @@ python-versions = "*"
 
 [[package]]
 name = "shapely"
-version = "1.8.0"
+version = "1.8.1.post1"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
@@ -671,7 +665,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "snowballstemmer"
-version = "2.1.0"
+version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 category = "dev"
 optional = false
@@ -702,7 +696,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "tomli"
-version = "1.2.2"
+version = "1.2.3"
 description = "A lil' TOML parser"
 category = "dev"
 optional = false
@@ -718,19 +712,19 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.10.0.2"
-description = "Backported and Experimental Type Hints for Python 3.5+"
+version = "4.1.1"
+description = "Backported and Experimental Type Hints for Python 3.6+"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "ujson"
-version = "4.2.0"
+version = "5.1.0"
 description = "Ultra fast JSON encoder and decoder for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "wcwidth"
@@ -750,7 +744,7 @@ python-versions = "*"
 
 [[package]]
 name = "yapf"
-version = "0.31.0"
+version = "0.32.0"
 description = "A formatter for Python code."
 category = "dev"
 optional = false
@@ -758,15 +752,15 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.6.0"
+version = "3.7.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [metadata]
 lock-version = "1.1"
@@ -787,24 +781,24 @@ atomicwrites = [
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
 ]
 attrs = [
-    {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
-    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
+    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
+    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
 ]
 autopep8 = [
     {file = "autopep8-1.5.7-py2.py3-none-any.whl", hash = "sha256:aa213493c30dcdac99537249ee65b24af0b2c29f2e83cd8b3f68760441ed0db9"},
     {file = "autopep8-1.5.7.tar.gz", hash = "sha256:276ced7e9e3cb22e5d7c14748384a5cf5d9002257c0ed50c0e075b68011bb6d0"},
 ]
 black = [
-    {file = "black-21.10b0-py3-none-any.whl", hash = "sha256:6eb7448da9143ee65b856a5f3676b7dda98ad9abe0f87fce8c59291f15e82a5b"},
-    {file = "black-21.10b0.tar.gz", hash = "sha256:a9952229092e325fe5f3dae56d81f639b23f7131eb840781947e4b2886030f33"},
+    {file = "black-21.12b0-py3-none-any.whl", hash = "sha256:a615e69ae185e08fdd73e4715e260e2479c861b5740057fde6e8b4e3b7dd589f"},
+    {file = "black-21.12b0.tar.gz", hash = "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3"},
 ]
 certifi = [
     {file = "certifi-2021.10.8-py2.py3-none-any.whl", hash = "sha256:d62a0163eb4c2344ac042ab2bdf75399a71a2d8c7d47eac2e2ee91b9d6339569"},
     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
 ]
 click = [
-    {file = "click-8.0.3-py3-none-any.whl", hash = "sha256:353f466495adaeb40b6b5f592f9f91cb22372351c84caeb068132442a4518ef3"},
-    {file = "click-8.0.3.tar.gz", hash = "sha256:410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b"},
+    {file = "click-8.0.4-py3-none-any.whl", hash = "sha256:6a7a62563bbfabfda3a38f3023a1db4a35978c0abd76f6c9605ecd6554d6d9b1"},
+    {file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"},
 ]
 click-plugins = [
     {file = "click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"},
@@ -819,15 +813,17 @@ colorama = [
     {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
 ]
 fiona = [
-    {file = "Fiona-1.8.20-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:02880556540e36ad6aac97687799d9b3093c354787a47bc0e73026c7fc15f1b3"},
-    {file = "Fiona-1.8.20-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:3f668c471fa2f8c9c0a9ca83639cb2c8dcc93edc3d93d43dba2f9e8da38ad53e"},
-    {file = "Fiona-1.8.20-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:54f81039e913d0f88728ef23edf5a69038dec94dea54f4c799f972ba8e2a7d40"},
-    {file = "Fiona-1.8.20-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:328340a448bed5c43d119f61f760368a04d13a302c59d2fccb051a3ff021f4b8"},
-    {file = "Fiona-1.8.20-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:03f910380dbe684730b59b817aa030e6e9a3ee79211b66c6db2d1c8fe6ea12de"},
-    {file = "Fiona-1.8.20-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:bef100ebd82afb9a4d67096216e82611b82ca9341330e4805832d7ff8c9bc1f7"},
-    {file = "Fiona-1.8.20-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:5e1cef608c6de9039eaa65b395024096e3189ab0559a5a328c68c4690c3302ce"},
-    {file = "Fiona-1.8.20-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:e72e4a5b84ec410be531d4fe4c1a5c87c6c0e92d01116c145c0f1b33f81c8080"},
-    {file = "Fiona-1.8.20.tar.gz", hash = "sha256:a70502d2857b82f749c09cb0dea3726787747933a2a1599b5ab787d74e3c143b"},
+    {file = "Fiona-1.8.21-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:39c656421e25b4d0d73d0b6acdcbf9848e71f3d9b74f44c27d2d516d463409ae"},
+    {file = "Fiona-1.8.21-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:43b1d2e45506e56cf3a9f59ba5d6f7981f3f75f4725d1e6cb9a33ba856371ebd"},
+    {file = "Fiona-1.8.21-cp36-cp36m-macosx_10_10_x86_64.whl", hash = "sha256:315e186cb880a8128e110312eb92f5956bbc54d7152af999d3483b463758d6f9"},
+    {file = "Fiona-1.8.21-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9fb2407623c4f44732a33b3f056f8c58c54152b51f0324bf8f10945e711eb549"},
+    {file = "Fiona-1.8.21-cp37-cp37m-macosx_10_10_x86_64.whl", hash = "sha256:b69054ed810eb7339d7effa88589afca48003206d7627d0b0b149715fc3fde41"},
+    {file = "Fiona-1.8.21-cp37-cp37m-manylinux2014_x86_64.whl", hash = "sha256:11532ccfda1073d3f5f558e4bb78d45b268e8680fd6e14993a394c564ddbd069"},
+    {file = "Fiona-1.8.21-cp38-cp38-macosx_10_10_x86_64.whl", hash = "sha256:3789523c811809a6e2e170cf9c437631f959f4c7a868f024081612d30afab468"},
+    {file = "Fiona-1.8.21-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:085f18d943097ac3396f3f9664ac1ae04ad0ff272f54829f03442187f01b6116"},
+    {file = "Fiona-1.8.21-cp39-cp39-macosx_10_10_x86_64.whl", hash = "sha256:388acc9fa07ba7858d508dfe826d4b04d813818bced16c4049de19cc7ca322ef"},
+    {file = "Fiona-1.8.21-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40b4eaf5b88407421d6c9e707520abd2ff16d7cd43efb59cd398aa41d2de332c"},
+    {file = "Fiona-1.8.21.tar.gz", hash = "sha256:3a0edca2a7a070db405d71187214a43d2333a57b4097544a3fcc282066a58bfc"},
 ]
 flake8 = [
     {file = "flake8-3.9.2-py2.py3-none-any.whl", hash = "sha256:bf8fd333346d844f616e8d47905ef3a3384edae6b4e9beb0c5101e25e3110907"},
@@ -845,6 +841,7 @@ greenlet = [
     {file = "greenlet-1.1.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:97e5306482182170ade15c4b0d8386ded995a07d7cc2ca8f27958d34d6736497"},
     {file = "greenlet-1.1.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:e6a36bb9474218c7a5b27ae476035497a6990e21d04c279884eb10d9b290f1b1"},
     {file = "greenlet-1.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:abb7a75ed8b968f3061327c433a0fbd17b729947b400747c334a9c29a9af6c58"},
+    {file = "greenlet-1.1.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:b336501a05e13b616ef81ce329c0e09ac5ed8c732d9ba7e3e983fcc1a9e86965"},
     {file = "greenlet-1.1.2-cp310-cp310-win_amd64.whl", hash = "sha256:14d4f3cd4e8b524ae9b8aa567858beed70c392fdec26dbdb0a8a418392e71708"},
     {file = "greenlet-1.1.2-cp35-cp35m-macosx_10_14_x86_64.whl", hash = "sha256:17ff94e7a83aa8671a25bf5b59326ec26da379ace2ebc4411d690d80a7fbcf23"},
     {file = "greenlet-1.1.2-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:9f3cba480d3deb69f6ee2c1825060177a22c7826431458c697df88e6aeb3caee"},
@@ -857,6 +854,7 @@ greenlet = [
     {file = "greenlet-1.1.2-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f9d29ca8a77117315101425ec7ec2a47a22ccf59f5593378fc4077ac5b754fce"},
     {file = "greenlet-1.1.2-cp36-cp36m-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:21915eb821a6b3d9d8eefdaf57d6c345b970ad722f856cd71739493ce003ad08"},
     {file = "greenlet-1.1.2-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eff9d20417ff9dcb0d25e2defc2574d10b491bf2e693b4e491914738b7908168"},
+    {file = "greenlet-1.1.2-cp36-cp36m-musllinux_1_1_x86_64.whl", hash = "sha256:b8c008de9d0daba7b6666aa5bbfdc23dcd78cafc33997c9b7741ff6353bafb7f"},
     {file = "greenlet-1.1.2-cp36-cp36m-win32.whl", hash = "sha256:32ca72bbc673adbcfecb935bb3fb1b74e663d10a4b241aaa2f5a75fe1d1f90aa"},
     {file = "greenlet-1.1.2-cp36-cp36m-win_amd64.whl", hash = "sha256:f0214eb2a23b85528310dad848ad2ac58e735612929c8072f6093f3585fd342d"},
     {file = "greenlet-1.1.2-cp37-cp37m-macosx_10_14_x86_64.whl", hash = "sha256:b92e29e58bef6d9cfd340c72b04d74c4b4e9f70c9fa7c78b674d1fec18896dc4"},
@@ -865,6 +863,7 @@ greenlet = [
     {file = "greenlet-1.1.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1e12bdc622676ce47ae9abbf455c189e442afdde8818d9da983085df6312e7a1"},
     {file = "greenlet-1.1.2-cp37-cp37m-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:8c790abda465726cfb8bb08bd4ca9a5d0a7bd77c7ac1ca1b839ad823b948ea28"},
     {file = "greenlet-1.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f276df9830dba7a333544bd41070e8175762a7ac20350786b322b714b0e654f5"},
+    {file = "greenlet-1.1.2-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:8c5d5b35f789a030ebb95bff352f1d27a93d81069f2adb3182d99882e095cefe"},
     {file = "greenlet-1.1.2-cp37-cp37m-win32.whl", hash = "sha256:64e6175c2e53195278d7388c454e0b30997573f3f4bd63697f88d855f7a6a1fc"},
     {file = "greenlet-1.1.2-cp37-cp37m-win_amd64.whl", hash = "sha256:b11548073a2213d950c3f671aa88e6f83cda6e2fb97a8b6317b1b5b33d850e06"},
     {file = "greenlet-1.1.2-cp38-cp38-macosx_10_14_x86_64.whl", hash = "sha256:9633b3034d3d901f0a46b7939f8c4d64427dfba6bbc5a36b1a67364cf148a1b0"},
@@ -873,6 +872,7 @@ greenlet = [
     {file = "greenlet-1.1.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e859fcb4cbe93504ea18008d1df98dee4f7766db66c435e4882ab35cf70cac43"},
     {file = "greenlet-1.1.2-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:00e44c8afdbe5467e4f7b5851be223be68adb4272f44696ee71fe46b7036a711"},
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+    {file = "ujson-5.1.0-pp37-pypy37_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:d0b26d9d6eb9a0979d37f28c715e717a409c9e03163e5cd8fa73aab806351ab5"},
+    {file = "ujson-5.1.0-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:b2c7e4afde0d36926b091fa9613b18b65e911fcaa60024e8721f2dcfedc25329"},
+    {file = "ujson-5.1.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:110633a8dda6c8ca78090292231e15381f8b2423e998399d4bc5f135149c722b"},
+    {file = "ujson-5.1.0-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:fdac161127ef8e0889180a4c07475457c55fe0bbd644436d8f4c7ef07565d653"},
+    {file = "ujson-5.1.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:452990c2b18445a7379a45873527d2ec47789b9289c13a17a3c1cc76b9641126"},
+    {file = "ujson-5.1.0-pp38-pypy38_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:5304ad25d100d50b5bc8513ef110335df678f66c7ccf3d4728c0c3aa69e08e0c"},
+    {file = "ujson-5.1.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:ce620a6563b21aa3fbb1658bc1bfddb484a6dad542de1efb5121eb7bb4f2b93a"},
+    {file = "ujson-5.1.0.tar.gz", hash = "sha256:a88944d2f99db71a3ca0c63d81f37e55b660edde0b07216fb65a3e46403ef004"},
 ]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
@@ -1338,10 +1306,10 @@ wrapt = [
     {file = "wrapt-1.12.1.tar.gz", hash = "sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"},
 ]
 yapf = [
-    {file = "yapf-0.31.0-py2.py3-none-any.whl", hash = "sha256:e3a234ba8455fe201eaa649cdac872d590089a18b661e39bbac7020978dd9c2e"},
-    {file = "yapf-0.31.0.tar.gz", hash = "sha256:408fb9a2b254c302f49db83c59f9aa0b4b0fd0ec25be3a5c51181327922ff63d"},
+    {file = "yapf-0.32.0-py2.py3-none-any.whl", hash = "sha256:8fea849025584e486fd06d6ba2bed717f396080fd3cc236ba10cb97c4c51cf32"},
+    {file = "yapf-0.32.0.tar.gz", hash = "sha256:a3f5085d37ef7e3e004c4ba9f9b3e40c54ff1901cd111f05145ae313a7c67d1b"},
 ]
 zipp = [
-    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
-    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
+    {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
+    {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
 ]

From 78af68c2b3d94b4868c5dabd909e11e2a56584a2 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 2 Mar 2022 15:21:17 -0500
Subject: [PATCH 044/105] Fix #45

* Environmental Modifications require special handling because they
  include a method and a number.
* The JSON value should be reported as `"<METHOD><VALUE>"` (e.g. `A2`
  which will add two to the value presented.
* The default value of all envmods should be "A0"
* If there is an error with the envmod, a logging error is reported and
  A0 is sent to the template.
* Use the type error to catch if the user puts in a physical value.
---
 pythia/functions.py | 10 ++++++++++
 pythia/template.py  | 26 +++++++++++++++++++++++++-
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/pythia/functions.py b/pythia/functions.py
index cee5fb86..43c493a6 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -221,3 +221,13 @@ def date_offset(k, run, context, _):
     else:
         logging.error("date_offset only works with references variables.")
         return None
+
+def string_to_number(term):
+    try:
+        if "." in term:
+            return float(term)
+        else:
+            return int(term)
+    except ValueError:
+        logging.error("string_to_number: %s is not a number", term)
+        return None
diff --git a/pythia/template.py b/pythia/template.py
index e8f1714e..81bd76b0 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -1,4 +1,6 @@
 from jinja2 import Environment, FileSystemLoader
+import logging
+import pythia.functions
 import pythia.util
 
 _t_formats = {
@@ -24,7 +26,6 @@
     "flhst": {"length": 5},
     "fhdur": {"length": 5},
     "irrig": {"length": 5},
-    "erain": {"raw": "M{:>4}"},
     "ph2ol": {"length": 5},
     "fodate": {"length": 7},
     "pdate": {"length": 5},
@@ -35,6 +36,7 @@
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]
 _t_date_fields_4 = ["fodate"]
+_t_envmod_fields = ["eday", "erad", "emax", "emin", "erain", "eco2", "edew", "ewind"]
 
 
 def init_engine(template_dir):
@@ -68,6 +70,24 @@ def wrap_format(k, v):
     return fmt.format(v)
 
 
+def envmod_format(v):
+    fmt = "{}{:>4}"
+    valid_mod = ["R", "A", "M", "S"]
+    try:
+        mod, raw = v[0], v[1:]
+    except TypeError:
+        logging.error("%s is not a valid value for envmod.", v)
+        return fmt.format("A", "0")
+    if mod not in valid_mod:
+        logging.error('"%s" is not a valid envmod modifier.', mod)
+        return fmt.format("A", "0")
+    val = pythia.functions.string_to_number(raw)
+    if val is None:
+        return fmt.format("A", "0")
+    return "{}{:>4}".format(mod, val)
+
+
+
 def auto_format_dict(d):
     if isinstance(d, str):
         return d
@@ -78,11 +98,15 @@ def auto_format_dict(d):
             clean[k] = wrap_format(k, v["default"])
         else:
             clean[k] = wrap_format(k, -99)
+    for k in _t_envmod_fields:
+        clean[k] = envmod_format("A0")
     for k, v in d.items():
         if k in _t_date_fields and "::" not in v:
             clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
         elif k in _t_date_fields_4 and "::" not in v:
             clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
+        elif k in _t_envmod_fields:
+            clean[k] = envmod_format(v)
         elif k in _t_formats:
             clean[k] = wrap_format(k, v)
         elif isinstance(v, dict):

From fa43600de330701607b815a63103eece6199ae76 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 4 Mar 2022 08:40:03 -0500
Subject: [PATCH 045/105] Fix #46

* In the case of the two offset function, do not apply the sensitivity
   analysis if the variable is not specified in the configuration.
* In the case of `env_mod`, you can just apply the factor, as it is an
   overwrite to the variable.
* This detects unusable factors per run and removes them from the factors list for that run.
* Error log is emitted during a list comprehension, and loops every time.
* Currently it is an overlogged issue.
---
 pythia/plugins/sensitivity_plugin/__init__.py | 57 ++++++++++++++++---
 1 file changed, 48 insertions(+), 9 deletions(-)

diff --git a/pythia/plugins/sensitivity_plugin/__init__.py b/pythia/plugins/sensitivity_plugin/__init__.py
index 1694ba1c..6605a317 100644
--- a/pythia/plugins/sensitivity_plugin/__init__.py
+++ b/pythia/plugins/sensitivity_plugin/__init__.py
@@ -1,6 +1,7 @@
 import datetime
 import itertools
 import logging
+import os
 from pythia.plugin import register_plugin_function, PluginHook
 import pythia.util
 
@@ -82,6 +83,22 @@ def merge_static(statics, factor):
     return list(factor) + statics
 
 
+def _uniq_factors(factor_list):
+    uniq = []
+    for factors in factor_list:
+        if len(uniq) == 0:
+            uniq.append(factors)
+        else:
+            uniq_test = [u == factors for u in uniq]
+            if True in uniq_test:
+                pass
+            else:
+                uniq.append(factors)
+    return uniq
+
+
+
+
 def generate_sensitivity_runs(plugin_config={}, full_config={}):
     sens = {
         "_sens_pre_context": {},
@@ -90,6 +107,7 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         "_sens_post_context_static": {},
     }
     # First we organize them
+    runs = full_config.get("runs", {})
     for k in plugin_config.keys():
         if k == "no_rename":
             continue
@@ -118,19 +136,20 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
             ]
         )
     )
-    factors = [merge_static(statics, f) for f in factorial]
+    combined_factors = [merge_static(statics, f) for f in factorial]
     # Next we generate the new runs for each analysis
-    runs = full_config.get("runs", [])
     out_runs = []
     for run in runs:
         current_name = run["name"]
         current_workDir = run["workDir"]
-        for factor in factors:
+        prefilter = [filter_unfactorable(run, f) for f in combined_factors]
+        uniq = _uniq_factors(prefilter)
+        for factors in uniq:
             if not plugin_config.get("no_rename", False):
-                f = generate_factorial_name(factor)
+                f = generate_factorial_name(factors)
                 run["name"] = current_name + "__" + f
                 run["workDir"] = current_workDir + "__" + f
-            out_runs.append({**run, **{"_sens": factor}})
+            out_runs.append({**run, **{"_sens": factors}})
     out_runs = [apply_factors("_sens_pre_context", run) for run in out_runs]
     out_runs = [apply_factors("_sens_pre_context_static", run) for run in out_runs]
     full_config["runs"] = out_runs
@@ -147,6 +166,22 @@ def generate_factorial_name(factors):
     )
 
 
+def _factorable(run, factor):
+    if factor["hook"].endswith("static"):
+        var = factor["from"]
+    else:
+        var = factor["var"]
+    if factor["method"] != "env_mod" and var not in run:
+        logging.error("sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied to run %s", factor["method"], var, run["name"]) 
+        return False 
+    else:
+        return True
+
+
+def filter_unfactorable(run, factors):
+    return [f for f in factors if _factorable(run, f)]
+
+
 def post_build_context_apply_factors(config={}, context={}):
     return apply_factors("_sens_post_context", context)
 
@@ -163,11 +198,15 @@ def apply_factors(hook, current_context):
     for cf in current_factors:
         cval = None
         if hook.endswith("static"):
-            cval = current_context[cf["from"]]
+            cvar = cf["from"]
+        else:
+            cvar = cf["var"]
+        cval = current_context.get(cvar, -99)
+        if cval == -99 and cf["method"] != "env_mod":
+            logging.error("sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied.", cf["method"], cvar) 
         else:
-            cval = current_context[cf["var"]]
-        if cf["method"] in call_list:
-            current_context[cf["var"]] = call_list[cf["method"]](cval, cf["val"])
+            if cf["method"] in call_list:
+                current_context[cf["var"]] = call_list[cf["method"]](cval, cf["val"])
     return current_context
 
 

From e120d9c3e80d56620755fd584ca40daa7b3205c7 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 4 Mar 2022 09:32:45 -0500
Subject: [PATCH 046/105] Release 2.1.5

Fix #46

* In the case of the two offset function, do not apply the sensitivity
  analysis if the variable is not specified in the configuration.
* In the case of `env_mod`, you can just apply the factor, as it is an
overwrite to the variable.
* This detects unusable factors per run and removes them from the factors list for that run.
* Error log is emitted during a list comprehension, and loops every time.
* Currently it is an overlogged issue.

Fix #45

* Environmental Modifications require special handling because they
  include a method and a number.
* The JSON value should be reported as `"<METHOD><VALUE>"` (e.g. `A2`
  which will add two to the value presented.
* The default value of all envmods should be "A0"
* If there is an error with the envmod, a logging error is reported and
  A0 is sent to the template.
* Use the type error to catch if the user puts in a physical value.

Fix #44

* Upgrade ujson
* Upgrade dev dependencies
* Update poetry.lock
* Upgrade Jinja2
---
 poetry.lock                                   | 954 ++++++++++--------
 pyproject.toml                                |   7 +-
 pythia/functions.py                           |  10 +
 pythia/plugins/sensitivity_plugin/__init__.py |  57 +-
 pythia/template.py                            |  26 +-
 5 files changed, 618 insertions(+), 436 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9ce53c74..5a414cb2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -9,6 +9,14 @@ python-versions = "*"
 [package.extras]
 test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
 
+[[package]]
+name = "appnope"
+version = "0.1.2"
+description = "Disable App Nap on macOS >= 10.9"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "astroid"
 version = "2.6.6"
@@ -19,10 +27,22 @@ python-versions = "~=3.6"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
-typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
-typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 wrapt = ">=1.11,<1.13"
 
+[[package]]
+name = "asttokens"
+version = "2.0.5"
+description = "Annotate AST trees with source code positions"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+six = "*"
+
+[package.extras]
+test = ["astroid", "pytest"]
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.0"
@@ -33,17 +53,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "autopep8"
@@ -57,9 +77,17 @@ python-versions = "*"
 pycodestyle = ">=2.7.0"
 toml = "*"
 
+[[package]]
+name = "backcall"
+version = "0.2.0"
+description = "Specifications for callback functions passed in to an API"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "black"
-version = "21.10b0"
+version = "21.12b0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
@@ -70,9 +98,7 @@ click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
 pathspec = ">=0.9.0,<1"
 platformdirs = ">=2"
-regex = ">=2020.1.8"
 tomli = ">=0.2.6,<2.0.0"
-typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
 typing-extensions = [
     {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
     {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
@@ -95,7 +121,7 @@ python-versions = "*"
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.0.4"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
@@ -103,7 +129,6 @@ python-versions = ">=3.6"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [[package]]
 name = "click-plugins"
@@ -141,9 +166,25 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
+name = "executing"
+version = "0.8.3"
+description = "Get the currently executing AST node of a frame, and other information"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "fiona"
-version = "1.8.20"
+version = "1.8.21"
 description = "Fiona reads and writes spatial data files"
 category = "main"
 optional = false
@@ -159,7 +200,7 @@ munch = "*"
 six = ">=1.7"
 
 [package.extras]
-all = ["pytest (>=3)", "boto3 (>=1.2.4)", "pytest-cov", "shapely", "mock"]
+all = ["boto3 (>=1.2.4)", "pytest-cov", "shapely", "pytest (>=3)", "mock"]
 calc = ["shapely"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["pytest (>=3)", "pytest-cov", "boto3 (>=1.2.4)", "mock"]
@@ -173,7 +214,6 @@ optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [package.dependencies]
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
@@ -190,25 +230,43 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 docs = ["sphinx"]
 
 [[package]]
-name = "importlib-metadata"
-version = "4.8.1"
-description = "Read metadata from Python packages"
-category = "main"
+name = "ipython"
+version = "8.1.0"
+description = "IPython: Productive Interactive Computing"
+category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 
 [package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
-zipp = ">=0.5"
+appnope = {version = "*", markers = "sys_platform == \"darwin\""}
+backcall = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+decorator = "*"
+jedi = ">=0.16"
+matplotlib-inline = "*"
+pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
+pickleshare = "*"
+prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
+pygments = ">=2.4.0"
+stack-data = "*"
+traitlets = ">=5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-perf = ["ipython"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+all = ["black", "Sphinx (>=1.3)", "ipykernel", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.19)", "pandas", "pytest", "testpath", "trio", "pytest-asyncio"]
+black = ["black"]
+doc = ["Sphinx (>=1.3)"]
+kernel = ["ipykernel"]
+nbconvert = ["nbconvert"]
+nbformat = ["nbformat"]
+notebook = ["ipywidgets", "notebook"]
+parallel = ["ipyparallel"]
+qtconsole = ["qtconsole"]
+test = ["pytest", "pytest-asyncio", "testpath"]
+test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest", "testpath", "trio"]
 
 [[package]]
 name = "isort"
-version = "5.10.0"
+version = "5.10.1"
 description = "A Python utility / library to sort Python imports."
 category = "dev"
 optional = false
@@ -222,7 +280,7 @@ plugins = ["setuptools"]
 
 [[package]]
 name = "jedi"
-version = "0.18.0"
+version = "0.18.1"
 description = "An autocompletion tool for Python that can be used for text editors."
 category = "dev"
 optional = false
@@ -233,37 +291,48 @@ parso = ">=0.8.0,<0.9.0"
 
 [package.extras]
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "2.11.3"
+version = "3.0.3"
 description = "A very fast and expressive template engine."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
 
 [package.dependencies]
-MarkupSafe = ">=0.23"
+MarkupSafe = ">=2.0"
 
 [package.extras]
-i18n = ["Babel (>=0.8)"]
+i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "lazy-object-proxy"
-version = "1.6.0"
+version = "1.7.1"
 description = "A fast and thorough lazy object proxy."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "markupsafe"
-version = "2.0.1"
+version = "2.1.0"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+
+[[package]]
+name = "matplotlib-inline"
+version = "0.1.3"
+description = "Inline Matplotlib backend for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+traitlets = "*"
 
 [[package]]
 name = "mccabe"
@@ -275,7 +344,7 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.10.0"
+version = "8.12.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
@@ -283,7 +352,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "msgpack"
-version = "1.0.2"
+version = "1.0.3"
 description = "MessagePack (de)serializer."
 category = "dev"
 optional = false
@@ -325,26 +394,26 @@ pynvim = ">=0.3.1"
 
 [[package]]
 name = "numpy"
-version = "1.21.1"
+version = "1.22.2"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [[package]]
 name = "packaging"
-version = "21.2"
+version = "21.3"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-pyparsing = ">=2.0.2,<3"
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "parso"
-version = "0.8.2"
+version = "0.8.3"
 description = "A Python Parser"
 category = "dev"
 optional = false
@@ -362,13 +431,32 @@ category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
+[[package]]
+name = "pexpect"
+version = "4.8.0"
+description = "Pexpect allows easy control of interactive console applications."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+ptyprocess = ">=0.5"
+
+[[package]]
+name = "pickleshare"
+version = "0.7.5"
+description = "Tiny 'shelve'-like database with concurrency support"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "platformdirs"
-version = "2.4.0"
+version = "2.5.1"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
@@ -382,11 +470,38 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.extras]
+dev = ["pre-commit", "tox"]
+
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.28"
+description = "Library for building powerful interactive command lines in Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
 [package.dependencies]
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+wcwidth = "*"
+
+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "pure-eval"
+version = "0.2.2"
+description = "Safely evaluate AST nodes without side effects"
+category = "dev"
+optional = false
+python-versions = "*"
 
 [package.extras]
-dev = ["pre-commit", "tox"]
+tests = ["pytest"]
 
 [[package]]
 name = "py"
@@ -426,6 +541,14 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pygments"
+version = "2.11.2"
+description = "Pygments is a syntax highlighting package written in Python."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "pylint"
 version = "2.9.6"
@@ -467,7 +590,7 @@ python-lsp-server = "*"
 
 [[package]]
 name = "pylsp-rope"
-version = "0.1.7"
+version = "0.1.8"
 description = "Extended refactoring capabilities for Python LSP Server using Rope."
 category = "dev"
 optional = false
@@ -476,7 +599,6 @@ python-versions = ">=3.6"
 [package.dependencies]
 python-lsp-server = "*"
 rope = ">=0.21.0"
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 dev = ["build", "pytest", "twine"]
@@ -500,11 +622,14 @@ test = ["pytest (>=3.4.0)"]
 
 [[package]]
 name = "pyparsing"
-version = "2.4.7"
+version = "3.0.7"
 description = "Python parsing module"
 category = "main"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = ">=3.6"
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
@@ -518,7 +643,6 @@ python-versions = ">=3.5"
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=17.4.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 more-itertools = ">=4.0.0"
 packaging = "*"
 pluggy = ">=0.12,<1.0"
@@ -531,7 +655,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 
 [[package]]
 name = "python-lsp-black"
-version = "1.0.0"
+version = "1.1.0"
 description = "Black plugin for the Python LSP Server"
 category = "dev"
 optional = false
@@ -543,7 +667,7 @@ python-lsp-server = "*"
 toml = "*"
 
 [package.extras]
-dev = ["isort (>=5.0)", "flake8", "pytest", "mypy"]
+dev = ["flake8", "isort (>=5.0)", "mypy", "pre-commit", "pytest", "types-pkg-resources", "types-setuptools", "types-toml"]
 
 [[package]]
 name = "python-lsp-jsonrpc"
@@ -621,24 +745,16 @@ plot = ["matplotlib"]
 s3 = ["boto3 (>=1.2.4)"]
 test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "pytest (>=2.8.2)", "shapely"]
 
-[[package]]
-name = "regex"
-version = "2021.11.2"
-description = "Alternative regular expression module, to replace re."
-category = "dev"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "rope"
-version = "0.21.0"
+version = "0.23.0"
 description = "a python refactoring library..."
 category = "dev"
 optional = false
 python-versions = "*"
 
 [package.extras]
-dev = ["pytest", "pytest-timeout"]
+dev = ["build", "pytest", "pytest-timeout"]
 
 [[package]]
 name = "rtree"
@@ -650,7 +766,7 @@ python-versions = "*"
 
 [[package]]
 name = "shapely"
-version = "1.8.0"
+version = "1.8.1.post1"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
@@ -671,7 +787,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "snowballstemmer"
-version = "2.1.0"
+version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 category = "dev"
 optional = false
@@ -692,6 +808,22 @@ pyparsing = ">=2.1.6"
 [package.extras]
 test = ["pytest", "hypothesis"]
 
+[[package]]
+name = "stack-data"
+version = "0.2.0"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+asttokens = "*"
+executing = "*"
+pure-eval = "*"
+
+[package.extras]
+tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -702,35 +834,38 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "tomli"
-version = "1.2.2"
+version = "1.2.3"
 description = "A lil' TOML parser"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [[package]]
-name = "typed-ast"
-version = "1.4.3"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
+name = "traitlets"
+version = "5.1.1"
+description = "Traitlets Python configuration system"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+
+[package.extras]
+test = ["pytest"]
 
 [[package]]
 name = "typing-extensions"
-version = "3.10.0.2"
-description = "Backported and Experimental Type Hints for Python 3.5+"
-category = "main"
+version = "4.1.1"
+description = "Backported and Experimental Type Hints for Python 3.6+"
+category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "ujson"
-version = "4.2.0"
+version = "5.1.0"
 description = "Ultra fast JSON encoder and decoder for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "wcwidth"
@@ -750,61 +885,61 @@ python-versions = "*"
 
 [[package]]
 name = "yapf"
-version = "0.31.0"
+version = "0.32.0"
 description = "A formatter for Python code."
 category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "zipp"
-version = "3.6.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
-
 [metadata]
 lock-version = "1.1"
-python-versions = "^3.7"
-content-hash = "f55eee3ae0ca41608fea98081bf32dbcf104db9105be41571dd3cd57dd449ef7"
+python-versions = "^3.8"
+content-hash = "f99cb43ca081505d52d25211f1dadde1a032af87a89732f01a768d2d7a4a9c50"
 
 [metadata.files]
 affine = [
     {file = "affine-2.3.0-py2.py3-none-any.whl", hash = "sha256:34b05b070d954c382e56f02c207a372d8a32621a87653cc30cdd31cd7f65799f"},
     {file = "affine-2.3.0.tar.gz", hash = "sha256:2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102"},
 ]
+appnope = [
+    {file = "appnope-0.1.2-py2.py3-none-any.whl", hash = "sha256:93aa393e9d6c54c5cd570ccadd8edad61ea0c4b9ea7a01409020c9aa019eb442"},
+    {file = "appnope-0.1.2.tar.gz", hash = "sha256:dd83cd4b5b460958838f6eb3000c660b1f9caf2a5b1de4264e941512f603258a"},
+]
 astroid = [
     {file = "astroid-2.6.6-py3-none-any.whl", hash = "sha256:ab7f36e8a78b8e54a62028ba6beef7561db4cdb6f2a5009ecc44a6f42b5697ef"},
     {file = "astroid-2.6.6.tar.gz", hash = "sha256:3975a0bd5373bdce166e60c851cfcbaf21ee96de80ec518c1f4cb3e94c3fb334"},
 ]
+asttokens = [
+    {file = "asttokens-2.0.5-py2.py3-none-any.whl", hash = "sha256:0844691e88552595a6f4a4281a9f7f79b8dd45ca4ccea82e5e05b4bbdb76705c"},
+    {file = "asttokens-2.0.5.tar.gz", hash = "sha256:9a54c114f02c7a9480d56550932546a3f1fe71d8a02f1bc7ccd0ee3ee35cf4d5"},
+]
 atomicwrites = [
     {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
 ]
 attrs = [
-    {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
-    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
+    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
+    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
 ]
 autopep8 = [
     {file = "autopep8-1.5.7-py2.py3-none-any.whl", hash = "sha256:aa213493c30dcdac99537249ee65b24af0b2c29f2e83cd8b3f68760441ed0db9"},
     {file = "autopep8-1.5.7.tar.gz", hash = "sha256:276ced7e9e3cb22e5d7c14748384a5cf5d9002257c0ed50c0e075b68011bb6d0"},
 ]
+backcall = [
+    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
+    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
+]
 black = [
-    {file = "black-21.10b0-py3-none-any.whl", hash = "sha256:6eb7448da9143ee65b856a5f3676b7dda98ad9abe0f87fce8c59291f15e82a5b"},
-    {file = "black-21.10b0.tar.gz", hash = "sha256:a9952229092e325fe5f3dae56d81f639b23f7131eb840781947e4b2886030f33"},
+    {file = "black-21.12b0-py3-none-any.whl", hash = "sha256:a615e69ae185e08fdd73e4715e260e2479c861b5740057fde6e8b4e3b7dd589f"},
+    {file = "black-21.12b0.tar.gz", hash = "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3"},
 ]
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-]
-zipp = [
-    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
-    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
+    {file = "yapf-0.32.0-py2.py3-none-any.whl", hash = "sha256:8fea849025584e486fd06d6ba2bed717f396080fd3cc236ba10cb97c4c51cf32"},
+    {file = "yapf-0.32.0.tar.gz", hash = "sha256:a3f5085d37ef7e3e004c4ba9f9b3e40c54ff1901cd111f05145ae313a7c67d1b"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 5e0a303e..9b8d370b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,14 +1,14 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.4"
+version = "2.1.5"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"
 
 [tool.poetry.dependencies]
-python = "^3.7"
+python = "^3.8"
 fiona = "^1.8"
-jinja2 = "^2.10"
+jinja2 = "^3.0"
 numpy = "^1.16"
 rasterio = "^1.0"
 shapely = "^1.6"
@@ -24,6 +24,7 @@ pyls-isort = "^0.2.2"
 python-lsp-black = "^1.0.0"
 pylsp-rope = "^0.1.7"
 pyls-flake8 = "^0.4.0"
+ipython = "^8.1.0"
 
 [tool.poetry.scripts]
 pythia = "pythia.cli:main"
diff --git a/pythia/functions.py b/pythia/functions.py
index cee5fb86..43c493a6 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -221,3 +221,13 @@ def date_offset(k, run, context, _):
     else:
         logging.error("date_offset only works with references variables.")
         return None
+
+def string_to_number(term):
+    try:
+        if "." in term:
+            return float(term)
+        else:
+            return int(term)
+    except ValueError:
+        logging.error("string_to_number: %s is not a number", term)
+        return None
diff --git a/pythia/plugins/sensitivity_plugin/__init__.py b/pythia/plugins/sensitivity_plugin/__init__.py
index 1694ba1c..6605a317 100644
--- a/pythia/plugins/sensitivity_plugin/__init__.py
+++ b/pythia/plugins/sensitivity_plugin/__init__.py
@@ -1,6 +1,7 @@
 import datetime
 import itertools
 import logging
+import os
 from pythia.plugin import register_plugin_function, PluginHook
 import pythia.util
 
@@ -82,6 +83,22 @@ def merge_static(statics, factor):
     return list(factor) + statics
 
 
+def _uniq_factors(factor_list):
+    uniq = []
+    for factors in factor_list:
+        if len(uniq) == 0:
+            uniq.append(factors)
+        else:
+            uniq_test = [u == factors for u in uniq]
+            if True in uniq_test:
+                pass
+            else:
+                uniq.append(factors)
+    return uniq
+
+
+
+
 def generate_sensitivity_runs(plugin_config={}, full_config={}):
     sens = {
         "_sens_pre_context": {},
@@ -90,6 +107,7 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
         "_sens_post_context_static": {},
     }
     # First we organize them
+    runs = full_config.get("runs", {})
     for k in plugin_config.keys():
         if k == "no_rename":
             continue
@@ -118,19 +136,20 @@ def generate_sensitivity_runs(plugin_config={}, full_config={}):
             ]
         )
     )
-    factors = [merge_static(statics, f) for f in factorial]
+    combined_factors = [merge_static(statics, f) for f in factorial]
     # Next we generate the new runs for each analysis
-    runs = full_config.get("runs", [])
     out_runs = []
     for run in runs:
         current_name = run["name"]
         current_workDir = run["workDir"]
-        for factor in factors:
+        prefilter = [filter_unfactorable(run, f) for f in combined_factors]
+        uniq = _uniq_factors(prefilter)
+        for factors in uniq:
             if not plugin_config.get("no_rename", False):
-                f = generate_factorial_name(factor)
+                f = generate_factorial_name(factors)
                 run["name"] = current_name + "__" + f
                 run["workDir"] = current_workDir + "__" + f
-            out_runs.append({**run, **{"_sens": factor}})
+            out_runs.append({**run, **{"_sens": factors}})
     out_runs = [apply_factors("_sens_pre_context", run) for run in out_runs]
     out_runs = [apply_factors("_sens_pre_context_static", run) for run in out_runs]
     full_config["runs"] = out_runs
@@ -147,6 +166,22 @@ def generate_factorial_name(factors):
     )
 
 
+def _factorable(run, factor):
+    if factor["hook"].endswith("static"):
+        var = factor["from"]
+    else:
+        var = factor["var"]
+    if factor["method"] != "env_mod" and var not in run:
+        logging.error("sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied to run %s", factor["method"], var, run["name"]) 
+        return False 
+    else:
+        return True
+
+
+def filter_unfactorable(run, factors):
+    return [f for f in factors if _factorable(run, f)]
+
+
 def post_build_context_apply_factors(config={}, context={}):
     return apply_factors("_sens_post_context", context)
 
@@ -163,11 +198,15 @@ def apply_factors(hook, current_context):
     for cf in current_factors:
         cval = None
         if hook.endswith("static"):
-            cval = current_context[cf["from"]]
+            cvar = cf["from"]
+        else:
+            cvar = cf["var"]
+        cval = current_context.get(cvar, -99)
+        if cval == -99 and cf["method"] != "env_mod":
+            logging.error("sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied.", cf["method"], cvar) 
         else:
-            cval = current_context[cf["var"]]
-        if cf["method"] in call_list:
-            current_context[cf["var"]] = call_list[cf["method"]](cval, cf["val"])
+            if cf["method"] in call_list:
+                current_context[cf["var"]] = call_list[cf["method"]](cval, cf["val"])
     return current_context
 
 
diff --git a/pythia/template.py b/pythia/template.py
index e8f1714e..81bd76b0 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -1,4 +1,6 @@
 from jinja2 import Environment, FileSystemLoader
+import logging
+import pythia.functions
 import pythia.util
 
 _t_formats = {
@@ -24,7 +26,6 @@
     "flhst": {"length": 5},
     "fhdur": {"length": 5},
     "irrig": {"length": 5},
-    "erain": {"raw": "M{:>4}"},
     "ph2ol": {"length": 5},
     "fodate": {"length": 7},
     "pdate": {"length": 5},
@@ -35,6 +36,7 @@
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]
 _t_date_fields_4 = ["fodate"]
+_t_envmod_fields = ["eday", "erad", "emax", "emin", "erain", "eco2", "edew", "ewind"]
 
 
 def init_engine(template_dir):
@@ -68,6 +70,24 @@ def wrap_format(k, v):
     return fmt.format(v)
 
 
+def envmod_format(v):
+    fmt = "{}{:>4}"
+    valid_mod = ["R", "A", "M", "S"]
+    try:
+        mod, raw = v[0], v[1:]
+    except TypeError:
+        logging.error("%s is not a valid value for envmod.", v)
+        return fmt.format("A", "0")
+    if mod not in valid_mod:
+        logging.error('"%s" is not a valid envmod modifier.', mod)
+        return fmt.format("A", "0")
+    val = pythia.functions.string_to_number(raw)
+    if val is None:
+        return fmt.format("A", "0")
+    return "{}{:>4}".format(mod, val)
+
+
+
 def auto_format_dict(d):
     if isinstance(d, str):
         return d
@@ -78,11 +98,15 @@ def auto_format_dict(d):
             clean[k] = wrap_format(k, v["default"])
         else:
             clean[k] = wrap_format(k, -99)
+    for k in _t_envmod_fields:
+        clean[k] = envmod_format("A0")
     for k, v in d.items():
         if k in _t_date_fields and "::" not in v:
             clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
         elif k in _t_date_fields_4 and "::" not in v:
             clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
+        elif k in _t_envmod_fields:
+            clean[k] = envmod_format(v)
         elif k in _t_formats:
             clean[k] = wrap_format(k, v)
         elif isinstance(v, dict):

From 91c986b88633015eed2016a436bbbec23de4c453 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Fri, 4 Mar 2022 10:53:12 -0500
Subject: [PATCH 047/105] Bump to next dev version (2.1.dev6)

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 67f7402d..4f3b7314 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.dev5"
+version = "2.1.dev6"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From b8871201148fb9909d114f4a416ae358b62b3eed Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 21 Mar 2022 22:29:08 -0400
Subject: [PATCH 048/105] Silence the output from pythia

* Add silence key to config
* Use the silence key to determine printing of .+X on the console.
---
 pythia/cli.py      |  9 +++++++++
 pythia/dssat.py    | 24 ++++++++++++++++++++++--
 pythia/peerless.py | 13 +++++++++----
 3 files changed, 40 insertions(+), 6 deletions(-)

diff --git a/pythia/cli.py b/pythia/cli.py
index f1be2007..438360f7 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -41,6 +41,11 @@ def main():
         default="pythia",
         help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log",
     )
+    parser.add_argument(
+            "--quiet",
+            action="store_true",
+            help="Enjoy the silence"
+            )
     args = parser.parse_args()
 
     if not args.config:
@@ -73,6 +78,10 @@ def main():
             config = pythia.plugin.run_plugin_functions(
                 pythia.plugin.PluginHook.post_config, plugins, full_config=config
             )
+            if args.quiet:
+                config["silence"] = True
+            else:
+                config["silence"] = False
             if args.all or args.setup:
                 print("Setting up points and directory structure")
                 pythia.peerless.execute(config, plugins)
diff --git a/pythia/dssat.py b/pythia/dssat.py
index 9130e424..0ab8c9dd 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -5,6 +5,8 @@
 from multiprocessing.pool import Pool
 
 
+async_error = False
+
 def _run_dssat(details, config):
     logging.debug("Current WD: {}".format(os.getcwd()))
     run_mode = "A"
@@ -66,16 +68,34 @@ def display_async(details):
             out.decode()[:-1],
         )
         print("X", end="", flush=True)
+        async_error = True
     else:
         print(".", end="", flush=True)
 
 
+def silent_async(details):
+    loc, xfile, out, error, retcode = details
+    error_count = len(out.decode().split("\n")) - 1
+    if error_count > 0:
+        logging.warning(
+            "Check the DSSAT summary file in %s. %d failures occured\n%s",
+            loc,
+            error_count,
+            out.decode()[:-1],
+        )
+        async_error = True
+
+
 def execute(config, plugins):
     pool_size = config.get("cores", mp.cpu_count())
     run_list = _generate_run_list(config)
     with Pool(processes=pool_size) as pool:
         for details in run_list:  # _generate_run_list(config):
-            pool.apply_async(_run_dssat, (details, config), callback=display_async)
+            if config["silence"]:
+                pool.apply_async(_run_dssat, (details, config), callback=silent_async)
+            else:
+                pool.apply_async(_run_dssat, (details, config), callback=display_async)
         pool.close()
         pool.join()
-    print("\nIf you see an X above, please check the pythia.log for more details")
+    if async_error:
+        print("\nOne or more simulations had failures. Please check the pythia log for more details")
diff --git a/pythia/peerless.py b/pythia/peerless.py
index 72459e14..eeea00c7 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -9,9 +9,11 @@
 import pythia.util
 
 
+
 def build_context(args):
-    print("+", end="", flush=True)
     run, ctx, config = args
+    if not config["silence"]:
+        print("+", end="", flush=True)
     context = run.copy()
     context = {**context, **ctx}
     y, x = pythia.util.translate_coords_news(context["lat"], context["lng"])
@@ -58,7 +60,8 @@ def symlink_wth_soil(output_dir, config, context):
 
 
 def compose_peerless(context, config, env):
-    print(".", end="", flush=True)
+    if not config["silence"]:
+        print(".", end="", flush=True)
     this_output_dir = context["contextWorkDir"]
     symlink_wth_soil(this_output_dir, config, context)
     xfile = pythia.template.render_template(env, context["template"], context)
@@ -93,8 +96,10 @@ def execute(config, plugins):
                 )
                 runlist.append(os.path.abspath(compose_peerless(context, config, env)))
             else:
-                print("X", end="", flush=True)
+                if not config["silence"]:
+                    print("X", end="", flush=True)
     if config["exportRunlist"]:
         with open(os.path.join(config["workDir"], "run_list.txt"), "w") as f:
             [f.write(f"{x}\n") for x in runlist]
-    print()
+    if not config["silence"]:
+        print()

From eaa16e0d22aa642abb7a12b0ccfd2b52daedcee0 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 21 Mar 2022 23:05:58 -0400
Subject: [PATCH 049/105] Release 2.1.6

* Enable --quiet option to remove progress marks on the console.
---
 pyproject.toml     |  2 +-
 pythia/cli.py      |  9 +++++++++
 pythia/dssat.py    | 24 ++++++++++++++++++++++--
 pythia/peerless.py | 13 +++++++++----
 4 files changed, 41 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9b8d370b..4d780f2d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.5"
+version = "2.1.6"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"
diff --git a/pythia/cli.py b/pythia/cli.py
index f1be2007..438360f7 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -41,6 +41,11 @@ def main():
         default="pythia",
         help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log",
     )
+    parser.add_argument(
+            "--quiet",
+            action="store_true",
+            help="Enjoy the silence"
+            )
     args = parser.parse_args()
 
     if not args.config:
@@ -73,6 +78,10 @@ def main():
             config = pythia.plugin.run_plugin_functions(
                 pythia.plugin.PluginHook.post_config, plugins, full_config=config
             )
+            if args.quiet:
+                config["silence"] = True
+            else:
+                config["silence"] = False
             if args.all or args.setup:
                 print("Setting up points and directory structure")
                 pythia.peerless.execute(config, plugins)
diff --git a/pythia/dssat.py b/pythia/dssat.py
index 9130e424..0ab8c9dd 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -5,6 +5,8 @@
 from multiprocessing.pool import Pool
 
 
+async_error = False
+
 def _run_dssat(details, config):
     logging.debug("Current WD: {}".format(os.getcwd()))
     run_mode = "A"
@@ -66,16 +68,34 @@ def display_async(details):
             out.decode()[:-1],
         )
         print("X", end="", flush=True)
+        async_error = True
     else:
         print(".", end="", flush=True)
 
 
+def silent_async(details):
+    loc, xfile, out, error, retcode = details
+    error_count = len(out.decode().split("\n")) - 1
+    if error_count > 0:
+        logging.warning(
+            "Check the DSSAT summary file in %s. %d failures occured\n%s",
+            loc,
+            error_count,
+            out.decode()[:-1],
+        )
+        async_error = True
+
+
 def execute(config, plugins):
     pool_size = config.get("cores", mp.cpu_count())
     run_list = _generate_run_list(config)
     with Pool(processes=pool_size) as pool:
         for details in run_list:  # _generate_run_list(config):
-            pool.apply_async(_run_dssat, (details, config), callback=display_async)
+            if config["silence"]:
+                pool.apply_async(_run_dssat, (details, config), callback=silent_async)
+            else:
+                pool.apply_async(_run_dssat, (details, config), callback=display_async)
         pool.close()
         pool.join()
-    print("\nIf you see an X above, please check the pythia.log for more details")
+    if async_error:
+        print("\nOne or more simulations had failures. Please check the pythia log for more details")
diff --git a/pythia/peerless.py b/pythia/peerless.py
index 72459e14..eeea00c7 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -9,9 +9,11 @@
 import pythia.util
 
 
+
 def build_context(args):
-    print("+", end="", flush=True)
     run, ctx, config = args
+    if not config["silence"]:
+        print("+", end="", flush=True)
     context = run.copy()
     context = {**context, **ctx}
     y, x = pythia.util.translate_coords_news(context["lat"], context["lng"])
@@ -58,7 +60,8 @@ def symlink_wth_soil(output_dir, config, context):
 
 
 def compose_peerless(context, config, env):
-    print(".", end="", flush=True)
+    if not config["silence"]:
+        print(".", end="", flush=True)
     this_output_dir = context["contextWorkDir"]
     symlink_wth_soil(this_output_dir, config, context)
     xfile = pythia.template.render_template(env, context["template"], context)
@@ -93,8 +96,10 @@ def execute(config, plugins):
                 )
                 runlist.append(os.path.abspath(compose_peerless(context, config, env)))
             else:
-                print("X", end="", flush=True)
+                if not config["silence"]:
+                    print("X", end="", flush=True)
     if config["exportRunlist"]:
         with open(os.path.join(config["workDir"], "run_list.txt"), "w") as f:
             [f.write(f"{x}\n") for x in runlist]
-    print()
+    if not config["silence"]:
+        print()

From 1cb7e503e2d2cbab8c789c2a9c14a2d619563b5d Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Mon, 21 Mar 2022 23:08:50 -0400
Subject: [PATCH 050/105] Bump to next dev version (2.1.dev7)

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4f3b7314..ad471fbc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.dev6"
+version = "2.1.dev7"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 2fc5957835fa404eebc7b41e911db7e07908864b Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 13 Apr 2022 16:27:50 -0400
Subject: [PATCH 051/105] Fix -99 for 4-digit dates

* If any 4-digit date field is passed -99, keep as is.
---
 pythia/template.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/pythia/template.py b/pythia/template.py
index 81bd76b0..006d5196 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -87,7 +87,6 @@ def envmod_format(v):
     return "{}{:>4}".format(mod, val)
 
 
-
 def auto_format_dict(d):
     if isinstance(d, str):
         return d
@@ -104,7 +103,10 @@ def auto_format_dict(d):
         if k in _t_date_fields and "::" not in v:
             clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
         elif k in _t_date_fields_4 and "::" not in v:
-            clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
+            if v == "-99" or v == -99:
+                clean[k] = v
+            else:
+                clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
         elif k in _t_envmod_fields:
             clean[k] = envmod_format(v)
         elif k in _t_formats:

From 56e878f232b9079c009c248497a1aa899c2c6961 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 13 Apr 2022 16:37:36 -0400
Subject: [PATCH 052/105] Format forced -99 values

* Any forced -99 values should respect the formatting for the key being
  presented.
---
 pythia/template.py | 35 +++++++++++++++++++----------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/pythia/template.py b/pythia/template.py
index 81bd76b0..e63038a7 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -101,23 +101,26 @@ def auto_format_dict(d):
     for k in _t_envmod_fields:
         clean[k] = envmod_format("A0")
     for k, v in d.items():
-        if k in _t_date_fields and "::" not in v:
-            clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
-        elif k in _t_date_fields_4 and "::" not in v:
-            clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
-        elif k in _t_envmod_fields:
-            clean[k] = envmod_format(v)
-        elif k in _t_formats:
-            clean[k] = wrap_format(k, v)
-        elif isinstance(v, dict):
-            clean[k] = auto_format_dict(v)
-        elif isinstance(v, list) and not isinstance(v, str):
-            if k == "sites":
-                continue
-            else:
-                clean[k] = [auto_format_dict(intern) for intern in v]
+        if v == "-99" or v == -99:
+            clean[k] = wrap_format(v)
         else:
-            clean[k] = v
+            if k in _t_date_fields and "::" not in v:
+                clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))
+            elif k in _t_date_fields_4 and "::" not in v:
+                clean[k] = pythia.util.to_julian_date_4(pythia.util.from_iso_date(v))
+            elif k in _t_envmod_fields:
+                clean[k] = envmod_format(v)
+            elif k in _t_formats:
+                clean[k] = wrap_format(k, v)
+            elif isinstance(v, dict):
+                clean[k] = auto_format_dict(v)
+            elif isinstance(v, list) and not isinstance(v, str):
+                if k == "sites":
+                    continue
+                else:
+                    clean[k] = [auto_format_dict(intern) for intern in v]
+            else:
+                clean[k] = v
     return clean
 
 

From bf59172a62cb7ec6b5ac49412f98dda5ae6a1355 Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Wed, 13 Apr 2022 19:08:46 -0400
Subject: [PATCH 053/105] Fix wrap_format call

* Add missing k parameter for the `wrap_format()` call
---
 pythia/template.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/template.py b/pythia/template.py
index e63038a7..08d7ea01 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -102,7 +102,7 @@ def auto_format_dict(d):
         clean[k] = envmod_format("A0")
     for k, v in d.items():
         if v == "-99" or v == -99:
-            clean[k] = wrap_format(v)
+            clean[k] = wrap_format(k, v)
         else:
             if k in _t_date_fields and "::" not in v:
                 clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))

From 0bc4be332d9c6973249cc205e93a902458db795e Mon Sep 17 00:00:00 2001
From: Christopher Villalobos <cvillalobos@ufl.edu>
Date: Tue, 27 Sep 2022 12:07:50 -0400
Subject: [PATCH 054/105] Update dependencies and format code

* Format all code with `black` code formatter.
* Update dependencies
---
 .gitignore                                    |   1 +
 bin/pythia                                    |   0
 docs/about.rst                                |   2 +-
 docs/conf.py                                  |  19 +-
 guide.adoc                                    |  39 -
 poetry.lock                                   | 844 ++++++++++--------
 project.adoc                                  |  55 --
 project.org                                   |  37 -
 pyproject.toml                                |   6 +-
 pythia/cli.py                                 |   6 +-
 pythia/dssat.py                               |   5 +-
 pythia/functions.py                           |   1 +
 pythia/io.py                                  |   1 +
 pythia/peerless.py                            |   3 +-
 pythia/plugins/sensitivity_plugin/__init__.py |  17 +-
 pythia/template.py                            |   2 +-
 16 files changed, 506 insertions(+), 532 deletions(-)
 mode change 100644 => 100755 .gitignore
 mode change 100644 => 100755 bin/pythia
 delete mode 100644 guide.adoc
 delete mode 100644 project.adoc
 delete mode 100644 project.org

diff --git a/.gitignore b/.gitignore
old mode 100644
new mode 100755
index 4748a48d..17e9f59e
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@ docs/build
 .venv
 dist
 *~
+.python-version
diff --git a/bin/pythia b/bin/pythia
old mode 100644
new mode 100755
diff --git a/docs/about.rst b/docs/about.rst
index 35d22ba2..1e97e348 100644
--- a/docs/about.rst
+++ b/docs/about.rst
@@ -1,7 +1,7 @@
 What is Pythia?
 ===============
 
-Pythia is a simple framework to assist users in running DSSAT over a spatial area based on grid points. Pythia can use any DSSAT v4.7 build. The inputs to the framework are:
+Pythia is a simple framework to assist users in running DSSAT over a spatial area based on grid points. Pythia can use any DSSAT v4.7 build or greater. The inputs to the framework are:
 
 - A JSON configuration file
 - Shape files
diff --git a/docs/conf.py b/docs/conf.py
index 104252c8..d38a504b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'Pythia'
-copyright = '2020, DSSAT Foundation'
-author = 'Christopher Villalobos'
+project = "Pythia"
+copyright = "2020 - 2022, DSSAT Foundation"
+author = "Christopher Villalobos"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = "1.0.0"
 
 
 # -- General configuration ---------------------------------------------------
@@ -30,11 +30,10 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-]
+extensions = []
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -47,15 +46,15 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # -- RTD Settings -------------------------------------------------------------
 
 # It seems that RTD needs to have this set in order for the build to occur.
 #
-master_doc = 'index'
+master_doc = "index"
diff --git a/guide.adoc b/guide.adoc
deleted file mode 100644
index 5a9bfb72..00000000
--- a/guide.adoc
+++ /dev/null
@@ -1,39 +0,0 @@
-= pythia User Guide =
-Christopher Villalobos <cvillalobos@ufl.edu>
-:toc:
-:icons:
-
-== pythia Stages ==
-1. Setup
-2. Execution
-3. Analysis
-
-
-== pythia Analysis ==
-Below is a sample of the analysis sections of the pythia configuration file.
-
-[source,json]
-{
-  "analysis_default": {
-    "per_pixel_prefix": "pp"
-  },
-  "analysis": [
-    {
-      "title": "Yield without scaling",
-      "filename_format": "yields-$run-$ts" // automatically append .tif
-      "output_type": "tiff",
-      "runs": ["each::", "combine::all_rf::a+b+c", "combine::all::a+b+c+d"],
-      "timeseries": {
-        "variable":"PDAT",
-        "timestep":"Y" //Y=Yearly, M=Monthly, D=Daily
-        "as": "year"
-      },
-      "variables": [
-        {
-          "variable": "HWAM",
-          "as": "Yield"
-        }
-      ]
-    }
-  ]
-}
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 5a414cb2..ca2c2d8f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,17 +1,17 @@
 [[package]]
 name = "affine"
-version = "2.3.0"
+version = "2.3.1"
 description = "Matrices describing affine transformation of the plane."
 category = "main"
 optional = false
 python-versions = "*"
 
 [package.extras]
-test = ["pytest (>=3.0)", "pytest-cov", "pydocstyle", "coveralls"]
+test = ["coveralls", "flake8", "pydocstyle", "pytest (>=4.6)", "pytest-cov"]
 
 [[package]]
 name = "appnope"
-version = "0.1.2"
+version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
 category = "dev"
 optional = false
@@ -27,11 +27,12 @@ python-versions = "~=3.6"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
+setuptools = ">=20.0"
 wrapt = ">=1.11,<1.13"
 
 [[package]]
 name = "asttokens"
-version = "2.0.5"
+version = "2.0.8"
 description = "Annotate AST trees with source code positions"
 category = "dev"
 optional = false
@@ -41,11 +42,11 @@ python-versions = "*"
 six = "*"
 
 [package.extras]
-test = ["astroid", "pytest"]
+test = ["astroid (<=2.5.3)", "pytest"]
 
 [[package]]
 name = "atomicwrites"
-version = "1.4.0"
+version = "1.4.1"
 description = "Atomic file writes."
 category = "dev"
 optional = false
@@ -53,17 +54,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.4.0"
+version = "22.1.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.5"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
+docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
+tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "autopep8"
@@ -87,45 +88,41 @@ python-versions = "*"
 
 [[package]]
 name = "black"
-version = "21.12b0"
+version = "22.8.0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
 python-versions = ">=3.6.2"
 
 [package.dependencies]
-click = ">=7.1.2"
+click = ">=8.0.0"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.9.0,<1"
+pathspec = ">=0.9.0"
 platformdirs = ">=2"
-tomli = ">=0.2.6,<2.0.0"
-typing-extensions = [
-    {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
-    {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
-]
+tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
 d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
-python2 = ["typed-ast (>=1.4.3)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2021.10.8"
+version = "2022.9.24"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "click"
-version = "8.0.4"
+version = "8.1.3"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -142,7 +139,7 @@ python-versions = "*"
 click = ">=4.0"
 
 [package.extras]
-dev = ["pytest (>=3.6)", "pytest-cov", "wheel", "coveralls"]
+dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"]
 
 [[package]]
 name = "cligj"
@@ -160,7 +157,7 @@ test = ["pytest-cov"]
 
 [[package]]
 name = "colorama"
-version = "0.4.4"
+version = "0.4.5"
 description = "Cross-platform colored terminal text."
 category = "main"
 optional = false
@@ -176,14 +173,17 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "executing"
-version = "0.8.3"
+version = "1.1.0"
 description = "Get the currently executing AST node of a frame, and other information"
 category = "dev"
 optional = false
 python-versions = "*"
 
+[package.extras]
+tests = ["asttokens", "littleutils", "pytest", "rich"]
+
 [[package]]
-name = "fiona"
+name = "Fiona"
 version = "1.8.21"
 description = "Fiona reads and writes spatial data files"
 category = "main"
@@ -197,13 +197,14 @@ click = ">=4.0"
 click-plugins = ">=1.0"
 cligj = ">=0.5"
 munch = "*"
+setuptools = "*"
 six = ">=1.7"
 
 [package.extras]
-all = ["boto3 (>=1.2.4)", "pytest-cov", "shapely", "pytest (>=3)", "mock"]
+all = ["boto3 (>=1.2.4)", "mock", "pytest (>=3)", "pytest-cov", "shapely"]
 calc = ["shapely"]
 s3 = ["boto3 (>=1.2.4)"]
-test = ["pytest (>=3)", "pytest-cov", "boto3 (>=1.2.4)", "mock"]
+test = ["boto3 (>=1.2.4)", "mock", "pytest (>=3)", "pytest-cov"]
 
 [[package]]
 name = "flake8"
@@ -220,18 +221,18 @@ pyflakes = ">=2.3.0,<2.4.0"
 
 [[package]]
 name = "greenlet"
-version = "1.1.2"
+version = "1.1.3"
 description = "Lightweight in-process concurrent programming"
 category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 
 [package.extras]
-docs = ["sphinx"]
+docs = ["Sphinx"]
 
 [[package]]
 name = "ipython"
-version = "8.1.0"
+version = "8.5.0"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
@@ -246,13 +247,13 @@ jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
+prompt-toolkit = ">3.0.1,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
 
 [package.extras]
-all = ["black", "Sphinx (>=1.3)", "ipykernel", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.19)", "pandas", "pytest", "testpath", "trio", "pytest-asyncio"]
+all = ["Sphinx (>=1.3)", "black", "curio", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "testpath", "trio"]
 black = ["black"]
 doc = ["Sphinx (>=1.3)"]
 kernel = ["ipykernel"]
@@ -261,8 +262,8 @@ nbformat = ["nbformat"]
 notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["pytest", "pytest-asyncio", "testpath"]
-test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest", "testpath", "trio"]
+test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
+test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
 
 [[package]]
 name = "isort"
@@ -273,10 +274,10 @@ optional = false
 python-versions = ">=3.6.1,<4.0"
 
 [package.extras]
-pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
-requirements_deprecated_finder = ["pipreqs", "pip-api"]
 colors = ["colorama (>=0.4.3,<0.5.0)"]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
 plugins = ["setuptools"]
+requirements_deprecated_finder = ["pip-api", "pipreqs"]
 
 [[package]]
 name = "jedi"
@@ -294,12 +295,12 @@ qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
 testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
-name = "jinja2"
-version = "3.0.3"
+name = "Jinja2"
+version = "3.1.2"
 description = "A very fast and expressive template engine."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -316,8 +317,8 @@ optional = false
 python-versions = ">=3.6"
 
 [[package]]
-name = "markupsafe"
-version = "2.1.0"
+name = "MarkupSafe"
+version = "2.1.1"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
@@ -325,7 +326,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "matplotlib-inline"
-version = "0.1.3"
+version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
 category = "dev"
 optional = false
@@ -344,7 +345,7 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.12.0"
+version = "8.14.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
@@ -352,8 +353,8 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "msgpack"
-version = "1.0.3"
-description = "MessagePack (de)serializer."
+version = "1.0.4"
+description = "MessagePack serializer"
 category = "dev"
 optional = false
 python-versions = "*"
@@ -370,7 +371,7 @@ python-versions = "*"
 six = "*"
 
 [package.extras]
-testing = ["pytest", "coverage", "astroid (>=1.5.3,<1.6.0)", "pylint (>=1.7.2,<1.8.0)", "astroid (>=2.0)", "pylint (>=2.3.1,<2.4.0)"]
+testing = ["astroid (>=1.5.3,<1.6.0)", "astroid (>=2.0)", "coverage", "pylint (>=1.7.2,<1.8.0)", "pylint (>=2.3.1,<2.4.0)", "pytest"]
 yaml = ["PyYAML (>=5.1.0)"]
 
 [[package]]
@@ -394,7 +395,7 @@ pynvim = ">=0.3.1"
 
 [[package]]
 name = "numpy"
-version = "1.22.2"
+version = "1.23.3"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -425,11 +426,11 @@ testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "pathspec"
-version = "0.9.0"
+version = "0.10.1"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.7"
 
 [[package]]
 name = "pexpect"
@@ -452,14 +453,14 @@ python-versions = "*"
 
 [[package]]
 name = "platformdirs"
-version = "2.5.1"
+version = "2.5.2"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
 test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
 
 [[package]]
@@ -475,7 +476,7 @@ dev = ["pre-commit", "tox"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.28"
+version = "3.0.31"
 description = "Library for building powerful interactive command lines in Python"
 category = "dev"
 optional = false
@@ -542,12 +543,15 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
-name = "pygments"
-version = "2.11.2"
+name = "Pygments"
+version = "2.13.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
+
+[package.extras]
+plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pylint"
@@ -590,7 +594,7 @@ python-lsp-server = "*"
 
 [[package]]
 name = "pylsp-rope"
-version = "0.1.8"
+version = "0.1.10"
 description = "Extended refactoring capabilities for Python LSP Server using Rope."
 category = "dev"
 optional = false
@@ -622,11 +626,11 @@ test = ["pytest (>=3.4.0)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.7"
-description = "Python parsing module"
+version = "3.0.9"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.8"
 
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
@@ -681,7 +685,7 @@ python-versions = "*"
 ujson = ">=3.0.0"
 
 [package.extras]
-test = ["pylint", "pycodestyle", "pyflakes", "pytest", "pytest-cov", "coverage"]
+test = ["coverage", "pycodestyle", "pyflakes", "pylint", "pytest", "pytest-cov"]
 
 [[package]]
 name = "python-lsp-server"
@@ -703,6 +707,7 @@ pyflakes = {version = ">=2.3.0,<2.4.0", optional = true, markers = "extra == \"a
 pylint = {version = ">=2.5.0,<2.10.0", optional = true, markers = "extra == \"all\""}
 python-lsp-jsonrpc = ">=1.0.0"
 rope = {version = ">=0.10.5", optional = true, markers = "extra == \"all\""}
+setuptools = ">=39.0.0"
 ujson = ">=3.0.0"
 yapf = {version = "*", optional = true, markers = "extra == \"all\""}
 
@@ -716,16 +721,16 @@ pydocstyle = ["pydocstyle (>=2.0.0)"]
 pyflakes = ["pyflakes (>=2.3.0,<2.4.0)"]
 pylint = ["pylint (>=2.5.0,<2.10.0)"]
 rope = ["rope (>0.10.5)"]
-test = ["pylint (>=2.5.0,<2.10.0)", "pytest", "pytest-cov", "coverage", "numpy", "pandas", "matplotlib", "pyqt5", "flaky"]
+test = ["coverage", "flaky", "matplotlib", "numpy", "pandas", "pylint (>=2.5.0,<2.10.0)", "pyqt5", "pytest", "pytest-cov"]
 yapf = ["yapf"]
 
 [[package]]
 name = "rasterio"
-version = "1.2.10"
+version = "1.3.2"
 description = "Fast and direct raster I/O for use with Numpy and SciPy"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 
 [package.dependencies]
 affine = "*"
@@ -734,46 +739,63 @@ certifi = "*"
 click = ">=4.0"
 click-plugins = "*"
 cligj = ">=0.5"
-numpy = "*"
+numpy = ">=1.18"
+setuptools = "*"
 snuggs = ">=1.4.1"
 
 [package.extras]
-all = ["numpydoc", "hypothesis", "matplotlib", "pytest-cov (>=2.2.0)", "sphinx", "ipython (>=2.0)", "boto3 (>=1.2.4)", "shapely", "pytest (>=2.8.2)", "packaging", "sphinx-rtd-theme", "ghp-import"]
+all = ["boto3 (>=1.2.4)", "ghp-import", "hypothesis", "ipython (>=2.0)", "matplotlib", "numpydoc", "packaging", "pytest (>=2.8.2)", "pytest-cov (>=2.2.0)", "shapely", "sphinx", "sphinx-rtd-theme"]
 docs = ["ghp-import", "numpydoc", "sphinx", "sphinx-rtd-theme"]
 ipython = ["ipython (>=2.0)"]
 plot = ["matplotlib"]
 s3 = ["boto3 (>=1.2.4)"]
-test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "pytest (>=2.8.2)", "shapely"]
+test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest (>=2.8.2)", "pytest-cov (>=2.2.0)", "shapely"]
 
 [[package]]
 name = "rope"
-version = "0.23.0"
+version = "1.1.1"
 description = "a python refactoring library..."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3"
 
 [package.extras]
 dev = ["build", "pytest", "pytest-timeout"]
 
 [[package]]
-name = "rtree"
+name = "Rtree"
 version = "0.8.3"
 description = "R-Tree spatial index for Python GIS"
 category = "main"
 optional = false
 python-versions = "*"
 
+[package.dependencies]
+setuptools = "*"
+
+[[package]]
+name = "setuptools"
+version = "65.4.0"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+
 [[package]]
-name = "shapely"
-version = "1.8.1.post1"
+name = "Shapely"
+version = "1.8.4"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-all = ["pytest", "pytest-cov", "numpy"]
+all = ["numpy", "pytest", "pytest-cov"]
 test = ["pytest", "pytest-cov"]
 vectorized = ["numpy"]
 
@@ -806,11 +828,11 @@ numpy = "*"
 pyparsing = ">=2.1.6"
 
 [package.extras]
-test = ["pytest", "hypothesis"]
+test = ["hypothesis", "pytest"]
 
 [[package]]
 name = "stack-data"
-version = "0.2.0"
+version = "0.5.1"
 description = "Extract data from python stack frames and tracebacks for informative displays"
 category = "dev"
 optional = false
@@ -822,7 +844,7 @@ executing = "*"
 pure-eval = "*"
 
 [package.extras]
-tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
+tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
 [[package]]
 name = "toml"
@@ -842,26 +864,26 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "traitlets"
-version = "5.1.1"
-description = "Traitlets Python configuration system"
+version = "5.4.0"
+description = ""
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-test = ["pytest"]
+test = ["pre-commit", "pytest"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.1.1"
-description = "Backported and Experimental Type Hints for Python 3.6+"
+version = "4.3.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "ujson"
-version = "5.1.0"
+version = "5.5.0"
 description = "Ultra fast JSON encoder and decoder for Python"
 category = "dev"
 optional = false
@@ -894,32 +916,31 @@ python-versions = "*"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "f99cb43ca081505d52d25211f1dadde1a032af87a89732f01a768d2d7a4a9c50"
+content-hash = "c18c34acb80d2b510d41362abfba75a3baa2f48165a1c257307bb0ceef8d63cf"
 
 [metadata.files]
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+    {file = "affine-2.3.1-py2.py3-none-any.whl", hash = "sha256:de17839ff05e965580870c3b15e14cefd7992fa05dba9202a0879bbed0c171e4"},
+    {file = "affine-2.3.1.tar.gz", hash = "sha256:d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0"},
 ]
 appnope = [
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+    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
 ]
 astroid = [
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     {file = "astroid-2.6.6.tar.gz", hash = "sha256:3975a0bd5373bdce166e60c851cfcbaf21ee96de80ec518c1f4cb3e94c3fb334"},
 ]
 asttokens = [
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+    {file = "asttokens-2.0.8-py2.py3-none-any.whl", hash = "sha256:e3305297c744ae53ffa032c45dc347286165e4ffce6875dc662b205db0623d86"},
+    {file = "asttokens-2.0.8.tar.gz", hash = "sha256:c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b"},
 ]
 atomicwrites = [
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+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
 ]
 attrs = [
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-    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
+    {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
+    {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
 ]
 autopep8 = [
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@@ -930,16 +951,37 @@ backcall = [
     {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
 ]
 black = [
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-    {file = "black-21.12b0.tar.gz", hash = "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3"},
+    {file = "black-22.8.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ce957f1d6b78a8a231b18e0dd2d94a33d2ba738cd88a7fe64f53f659eea49fdd"},
+    {file = "black-22.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5107ea36b2b61917956d018bd25129baf9ad1125e39324a9b18248d362156a27"},
+    {file = "black-22.8.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e8166b7bfe5dcb56d325385bd1d1e0f635f24aae14b3ae437102dedc0c186747"},
+    {file = "black-22.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dd82842bb272297503cbec1a2600b6bfb338dae017186f8f215c8958f8acf869"},
+    {file = "black-22.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:d839150f61d09e7217f52917259831fe2b689f5c8e5e32611736351b89bb2a90"},
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 certifi = [
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+    {file = "certifi-2022.9.24.tar.gz", hash = "sha256:0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14"},
 ]
 click = [
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 ]
 click-plugins = [
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@@ -950,18 +992,18 @@ cligj = [
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 ]
 colorama = [
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+    {file = "colorama-0.4.5.tar.gz", hash = "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"},
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 executing = [
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 ]
-fiona = [
+Fiona = [
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+    {file = "ujson-5.5.0.tar.gz", hash = "sha256:b25077a971c7da47bd6846a912a747f6963776d90720c88603b1b55d81790780"},
 ]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
diff --git a/project.adoc b/project.adoc
deleted file mode 100644
index 09e160c6..00000000
--- a/project.adoc
+++ /dev/null
@@ -1,55 +0,0 @@
-= Pythia Project Notes
-Christopher Villalobos <cvillalobos@ufl.edu>
-:toc:
-
-== Task List
-* [x] Implement `run_mode` in the `dssat` configuration.
-** Default is `A`
-** Used to support `forecast mode`
-* [x] Add `FODATE` to template
-** Default is `-99`
-* [x] Validate `vector::` function works to feed any fields.
-* [x] Batch mode support
-** [x] Configuration option to specify batch file to use.
-** [x] Default the batch file to DSSBatch.v4x
-* [ ] Auto-include LAT/LNG if -99 in the DSSAT XFile
-* [ ] Auto-generate DSSBatch.v4x when needed for batch mode.
-* [x] Hardwire "season" variable in output
-* [x] Hardwire "management" variable in output
-* [x] Hardwire "late_season" variable in output (binary)
-
-== Execution Notes
-=== Batch file support
-In order to use batch file support modes (specified by `CheckRunMode.f90`), you should use `includes` to copy the batch file to every run directory. This should be in your `default_setup` or `runs` blocks.
-NOTE: Forecast mode (`"run_mode": "Y"`) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
-
-= Breaking Changes (v3.0)
-== Move analytics to output
-----
-"output": [
-{
-"filename": "summary.csv",
-----
-
-* Support for single output file
-----
-"singleOutput": true,
-----
-
-* Support for adding columns
-----
-"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
-----
-
-* Support for filtering columns
-
-NOTE: All hardwired variables will be removed in 3.0
-
-----
-"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
-},
-"filename": "daily.csv",
-"singleOutput": true,
-"outputColumns": ["SOME", "VARIABLE"]
-]
-----
diff --git a/project.org b/project.org
deleted file mode 100644
index c203f399..00000000
--- a/project.org
+++ /dev/null
@@ -1,37 +0,0 @@
-#+TITLE: Pythia Project Notes
-
-* Task List
-** DONE Implement ~run_mode~ in the ~dssat~ configuration.
-- Default is ~A~
-- Used to support ~forecast mode~
-** DONE Add ~FODATE~ to template
-- Default is ~-99~
-** DONE Validate ~vector::~ function works to feed any fields.
-** DONE Batch mode support
-- [X] Configuration option to specify batch file to use.
-- [X] Default the batch file to DSSBatch.v4x
-** TODO auto-include LAT/LNG if -99 in the DSSAT XFile
-** TODO Auto-generate DSSBatch.v4x when needed for batch mode.
-** DONE Hardwire "season" variable in output
-* Execution Notes
-** Batch file support
-In order to use batch file support modes (specified by ~CheckRunMode.f90~), you should use ~includes~ to copy the batch file to every run directory. This should be in your ~default_setup~ or ~runs~ blocks.
-*NOTE* Forecast mode (~"run_mode": "Y"~) only works with DSSAT v4.8 and higher. The FileX should include any forecast mode parameters, even if they aren't specified in the configuration file. Defaults will be used.
-
-* Breaking Changes (v3.0)
-** Move analytics to output
-"output": [
-{
-"filename": "summary.csv",
-** Support for single output file
-"singleOutput": true,
-** Suppffort for adding columns
-"outputColumns": [{"HARVEST_AREA": "from_config::harvestArea"}. {"VNAM": "subtract::$cnam, $gnam"}],
-** Support for filtering columns
-** All these hardwired variables will be removed in 3.0
-"outputColumns": [HARVEST_AREA, "NVAM", "LAT", "LNG"],
-},
-"filename": "daily.csv",
-"singleOutput": true,
-"outputColumns": ["SOME", "VARIABLE"]
-]
diff --git a/pyproject.toml b/pyproject.toml
index 3a71eb2b..ae5fa1de 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ license = "BSD-3-Clause"
 
 [tool.poetry.dependencies]
 python = "^3.8"
-fiona = "^1.8"
+Fiona = "^1.8"
 jinja2 = "^3.0"
 numpy = "^1.16"
 rasterio = "^1.0"
@@ -16,7 +16,6 @@ rtree = "^0.8"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.1"
-black = "^21.5b2"
 flake8 = "^3.9.2"
 neovim = "^0.3.1"
 python-lsp-server = {extras = ["all"], version = "^1.2.4"}
@@ -29,6 +28,9 @@ ipython = "^8.1.0"
 [tool.poetry.scripts]
 pythia = "pythia.cli:main"
 
+[tool.poetry.group.dev.dependencies]
+black = "^22.8.0"
+
 [build-system]
 requires = ["setuptools", "poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
diff --git a/pythia/cli.py b/pythia/cli.py
index 438360f7..0d0761aa 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -41,11 +41,7 @@ def main():
         default="pythia",
         help="Prefix the log file with this string. <prefix|pythia>-YYYYmmdd-hhMMSS.log",
     )
-    parser.add_argument(
-            "--quiet",
-            action="store_true",
-            help="Enjoy the silence"
-            )
+    parser.add_argument("--quiet", action="store_true", help="Enjoy the silence")
     args = parser.parse_args()
 
     if not args.config:
diff --git a/pythia/dssat.py b/pythia/dssat.py
index 0ab8c9dd..9efbe2fe 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -7,6 +7,7 @@
 
 async_error = False
 
+
 def _run_dssat(details, config):
     logging.debug("Current WD: {}".format(os.getcwd()))
     run_mode = "A"
@@ -98,4 +99,6 @@ def execute(config, plugins):
         pool.close()
         pool.join()
     if async_error:
-        print("\nOne or more simulations had failures. Please check the pythia log for more details")
+        print(
+            "\nOne or more simulations had failures. Please check the pythia log for more details"
+        )
diff --git a/pythia/functions.py b/pythia/functions.py
index 43c493a6..a562f8b7 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -222,6 +222,7 @@ def date_offset(k, run, context, _):
         logging.error("date_offset only works with references variables.")
         return None
 
+
 def string_to_number(term):
     try:
         if "." in term:
diff --git a/pythia/io.py b/pythia/io.py
index e4f35fab..08ae65c4 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -9,6 +9,7 @@
 import pythia.functions
 import pythia.util
 
+
 """rasterio reads x/y which is longitude/latitude"""
 
 
diff --git a/pythia/peerless.py b/pythia/peerless.py
index eeea00c7..5f4aaaed 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -4,12 +4,11 @@
 
 import pythia.functions
 import pythia.io
-import pythia.template
 import pythia.plugin
+import pythia.template
 import pythia.util
 
 
-
 def build_context(args):
     run, ctx, config = args
     if not config["silence"]:
diff --git a/pythia/plugins/sensitivity_plugin/__init__.py b/pythia/plugins/sensitivity_plugin/__init__.py
index 6605a317..41e00cbb 100644
--- a/pythia/plugins/sensitivity_plugin/__init__.py
+++ b/pythia/plugins/sensitivity_plugin/__init__.py
@@ -97,8 +97,6 @@ def _uniq_factors(factor_list):
     return uniq
 
 
-
-
 def generate_sensitivity_runs(plugin_config={}, full_config={}):
     sens = {
         "_sens_pre_context": {},
@@ -172,8 +170,13 @@ def _factorable(run, factor):
     else:
         var = factor["var"]
     if factor["method"] != "env_mod" and var not in run:
-        logging.error("sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied to run %s", factor["method"], var, run["name"]) 
-        return False 
+        logging.error(
+            "sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied to run %s",
+            factor["method"],
+            var,
+            run["name"],
+        )
+        return False
     else:
         return True
 
@@ -203,7 +206,11 @@ def apply_factors(hook, current_context):
             cvar = cf["var"]
         cval = current_context.get(cvar, -99)
         if cval == -99 and cf["method"] != "env_mod":
-            logging.error("sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied.", cf["method"], cvar) 
+            logging.error(
+                "sensitivity_plugin: %s requires %s to be specified in the JSON config file. This factor is NOT being applied.",
+                cf["method"],
+                cvar,
+            )
         else:
             if cf["method"] in call_list:
                 current_context[cf["var"]] = call_list[cf["method"]](cval, cf["val"])
diff --git a/pythia/template.py b/pythia/template.py
index 0a3007db..945e552f 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -31,7 +31,7 @@
     "pdate": {"length": 5},
     "pfrst": {"length": 5},
     "plast": {"length": 5},
-    "hdate": {"length": 5}
+    "hdate": {"length": 5},
 }
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]

From dc831ef191a2eb06d60258ece175a634725094ed Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 30 Dec 2023 19:09:21 -0300
Subject: [PATCH 055/105] feat!: improve hook plugin framework to easily add
 new hooks.

Each hook execution should modify and return the given kwargs
---
 pythia/cli.py                          |  2 +-
 pythia/peerless.py                     |  2 +-
 pythia/plugin.py                       | 22 +++++++---------------
 pythia/plugins/test_plugin/__init__.py |  8 ++++----
 pythia/tests/plugin_test.py            |  8 ++++----
 5 files changed, 17 insertions(+), 25 deletions(-)

diff --git a/pythia/cli.py b/pythia/cli.py
index 438360f7..2ea54430 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -77,7 +77,7 @@ def main():
             plugins = pythia.plugin.load_plugins(config, {})
             config = pythia.plugin.run_plugin_functions(
                 pythia.plugin.PluginHook.post_config, plugins, full_config=config
-            )
+            ).get("full_config", config)
             if args.quiet:
                 config["silence"] = True
             else:
diff --git a/pythia/peerless.py b/pythia/peerless.py
index eeea00c7..9e281a8b 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -93,7 +93,7 @@ def execute(config, plugins):
                     pythia.plugin.PluginHook.post_build_context,
                     plugins,
                     context=context,
-                )
+                ).get("context", context)
                 runlist.append(os.path.abspath(compose_peerless(context, config, env)))
             else:
                 if not config["silence"]:
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 9740aadf..75317bf3 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -94,21 +94,13 @@ def load_plugins(config, plugins={}, module_prefix="pythia.plugins"):
 
 
 def run_plugin_functions(hook, plugins, **kwargs):
-    _return = {}
-    if hook == PluginHook.post_config:
-        _return = {**kwargs.get("full_config", {})}
-    elif hook == PluginHook.post_build_context:
-        _return = {**kwargs.get("context", {})}
+    _return = {**kwargs}
     if hook in plugins:
         for plugin_fun in plugins[hook]:
-            if hook == PluginHook.post_config:
-                _return = {
-                    **_return,
-                    **plugin_fun["fun"](plugin_fun.get("config", {}), _return),
-                }
-            elif hook == PluginHook.post_build_context:
-                _return = {
-                    **_return,
-                    **plugin_fun["fun"](plugin_fun.get("config", {}), _return),
-                }
+            plugin_fun_return = plugin_fun["fun"](plugin_fun.get("config", {}), _return, **kwargs)
+            _return = {
+                **_return,
+                **({} if plugin_fun_return is None else plugin_fun_return)
+            }
+
     return _return
diff --git a/pythia/plugins/test_plugin/__init__.py b/pythia/plugins/test_plugin/__init__.py
index b4a1e4ac..5d651cd2 100644
--- a/pythia/plugins/test_plugin/__init__.py
+++ b/pythia/plugins/test_plugin/__init__.py
@@ -13,13 +13,13 @@ def initialize(config, plugins, full_config):
     return plugins
 
 
-def sample_function(config={}):
+def sample_function(config={}, **kwargs):
     retval = config.get("value", 1)
     logging.info("[TEST PLUGIN] Running the sample_function()")
-    return retval
+    return {**kwargs, "config": config, "retval": retval}
 
 
-def contexted_function(config={}, context={}):
+def contexted_function(context={}, **kwargs):
     logging.info("[TEST PLUGIN] Running the contexted_function()")
     context["context_value"] = context.get("context_value", 2) + 1
-    return context
+    return {**kwargs, "context": context}
diff --git a/pythia/tests/plugin_test.py b/pythia/tests/plugin_test.py
index 345fee77..682d8dc9 100644
--- a/pythia/tests/plugin_test.py
+++ b/pythia/tests/plugin_test.py
@@ -93,8 +93,8 @@ def test_plugin_auto_execution():
     context = {"context_value": 7}
     context1 = run_plugin_functions(
         PluginHook.post_build_context, plugins1, context=context
-    )
-    context2 = run_plugin_functions(PluginHook.post_build_context, plugins1)
+    ).get("context")
+    context2 = run_plugin_functions(PluginHook.post_build_context, plugins1).get("context", None)
     assert context1 != context
     assert context1["context_value"] == 8
     assert context2["context_value"] == 3
@@ -107,10 +107,10 @@ def test_no_plugin_does_not_change_context():
     context = {"hello": "there"}
     context1 = run_plugin_functions(
         PluginHook.post_build_context, plugins, context=context
-    )
+    ).get("context")
     assert context == context1
     context2 = run_plugin_functions(
         PluginHook.post_build_context, plugins1, context=context
-    )
+    ).get("context")
     assert context1 != context2
     assert context2 == {**context, **{"context_value": 3}}

From bc8ab7444f8db30ccbea7f6569a589e9ce50e74e Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 30 Dec 2023 19:10:51 -0300
Subject: [PATCH 056/105] feat: add new hooks (post_peerless_pixel_success,
 post_peerless_pixel_skip, post_compose_peerless_pixel_success,
 post_compose_peerless_pixel_skip, post_run_pixel_success and
 post_run_pixel_failed)

---
 pythia/dssat.py                        | 26 ++++++++++++++----
 pythia/peerless.py                     | 38 ++++++++++++++++++++++----
 pythia/plugin.py                       |  6 ++++
 pythia/plugins/test_plugin/__init__.py | 32 ++++++++++++++++++----
 4 files changed, 85 insertions(+), 17 deletions(-)

diff --git a/pythia/dssat.py b/pythia/dssat.py
index 0ab8c9dd..87d5d7f2 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -4,10 +4,11 @@
 import subprocess
 from multiprocessing.pool import Pool
 
+import pythia.plugin
 
 async_error = False
 
-def _run_dssat(details, config):
+def _run_dssat(details, config, plugins):
     logging.debug("Current WD: {}".format(os.getcwd()))
     run_mode = "A"
     if "run_mode" in config["dssat"]:
@@ -21,7 +22,20 @@ def _run_dssat(details, config):
     )
     out, err = dssat.communicate()
     # print("+", end="", flush=True)
-    return details["dir"], details["file"], out, err, dssat.returncode
+
+    error_count = len(out.decode().split("\n")) - 1
+    hook = pythia.plugin.PluginHook.post_run_pixel_success
+    if error_count > 0:
+        hook = pythia.plugin.PluginHook.post_run_pixel_failed
+
+    plugin_transform = pythia.plugin.run_plugin_functions(
+        hook,
+        plugins,
+        input={"details": details, "config": config},
+        output={"loc": details["dir"], "xfile": details["file"], "out": out, "err": err, "retcode": dssat.returncode}
+    ).get("output", {})
+
+    return plugin_transform.get("loc", details["dir"]), plugin_transform.get("xfile", details["file"]), plugin_transform.get("out", out), plugin_transform.get("err", err), plugin_transform.get("retcode", dssat.returncode)
 
 
 def _generate_run_list(config):
@@ -92,10 +106,12 @@ def execute(config, plugins):
     with Pool(processes=pool_size) as pool:
         for details in run_list:  # _generate_run_list(config):
             if config["silence"]:
-                pool.apply_async(_run_dssat, (details, config), callback=silent_async)
+                pool.apply_async(_run_dssat, (details, config, plugins), callback=silent_async)
             else:
-                pool.apply_async(_run_dssat, (details, config), callback=display_async)
+                pool.apply_async(_run_dssat, (details, config, plugins), callback=display_async)
         pool.close()
         pool.join()
     if async_error:
-        print("\nOne or more simulations had failures. Please check the pythia log for more details")
+        print(
+            "\nOne or more simulations had failures. Please check the pythia log for more details"
+        )
diff --git a/pythia/peerless.py b/pythia/peerless.py
index 9e281a8b..42011e83 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -11,7 +11,7 @@
 
 
 def build_context(args):
-    run, ctx, config = args
+    run, ctx, config, plugins = args
     if not config["silence"]:
         print("+", end="", flush=True)
     context = run.copy()
@@ -28,13 +28,25 @@ def build_context(args):
                 else:
                     context = None
                     break
-    return context
 
+    hook = pythia.plugin.PluginHook.post_peerless_pixel_success
+    if context is None:
+        hook = pythia.plugin.PluginHook.post_peerless_pixel_skip
 
-def _generate_context_args(runs, peers, config):
+    context = pythia.plugin.run_plugin_functions(
+        hook,
+        plugins,
+        context=context,
+        args={"run": run, "config": config, "ctx": ctx},
+    ).get("context", context)
+
+    return context, args
+
+
+def _generate_context_args(runs, peers, config, plugins):
     for idx, run in enumerate(runs):
         for peer in peers[idx]:
-            yield run, peer, config
+            yield run, peer, config, plugins
 
 
 def symlink_wth_soil(output_dir, config, context):
@@ -82,8 +94,8 @@ def execute(config, plugins):
     print("RUNNING WITH POOL SIZE: {}".format(pool_size))
     env = pythia.template.init_engine(config["templateDir"])
     with mp.pool.ThreadPool(pool_size) as pool:
-        for context in pool.imap_unordered(
-            build_context, _generate_context_args(runs, peers, config), 250
+        for context, args in pool.imap_unordered(
+            build_context, _generate_context_args(runs, peers, config, plugins), 250
         ):
             if context is not None:
                 pythia.io.make_run_directory(context["contextWorkDir"])
@@ -95,7 +107,21 @@ def execute(config, plugins):
                     context=context,
                 ).get("context", context)
                 runlist.append(os.path.abspath(compose_peerless(context, config, env)))
+                pythia.plugin.run_plugin_functions(
+                    pythia.plugin.PluginHook.post_compose_peerless_pixel_success,
+                    plugins,
+                    input=context,
+                    config=config,
+                    env=env,
+                )
             else:
+                pythia.plugin.run_plugin_functions(
+                    pythia.plugin.PluginHook.post_compose_peerless_pixel_skip,
+                    plugins,
+                    input=context,
+                    config=config,
+                    env=env,
+                )
                 if not config["silence"]:
                     print("X", end="", flush=True)
     if config["exportRunlist"]:
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 75317bf3..4e465dc5 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -7,9 +7,15 @@ class PluginHook(Enum):
     post_config = 100
     pre_build_context = 200
     post_build_context = 300
+    post_peerless_pixel_success = 350
+    post_peerless_pixel_skip = 351
+    post_compose_peerless_pixel_success = 352
+    post_compose_peerless_pixel_skip = 353
     post_setup = 400
     pre_run = 500
     run_pixel = 600
+    post_run_pixel_success = 650
+    post_run_pixel_failed = 651
     post_run = 700
     pre_analysis = 800
     analyze_file = 900
diff --git a/pythia/plugins/test_plugin/__init__.py b/pythia/plugins/test_plugin/__init__.py
index 5d651cd2..c5c21508 100644
--- a/pythia/plugins/test_plugin/__init__.py
+++ b/pythia/plugins/test_plugin/__init__.py
@@ -4,12 +4,12 @@
 
 def initialize(config, plugins, full_config):
     logging.info("[TEST PLUGIN] Initializing plugin")
-    plugins = register_plugin_function(
-        PluginHook.post_config, sample_function, config, plugins
-    )
-    plugins = register_plugin_function(
-        PluginHook.post_build_context, contexted_function, config, plugins
-    )
+    plugins = register_plugin_function(PluginHook.post_config, sample_function, config, plugins)
+    plugins = register_plugin_function(PluginHook.post_build_context, contexted_function, config, plugins)
+    plugins = register_plugin_function(PluginHook.post_peerless_pixel_success, on_peerless_success, config, plugins)
+    plugins = register_plugin_function(PluginHook.post_peerless_pixel_skip, on_peerless_skip, config, plugins)
+    plugins = register_plugin_function(PluginHook.post_run_pixel_success, on_run_pixel_success, config, plugins)
+    plugins = register_plugin_function(PluginHook.post_run_pixel_failed, on_run_pixel_failed, config, plugins)
     return plugins
 
 
@@ -23,3 +23,23 @@ def contexted_function(context={}, **kwargs):
     logging.info("[TEST PLUGIN] Running the contexted_function()")
     context["context_value"] = context.get("context_value", 2) + 1
     return {**kwargs, "context": context}
+
+
+def on_peerless_success(*args, **kwargs):
+    logging.info("[TEST PLUGIN] peerless success")
+    return kwargs
+
+
+def on_peerless_skip(*args, **kwargs):
+    logging.info("[TEST PLUGIN] peerless skip")
+    return kwargs
+
+
+def on_run_pixel_success(*args, **kwargs):
+    logging.info("[TEST PLUGIN] run pixel success")
+    return kwargs
+
+
+def on_run_pixel_failed(*args, **kwargs):
+    logging.info("[TEST PLUGIN] run pixel failed")
+    return kwargs

From 589afbe2e1ac98a3d8a574a7f51dbecceab6f414 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 30 Dec 2023 21:05:34 -0300
Subject: [PATCH 057/105] feat: add new hook post_compose_peerless

---
 pythia/peerless.py | 11 +++++++++--
 pythia/plugin.py   |  1 +
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/pythia/peerless.py b/pythia/peerless.py
index 42011e83..2bdcafed 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -124,8 +124,15 @@ def execute(config, plugins):
                 )
                 if not config["silence"]:
                     print("X", end="", flush=True)
+
     if config["exportRunlist"]:
         with open(os.path.join(config["workDir"], "run_list.txt"), "w") as f:
             [f.write(f"{x}\n") for x in runlist]
-    if not config["silence"]:
-        print()
+
+    pythia.plugin.run_plugin_functions(
+        pythia.plugin.PluginHook.post_compose_peerless_all,
+        plugins,
+        runlist=runlist,
+        config=config,
+        env=env,
+    )
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 4e465dc5..51c47680 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -11,6 +11,7 @@ class PluginHook(Enum):
     post_peerless_pixel_skip = 351
     post_compose_peerless_pixel_success = 352
     post_compose_peerless_pixel_skip = 353
+    post_compose_peerless_all = 354
     post_setup = 400
     pre_run = 500
     run_pixel = 600

From df127fcd6ffd2ca9b366ef25bd85348010ae266e Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 30 Dec 2023 22:01:25 -0300
Subject: [PATCH 058/105] feat: implement hook post_run_all

---
 pythia/dssat.py  | 8 ++++++++
 pythia/plugin.py | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/pythia/dssat.py b/pythia/dssat.py
index 87d5d7f2..741f5414 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -111,7 +111,15 @@ def execute(config, plugins):
                 pool.apply_async(_run_dssat, (details, config, plugins), callback=display_async)
         pool.close()
         pool.join()
+
     if async_error:
         print(
             "\nOne or more simulations had failures. Please check the pythia log for more details"
         )
+
+    pythia.plugin.run_plugin_functions(
+        pythia.plugin.PluginHook.post_run_all,
+        plugins,
+        config=config,
+        run_list=run_list,
+    )
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 51c47680..b508231e 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -17,7 +17,7 @@ class PluginHook(Enum):
     run_pixel = 600
     post_run_pixel_success = 650
     post_run_pixel_failed = 651
-    post_run = 700
+    post_run_all = 700
     pre_analysis = 800
     analyze_file = 900
     analyze_pixel = 1000

From 1afa78cf0518d131d050d1c2957603cba9259846 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 30 Dec 2023 22:02:24 -0300
Subject: [PATCH 059/105] dev: rename hook argument runlist to run_list

---
 pythia/peerless.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/peerless.py b/pythia/peerless.py
index 2bdcafed..a0c07e9c 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -132,7 +132,7 @@ def execute(config, plugins):
     pythia.plugin.run_plugin_functions(
         pythia.plugin.PluginHook.post_compose_peerless_all,
         plugins,
-        runlist=runlist,
+        run_list=runlist,
         config=config,
         env=env,
     )

From abe2aa4358cd05f718eee58529c03cc743c2a1ce Mon Sep 17 00:00:00 2001
From: Anol Kurian <anolkurian@gmail.com>
Date: Fri, 12 Jan 2024 15:16:59 -0300
Subject: [PATCH 060/105] fix: fix peerless parallelization

Co-authored-by: Nathan P. Bombana <nathan.pbombana@gmail.com>
---
 pythia/peerless.py | 53 +++++++++++++++++++++++++++++++---------------
 1 file changed, 36 insertions(+), 17 deletions(-)

diff --git a/pythia/peerless.py b/pythia/peerless.py
index 5f4aaaed..cde2cea7 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -1,5 +1,6 @@
 import logging
 import multiprocessing as mp
+import concurrent.futures
 import os
 
 import pythia.functions
@@ -68,6 +69,20 @@ def compose_peerless(context, config, env):
         f.write(xfile)
     return context["contextWorkDir"]
 
+def process_context(context, plugins, config, env):
+    if context is not None:
+        pythia.io.make_run_directory(context["contextWorkDir"])
+        # Post context hook
+        logging.debug("[PEERLESS] Running post_build_context plugins")
+        context = pythia.plugin.run_plugin_functions(
+            pythia.plugin.PluginHook.post_build_context,
+            plugins,
+            context=context,
+        )
+        return os.path.abspath(compose_peerless(context, config, env))
+    else:
+        if not config["silence"]:
+            print("X", end="", flush=True)
 
 def execute(config, plugins):
     runs = config.get("runs", [])
@@ -77,26 +92,30 @@ def execute(config, plugins):
     for run in runs:
         pythia.io.make_run_directory(os.path.join(config["workDir"], run["name"]))
     peers = [pythia.io.peer(r, config.get("sample", None)) for r in runs]
-    pool_size = config.get("threads", mp.cpu_count() * 10)
+    pool_size = config.get("threads", mp.cpu_count())
     print("RUNNING WITH POOL SIZE: {}".format(pool_size))
     env = pythia.template.init_engine(config["templateDir"])
-    with mp.pool.ThreadPool(pool_size) as pool:
-        for context in pool.imap_unordered(
+    pythia.functions.build_ghr_cache(config)
+
+    with mp.Pool(pool_size) as pool:
+        results = pool.imap_unordered(
             build_context, _generate_context_args(runs, peers, config), 250
-        ):
-            if context is not None:
-                pythia.io.make_run_directory(context["contextWorkDir"])
-                # Post context hook
-                logging.debug("[PEERLESS] Running post_build_context plugins")
-                context = pythia.plugin.run_plugin_functions(
-                    pythia.plugin.PluginHook.post_build_context,
-                    plugins,
-                    context=context,
-                )
-                runlist.append(os.path.abspath(compose_peerless(context, config, env)))
-            else:
-                if not config["silence"]:
-                    print("X", end="", flush=True)
+        )
+        with concurrent.futures.ProcessPoolExecutor(max_workers=pool_size) as executor:
+            # Use submit to asynchronously execute the process_context function for each context
+            future_to_result = {executor.submit(process_context, context, plugins, config, env): context for context in results}
+
+            # Iterate through the completed futures
+            runlist = []
+            for future in concurrent.futures.as_completed(future_to_result):
+                try:
+                    result = future.result()
+                    if result is not None:
+                        runlist.append(result)
+                except Exception as e:
+                    # Handle exceptions if any occurred during processing
+                    print(f"Error processing context: {e}")
+
     if config["exportRunlist"]:
         with open(os.path.join(config["workDir"], "run_list.txt"), "w") as f:
             [f.write(f"{x}\n") for x in runlist]

From a8adf2051c957d243f258393f6c6e788f80cc913 Mon Sep 17 00:00:00 2001
From: Anol Kurian <anolkurian@gmail.com>
Date: Fri, 12 Jan 2024 15:32:39 -0300
Subject: [PATCH 061/105] fix: fix duplicate newlines on windows

Co-authored-by: Nathan P. Bombana <nathan.pbombana@gmail.com>
---
 pythia/analytics.py                                | 4 ++--
 pythia/plugins/weather_forecast_simple/__init__.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 16c2cded..048c4731 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -54,7 +54,7 @@ def filter_columns(config, outputs):
         out_file = os.path.join(
             out_dir, "filtered_{}".format(os.path.basename(current_file))
         )
-        with open(current_file) as source, open(out_file, "w") as dest:
+        with open(current_file) as source, open(out_file, "w", newline = '') as dest:
             dssat_in = csv.reader(source)
             dssat_out = csv.writer(dest)
             try:
@@ -93,7 +93,7 @@ def calculate_columns(config, outputs):
         out_file = os.path.join(
             out_dir, "calculated_{}".format(os.path.basename(current_file))
         )
-        with open(current_file) as source, open(out_file, "w") as dest:
+        with open(current_file) as source, open(out_file, "w", newline = '') as dest:
             dssat_in = csv.reader(source)
             dssat_out = csv.writer(dest)
             num_cols = 0
diff --git a/pythia/plugins/weather_forecast_simple/__init__.py b/pythia/plugins/weather_forecast_simple/__init__.py
index 30071fb3..cf9ab88e 100644
--- a/pythia/plugins/weather_forecast_simple/__init__.py
+++ b/pythia/plugins/weather_forecast_simple/__init__.py
@@ -57,7 +57,7 @@ def construct_pixel_forecast(config={}, context={}):
                 scraping_lines = False
                 break
 
-    with open(source_weather) as source, open(dest_weather, "w") as dest:
+    with open(source_weather) as source, open(dest_weather, "w", newline = '') as dest:
         in_target = False
         wrote_target = False
         for line in source:

From 49fa57768b9f25ca352327f4a750466014edec0f Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sun, 25 Sep 2022 22:56:33 -0300
Subject: [PATCH 062/105] make pythia accept floats in dbf but convert it back
 to int

(cherry picked from commit 290b11234e88d0e57a8167a131c72edfdd318d0f)
---
 pythia/functions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/functions.py b/pythia/functions.py
index a562f8b7..76207876 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -99,7 +99,7 @@ def lookup_ghr(k, run, context, config):
         logging.debug("lookup_ghr - context[%s] => %s", k, context[k])
         if "ghr_profiles" not in cache:
             build_ghr_cache(config)
-        tif_profile_id = int(str(context[k]))
+        tif_profile_id = int(float(str(context[k])))
         if tif_profile_id not in cache["ghr_profiles"]:
             logging.error(
                 "Invalid soil ID (%d) at (%f,%f)",

From f9eea407ed9d0027799f6770f4854061fb458435 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Tue, 25 Oct 2022 11:16:41 -0300
Subject: [PATCH 063/105] fix converting ID from decimal to integer

(cherry picked from commit 7b7eea8959dca17fd6b4b1b80831482d337d834b)
---
 pythia/functions.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pythia/functions.py b/pythia/functions.py
index 76207876..df17b455 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -57,8 +57,7 @@ def lookup_wth(k, run, context, _):
     if "vector" in args:
         idx = args.index("vector")
         cell_id = finder(args[idx + 1], context["lng"], context["lat"], args[idx + 2])
-    return {k: args[0], "wthFile": "{}.WTH".format(cell_id)}
-
+    return {k: args[0], "wthFile": "{}.WTH".format(int(cell_id))}
 
 def generate_ic_layers(k, run, context, _):
     args = run[k].split("::")[1:]

From 4e6bfdf67562a20b76b82f3651ff8ef9af86a9a3 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Tue, 4 Apr 2023 09:56:58 -0300
Subject: [PATCH 064/105] increase performance of build_ghr_cache by filtering
 out rows in sqlite3 layer

(cherry picked from commit b3af8eeb0f36c70fcc0afd9d5d1574b9aa3f427c)
---
 pythia/functions.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/pythia/functions.py b/pythia/functions.py
index df17b455..3787034b 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -78,16 +78,14 @@ def build_ghr_cache(config):
     import sqlite3
 
     with sqlite3.connect(os.path.join(config["ghr_root"], "GHR.db")) as conn:
-        cache["ghr_profiles"] = {}
+        ghr_profiles = {}
         conn.row_factory = sqlite3.Row
         cursor = conn.cursor()
-        cursor.execute("SELECT * FROM profile_map")
+        cursor.execute("SELECT * FROM profile_map where profile != ''")
         for row in cursor.fetchall():
-            if row["profile"] == "":
-                profile = None
-            else:
-                profile = row["profile"]
-            cache["ghr_profiles"][row["id"]] = profile
+            ghr_profiles[row["id"]] = row["profile"]
+
+        cache["ghr_profiles"] = ghr_profiles;
 
     pass
 

From e0dccec479476be215b8907a098ccfb9912679f9 Mon Sep 17 00:00:00 2001
From: Willingthon Pavan <wpavan@ifdc.org>
Date: Mon, 28 Nov 2022 15:46:47 -0600
Subject: [PATCH 065/105] fix: new function to resolve planting date as DOY
 (day of year)

(cherry picked from commit 76efdfd278d001099c7b1c1d63b631f31bd9a909)
---
 pythia/functions.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/pythia/functions.py b/pythia/functions.py
index 3787034b..5ce39fd0 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -41,6 +41,21 @@ def auto_planting_window(k, run, context, _):
         "plast": pythia.util.to_iso_date(last),
     }
 
+def auto_planting_window_doy(k, run, context, _):
+    """multiple rasters not yet supported"""
+    args = run[k].split("::")[1:]
+    raster_idx = args.index("raster")
+    args[raster_idx + 1] = context[k]
+    args.pop(raster_idx)
+    vals = [int(v) for v in args]
+    first = datetime.datetime(run["startYear"], 1, 1) + datetime.timedelta(vals[0] + vals[1] - 1)
+    td = datetime.timedelta(days=vals[2])
+    last = first + td
+    return {
+        "pdate": pythia.util.to_iso_date(first),
+        "pfrst": pythia.util.to_iso_date(first),
+        "plast": pythia.util.to_iso_date(last),
+    }
 
 def lookup_hc27(k, run, context, _):
     args = run[k].split("::")[1:]

From 0702524475df109eda79f38e6558af20e4654458 Mon Sep 17 00:00:00 2001
From: Willingthon Pavan <wpavan@ifdc.org>
Date: Wed, 7 Dec 2022 15:06:49 -0600
Subject: [PATCH 066/105] feat: planting window based on shape files and doy

(cherry picked from commit 7c2bdd1974f83c0f52232a73695d786227e0ee69)
---
 pythia/functions.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/pythia/functions.py b/pythia/functions.py
index 5ce39fd0..bfd3897b 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -57,6 +57,24 @@ def auto_planting_window_doy(k, run, context, _):
         "plast": pythia.util.to_iso_date(last),
     }
 
+def auto_planting_window_doy_shape(k, run, context, _):
+    """multiple rasters not yet supported"""
+    args = run[k].split("::")[1:]
+    finder = pythia.io.find_closest_vector_coords
+    cell_doy = None
+    if "vector" in args:
+        idx = args.index("vector")
+        cell_doy = finder(args[idx + 1], context["lng"], context["lat"], args[idx + 2])
+
+    first = datetime.datetime(run["startYear"], 1, 1) + datetime.timedelta(int(cell_doy) + int(args[idx + 3]) )
+    td = datetime.timedelta(days=int(args[idx + 4]))
+    last = first + td
+    return {
+        "pdate": pythia.util.to_iso_date(first),
+        "pfrst": pythia.util.to_iso_date(first),
+        "plast": pythia.util.to_iso_date(last),
+    }
+
 def lookup_hc27(k, run, context, _):
     args = run[k].split("::")[1:]
     if "raster" in args:
@@ -74,6 +92,7 @@ def lookup_wth(k, run, context, _):
         cell_id = finder(args[idx + 1], context["lng"], context["lat"], args[idx + 2])
     return {k: args[0], "wthFile": "{}.WTH".format(int(cell_id))}
 
+
 def generate_ic_layers(k, run, context, _):
     args = run[k].split("::")[1:]
     if args[0].startswith("$"):

From c815b232303e263ddf694b21b8bbde96a0f7468b Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Mon, 22 Jan 2024 18:51:38 -0300
Subject: [PATCH 067/105] fix: fix Dockerfile

---
 .dockerignore  |    2 +
 Dockerfile     |   62 +-
 bin/pythia     |    5 +-
 poetry.lock    | 1724 ++++++++++++++++++++++++------------------------
 pyproject.toml |    2 +-
 5 files changed, 906 insertions(+), 889 deletions(-)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..60cc45ec
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,2 @@
+.dockerignore
+.venv
diff --git a/Dockerfile b/Dockerfile
index 47282c12..6a7129e7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,39 +1,27 @@
-FROM dssat/dssat-csm
+FROM dssat/dssat-csm:v4.8.2.0
 
-COPY . /app/pythia
-RUN ln -sf /bin/bash /bin/sh && \
-# install pre-reqs for pyenv installed pythons
-apt-get install -y build-essential libssl-dev zlib1g-dev libbz2-dev \
-libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
-xz-utils tk-dev libffi-dev liblzma-dev python-openssl git libspatialindex-dev && \
-# setup pyenv
-curl https://pyenv.run | bash && \                          
-echo 'export PATH="/root/.pyenv/bin:/root/.local/bin:$PATH"' >> ~/.bashrc && \
-echo 'eval "$(pyenv init -)"' >> ~/.bashrc && \
-echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.bashrc && \
-export PATH="/root/.pyenv/bin:/root/.local/bin:$PATH" && \
-eval "$(pyenv init -)" && \
-eval "$(pyenv virtualenv-init i)" && \
-# install python 3.7.9
-pyenv install 3.7.9 && \
-pyenv rehash && \
-pyenv virtualenv 3.7.9 pythia-3.7.9 && \
-pyenv activate pythia-3.7.9 && \
-pip install --upgrade pip && \
-pip install pipenv && \
-# install dependencies
-cd /app/pythia && \
-pipenv install && \
-echo "#!/bin/bash" > /app/pythia.sh && \
-echo "" >> /app/pythia.sh && \
-echo 'export PATH="/root/.pyenv/bin:/root/.local/bin:$PATH"' >> /app/pythia.sh && \
-echo 'export PYENV_VIRTUALENV_DISABLE_PROMPT=1' >> /app/pythia.sh && \
-echo 'eval "$(pyenv init -)"' >> /app/pythia.sh && \
-echo 'eval "$(pyenv virtualenv-init -)"' >> /app/pythia.sh && \
-echo "pyenv activate pythia-3.7.9" >> /app/pythia.sh && \
-echo "python /app/pythia/pythia.py \$@" >> /app/pythia.sh && \
-echo "pyenv deactivate" && \
-chmod 755 /app/pythia.sh
+RUN apt-get update && apt-get install -y \
+    python3.11 \
+    python3.11-dev \
+    python3-pip \
+    python3-venv \
+    python3-poetry \
+    python3-virtualenv \
+    curl \
+    gdal-bin=3.6.2+dfsg-1+b2 \
+    libgdal-dev=3.6.2+dfsg-1+b2 \
+    && rm -rf /var/lib/apt/lists/*
 
-ENTRYPOINT ["/app/pythia.sh"]
-CMD ["-h"]
+ENV GDAL_VERSION 3.6.2
+ENV C_INCLUDE_PATH=/usr/include/python3.11/cpython
+ENV CPLUS_INCLUDE_PATH=/usr/include/python3.11/cpython
+
+WORKDIR /app/pythia
+
+COPY pyproject.toml poetry.toml poetry.lock ./
+RUN POETRY_VIRTUALENVS_CREATE=false poetry install --no-interaction --no-ansi
+
+COPY . ./
+ENV PATH="${PATH}:/app/pythia/bin"
+
+ENTRYPOINT ["pythia"]
diff --git a/bin/pythia b/bin/pythia
index ed90256b..1d17ae7c 100755
--- a/bin/pythia
+++ b/bin/pythia
@@ -1,3 +1,4 @@
-#!/usr/bin/env sh
+#!/usr/bin/env bash
 
-python -m pythia $@
+source .venv/bin/activate
+python3 -m pythia $@
diff --git a/poetry.lock b/poetry.lock
index ca2c2d8f..995a6947 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,29 +1,41 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
 [[package]]
 name = "affine"
-version = "2.3.1"
-description = "Matrices describing affine transformation of the plane."
-category = "main"
+version = "2.4.0"
+description = "Matrices describing affine transformation of the plane"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+files = [
+    {file = "affine-2.4.0-py3-none-any.whl", hash = "sha256:8a3df80e2b2378aef598a83c1392efd47967afec4242021a0b06b4c7cbc61a92"},
+    {file = "affine-2.4.0.tar.gz", hash = "sha256:a24d818d6a836c131976d22f8c27b8d3ca32d0af64c1d8d29deb7bafa4da1eea"},
+]
 
 [package.extras]
-test = ["coveralls", "flake8", "pydocstyle", "pytest (>=4.6)", "pytest-cov"]
+dev = ["coveralls", "flake8", "pydocstyle"]
+test = ["pytest (>=4.6)", "pytest-cov"]
 
 [[package]]
 name = "appnope"
 version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
+    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
+]
 
 [[package]]
 name = "astroid"
 version = "2.6.6"
 description = "An abstract syntax tree for Python with inference support."
-category = "dev"
 optional = false
 python-versions = "~=3.6"
+files = [
+    {file = "astroid-2.6.6-py3-none-any.whl", hash = "sha256:ab7f36e8a78b8e54a62028ba6beef7561db4cdb6f2a5009ecc44a6f42b5697ef"},
+    {file = "astroid-2.6.6.tar.gz", hash = "sha256:3975a0bd5373bdce166e60c851cfcbaf21ee96de80ec518c1f4cb3e94c3fb334"},
+]
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
@@ -32,47 +44,61 @@ wrapt = ">=1.11,<1.13"
 
 [[package]]
 name = "asttokens"
-version = "2.0.8"
+version = "2.4.1"
 description = "Annotate AST trees with source code positions"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+]
 
 [package.dependencies]
-six = "*"
+six = ">=1.12.0"
 
 [package.extras]
-test = ["astroid (<=2.5.3)", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "atomicwrites"
 version = "1.4.1"
 description = "Atomic file writes."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
 
 [[package]]
 name = "attrs"
-version = "22.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
+files = [
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+]
 
 [package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "autopep8"
 version = "1.5.7"
 description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "autopep8-1.5.7-py2.py3-none-any.whl", hash = "sha256:aa213493c30dcdac99537249ee65b24af0b2c29f2e83cd8b3f68760441ed0db9"},
+    {file = "autopep8-1.5.7.tar.gz", hash = "sha256:276ced7e9e3cb22e5d7c14748384a5cf5d9002257c0ed50c0e075b68011bb6d0"},
+]
 
 [package.dependencies]
 pycodestyle = ">=2.7.0"
@@ -82,17 +108,33 @@ toml = "*"
 name = "backcall"
 version = "0.2.0"
 description = "Specifications for callback functions passed in to an API"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
+    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
+]
 
 [[package]]
 name = "black"
-version = "22.8.0"
+version = "22.12.0"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.7"
+files = [
+    {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
+    {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
+    {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
+    {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
+    {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
+    {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
+    {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
+    {file = "black-22.12.0-cp38-cp38-win_amd64.whl", hash = "sha256:82d9fe8fee3401e02e79767016b4907820a7dc28d70d137eb397b92ef3cc5bfc"},
+    {file = "black-22.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:101c69b23df9b44247bd88e1d7e90154336ac4992502d4197bdac35dd7ee3320"},
+    {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
+    {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
+    {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
+]
 
 [package.dependencies]
 click = ">=8.0.0"
@@ -110,19 +152,25 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2022.9.24"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+]
 
 [[package]]
 name = "click"
-version = "8.1.3"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -131,9 +179,12 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "click-plugins"
 version = "1.1.1"
 description = "An extension module for click to enable registering CLI commands via setuptools entry-points."
-category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"},
+    {file = "click_plugins-1.1.1-py2.py3-none-any.whl", hash = "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"},
+]
 
 [package.dependencies]
 click = ">=4.0"
@@ -145,9 +196,12 @@ dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"]
 name = "cligj"
 version = "0.7.2"
 description = "Click params for commmand line interfaces to GeoJSON"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4"
+files = [
+    {file = "cligj-0.7.2-py3-none-any.whl", hash = "sha256:c1ca117dbce1fe20a5809dc96f01e1c2840f6dcc939b3ddbb1111bf330ba82df"},
+    {file = "cligj-0.7.2.tar.gz", hash = "sha256:a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27"},
+]
 
 [package.dependencies]
 click = ">=4.0"
@@ -157,62 +211,99 @@ test = ["pytest-cov"]
 
 [[package]]
 name = "colorama"
-version = "0.4.5"
+version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
 
 [[package]]
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
 
 [[package]]
 name = "executing"
-version = "1.1.0"
+version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
-category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
+files = [
+    {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"},
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-version = "1.8.21"
+name = "fiona"
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 description = "Fiona reads and writes spatial data files"
-category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
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 [package.dependencies]
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+attrs = ">=19.2.0"
 certifi = "*"
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+click = ">=8.0,<9.0"
 click-plugins = ">=1.0"
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-munch = "*"
+importlib-metadata = {version = "*", markers = "python_version < \"3.10\""}
 setuptools = "*"
-six = ">=1.7"
+six = "*"
 
 [package.extras]
-all = ["boto3 (>=1.2.4)", "mock", "pytest (>=3)", "pytest-cov", "shapely"]
+all = ["Fiona[calc,s3,test]"]
 calc = ["shapely"]
-s3 = ["boto3 (>=1.2.4)"]
-test = ["boto3 (>=1.2.4)", "mock", "pytest (>=3)", "pytest-cov"]
+s3 = ["boto3 (>=1.3.1)"]
+test = ["Fiona[s3]", "pytest (>=7)", "pytest-cov", "pytz"]
 
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-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
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+]
 
 [package.dependencies]
 mccabe = ">=0.6.0,<0.7.0"
@@ -221,22 +312,104 @@ pyflakes = ">=2.3.0,<2.4.0"
 
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+python-versions = ">=3.8"
+files = [
+    {file = "importlib_metadata-7.0.1-py3-none-any.whl", hash = "sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e"},
+    {file = "importlib_metadata-7.0.1.tar.gz", hash = "sha256:f238736bb06590ae52ac1fab06a3a9ef1d8dce2b7a35b5ab329371d6c8f5d2cc"},
+]
+
+[package.dependencies]
+zipp = ">=0.5"
 
 [package.extras]
-docs = ["Sphinx"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+perf = ["ipython"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "ipython"
-version = "8.5.0"
+version = "8.12.3"
 description = "IPython: Productive Interactive Computing"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "ipython-8.12.3-py3-none-any.whl", hash = "sha256:b0340d46a933d27c657b211a329d0be23793c36595acf9e6ef4164bc01a1804c"},
+    {file = "ipython-8.12.3.tar.gz", hash = "sha256:3910c4b54543c2ad73d06579aa771041b7d5707b033bd488669b4cf544e3b363"},
+]
 
 [package.dependencies]
 appnope = {version = "*", markers = "sys_platform == \"darwin\""}
@@ -247,15 +420,16 @@ jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">3.0.1,<3.1.0"
+prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
+typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["Sphinx (>=1.3)", "black", "curio", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "testpath", "trio"]
+all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["Sphinx (>=1.3)"]
+doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
@@ -263,44 +437,51 @@ notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
 test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
-test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
 
 [[package]]
 name = "isort"
-version = "5.10.1"
+version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
-python-versions = ">=3.6.1,<4.0"
+python-versions = ">=3.8.0"
+files = [
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+    {file = "isort-5.13.2.tar.gz", hash = "sha256:48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109"},
+]
 
 [package.extras]
-colors = ["colorama (>=0.4.3,<0.5.0)"]
-pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
-plugins = ["setuptools"]
-requirements_deprecated_finder = ["pip-api", "pipreqs"]
+colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jedi"
-version = "0.18.1"
+version = "0.18.2"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+    {file = "jedi-0.18.2.tar.gz", hash = "sha256:bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612"},
+]
 
 [package.dependencies]
 parso = ">=0.8.0,<0.9.0"
 
 [package.extras]
+docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
-name = "Jinja2"
-version = "3.1.2"
+name = "jinja2"
+version = "3.1.3"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
+    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -310,27 +491,129 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "lazy-object-proxy"
-version = "1.7.1"
+version = "1.10.0"
 description = "A fast and thorough lazy object proxy."
-category = "dev"
 optional = false
-python-versions = ">=3.6"
-
-[[package]]
-name = "MarkupSafe"
-version = "2.1.1"
+python-versions = ">=3.8"
+files = [
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 python-versions = ">=3.7"
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 version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
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 [package.dependencies]
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-python-versions = ">=3.5"
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-python-versions = "*"
-
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 pynvim = ">=0.3.1"
 
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-version = "21.3"
+version = "23.2"
 description = "Core utilities for Python packages"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+python-versions = ">=3.7"
+files = [
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+]
 
 [[package]]
 name = "parso"
 version = "0.8.3"
 description = "A Python Parser"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
 [package.extras]
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
@@ -426,19 +794,25 @@ testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "pathspec"
-version = "0.10.1"
+version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+files = [
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+]
 
 [[package]]
 name = "pexpect"
-version = "4.8.0"
+version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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+]
 
 [package.dependencies]
 ptyprocess = ">=0.5"
@@ -447,40 +821,52 @@ ptyprocess = ">=0.5"
 name = "pickleshare"
 version = "0.7.5"
 description = "Tiny 'shelve'-like database with concurrency support"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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+    {file = "pickleshare-0.7.5.tar.gz", hash = "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca"},
+]
 
 [[package]]
 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
+version = "4.1.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+files = [
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+    {file = "platformdirs-4.1.0.tar.gz", hash = "sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420"},
+]
 
 [package.extras]
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-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
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 version = "0.13.1"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+    {file = "pluggy-0.13.1.tar.gz", hash = "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0"},
+]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.31"
+version = "3.0.43"
 description = "Library for building powerful interactive command lines in Python"
-category = "dev"
 optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.7.0"
+files = [
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+]
 
 [package.dependencies]
 wcwidth = "*"
@@ -489,17 +875,23 @@ wcwidth = "*"
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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+    {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
+]
 
 [[package]]
 name = "pure-eval"
 version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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+    {file = "pure_eval-0.2.2.tar.gz", hash = "sha256:2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3"},
+]
 
 [package.extras]
 tests = ["pytest"]
@@ -508,58 +900,77 @@ tests = ["pytest"]
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 version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
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+    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
+]
 
 [[package]]
 name = "pycodestyle"
 version = "2.7.0"
 description = "Python style guide checker"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+    {file = "pycodestyle-2.7.0.tar.gz", hash = "sha256:c389c1d06bf7904078ca03399a4816f974a1d590090fecea0c63ec26ebaf1cef"},
+]
 
 [[package]]
 name = "pydocstyle"
-version = "6.1.1"
+version = "6.3.0"
 description = "Python docstring style checker"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
 [package.dependencies]
-snowballstemmer = "*"
+snowballstemmer = ">=2.2.0"
 
 [package.extras]
-toml = ["toml"]
+toml = ["tomli (>=1.2.3)"]
 
 [[package]]
 name = "pyflakes"
 version = "2.3.1"
 description = "passive checker of Python programs"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+    {file = "pyflakes-2.3.1.tar.gz", hash = "sha256:f5bc8ecabc05bb9d291eb5203d6810b49040f6ff446a756326104746cc00c1db"},
+]
 
 [[package]]
-name = "Pygments"
-version = "2.13.0"
+name = "pygments"
+version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+files = [
+    {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
+    {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
+]
 
 [package.extras]
 plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pylint"
 version = "2.9.6"
 description = "python code static checker"
-category = "dev"
 optional = false
 python-versions = "~=3.6"
+files = [
+    {file = "pylint-2.9.6-py3-none-any.whl", hash = "sha256:2e1a0eb2e8ab41d6b5dbada87f066492bb1557b12b76c47c2ee8aa8a11186594"},
+    {file = "pylint-2.9.6.tar.gz", hash = "sha256:8b838c8983ee1904b2de66cce9d0b96649a91901350e956d78f289c3bc87b48e"},
+]
 
 [package.dependencies]
 astroid = ">=2.6.5,<2.7"
@@ -572,9 +983,12 @@ toml = ">=0.7.1"
 name = "pyls-flake8"
 version = "0.4.0"
 description = "A Flake8 plugin for the Python Language Server"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "pyls-flake8-0.4.0.tar.gz", hash = "sha256:630cec96e494c0f3bffa381451d71a05f46b4f4e6d9b897ad6377e81cc4f8f70"},
+    {file = "pyls_flake8-0.4.0-py2.py3-none-any.whl", hash = "sha256:ca8051e53ee0e06e621abfa7bdc72c9a7f56d5bede51fa7c17caba166b7101a2"},
+]
 
 [package.dependencies]
 flake8 = ">=3.6.0"
@@ -584,9 +998,11 @@ python-lsp-server = "*"
 name = "pyls-isort"
 version = "0.2.2"
 description = "Isort plugin for python-lsp-server"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "pyls-isort-0.2.2.tar.gz", hash = "sha256:2192bd2203db00459f85eb329521feba58af63075d2dd10a051a4eccd000bba0"},
+]
 
 [package.dependencies]
 isort = "*"
@@ -594,11 +1010,14 @@ python-lsp-server = "*"
 
 [[package]]
 name = "pylsp-rope"
-version = "0.1.10"
+version = "0.1.11"
 description = "Extended refactoring capabilities for Python LSP Server using Rope."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "pylsp-rope-0.1.11.tar.gz", hash = "sha256:48aadf993dafa5e8fca1108b4a5431314cf80bc78cffdd56400ead9c407553be"},
+    {file = "pylsp_rope-0.1.11-py3-none-any.whl", hash = "sha256:71fb08dc6ead9a69202f2e7c5f7bbc5ada037a0f0722d7eb2d1f8cac2c9a18af"},
+]
 
 [package.dependencies]
 python-lsp-server = "*"
@@ -610,27 +1029,33 @@ test = ["pytest"]
 
 [[package]]
 name = "pynvim"
-version = "0.4.3"
-description = "Python client to neovim"
-category = "dev"
+version = "0.5.0"
+description = "Python client for Neovim"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+files = [
+    {file = "pynvim-0.5.0-py2.py3-none-any.whl", hash = "sha256:2ac197ef0cdfff53719184a45c33cfb7cef88d1c9bf7f0525c21b3239cb5365f"},
+    {file = "pynvim-0.5.0.tar.gz", hash = "sha256:e80a11f6f5d194c6a47bea4135b90b55faca24da3544da7cf4a5f7ba8fb09215"},
+]
 
 [package.dependencies]
-greenlet = "*"
+greenlet = ">=3.0"
 msgpack = ">=0.5.0"
 
 [package.extras]
 pyuv = ["pyuv (>=1.0.0)"]
-test = ["pytest (>=3.4.0)"]
+test = ["pytest"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.9"
+version = "3.1.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
+files = [
+    {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
+    {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
+]
 
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
@@ -639,9 +1064,12 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "5.4.3"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "pytest-5.4.3-py3-none-any.whl", hash = "sha256:5c0db86b698e8f170ba4582a492248919255fcd4c79b1ee64ace34301fb589a1"},
+    {file = "pytest-5.4.3.tar.gz", hash = "sha256:7979331bfcba207414f5e1263b5a0f8f521d0f457318836a7355531ed1a4c7d8"},
+]
 
 [package.dependencies]
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
@@ -661,9 +1089,12 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 name = "python-lsp-black"
 version = "1.1.0"
 description = "Black plugin for the Python LSP Server"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "python-lsp-black-1.1.0.tar.gz", hash = "sha256:4f665aca0fd1611f9e2a4c1ea09de8809810bbe5013eeee5dfb8796c90a12d4c"},
+    {file = "python_lsp_black-1.1.0-py3-none-any.whl", hash = "sha256:1d2a9eb1f46c28cb994b22bfd1463a90d4779ad314d12db65d91940b0f1bd137"},
+]
 
 [package.dependencies]
 black = ">=19.3b0"
@@ -675,11 +1106,14 @@ dev = ["flake8", "isort (>=5.0)", "mypy", "pre-commit", "pytest", "types-pkg-res
 
 [[package]]
 name = "python-lsp-jsonrpc"
-version = "1.0.0"
+version = "1.1.2"
 description = "JSON RPC 2.0 server library"
-category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
+files = [
+    {file = "python-lsp-jsonrpc-1.1.2.tar.gz", hash = "sha256:4688e453eef55cd952bff762c705cedefa12055c0aec17a06f595bcc002cc912"},
+    {file = "python_lsp_jsonrpc-1.1.2-py3-none-any.whl", hash = "sha256:7339c2e9630ae98903fdaea1ace8c47fba0484983794d6aafd0bd8989be2b03c"},
+]
 
 [package.dependencies]
 ujson = ">=3.0.0"
@@ -691,9 +1125,12 @@ test = ["coverage", "pycodestyle", "pyflakes", "pylint", "pytest", "pytest-cov"]
 name = "python-lsp-server"
 version = "1.2.4"
 description = "Python Language Server for the Language Server Protocol"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "python-lsp-server-1.2.4.tar.gz", hash = "sha256:007278c4419339bd3a61ca6d7eb8648ead28b5f1b9eba3b6bae8540046116335"},
+    {file = "python_lsp_server-1.2.4-py3-none-any.whl", hash = "sha256:a163907c83ba7bae6b45a9bc9e407b7001fbed7c7561d032a5fd355ae6fae42c"},
+]
 
 [package.dependencies]
 autopep8 = {version = "*", optional = true, markers = "extra == \"all\""}
@@ -724,13 +1161,57 @@ rope = ["rope (>0.10.5)"]
 test = ["coverage", "flaky", "matplotlib", "numpy", "pandas", "pylint (>=2.5.0,<2.10.0)", "pyqt5", "pytest", "pytest-cov"]
 yapf = ["yapf"]
 
+[[package]]
+name = "pytoolconfig"
+version = "1.3.1"
+description = "Python tool configuration"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytoolconfig-1.3.1-py3-none-any.whl", hash = "sha256:5d8cea8ae1996938ec3eaf44567bbc5ef1bc900742190c439a44a704d6e1b62b"},
+    {file = "pytoolconfig-1.3.1.tar.gz", hash = "sha256:51e6bd1a6f108238ae6aab6a65e5eed5e75d456be1c2bf29b04e5c1e7d7adbae"},
+]
+
+[package.dependencies]
+packaging = ">=23.2"
+platformdirs = {version = ">=3.11.0", optional = true, markers = "extra == \"global\""}
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+doc = ["sphinx (>=7.1.2)", "tabulate (>=0.9.0)"]
+gendocs = ["pytoolconfig[doc]", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.25.2)", "sphinx-rtd-theme (>=2.0.0)"]
+global = ["platformdirs (>=3.11.0)"]
+validation = ["pydantic (>=2.5.3)"]
+
 [[package]]
 name = "rasterio"
-version = "1.3.2"
+version = "1.3.9"
 description = "Fast and direct raster I/O for use with Numpy and SciPy"
-category = "main"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "rasterio-1.3.9-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:04247da9f4002587ac2bec967c3a72f63fc0e6654101c06850bae3d8131b700d"},
+    {file = "rasterio-1.3.9-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c9edce37b70f4cd4be5d3f5d314877e3130aeebb612120405cd28f83fe200865"},
+    {file = "rasterio-1.3.9-cp310-cp310-manylinux2014_x86_64.whl", hash = "sha256:fd6a850a37840ba590ddcf7ff90ba007b1e231b04434d8b4ac5ce0f746ada91a"},
+    {file = "rasterio-1.3.9-cp310-cp310-win_amd64.whl", hash = "sha256:0c83156a44f8fda11876ff9f2ff1b602d7e7434447f7d621353f2929cefb1bf1"},
+    {file = "rasterio-1.3.9-cp311-cp311-macosx_10_15_x86_64.whl", hash = "sha256:0172dbd80bd9adc105ec2c9bd207dbd5519ea06b438a4d965c6290ae8ed6ff9f"},
+    {file = "rasterio-1.3.9-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:0ea5b42597d85868ee88c750cc33f2ae729e1b5e3fe28f99071f39e1417bf1c0"},
+    {file = "rasterio-1.3.9-cp311-cp311-manylinux2014_x86_64.whl", hash = "sha256:be9b343bd08245df22115775dc9513c912afb4134d832662fa165d70cb805c34"},
+    {file = "rasterio-1.3.9-cp311-cp311-win_amd64.whl", hash = "sha256:06d53e2e0885f039f960beb7c861400b92ea3e0e5abc2c67483fb56b1e5cbc13"},
+    {file = "rasterio-1.3.9-cp312-cp312-macosx_10_15_x86_64.whl", hash = "sha256:a34bb9eef67b7896e2dfb39e10ba6372f9894226fb790bd7a46f5748f205b7d8"},
+    {file = "rasterio-1.3.9-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:67b144b9678f9ad4cf5f2c3f455cbc6a7166c0523179249cee8f2e2c57d76c5b"},
+    {file = "rasterio-1.3.9-cp312-cp312-manylinux2014_x86_64.whl", hash = "sha256:99b72fccb702a921f43e56a4507b4cafe2a9196b478b993b98e82ec6851916d7"},
+    {file = "rasterio-1.3.9-cp312-cp312-win_amd64.whl", hash = "sha256:6777fad3c31eb3e5da0ccaa28a032ad07c20d003bcd14f8bc13e16ca2f62348c"},
+    {file = "rasterio-1.3.9-cp38-cp38-macosx_10_15_x86_64.whl", hash = "sha256:55bb1a2701dd67c1952b261a2ffbabd947a435d4457f13c25092a32ab7a4b36e"},
+    {file = "rasterio-1.3.9-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:726d8e8884359c34f672312171310052d5483af550ef00fb4f2562cc022a6f5a"},
+    {file = "rasterio-1.3.9-cp38-cp38-manylinux2014_x86_64.whl", hash = "sha256:f65879415df188fdc9388ccf2ee01e0659abae370d12518a17b60151e7d04efe"},
+    {file = "rasterio-1.3.9-cp38-cp38-win_amd64.whl", hash = "sha256:89771b70ee722c4cc808e2a6139b367bef1a736ecd497b311b3515d78a5d16bc"},
+    {file = "rasterio-1.3.9-cp39-cp39-macosx_10_15_x86_64.whl", hash = "sha256:14df8413c030b04e54d478d6ecec4e5958b46585c3cb970bf0dc19b4831146c8"},
+    {file = "rasterio-1.3.9-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:911e54e0bb97c456a045f6d8e24b00aeb055a235d2aa7c2c1f9128f4c6c7a52d"},
+    {file = "rasterio-1.3.9-cp39-cp39-manylinux2014_x86_64.whl", hash = "sha256:01e428ee5ba8444f5cb4fff56225acb1ab9bc8b77209b6e4198e04565d8a8509"},
+    {file = "rasterio-1.3.9-cp39-cp39-win_amd64.whl", hash = "sha256:26d9aea05b035927647bb32cc04fad0a68346a2f5186224dc1c2555c33515183"},
+    {file = "rasterio-1.3.9.tar.gz", hash = "sha256:fc6d0d290492fa1a5068711cfebb21cc936968891b7ed9da0690c8a7388885c5"},
+]
 
 [package.dependencies]
 affine = "*"
@@ -739,7 +1220,7 @@ certifi = "*"
 click = ">=4.0"
 click-plugins = "*"
 cligj = ">=0.5"
-numpy = ">=1.18"
+numpy = "*"
 setuptools = "*"
 snuggs = ">=1.4.1"
 
@@ -753,46 +1234,104 @@ test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest (>=2.8.2)", "pytes
 
 [[package]]
 name = "rope"
-version = "1.1.1"
+version = "1.12.0"
 description = "a python refactoring library..."
-category = "dev"
 optional = false
-python-versions = ">=3"
+python-versions = ">=3.8"
+files = [
+    {file = "rope-1.12.0-py3-none-any.whl", hash = "sha256:01f06624159e6b2ec9b94412d519e8877a19eeabe392f469c36f7236df05d443"},
+    {file = "rope-1.12.0.tar.gz", hash = "sha256:93a1bb991fbf0426e8d415102d1c092ccc42e826ce9a42c4d61ce53d7786d9d9"},
+]
+
+[package.dependencies]
+pytoolconfig = {version = ">=1.2.2", extras = ["global"]}
 
 [package.extras]
-dev = ["build", "pytest", "pytest-timeout"]
+dev = ["build (>=0.7.0)", "pre-commit (>=2.20.0)", "pytest (>=7.0.1)", "pytest-timeout (>=2.1.0)"]
+doc = ["pytoolconfig[doc]", "sphinx (>=4.5.0)", "sphinx-autodoc-typehints (>=1.18.1)", "sphinx-rtd-theme (>=1.0.0)"]
+release = ["pip-tools (>=6.12.1)", "toml (>=0.10.2)", "twine (>=4.0.2)"]
 
 [[package]]
-name = "Rtree"
+name = "rtree"
 version = "0.8.3"
 description = "R-Tree spatial index for Python GIS"
-category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "Rtree-0.8.3-py2-none-any.whl", hash = "sha256:8526431aa15d8cea1c07b451ce853b62b1da4cf6b74c07810aba5b81d12efe66"},
+    {file = "Rtree-0.8.3-py3-none-any.whl", hash = "sha256:a9e67386073f93f22449f396d5993dfe479335169c376f3f7fb04a396391f0dc"},
+    {file = "Rtree-0.8.3.tar.gz", hash = "sha256:6cb9cf3000963ea6a3db777a597baee2bc55c4fc891e4f1967f262cc96148649"},
+]
 
 [package.dependencies]
 setuptools = "*"
 
 [[package]]
 name = "setuptools"
-version = "65.4.0"
+version = "69.0.3"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+files = [
+    {file = "setuptools-69.0.3-py3-none-any.whl", hash = "sha256:385eb4edd9c9d5c17540511303e39a147ce2fc04bc55289c322b9e5904fe2c05"},
+    {file = "setuptools-69.0.3.tar.gz", hash = "sha256:be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78"},
+]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
-name = "Shapely"
-version = "1.8.4"
+name = "shapely"
+version = "1.8.5.post1"
 description = "Geometric objects, predicates, and operations"
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "Shapely-1.8.5.post1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d048f93e42ba578b82758c15d8ae037d08e69d91d9872bca5a1895b118f4e2b0"},
+    {file = "Shapely-1.8.5.post1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:99ab0ddc05e44acabdbe657c599fdb9b2d82e86c5493bdae216c0c4018a82dee"},
+    {file = "Shapely-1.8.5.post1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:99a2f0da0109e81e0c101a2b4cd8412f73f5f299e7b5b2deaf64cd2a100ac118"},
+    {file = "Shapely-1.8.5.post1-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:6fe855e7d45685926b6ba00aaeb5eba5862611f7465775dacd527e081a8ced6d"},
+    {file = "Shapely-1.8.5.post1-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:ec14ceca36f67cb48b34d02d7f65a9acae15cd72b48e303531893ba4a960f3ea"},
+    {file = "Shapely-1.8.5.post1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d8a2b2a65fa7f97115c1cd989fe9d6f39281ca2a8a014f1d4904c1a6e34d7f25"},
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 [package.extras]
 all = ["numpy", "pytest", "pytest-cov"]
@@ -803,25 +1342,34 @@ vectorized = ["numpy"]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
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+]
 
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 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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+]
 
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 name = "snuggs"
 version = "1.4.7"
 description = "Snuggs are s-expressions for Numpy"
-category = "main"
 optional = false
 python-versions = "*"
+files = [
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+]
 
 [package.dependencies]
 numpy = "*"
@@ -832,15 +1380,18 @@ test = ["hypothesis", "pytest"]
 
 [[package]]
 name = "stack-data"
-version = "0.5.1"
+version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "dev"
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 python-versions = "*"
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 [package.dependencies]
-asttokens = "*"
-executing = "*"
+asttokens = ">=2.1.0"
+executing = ">=1.2.0"
 pure-eval = "*"
 
 [package.extras]
@@ -850,702 +1401,177 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
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 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
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-version = "1.2.3"
+version = "2.0.1"
 description = "A lil' TOML parser"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
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 [[package]]
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-version = "5.4.0"
-description = ""
-category = "dev"
+version = "5.14.1"
+description = "Traitlets Python configuration system"
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-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 [package.extras]
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-version = "4.3.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "dev"
+version = "4.9.0"
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+version = "5.9.0"
 description = "Ultra fast JSON encoder and decoder for Python"
-category = "dev"
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-wcwidth = [
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-]
-wrapt = [
-    {file = "wrapt-1.12.1.tar.gz", hash = "sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"},
-]
-yapf = [
-    {file = "yapf-0.32.0-py2.py3-none-any.whl", hash = "sha256:8fea849025584e486fd06d6ba2bed717f396080fd3cc236ba10cb97c4c51cf32"},
-    {file = "yapf-0.32.0.tar.gz", hash = "sha256:a3f5085d37ef7e3e004c4ba9f9b3e40c54ff1901cd111f05145ae313a7c67d1b"},
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.8"
+content-hash = "07a6a34a534ac6229a9dba81e4fcd47d39017999aa311c40f443bb1811f476e7"
diff --git a/pyproject.toml b/pyproject.toml
index ae5fa1de..13d176b0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ license = "BSD-3-Clause"
 
 [tool.poetry.dependencies]
 python = "^3.8"
-Fiona = "^1.8"
+Fiona = "^1.9"
 jinja2 = "^3.0"
 numpy = "^1.16"
 rasterio = "^1.0"

From 4292ce0fd950999f3a15a5224f8b7b2da89a5e53 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Mon, 22 Jan 2024 19:06:36 -0300
Subject: [PATCH 068/105] ci: add automated deploy to docker

---
 .github/workflows/release.yml | 57 +++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 00000000..6d2378ac
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,57 @@
+name: Release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'New version'
+        required: true
+
+jobs:
+  update-and-build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Update pyproject.toml version
+        run: |
+          sed -i "s/^version = .*/version = \"${{ github.event.inputs.version }}\"/" pyproject.toml
+          git config --global user.name 'GitHub Actions'
+          git config --global user.email 'actions@github.com'
+          git commit -am "ci: Version bump ${{ github.event.inputs.version }}"
+          git push
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ vars.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Build and push Docker Image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          platforms: linux/amd64 #,linux/arm64 future ;)
+          push: true
+          tags: ${{ vars.DOCKER_IMAGE_NAME }}:${{ github.event.inputs.version }}, ${{ secrets.DOCKER_IMAGE_NAME }}:latest
+
+      - name: Push version bump commit
+        run: |
+          git tag ${{ github.event.inputs.version }}
+          git push origin ${{ github.event.inputs.version }}
+          git push
+
+      - name: Create GitHub Release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.event.inputs.version }}
+          release_name: Release ${{ github.event.inputs.version }}
+          draft: false
+          prerelease: false

From 4acd1f74a90e366402b5c353265479036074091d Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Tue, 23 Jan 2024 00:41:43 -0300
Subject: [PATCH 069/105] fix(peerless): fix parallelization performance issues
 when building the context

---
 pythia/peerless.py | 33 +++++++++++++++------------------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/pythia/peerless.py b/pythia/peerless.py
index cde2cea7..8dab3d26 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -84,6 +84,7 @@ def process_context(context, plugins, config, env):
         if not config["silence"]:
             print("X", end="", flush=True)
 
+
 def execute(config, plugins):
     runs = config.get("runs", [])
     if len(runs) == 0:
@@ -91,30 +92,26 @@ def execute(config, plugins):
     runlist = []
     for run in runs:
         pythia.io.make_run_directory(os.path.join(config["workDir"], run["name"]))
+
     peers = [pythia.io.peer(r, config.get("sample", None)) for r in runs]
     pool_size = config.get("threads", mp.cpu_count())
     print("RUNNING WITH POOL SIZE: {}".format(pool_size))
     env = pythia.template.init_engine(config["templateDir"])
     pythia.functions.build_ghr_cache(config)
 
-    with mp.Pool(pool_size) as pool:
-        results = pool.imap_unordered(
-            build_context, _generate_context_args(runs, peers, config), 250
-        )
-        with concurrent.futures.ProcessPoolExecutor(max_workers=pool_size) as executor:
-            # Use submit to asynchronously execute the process_context function for each context
-            future_to_result = {executor.submit(process_context, context, plugins, config, env): context for context in results}
-
-            # Iterate through the completed futures
-            runlist = []
-            for future in concurrent.futures.as_completed(future_to_result):
-                try:
-                    result = future.result()
-                    if result is not None:
-                        runlist.append(result)
-                except Exception as e:
-                    # Handle exceptions if any occurred during processing
-                    print(f"Error processing context: {e}")
+    # Parallelize the context build (build_context), it is CPU intensive because it
+    #  runs the functions (functions.py) declared in the config files.
+    with concurrent.futures.ProcessPoolExecutor(max_workers=pool_size) as executor:
+        tasks = _generate_context_args(runs, peers, config)
+        future_to_context = {executor.submit(build_context, task): task for task in tasks}
+
+        # process_context is mostly I/O intensive, no reason to parallelize it.
+        for future in concurrent.futures.as_completed(future_to_context):
+            context_result = future.result()
+            if context_result is not None:
+                processed_result = process_context(context_result, plugins, config, env)
+                if processed_result is not None:
+                    runlist.append(processed_result)
 
     if config["exportRunlist"]:
         with open(os.path.join(config["workDir"], "run_list.txt"), "w") as f:

From 8bf58ebfb11cac9728a7976c9a290868c04950fe Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Tue, 23 Jan 2024 01:07:46 -0300
Subject: [PATCH 070/105] feat: add ppop and plrs field support

---
 pythia/template.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pythia/template.py b/pythia/template.py
index 945e552f..8b544d63 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -32,6 +32,8 @@
     "pfrst": {"length": 5},
     "plast": {"length": 5},
     "hdate": {"length": 5},
+    "ppop": {"fmt": ":>2.1f"},
+    "plrs": {"length": 3},
 }
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]

From 07516b0dff741b33f524bc4ecf3f72ad2bd83c6e Mon Sep 17 00:00:00 2001
From: Willingthon Pavan <wpavan@ufl.edu>
Date: Mon, 5 Feb 2024 16:56:07 -0500
Subject: [PATCH 071/105] ci: bump version v2.2.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 13d176b0..127ec27e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.1.7"
+version = "2.2.0"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From fd2d6e1120056f0b85b7f3e2f1e73a364e3b55c8 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Thu, 8 Feb 2024 10:19:05 -0300
Subject: [PATCH 072/105] fix: allow pythia to have ppop greater than 3 digits

---
 pythia/template.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/template.py b/pythia/template.py
index 8b544d63..2092dee9 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -32,7 +32,7 @@
     "pfrst": {"length": 5},
     "plast": {"length": 5},
     "hdate": {"length": 5},
-    "ppop": {"fmt": ":>2.1f"},
+    "ppop": {"length": 5},
     "plrs": {"length": 3},
 }
 

From 86a4c7cbe7c18cb6576a59c7cda6885c14641f69 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Thu, 8 Feb 2024 13:29:03 +0000
Subject: [PATCH 073/105] ci: Version bump 2.2.1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 127ec27e..ca57adcb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.2.0"
+version = "2.2.1"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 7958295d5655e462c3acfa92ba81e4c1d913e21a Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Thu, 8 Feb 2024 10:31:54 -0300
Subject: [PATCH 074/105] ci: fix pulling image name from secrets

---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 6d2378ac..c217fed9 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -38,7 +38,7 @@ jobs:
           file: ./Dockerfile
           platforms: linux/amd64 #,linux/arm64 future ;)
           push: true
-          tags: ${{ vars.DOCKER_IMAGE_NAME }}:${{ github.event.inputs.version }}, ${{ secrets.DOCKER_IMAGE_NAME }}:latest
+          tags: ${{ vars.DOCKER_IMAGE_NAME }}:${{ github.event.inputs.version }}, ${{ vars.DOCKER_IMAGE_NAME }}:latest
 
       - name: Push version bump commit
         run: |

From 490d480d7032871f2adad7c98381e77c462dea54 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Thu, 8 Feb 2024 10:45:20 -0300
Subject: [PATCH 075/105] Revert 86a4c7cbe7c18cb6576a59c7cda6885c14641f69

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ca57adcb..127ec27e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.2.1"
+version = "2.2.0"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 2138f0627b295ab23af8028460e130b70a0eba92 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Thu, 8 Feb 2024 13:52:55 +0000
Subject: [PATCH 076/105] ci: Version bump 2.2.1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 127ec27e..ca57adcb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.2.0"
+version = "2.2.1"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 85a7a0e32408d7f80b84f8d696a3d8c7b89d2fa7 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 30 Dec 2023 19:09:21 -0300
Subject: [PATCH 077/105] feat(hooks): add pre_analytics and post_analytics
 hooks

---
 pythia/analytics.py         | 26 ++++++++++++++++++++++----
 pythia/plugin.py            |  6 ++----
 pythia/tests/plugin_test.py | 10 +++++-----
 3 files changed, 29 insertions(+), 13 deletions(-)

diff --git a/pythia/analytics.py b/pythia/analytics.py
index 048c4731..0efeb456 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -8,6 +8,7 @@
 import pythia.analytic_functions
 import pythia.io
 import pythia.util
+import pythia.plugin
 from contextlib import _GeneratorContextManager
 
 
@@ -250,13 +251,21 @@ def collate_outputs(config, run):
 def execute(config, plugins):
     runs = config.get("runs", [])
     analytics_config = config.get("analytics_setup", None)
+
+    if not analytics_config or len(runs) == 0:
+        logging.warning("Skipping analytics: no configuration or runs found.")
+        return
+
+    pythia.plugin.run_plugin_functions(
+        pythia.plugin.PluginHook.pre_analytics,
+        plugins,
+        config=config,
+    )
+
     run_outputs = []
     calculated = None
     filtered = None
-    if not analytics_config:
-        return
-    if len(runs) == 0:
-        return
+
     for run in runs:
         run_outputs.append(collate_outputs(config, run))
     # Apply all the filters first
@@ -272,3 +281,12 @@ def execute(config, plugins):
         combine_outputs(config, filtered)
     else:
         final_outputs(config, filtered)
+
+    pythia.plugin.run_plugin_functions(
+        pythia.plugin.PluginHook.post_analytics,
+        plugins,
+        config=config,
+        run_outputs=run_outputs,
+        calculated=calculated,
+        filtered=filtered,
+    )
diff --git a/pythia/plugin.py b/pythia/plugin.py
index b508231e..004bc730 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -18,10 +18,8 @@ class PluginHook(Enum):
     post_run_pixel_success = 650
     post_run_pixel_failed = 651
     post_run_all = 700
-    pre_analysis = 800
-    analyze_file = 900
-    analyze_pixel = 1000
-    post_analysis = 1100
+    pre_analytics = 800
+    post_analytics = 900
 
 
 def register_plugin_function(hook, fun, config, plugins):
diff --git a/pythia/tests/plugin_test.py b/pythia/tests/plugin_test.py
index 682d8dc9..fa197a57 100644
--- a/pythia/tests/plugin_test.py
+++ b/pythia/tests/plugin_test.py
@@ -15,7 +15,7 @@ def test_register_with_invalid_hook():
 def test_register_with_invalid_fun():
     plugins = {}
     plugins1 = register_plugin_function(
-        PluginHook.analyze_file, "not a function", "", plugins
+        PluginHook.pre_analytics, "not a function", "", plugins
     )
     assert plugins1 == {}
 
@@ -23,7 +23,7 @@ def test_register_with_invalid_fun():
 def test_register_with_invalid_config():
     plugins = {}
     plugins1 = register_plugin_function(
-        PluginHook.post_analysis, sample_function, "", plugins
+        PluginHook.post_analytics, sample_function, "", plugins
     )
     assert plugins1 == {}
 
@@ -33,13 +33,13 @@ def test_register_twice():
     plugins1 = {}
     plugins2 = {}
     plugins1 = register_plugin_function(
-        PluginHook.analyze_file, sample_function, {}, plugins
+        PluginHook.pre_analytics, sample_function, {}, plugins
     )
     plugins2 = register_plugin_function(
-        PluginHook.analyze_file, sample_function, {"a": 1}, plugins1
+        PluginHook.pre_analytics, sample_function, {"a": 1}, plugins1
     )
     assert plugins1 == {
-        PluginHook.analyze_file: [{"fun": sample_function, "config": {}}]
+        PluginHook.pre_analytics: [{"fun": sample_function, "config": {}}]
     }
     assert plugins1 == plugins2
 

From 802ce6220e1edeae1480088df4cb692d7ad4ddd0 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Mon, 4 Mar 2024 18:35:42 -0300
Subject: [PATCH 078/105] docs: add docs for releasing Pythia

---
 docs/RELEASING.md | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 docs/RELEASING.md

diff --git a/docs/RELEASING.md b/docs/RELEASING.md
new file mode 100644
index 00000000..a9827a69
--- /dev/null
+++ b/docs/RELEASING.md
@@ -0,0 +1,26 @@
+# Pythia - Release Guide
+
+## Versioning
+
+When it comes to managing software releases for Pythia, understanding how to properly version each release is crucial. Pythia follows the principles of [semantic versioning](https://semver.org/), a widely adopted system designed to give meaning to version numbers. In semantic versioning, a version number is made up of three parts: ``MAJOR.MINOR.PATCH``, with each part serving a specific purpose:
+
+ - **MAJOR** version when you make incompatible API changes,
+ - **MINOR** version when you add functionality in a backwards compatible manner, and
+ - **PATCH** version when you make backwards compatible bug fixes.
+
+This system helps developers and users understand the scope and impact of each release. Here's a breakdown of when to increment each part of the version number:
+
+ - Increment the **MAJOR** version when there are significant changes that break backward compatibility with the previous versions. This could include changes to the software's architecture, removal of functionalities, or any other changes that would require users to make modifications to their existing setups.
+ - Increment the **MINOR** version when new features or functionalities are added in a backward-compatible manner. This means that the new version adds value to the software without disrupting the existing functionalities or forcing changes in the users' setups.
+ - Increment the **PATCH** version for minor changes that fix bugs without adding new features or changing existing ones. These should not affect the software's functionality beyond the specific fixes.
+
+## Release Process
+Pythia is released through GitHub Actions. Once a release is triggered, the CI/CD pipeline will automatically build the software and publish a Docker image to Dockerhub. A GitHub release is also created.
+
+In order to deploy new versions of Pythia, go to "([Actions > Release](https://github.com/DSSAT/pythia/actions/workflows/release.yml) > Run Workflow > fill in the version number, follow [versioning](#versioning) to figure out this information > Run workflow).
+
+![image](https://github.com/DSSAT/pythia/assets/18128642/a5db0435-9d17-4be8-82c8-54adcbcf860d)
+
+> **IMPORTANT:** The version number must strictly match what is described in [versioning](#versioning). **Do not** add any kind of prefix or suffix that is not semantically valid.
+ 
+> **IMPORTANT:** The version number on ``pyproject.toml`` is automatically updated by the CI/CD pipeline. **Do not** change it manually.

From 1d9fd97541d63f640e3e78d33c84d2f79d9faa14 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 12 Mar 2024 15:41:28 +0000
Subject: [PATCH 079/105] ci: Version bump 2.3.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ca57adcb..50309d63 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pythia"
-version = "2.2.1"
+version = "2.3.0"
 description = "An extensible gridded modeling framework for point-based modeling."
 authors = ["Christopher Villalobos <cvillalobos@ufl.edu>"]
 license = "BSD-3-Clause"

From 352839896c57d5e0438bf6fa6f68af4ade8f3cc0 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Tue, 30 Jul 2024 17:35:04 -0300
Subject: [PATCH 080/105] feat: add support (or rearranged) for new ic
 variables in the template engine: icbl, sh2o, snh4, sno3, icrt, icnd, icrn,
 icre, icwd, icres, icren, icrep, icrip and icrid

---
 pythia/template.py | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/pythia/template.py b/pythia/template.py
index 2092dee9..3eb3063d 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -10,13 +10,6 @@
     "id_soil": {"align": ":<", "length": 10},
     "xcrd": {"fmt": ":>15.3f"},
     "ycrd": {"fmt": ":>15.3f"},
-    "icrt": {"length": 6},
-    "icres": {"length": 6},
-    "icren": {"length": 6},
-    "icbl": {"length": 6},
-    "sh2o": {"fmt": ":>6.3f"},
-    "snh4": {"fmt": ":>6.2f"},
-    "sno3": {"fmt": ":>6.2f"},
     "fdate": {"length": 5},
     "fdap": {"length": 5},
     "famn": {"length": 5},
@@ -34,6 +27,24 @@
     "hdate": {"length": 5},
     "ppop": {"length": 5},
     "plrs": {"length": 3},
+
+    # Initial Conditions (Soil Profiles)
+    "icbl": {"length": 6},
+    "sh2o": {"fmt": ":>6.3f"},
+    "snh4": {"fmt": ":>6.2f"},
+    "sno3": {"fmt": ":>6.2f"},
+
+    # Initial Conditions (Residue)
+    "icrt": {"length": 6},
+    "icnd": {"length": 6},
+    "icrn": {"length": 6},
+    "icre": {"length": 6},
+    "icwd": {"length": 6},
+    "icres": {"length": 6},
+    "icren": {"length": 6},
+    "icrep": {"length": 6},
+    "icrip": {"length": 6},
+    "icrid": {"length": 6},
 }
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]

From 7ea8be90be6a2616532a195c385c035ab7de081f Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Thu, 1 Aug 2024 18:51:08 -0300
Subject: [PATCH 081/105] docs: add parameters (added in
 352839896c57d5e0438bf6fa6f68af4ade8f3cc0) to the list of available variables

---
 docs/json.rst | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/docs/json.rst b/docs/json.rst
index a50533fa..247c8100 100644
--- a/docs/json.rst
+++ b/docs/json.rst
@@ -82,21 +82,23 @@ Supported DSSAT variables
 The following are the supported DSSAT variables. To add more variables, please extend ``template.py``.
 
 +-------+---------+-------+-------+
-| cname | icbl    | pdate | sno3  |
+| cname | nyers   | pdate | irrig |
 +-------+---------+-------+-------+
-| erain | icren   | pfrst | wsta  |
+| erain | flhst   | pfrst | wsta  |
 +-------+---------+-------+-------+
-| famn  | icres   | ph2ol | xcrd  |
+| famn  | fhdur   | ph2ol | xcrd  |
 +-------+---------+-------+-------+
-| fdap  | icrt    | plast | ycrd  |
+| fdap  | sdate   | plast | ycrd  |
 +-------+---------+-------+-------+
-| fdate | id_soil | ramt  |       |
+| fdate | id_soil | ramt  | ingeno|
 +-------+---------+-------+-------+
-| fdate | ingeno  | sdate |       |
+| fdate | icbl    | sh2o  | snh4  |
 +-------+---------+-------+-------+
-| fhdur | irrig   | sh2o  |       |
+| sno3  | icrt    | icnr  | icrn  |
 +-------+---------+-------+-------+
-| flhst | nyers   | snh4  |       |
+| icre  | icwd    | icres | icren |
++-------+---------+-------+-------+
+| icrep | icrip   | icrid |       |
 +-------+---------+-------+-------+
 
 **Note:** All dates are ISO formatted as ``YYYY-MM-DD``

From 7e6464493b0024376e87ec3296e7302c113125bf Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Thu, 29 Aug 2024 15:27:20 -0300
Subject: [PATCH 082/105] feat: automatically convert `None` to `-99` in the
 template engine

---
 pythia/template.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pythia/template.py b/pythia/template.py
index 2092dee9..f51ed627 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -102,8 +102,8 @@ def auto_format_dict(d):
     for k in _t_envmod_fields:
         clean[k] = envmod_format("A0")
     for k, v in d.items():
-        if v == "-99" or v == -99:
-            clean[k] = wrap_format(k, v)
+        if v == "-99" or v == -99 or v is None:
+            clean[k] = wrap_format(k, -99)
         else:
             if k in _t_date_fields and "::" not in v:
                 clean[k] = pythia.util.to_julian_date(pythia.util.from_iso_date(v))

From ffd23dfbb48862769fb09785f649d7251c44dfe2 Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Thu, 29 Aug 2024 15:32:23 -0300
Subject: [PATCH 083/105] feat: add support for Soil Analysis variables:
 ``sadat``, ``smhb``, ``smpx`` and ``smke``

---
 docs/json.rst      | 2 ++
 pythia/template.py | 6 ++++++
 2 files changed, 8 insertions(+)

diff --git a/docs/json.rst b/docs/json.rst
index a50533fa..b9ab7167 100644
--- a/docs/json.rst
+++ b/docs/json.rst
@@ -98,6 +98,8 @@ The following are the supported DSSAT variables. To add more variables, please e
 +-------+---------+-------+-------+
 | flhst | nyers   | snh4  |       |
 +-------+---------+-------+-------+
+| sadat | smhb    | smpx  | smke  |
++-------+---------+-------+-------+
 
 **Note:** All dates are ISO formatted as ``YYYY-MM-DD``
 
diff --git a/pythia/template.py b/pythia/template.py
index f51ed627..2b889075 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -34,6 +34,12 @@
     "hdate": {"length": 5},
     "ppop": {"length": 5},
     "plrs": {"length": 3},
+
+    # Soil Analysis
+    "sadat": {"length": 5},
+    "smhb": {"length": 6},
+    "smpx": {"length": 6},
+    "smke": {"length": 6},
 }
 
 _t_date_fields = ["sdate", "fdate", "pfrst", "plast", "pdate", "hdate"]

From 041cd3411b37f132a2ddb1b251459766cc517104 Mon Sep 17 00:00:00 2001
From: Willingthon Pavan <wpavan@ufl.edu>
Date: Sat, 14 Sep 2024 13:43:27 -0400
Subject: [PATCH 084/105] Create README.md

First README file
---
 README.md | 122 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100644 README.md

diff --git a/README.md b/README.md
new file mode 100644
index 00000000..b8f0c154
--- /dev/null
+++ b/README.md
@@ -0,0 +1,122 @@
+# DSSAT-Pythia Installation Guide
+
+## Software Requirements
+To install and run DSSAT-Pythia on your PC, you will need the following software:
+
+1. **DSSAT**:  
+   Download and install DSSAT from [DSSAT website](https://get.dssat.net/request/?sft=4).
+
+2. **Python 3.8**:  
+   Download the Python 3.8 installer for Windows or macOS from [Python 3.8 release page](https://www.python.org/downloads/release/python-389/).  
+   - During installation, select “Customize installation.”
+   - Select all options under “Optional Features” and “Advanced Options.”
+   - Note: DSSAT-Pythia only works with Python 3.8. If you have another version, uninstall it and download Python 3.8 from the above link.
+
+3. **Git**:  
+   Download and install Git from [Git download page](https://git-scm.com/download/win).
+
+4. **Community Version of Visual Studio**:  
+   Download and install Visual Studio from [Visual Studio website](https://visualstudio.microsoft.com/downloads/).  
+   Select the **Desktop development with C++** workload during installation.
+
+5. **RStudio**:  
+   To use RStudio on your PC, install both R and RStudio:
+   - Download and install R from [CRAN website](https://cran.rstudio.com/).
+   - Download and install RStudio from [RStudio website](https://posit.co/download/rstudio-desktop/).
+
+---
+
+
+## Steps to Install DSSAT-Pythia on PC
+
+1. Enable **Developer Mode**:
+   - Open Windows Settings > Update & Security > For Developers.
+   - Switch on Developer Mode and restart the computer.
+
+2. Open the **Command Prompt** in the C Drive:
+   - Open the C drive and type `cmd` in the address bar and press Enter.
+
+3. Clone the DSSAT-Pythia repository:
+   ```bash
+   git clone https://github.com/dssat/pythia.git pythia
+   ```
+
+4. Navigate to the cloned directory:
+   ```bash
+   cd pythia
+   ```
+
+5. Delete the `poetry.lock` file:
+   ```bash
+   del poetry.lock
+   ```
+
+6. Install Poetry:
+   ```bash
+   pip install poetry
+   ```
+
+7. Install DSSAT-Pythia:
+   ```bash
+   <full path to poetry>\poetry install
+   <full path to poetry>\poetry build
+   ```
+
+8. Install the Pythia wheel file:
+   - Navigate to the `dist` folder and install the `.whl` file:
+     ```bash
+     cd dist
+     pip install pythia-2.2.1-py3-none-any.whl
+     ```
+   - **Note**: Check the version in the `dist` folder and adjust the command if necessary.
+
+9. Add the path to `pythia.exe` to your environment variables.
+
+10. Close the command prompt.
+
+---
+
+## Troubleshooting
+
+- If you encounter any issues during installation, delete the folder `C:\pythia` and repeat the installation steps.
+
+---
+
+## Input Files Setup
+
+1. Download the `InputFiles.zip` folder from [Google Drive link](https://drive.google.com/file/d/1vlBeWEavNggcuhRMgmO79aHTYZ7aq_Im/view?usp=sharing), unzip it, and save the `Simulation_Data` folder in `C:\pythia\`.
+
+2. Open the folder `C:\pythia\Simulation_Data\OUTPUT\Sri_Lanka` and remove all folders (if any).
+
+   **Note**: Remove the contents from the `OUTPUT` folder every time you run the model.
+
+---
+
+## Running the Model
+
+1. Open the command prompt at `C:\pythia\Simulation_Data\Sri_Lanka` by typing `cmd` in the folder address bar.
+
+2. Run the following commands to simulate maize and rice:
+   ```bash
+   pythia --all C:/pythia/Simulation_Data/Sri_Lanka/SL_Maize.json
+   pythia --all C:/pythia/Simulation_Data/Sri_Lanka/SL_Rice.json
+   ```
+
+3. To view the output:
+   - Open the `.json` file in `C:\pythia\Simulation_Data\Sri_Lanka\`.
+   - Find the working directory in `"workDir": "C:/pythia/Simulation_Data/OUTPUT/Sri_Lanka/…"` and navigate to that folder.
+   - The output will be available in `.csv` format.
+
+---
+
+## Plotting Output in RStudio
+
+1. Open the R code file: `C:\pythia\Simulation_Data\OUTPUT\ACASA_Sri_Lanka_maize.R`.
+
+2. Install all required packages and modify the file location on line 22 to match the output `.csv` file.
+
+3. Run the R script to generate the yield plot.
+
+4. The plot will be saved at the location specified in line 62.
+
+   **Note**: If you encounter errors reading the `.csv` file, open the file and delete all columns except `LATITUDE`, `LONGITUDE`, and `HWAH`.

From 8a74a3314c348411af08113314e2715e1788e538 Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Fri, 25 Oct 2024 12:51:53 -0400
Subject: [PATCH 085/105] Added rescale argument to parser; added rescale.py;
 implemented initial functionality for getting raster and vector resolution
 from detected inputs (dynamically); began work on implementing functions for
 changing raster and vector resolution.

---
 .gitignore          |   2 +
 pythia/cli.py       |   7 ++
 pythia/functions.py |  26 +++++++
 pythia/rescale.py   | 160 ++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 195 insertions(+)
 create mode 100644 pythia/rescale.py

diff --git a/.gitignore b/.gitignore
index 17e9f59e..fdcd2c5f 100755
--- a/.gitignore
+++ b/.gitignore
@@ -14,3 +14,5 @@ docs/build
 dist
 *~
 .python-version
+Simulation_Data/
+.idea/
\ No newline at end of file
diff --git a/pythia/cli.py b/pythia/cli.py
index 19581009..c4df036d 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -8,6 +8,7 @@
 import pythia.analytics
 import pythia.io
 import pythia.peerless
+import pythia.rescale
 import pythia.plugin
 
 
@@ -22,6 +23,9 @@ def main():
         action="store_true",
         help="Export a list of all the directories to be run",
     )
+    parser.add_argument(
+        "--rescale", action="store_true", help="Rescale the input files"
+    )
     parser.add_argument(
         "--setup", action="store_true", help="Setup DSSAT run structure and files"
     )
@@ -78,6 +82,9 @@ def main():
                 config["silence"] = True
             else:
                 config["silence"] = False
+            if args.all or args.rescale:
+                print("Rescaling the input files")
+                pythia.rescale.execute(config, plugins)
             if args.all or args.setup:
                 print("Setting up points and directory structure")
                 pythia.peerless.execute(config, plugins)
diff --git a/pythia/functions.py b/pythia/functions.py
index bfd3897b..b27c93a8 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -192,6 +192,32 @@ def split_fert_dap_percent(k, run, context, _):
     return {k: out}
 
 
+def split_fert_dap_qty(k, run, context, _):
+    args = run[k].split("::")[1:]
+    split_amounts = args
+    for i,split_amount in enumerate(split_amounts):
+        if split_amount.startswith("$"):
+            search_context = split_amount[1:]
+            value = float(context[search_context])
+        else:
+            value = float(split_amount)
+        split_amounts[i]=value
+    daps = [int(i) for i in split_amounts[0::2]]
+    qty = [int(i) for i in split_amounts[1::2]]
+    if len(daps) != len(qty):
+        logging.error("Not enough arguments for split_applications_dap_qty")
+        return None
+    if len(daps) != len(set(daps)):
+        logging.error("Days should not be the same in split_applications_dap_percent")
+        return None
+    out = []
+    for i in range(len(daps)):
+        app_total = qty[i]
+        app_dap = daps[i]
+        out.append({"fdap": app_dap, "famn": app_total})
+    return {k: out}
+
+
 def assign_by_raster_value(k, run, context, _):
     init_args = run[k].split("::")[1:]
     if "raster" in init_args:
diff --git a/pythia/rescale.py b/pythia/rescale.py
new file mode 100644
index 00000000..89a66a78
--- /dev/null
+++ b/pythia/rescale.py
@@ -0,0 +1,160 @@
+import json
+import logging
+import os
+
+import fiona
+import rasterio
+
+import pythia.functions
+
+
+def get_raster_resolution(file_path):
+    with rasterio.open(file_path, 'r') as raster:
+        return (raster.profile['transform'][0], raster.profile['transform'][4])
+
+
+def get_vector_resolution(file_path):
+    with fiona.open(file_path, 'r') as src:
+        min_x_dist, min_y_dist = None, None
+        for i in range(len(src)-1):
+            x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i+1]['geometry']['coordinates'][0])
+            y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i+1]['geometry']['coordinates'][1])
+            if 0 < x_dist:
+                if min_x_dist is None or x_dist < min_x_dist:
+                    min_x_dist = x_dist
+            if 0 < y_dist:
+                if min_y_dist is None or y_dist < min_y_dist:
+                    min_y_dist = y_dist
+        return (min_x_dist, min_y_dist)
+
+
+def change_raster_resolution(file_path, scale_factor, config, dst_path=None):
+    file_name = file_path.split('/')[-1].split('.')[0]
+
+    with rasterio.open(file_path, 'r') as src:
+        data = src.read()
+        profile = src.profile
+
+        # Use resampling method defined
+        resampling_mode = rasterio.enums.Resampling.nearest
+
+        # Define the new resolution
+        new_width = int(profile['width'] * scale_factor)
+        new_height = int(profile['height'] * scale_factor)
+
+        # Compute the new transform
+        transform = profile['transform'] * profile['transform'].scale(
+            profile['width'] / new_width,
+            profile['height'] / new_height
+        )
+
+        # Update the profile for the new raster
+        profile.update({
+            'height': new_height,
+            'width': new_width,
+            'transform': transform
+        })
+
+        rescale_dir = config['workDir']
+        rescale_dir += "/rescale/" if rescale_dir[-1] != '/' else 'rescale/'
+        new_filename = file_name + '_rescaled.tif'
+        new_path = rescale_dir + new_filename if dst_path is None else dst_path
+
+        try:
+            os.makedirs(rescale_dir, exist_ok=True)
+        except OSError as e:
+            logging.error(
+                "OSError encountered when attempting to create rescale_dir: " + str(e)
+            )
+            raise e
+
+        with rasterio.open(new_path, 'w', **profile) as out_file:
+            for i in range(1, profile['count'] + 1):
+                rasterio.warp.reproject(
+                    source=rasterio.band(src, i),
+                    destination=rasterio.band(out_file, i),
+                    src_transform=profile['transform'],
+                    src_crs=profile['crs'],
+                    dst_transform=transform,
+                    dst_crs=profile['crs'],
+                    resampling=resampling_mode
+                )
+
+
+def change_vector_resolution(file_path, scale_factor, config, dst_path=None):
+    pass
+
+
+def execute(config, plugins):
+    # print(json.dumps(config, indent=4))
+    """
+    Keep track of all the resolutions and what they point to.
+    To do this, create a template dictionary containing all of the files.
+    None values indicate a placeholder.
+    """
+    print(json.dumps(config, indent=4), "\n\n\n")
+
+    # Create runs sub-dictionary with the same number of runs as the orginal
+    resolutions = {"runs": [{key: None for key in run.keys()} for run in config['runs']]}
+
+    # Create a sub-dictionary for fertilizers since an arbitrary number of arguments may be used
+    # Only add values if they start in $, this indicates it is an arg (may or may not be file)
+    for i in range(len(config['runs'])):
+        fertilizer_dict = {arg[1:]: None for arg in config['runs'][i]['fertilizers'].split("::")[1:] if arg[0]=='$'}
+        resolutions["runs"][i].update(fertilizer_dict)
+
+    # Find file path of a key
+    # sites
+    i = 0
+    sites_functions = [pythia.functions.xy_from_vector.__name__]
+    for run in config['runs']:
+        site_path = run['sites'].split("::")[1] if run['sites'].split("::")[0] in sites_functions else None
+        print(site_path)
+        try:
+            resolutions["runs"][i]['sites'] = get_vector_resolution(site_path) if site_path is not None else None
+        except fiona.errors.DriverError:
+            logging.error(
+                "Specified file path for \"sites\" does not point to a vector file. Path: %s",
+                site_path
+            )
+        i += 1
+
+    to_delete = []
+    for i in range(len(config['runs'])):
+        for key, value in config['runs'][i].items():
+            if key == "sites":
+                continue
+            elif isinstance(value, str):
+                try:
+                    raster_pos = value.split('::').index('raster')
+                    try:
+                        resolutions['runs'][i][key] = get_raster_resolution(value.split("::")[raster_pos + 1])
+                    except rasterio.errors.RasterioIOError:
+                        logging.error(
+                            "Specified file path for \"%s\" does not point to a raster file. Path: %s",
+                            key, value.split("::")[raster_pos + 1]
+                        )
+                except ValueError:
+                    try:
+                        vector_pos = value.split('::').index('vector')
+                        try:
+                            resolutions['runs'][i][key] = get_vector_resolution(value.split("::")[vector_pos + 1])
+                        except fiona.errors.DriverError:
+                            logging.error(
+                                "Specified file path for \"%s\" does not point to a raster file. Path: %s",
+                                key,
+                                value.split("::")[vector_pos + 1]
+                            )
+                    except ValueError:
+                        to_delete.append(key)
+            else:
+                to_delete.append(key)
+
+    # Remove non-file keys from resolutions dict
+    for key in to_delete:
+        for i in range(len(config['runs'])):
+            del resolutions['runs'][i][key]
+
+
+
+    print(json.dumps(resolutions, indent=4))

From 6ad812884d48700dba3ba22b453c5b2810bb07d6 Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Tue, 12 Nov 2024 21:28:37 -0500
Subject: [PATCH 086/105] Added rescaling functionality after automatic config
 searching.

---
 pythia/cli.py     |   2 +-
 pythia/rescale.py | 202 +++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 175 insertions(+), 29 deletions(-)

diff --git a/pythia/cli.py b/pythia/cli.py
index c4df036d..5d83da88 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -84,7 +84,7 @@ def main():
                 config["silence"] = False
             if args.all or args.rescale:
                 print("Rescaling the input files")
-                pythia.rescale.execute(config, plugins)
+                config = pythia.rescale.execute(config, plugins)
             if args.all or args.setup:
                 print("Setting up points and directory structure")
                 pythia.peerless.execute(config, plugins)
diff --git a/pythia/rescale.py b/pythia/rescale.py
index 89a66a78..31174082 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -4,35 +4,50 @@
 
 import fiona
 import rasterio
+from rasterio.warp import reproject
 
 import pythia.functions
 
 
 def get_raster_resolution(file_path):
     with rasterio.open(file_path, 'r') as raster:
-        return (raster.profile['transform'][0], raster.profile['transform'][4])
+        return [round(raster.profile['transform'][0], 6), round(raster.profile['transform'][4], 6)]
 
 
 def get_vector_resolution(file_path):
     with fiona.open(file_path, 'r') as src:
         min_x_dist, min_y_dist = None, None
-        for i in range(len(src)-1):
-            x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i+1]['geometry']['coordinates'][0])
-            y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i+1]['geometry']['coordinates'][1])
-            if 0 < x_dist:
-                if min_x_dist is None or x_dist < min_x_dist:
-                    min_x_dist = x_dist
-            if 0 < y_dist:
-                if min_y_dist is None or y_dist < min_y_dist:
-                    min_y_dist = y_dist
-        return (min_x_dist, min_y_dist)
+        if src[0]['geometry']['type'] == 'Polygon':
+            x_min, y_min, x_max, y_min = None, None
+            for coords in src[0]['geometry']['coordinates']:
+                if x_min is None or coords[0] < x_min:
+                    x_min = coords[0]
+                if x_max is None or x_max < coords[0]:
+                    x_max = coords[0]
+                if y_min is None or coords[1] < y_min:
+                    y_min = coords[1]
+                if y_max is None or y_max < coords[1]:
+                    y_max = coords[1]
+            x_dist = x_max - x_min
+            y_dist = y_max - y_min
+            return (x_dist, y_dist)
+        else:
+            for i in range(len(src) - 1):
+                x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i + 1]['geometry']['coordinates'][0])
+                y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i + 1]['geometry']['coordinates'][1])
+                if 0 < x_dist:
+                    if min_x_dist is None or x_dist < min_x_dist:
+                        min_x_dist = x_dist
+                if 0 < y_dist:
+                    if min_y_dist is None or y_dist < min_y_dist:
+                        min_y_dist = y_dist
+            return [round(min_x_dist, 6), round(min_y_dist, 6)]
 
 
 def change_raster_resolution(file_path, scale_factor, config, dst_path=None):
     file_name = file_path.split('/')[-1].split('.')[0]
 
     with rasterio.open(file_path, 'r') as src:
-        data = src.read()
         profile = src.profile
 
         # Use resampling method defined
@@ -58,7 +73,7 @@ def change_raster_resolution(file_path, scale_factor, config, dst_path=None):
         rescale_dir = config['workDir']
         rescale_dir += "/rescale/" if rescale_dir[-1] != '/' else 'rescale/'
         new_filename = file_name + '_rescaled.tif'
-        new_path = rescale_dir + new_filename if dst_path is None else dst_path
+        dst_path = rescale_dir + new_filename if dst_path is None else dst_path
 
         try:
             os.makedirs(rescale_dir, exist_ok=True)
@@ -68,39 +83,157 @@ def change_raster_resolution(file_path, scale_factor, config, dst_path=None):
             )
             raise e
 
-        with rasterio.open(new_path, 'w', **profile) as out_file:
+        with rasterio.open(dst_path, 'w', **profile) as dst:
             for i in range(1, profile['count'] + 1):
-                rasterio.warp.reproject(
+                reproject(
                     source=rasterio.band(src, i),
-                    destination=rasterio.band(out_file, i),
+                    destination=rasterio.band(dst, i),
                     src_transform=profile['transform'],
                     src_crs=profile['crs'],
                     dst_transform=transform,
                     dst_crs=profile['crs'],
                     resampling=resampling_mode
                 )
+    return dst_path
 
 
-def change_vector_resolution(file_path, scale_factor, config, dst_path=None):
-    pass
+def change_vector_resolution(file_path, scale_factor, config, current_res, dst_path=None):
+    """
+    Rescale the original file by a defined factor.
+
+    :param upscaling_factor: Must be an integer >= 2.
+    2 will result in a 2x2 grid of points created where 1 used to be.
+
+    :return:
+    """
+    file_name = file_path.split('/')[-1].split('.')[0]
+
+    with fiona.open(file_path, 'r') as src:
+        components = [abs(component_res) for component_res in current_res]
+        d = max(components)
+
+        new_features = []
+        id = 0
+
+        rescale_dir = config['workDir']
+        rescale_dir += "/rescale/" if rescale_dir[-1] != '/' else 'rescale/'
+        new_filename = file_name + '_rescaled.shp'
+        dst_path = rescale_dir + new_filename if dst_path is None else dst_path
+
+        try:
+            os.makedirs(rescale_dir, exist_ok=True)
+        except OSError as e:
+            logging.error(
+                "OSError encountered when attempting to create rescale_dir: " + str(e)
+            )
+            raise e
+
+        with fiona.open(dst_path, 'w',
+                        crs=src.crs,
+                        driver="ESRI Shapefile",
+                        schema=src.schema) as dst:
+            for feature in src:
+                if feature['geometry']['type'] == 'Point':
+                    x_old = feature['geometry']['coordinates'][0]
+                    y_old = feature['geometry']['coordinates'][1]
+
+                    old_properties = feature['properties']
+
+                    for i in range(scale_factor):
+                        for j in range(scale_factor):
+                            x_new = x_old + d * (2 * i - scale_factor + 1) / (2 * scale_factor)
+                            y_new = y_old + d * (2 * j - scale_factor + 1) / (2 * scale_factor)
+
+                            # Because of impending deprecation in fiona, new Geometry, Properties
+                            # and Feature objs must be made
+                            new_geometry = fiona.Geometry((x_new, y_new), type='Point')
+
+                            # TODO: find out how slimmed down we can get the properties (what is necessary)
+                            properties = {
+                                'ID': old_properties['ID'],
+                                'Latitude': old_properties['Latitude'],
+                                'Longitude': old_properties['Longitude'],
+                                'nasapid': old_properties['nasapid'],
+                                'LatNP': old_properties['LatNP'],
+                                'LonNP': old_properties['LonNP'],
+                            }
+
+                            new_properties = fiona.Properties.from_dict(properties)
+
+                            dst.write(fiona.Feature(new_geometry, str(id), new_properties))
+                            id += 1
+    return dst_path
+
+
+def get_desired_res(resolutions, desired='highest'):
+    desired = desired.lower()
+    if desired not in ['highest', 'high', 'lowest', 'low']:
+        raise ValueError('desired must be one of \"highest, high, lowest, low\"')
+
+    target_res = [None, None]
+    if desired in ['highest', "high"]:
+        for key, value in resolutions['runs'][0].items():
+            if target_res[0] is None or abs(value[0]) < abs(target_res[0]):
+                target_res[0] = value[0]
+            if target_res[1] is None or abs(value[1]) < abs(target_res[1]):
+                target_res[1] = value[1]
+    elif desired in ['lowest', "low"]:
+        for key, value in resolutions['runs'][0].items():
+            if target_res[0] is None or abs(value[0]) > abs(target_res[0]):
+                target_res[0] = value[0]
+            if target_res[1] is None or abs(value[1]) > abs(target_res[1]):
+                target_res[1] = value[1]
+
+    return target_res
+
+
+def assign_scale_factors(target_res, resolutions):
+    for run in resolutions['runs']:
+        for value in run.values():
+            value.append(abs(round(value[0] / target_res[0], 1)))
+            value.append(abs(round(value[1] / target_res[1], 1)))
+
+
+def change_resolutions(config, resolutions):
+    for run in resolutions['runs']:
+        for key, value in run.items():
+            if value[4] != 1 or value[5] != 1:
+                if value[2] == 'vector':
+                    updated_path = change_vector_resolution(value[3], int(value[4]), config, (value[0], value[1]))
+                    value[3] = updated_path
+                elif value[2] == 'raster':
+                    updated_path = change_raster_resolution(value[3], value[4], config)
+                    value[3] = updated_path
+
+
+def alter_config(config, resolutions):
+    for i in range(len(resolutions['runs'])):
+        for key, value in resolutions['runs'][i].items():
+            if key == "wsta" or config['runs'][i][key].split('::')[0] == "lookup_wth":
+                config_val = config['runs'][i][key].split('::')
+                config_val[-2] = value[3]
+                config['runs'][i][key] = '::'.join(config_val)
+            else:
+                config_val = config['runs'][i][key].split('::')
+                config_val[-1] = value[3]
+                config['runs'][i][key] = '::'.join(config_val)
 
 
 def execute(config, plugins):
-    # print(json.dumps(config, indent=4))
     """
     Keep track of all the resolutions and what they point to.
     To do this, create a template dictionary containing all of the files.
     None values indicate a placeholder.
     """
-    print(json.dumps(config, indent=4), "\n\n\n")
-
     # Create runs sub-dictionary with the same number of runs as the orginal
     resolutions = {"runs": [{key: None for key in run.keys()} for run in config['runs']]}
 
+    print(json.dumps(resolutions, indent=4))
+
     # Create a sub-dictionary for fertilizers since an arbitrary number of arguments may be used
     # Only add values if they start in $, this indicates it is an arg (may or may not be file)
     for i in range(len(config['runs'])):
-        fertilizer_dict = {arg[1:]: None for arg in config['runs'][i]['fertilizers'].split("::")[1:] if arg[0]=='$'}
+        fertilizer_dict = {arg[1:]: None for arg in config['runs'][i]['fertilizers'].split("::")[1:] if arg[0] == '$'}
         resolutions["runs"][i].update(fertilizer_dict)
 
     # Find file path of a key
@@ -109,9 +242,10 @@ def execute(config, plugins):
     sites_functions = [pythia.functions.xy_from_vector.__name__]
     for run in config['runs']:
         site_path = run['sites'].split("::")[1] if run['sites'].split("::")[0] in sites_functions else None
-        print(site_path)
         try:
-            resolutions["runs"][i]['sites'] = get_vector_resolution(site_path) if site_path is not None else None
+            resolutions['runs'][i]['sites'] = get_vector_resolution(site_path) if site_path is not None else None
+            resolutions['runs'][i]['sites'].append('vector')
+            resolutions['runs'][i]['sites'].append(site_path)
         except fiona.errors.DriverError:
             logging.error(
                 "Specified file path for \"sites\" does not point to a vector file. Path: %s",
@@ -122,13 +256,15 @@ def execute(config, plugins):
     to_delete = []
     for i in range(len(config['runs'])):
         for key, value in config['runs'][i].items():
-            if key == "sites":
+            if key in ["sites"]:
                 continue
             elif isinstance(value, str):
                 try:
                     raster_pos = value.split('::').index('raster')
                     try:
                         resolutions['runs'][i][key] = get_raster_resolution(value.split("::")[raster_pos + 1])
+                        resolutions['runs'][i][key].append('raster')
+                        resolutions['runs'][i][key].append(value.split("::")[raster_pos + 1])
                     except rasterio.errors.RasterioIOError:
                         logging.error(
                             "Specified file path for \"%s\" does not point to a raster file. Path: %s",
@@ -139,6 +275,8 @@ def execute(config, plugins):
                         vector_pos = value.split('::').index('vector')
                         try:
                             resolutions['runs'][i][key] = get_vector_resolution(value.split("::")[vector_pos + 1])
+                            resolutions['runs'][i][key].append('vector')
+                            resolutions['runs'][i][key].append(value.split("::")[vector_pos + 1])
                         except fiona.errors.DriverError:
                             logging.error(
                                 "Specified file path for \"%s\" does not point to a raster file. Path: %s",
@@ -146,15 +284,23 @@ def execute(config, plugins):
                                 value.split("::")[vector_pos + 1]
                             )
                     except ValueError:
-                        to_delete.append(key)
+                        if key not in to_delete:
+                            to_delete.append(key)
             else:
-                to_delete.append(key)
+                if key not in to_delete:
+                    to_delete.append(key)
 
     # Remove non-file keys from resolutions dict
     for key in to_delete:
         for i in range(len(config['runs'])):
             del resolutions['runs'][i][key]
 
-
+    assign_scale_factors(get_desired_res(resolutions, "highest"), resolutions)
+    change_resolutions(config, resolutions)
 
     print(json.dumps(resolutions, indent=4))
+
+    alter_config(config, resolutions)
+
+    print(json.dumps(config, indent=4))
+    return config

From 0c2f0d8939ea70ec1f72ade8fa5f052e59d41d2d Mon Sep 17 00:00:00 2001
From: alwinhopf <34645594+alwinhopf@users.noreply.github.com>
Date: Fri, 13 Dec 2024 09:58:09 -0700
Subject: [PATCH 087/105] Update README.md

Updated from
pythia-2.2.1-py3-none-any.whl
to
pythia-2.3.0-py3-none-any.whl
in 8. Install the Pythia wheel file

Added exemplary path under Windows where the poetry script is found for "7. Install DSSAT-Pythia:"
---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index b8f0c154..cb65e556 100644
--- a/README.md
+++ b/README.md
@@ -61,12 +61,13 @@ To install and run DSSAT-Pythia on your PC, you will need the following software
    <full path to poetry>\poetry install
    <full path to poetry>\poetry build
    ```
-
+   - On Windows, poetry will be found in "C:\Users\username\AppData\Local\Programs\Python\Python38\Scripts"
+     
 8. Install the Pythia wheel file:
    - Navigate to the `dist` folder and install the `.whl` file:
      ```bash
      cd dist
-     pip install pythia-2.2.1-py3-none-any.whl
+     pip install pythia-2.3.0-py3-none-any.whl
      ```
    - **Note**: Check the version in the `dist` folder and adjust the command if necessary.
 

From 63e4ec0479117812209ffc4240d162c6d11f5a23 Mon Sep 17 00:00:00 2001
From: Virginia Covert <66711984+VirginiaBee47@users.noreply.github.com>
Date: Fri, 10 Jan 2025 11:23:39 -0500
Subject: [PATCH 088/105] Create LICENSE

---
 LICENSE | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 LICENSE

diff --git a/LICENSE b/LICENSE
new file mode 100644
index 00000000..a495892d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, DSSAT Foundation
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

From f1c040a6c3b18345bfe33b7c8490625477ba971d Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Fri, 10 Jan 2025 11:25:11 -0500
Subject: [PATCH 089/105] Changed output stream for error checking from warning
 messages to true errors. This should allow for more consistent plugin
 operation.

---
 pythia/dssat.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/dssat.py b/pythia/dssat.py
index ada9f465..cdb60553 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -24,7 +24,7 @@ def _run_dssat(details, config, plugins):
     out, err = dssat.communicate()
     # print("+", end="", flush=True)
 
-    error_count = len(out.decode().split("\n")) - 1
+    error_count = len(err.decode().split("\n")) - 1
     hook = pythia.plugin.PluginHook.post_run_pixel_success
     if error_count > 0:
         hook = pythia.plugin.PluginHook.post_run_pixel_failed

From 9554919a29f33268cb6a627f34f41df5680fe126 Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Fri, 10 Jan 2025 14:56:42 -0500
Subject: [PATCH 090/105] Added licenses to source files.

---
 pythia/__init__.py           | 2 ++
 pythia/__main__.py           | 2 ++
 pythia/analytic_functions.py | 2 ++
 pythia/analytics.py          | 2 ++
 pythia/cache_manager.py      | 2 ++
 pythia/cli.py                | 2 ++
 pythia/config.py             | 2 ++
 pythia/dssat.py              | 2 ++
 pythia/functions.py          | 2 ++
 pythia/io.py                 | 3 ++-
 pythia/peerless.py           | 2 ++
 pythia/plugin.py             | 2 ++
 pythia/rescale.py            | 2 ++
 pythia/soil_handler.py       | 2 ++
 pythia/template.py           | 2 ++
 pythia/util.py               | 2 ++
 16 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/pythia/__init__.py b/pythia/__init__.py
index d4b07020..2c41930a 100644
--- a/pythia/__init__.py
+++ b/pythia/__init__.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import logging
 from logging import NullHandler
 
diff --git a/pythia/__main__.py b/pythia/__main__.py
index 06137fa9..cd84287e 100644
--- a/pythia/__main__.py
+++ b/pythia/__main__.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import sys
 from pythia.cli import main
 
diff --git a/pythia/analytic_functions.py b/pythia/analytic_functions.py
index 1e6e8fe5..f2919b2e 100644
--- a/pythia/analytic_functions.py
+++ b/pythia/analytic_functions.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 def generate_funs(config):
     funcs = []
     for key, funs in config.items():
diff --git a/pythia/analytics.py b/pythia/analytics.py
index 0efeb456..17c1ee35 100644
--- a/pythia/analytics.py
+++ b/pythia/analytics.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import csv
 import logging
 import os
diff --git a/pythia/cache_manager.py b/pythia/cache_manager.py
index 039e6af9..65db5578 100644
--- a/pythia/cache_manager.py
+++ b/pythia/cache_manager.py
@@ -1 +1,3 @@
+__license__ = "BSD-3-Clause"
+
 cache = {}
diff --git a/pythia/cli.py b/pythia/cli.py
index 5d83da88..917f7664 100644
--- a/pythia/cli.py
+++ b/pythia/cli.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import argparse
 import datetime
 import logging
diff --git a/pythia/config.py b/pythia/config.py
index d4a66029..26e53fa6 100644
--- a/pythia/config.py
+++ b/pythia/config.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import itertools
 import json
 import logging
diff --git a/pythia/dssat.py b/pythia/dssat.py
index cdb60553..173298b4 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import logging
 import multiprocessing as mp
 import os
diff --git a/pythia/functions.py b/pythia/functions.py
index b27c93a8..1e5d7126 100644
--- a/pythia/functions.py
+++ b/pythia/functions.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import datetime
 
 import logging
diff --git a/pythia/io.py b/pythia/io.py
index 08ae65c4..7dce4c93 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import os
 
 import fiona
@@ -12,7 +14,6 @@
 
 """rasterio reads x/y which is longitude/latitude"""
 
-
 def get_site_raster_value(dataset, band, site):
     lng, lat = site
     row, col = dataset.index(lng, lat)
diff --git a/pythia/peerless.py b/pythia/peerless.py
index dc842176..84e5bf71 100644
--- a/pythia/peerless.py
+++ b/pythia/peerless.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import logging
 import multiprocessing as mp
 import concurrent.futures
diff --git a/pythia/plugin.py b/pythia/plugin.py
index 004bc730..b682d4d4 100644
--- a/pythia/plugin.py
+++ b/pythia/plugin.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import logging
 from enum import Enum, unique
 
diff --git a/pythia/rescale.py b/pythia/rescale.py
index 31174082..ab14407f 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import json
 import logging
 import os
diff --git a/pythia/soil_handler.py b/pythia/soil_handler.py
index 65231d47..b7ce6f46 100644
--- a/pythia/soil_handler.py
+++ b/pythia/soil_handler.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 def findSoilProfile(profile, soilFiles):
     profile = "*{}".format(profile)
     for sf in soilFiles:
diff --git a/pythia/template.py b/pythia/template.py
index 3eb3063d..eababa4e 100644
--- a/pythia/template.py
+++ b/pythia/template.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 from jinja2 import Environment, FileSystemLoader
 import logging
 import pythia.functions
diff --git a/pythia/util.py b/pythia/util.py
index f7a69e87..7186704f 100644
--- a/pythia/util.py
+++ b/pythia/util.py
@@ -1,3 +1,5 @@
+__license__ = "BSD-3-Clause"
+
 import datetime
 import logging
 

From 285c04688cc18d260ec44b440f51d7c57823259e Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Mon, 13 Jan 2025 15:06:10 -0500
Subject: [PATCH 091/105] Renamed LICENSE to LICENSE.txt

---
 LICENSE => LICENSE.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename LICENSE => LICENSE.txt (100%)

diff --git a/LICENSE b/LICENSE.txt
similarity index 100%
rename from LICENSE
rename to LICENSE.txt

From 60506e65a0d620d437db03afa13efff94b2f063f Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Thu, 13 Feb 2025 12:48:10 -0500
Subject: [PATCH 092/105] Removed debugging print statements. Modified
 rescaling to apply sepaarately per run.

---
 pythia/rescale.py | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index ab14407f..b4f4e499 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -167,20 +167,20 @@ def change_vector_resolution(file_path, scale_factor, config, current_res, dst_p
     return dst_path
 
 
-def get_desired_res(resolutions, desired='highest'):
+def get_desired_res(run, desired='highest'):
     desired = desired.lower()
     if desired not in ['highest', 'high', 'lowest', 'low']:
         raise ValueError('desired must be one of \"highest, high, lowest, low\"')
 
     target_res = [None, None]
     if desired in ['highest', "high"]:
-        for key, value in resolutions['runs'][0].items():
+        for key, value in run.items():
             if target_res[0] is None or abs(value[0]) < abs(target_res[0]):
                 target_res[0] = value[0]
             if target_res[1] is None or abs(value[1]) < abs(target_res[1]):
                 target_res[1] = value[1]
     elif desired in ['lowest', "low"]:
-        for key, value in resolutions['runs'][0].items():
+        for key, value in run.items():
             if target_res[0] is None or abs(value[0]) > abs(target_res[0]):
                 target_res[0] = value[0]
             if target_res[1] is None or abs(value[1]) > abs(target_res[1]):
@@ -189,11 +189,10 @@ def get_desired_res(resolutions, desired='highest'):
     return target_res
 
 
-def assign_scale_factors(target_res, resolutions):
-    for run in resolutions['runs']:
-        for value in run.values():
-            value.append(abs(round(value[0] / target_res[0], 1)))
-            value.append(abs(round(value[1] / target_res[1], 1)))
+def assign_scale_factors(target_res, run):
+    for value in run.values():
+        value.append(abs(round(value[0] / target_res[0], 1)))
+        value.append(abs(round(value[1] / target_res[1], 1)))
 
 
 def change_resolutions(config, resolutions):
@@ -230,7 +229,7 @@ def execute(config, plugins):
     # Create runs sub-dictionary with the same number of runs as the orginal
     resolutions = {"runs": [{key: None for key in run.keys()} for run in config['runs']]}
 
-    print(json.dumps(resolutions, indent=4))
+    # print(json.dumps(resolutions, indent=4))
 
     # Create a sub-dictionary for fertilizers since an arbitrary number of arguments may be used
     # Only add values if they start in $, this indicates it is an arg (may or may not be file)
@@ -256,6 +255,7 @@ def execute(config, plugins):
         i += 1
 
     to_delete = []
+    # Iterate through every run in the config file
     for i in range(len(config['runs'])):
         for key, value in config['runs'][i].items():
             if key in ["sites"]:
@@ -297,11 +297,10 @@ def execute(config, plugins):
         for i in range(len(config['runs'])):
             del resolutions['runs'][i][key]
 
-    assign_scale_factors(get_desired_res(resolutions, "highest"), resolutions)
+    for run in resolutions['runs']:
+        assign_scale_factors(get_desired_res(run, "highest"), run)
     change_resolutions(config, resolutions)
 
-    print(json.dumps(resolutions, indent=4))
-
     alter_config(config, resolutions)
 
     print(json.dumps(config, indent=4))

From 7a36e732434f922acee5740079f152e4e487f001 Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Thu, 13 Feb 2025 12:56:33 -0500
Subject: [PATCH 093/105] Removed debug print statement.

---
 pythia/rescale.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index b4f4e499..ddd19673 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -303,5 +303,5 @@ def execute(config, plugins):
 
     alter_config(config, resolutions)
 
-    print(json.dumps(config, indent=4))
+    # print(json.dumps(config, indent=4))
     return config

From a77a343c7b4dcead7fdc33de9455f80395810812 Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Fri, 14 Feb 2025 16:13:05 -0500
Subject: [PATCH 094/105] Updated .gitignore for cleanliness.

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 17e9f59e..13e1e34d 100755
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@
 tags
 data/*
 pythia/__pycache__/*
+pythia/.idea/*
 .idea/*
 .vscode/*
 *.pyc

From 6c84e2186acabf45bc9d0b9f3c11388fb73f9a59 Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Fri, 10 Jan 2025 11:25:11 -0500
Subject: [PATCH 095/105] Changed output stream for error checking from warning
 messages to true errors. This should allow for more consistent plugin
 operation.

(cherry picked from commit f1c040a6c3b18345bfe33b7c8490625477ba971d)
---
 pythia/dssat.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pythia/dssat.py b/pythia/dssat.py
index ada9f465..cdb60553 100644
--- a/pythia/dssat.py
+++ b/pythia/dssat.py
@@ -24,7 +24,7 @@ def _run_dssat(details, config, plugins):
     out, err = dssat.communicate()
     # print("+", end="", flush=True)
 
-    error_count = len(out.decode().split("\n")) - 1
+    error_count = len(err.decode().split("\n")) - 1
     hook = pythia.plugin.PluginHook.post_run_pixel_success
     if error_count > 0:
         hook = pythia.plugin.PluginHook.post_run_pixel_failed

From cacc6d4519bb0095f23246f02b2d0cdb06a9877b Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Thu, 10 Apr 2025 18:32:40 -0400
Subject: [PATCH 096/105] Edited rescale.py to accomodate shapes files that
 have non-standard 'properties'.

---
 pythia/rescale.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index ddd19673..bf95c641 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -151,15 +151,9 @@ def change_vector_resolution(file_path, scale_factor, config, current_res, dst_p
                             new_geometry = fiona.Geometry((x_new, y_new), type='Point')
 
                             # TODO: find out how slimmed down we can get the properties (what is necessary)
-                            properties = {
-                                'ID': old_properties['ID'],
-                                'Latitude': old_properties['Latitude'],
-                                'Longitude': old_properties['Longitude'],
-                                'nasapid': old_properties['nasapid'],
-                                'LatNP': old_properties['LatNP'],
-                                'LonNP': old_properties['LonNP'],
-                            }
-
+                            properties = {}
+                            [properties.update({key: value}) for key, value in old_properties.items() if key != 'id']
+                            
                             new_properties = fiona.Properties.from_dict(properties)
 
                             dst.write(fiona.Feature(new_geometry, str(id), new_properties))

From 672a446d17763516d284f157e7829a2fa1b08e3c Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Thu, 10 Apr 2025 18:45:54 -0400
Subject: [PATCH 097/105] Harvest area rescaling fix.

---
 .gitignore        |  4 ++--
 pythia/rescale.py | 28 +++++++++++++++++++++-------
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index fdcd2c5f..9358d9ce 100755
--- a/.gitignore
+++ b/.gitignore
@@ -14,5 +14,5 @@ docs/build
 dist
 *~
 .python-version
-Simulation_Data/
-.idea/
\ No newline at end of file
+.idea/
+pythia-data/
\ No newline at end of file
diff --git a/pythia/rescale.py b/pythia/rescale.py
index bf95c641..1a848da2 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -46,7 +46,7 @@ def get_vector_resolution(file_path):
             return [round(min_x_dist, 6), round(min_y_dist, 6)]
 
 
-def change_raster_resolution(file_path, scale_factor, config, dst_path=None):
+def change_raster_resolution(file_path, scale_factor, config, dst_path=None, need_val_scaling=False):
     file_name = file_path.split('/')[-1].split('.')[0]
 
     with rasterio.open(file_path, 'r') as src:
@@ -87,15 +87,25 @@ def change_raster_resolution(file_path, scale_factor, config, dst_path=None):
 
         with rasterio.open(dst_path, 'w', **profile) as dst:
             for i in range(1, profile['count'] + 1):
+                src_array = src.read(i)
+
+                dst_array = rasterio.band(dst, i).read(1)
                 reproject(
-                    source=rasterio.band(src, i),
-                    destination=rasterio.band(dst, i),
-                    src_transform=profile['transform'],
-                    src_crs=profile['crs'],
+                    source=src_array,
+                    destination=dst_array,
+                    src_transform=src.transform,
+                    src_crs=src.crs,
                     dst_transform=transform,
-                    dst_crs=profile['crs'],
+                    dst_crs=src.crs,
                     resampling=resampling_mode
                 )
+
+                if need_val_scaling:
+                    area_scaling_factor = (1 / scale_factor) ** 2
+                    dst_array *= area_scaling_factor
+
+                dst.write(dst_array, i)
+
     return dst_path
 
 
@@ -197,7 +207,11 @@ def change_resolutions(config, resolutions):
                     updated_path = change_vector_resolution(value[3], int(value[4]), config, (value[0], value[1]))
                     value[3] = updated_path
                 elif value[2] == 'raster':
-                    updated_path = change_raster_resolution(value[3], value[4], config)
+                    # Hardcoded harvestArea rescaling of value.
+                    if key == "harvestArea":
+                        updated_path = change_raster_resolution(value[3], value[4], config)
+                    else:
+                        updated_path = change_raster_resolution(value[3], value[4], config)
                     value[3] = updated_path
 
 

From 0f1e3dfb9aa31c21dd28badb3b5d4b73b1df462e Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sat, 26 Apr 2025 19:45:54 -0300
Subject: [PATCH 098/105] perf: add early-return and on-the-fly computing to
 the io.py/find_closest_vector_coords function.

The following report originates from running this function twice per pixel on Tanzania 10x10 km grid:

BEFORE (041cd3411b37f132a2ddb1b251459766cc517104) ->
Performance counter stats for 'python -X perf -m pythia --clean-work-dir --setup test2/pythia-config.json' (5 runs):

     17,438,093.49 msec task-clock                       #   27.858 CPUs utilized               ( +-  0.08% )
           568,468      context-switches                 #   32.599 /sec                        ( +-  2.15% )
            16,541      cpu-migrations                   #    0.949 /sec                        ( +-  1.30% )
           341,541      page-faults                      #   19.586 /sec                        ( +-  0.52% )
85,137,469,787,762      instructions                     #    1.22  insn per cycle
                                                  #    0.29  stalled cycles per insn     ( +-  0.08% )
69,737,313,303,103      cycles                           #    3.999 GHz                         ( +-  0.08% )
24,862,264,765,548      stalled-cycles-frontend          #   35.65% frontend cycles idle        ( +-  0.25% )
18,281,479,410,162      branches                         #    1.048 G/sec                       ( +-  0.07% )
   172,136,315,036      branch-misses                    #    0.94% of all branches             ( +-  0.75% )

           625.953 +- 0.429 seconds time elapsed  ( +-  0.07% )

AFTER ->
Performance counter stats for 'python -X perf -m pythia --clean-work-dir --setup test2/pythia-config.json' (5 runs):

      4,436,558.37 msec task-clock                       #   27.514 CPUs utilized               ( +-  0.22% )
           255,284      context-switches                 #   57.541 /sec                        ( +-  1.80% )
            14,824      cpu-migrations                   #    3.341 /sec                        ( +-  1.76% )
           223,269      page-faults                      #   50.325 /sec                        ( +-  0.11% )
22,793,963,559,968      instructions                     #    1.28  insn per cycle
                                                  #    0.27  stalled cycles per insn     ( +-  0.15% )
17,739,586,160,894      cycles                           #    3.999 GHz                         ( +-  0.22% )
 6,203,511,000,548      stalled-cycles-frontend          #   34.97% frontend cycles idle        ( +-  0.34% )
 4,890,648,814,890      branches                         #    1.102 G/sec                       ( +-  0.13% )
    42,420,497,493      branch-misses                    #    0.87% of all branches             ( +-  0.64% )

           161.248 +- 0.403 seconds time elapsed  ( +-  0.25% )
---
 pythia/gis.py | 19 +++++++++++++++++++
 pythia/io.py  | 38 +++++++++++++++++++-------------------
 2 files changed, 38 insertions(+), 19 deletions(-)
 create mode 100644 pythia/gis.py

diff --git a/pythia/gis.py b/pythia/gis.py
new file mode 100644
index 00000000..39a9d0b1
--- /dev/null
+++ b/pythia/gis.py
@@ -0,0 +1,19 @@
+def euclidean_distance(lat1: float, lon1: float, lat2: float, lon2: float) -> float:
+    """
+    Calculates the euclidean distance between two lat/lon points.
+
+    Designed for fast comparisons (e.g., finding the closest point in a list).
+    Smaller values indicate closer proximity, but the output is NOT in any standard
+    unit (km, miles, etc.) and should not be used for actual distance calculations.
+
+    Args:
+        lat1, lon1: Latitude/longitude of the first point (decimal degrees).
+        lat2, lon2: Latitude/longitude of the second point (decimal degrees).
+
+    Returns:
+        A non-negative float representing relative 'distance' (dimensionless).
+        Only meaningful for comparing proximity between points.
+    """
+    if lat1 == lat2 and lon1 == lon2:
+        return 0.0
+    return (lat1 - lat2)**2 + (lon1 - lon2)**2
diff --git a/pythia/io.py b/pythia/io.py
index 08ae65c4..6663f4c4 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -1,10 +1,12 @@
 import os
+import sys
 
 import fiona
 import numpy.ma as ma
 import rasterio
 from shapely.geometry import Point, MultiPoint
 from shapely.ops import nearest_points
+from pythia.gis import euclidean_distance
 
 import pythia.functions
 import pythia.util
@@ -101,26 +103,24 @@ def find_vector_coords(f, lng, lat, a):
 
 
 def find_closest_vector_coords(f, lng, lat, a):
-    coords = Point(lng, lat)
-    points = []
-    ids = []
+    closest_id = None
     with fiona.open(f, "r") as source:
+        closest_distance = sys.float_info.max
         for feature in source:
             if feature["geometry"]["type"] == "MultiPoint":
-                points.extend(
-                    [Point(p[0], p[1]) for p in feature["geometry"]["coordinates"]]
-                )
-                ids.extend(
-                    [feature["properties"][a]] * len(feature["geometry"]["coordinates"])
-                )
+                for coords in feature["geometry"]["coordinates"]:
+                    res = euclidean_distance(coords[1], coords[0], lat, lng)
+                    if res < closest_distance:
+                        closest_distance = res
+                        closest_id = feature["properties"][a]
+                    if res == 0:
+                        break
             if feature["geometry"]["type"] == "Point":
-                points.append(
-                    Point(
-                        feature["geometry"]["coordinates"][0],
-                        feature["geometry"]["coordinates"][1],
-                    )
-                )
-                ids.append(feature["properties"][a])
-    mp = MultiPoint(points)
-    nearest = nearest_points(coords, mp)[1]
-    return ids[points.index(nearest)]
+                coords = feature["geometry"]["coordinates"]
+                res = euclidean_distance(coords[1], coords[0], lat, lng)
+                if res < closest_distance:
+                    closest_distance = res
+                    closest_id = feature["properties"][a]
+                if res == 0:
+                    return feature["properties"][a]
+    return closest_id

From 4ad13a605fbfe83b00f6ffc3e9914d521daa698a Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sun, 27 Apr 2025 19:13:32 -0300
Subject: [PATCH 099/105] chore: remove ``shapely`` dependency

---
 poetry.lock    | 170 ++++++++++++++++++++++++++++---------------------
 pyproject.toml |   1 -
 pythia/io.py   |   2 -
 3 files changed, 99 insertions(+), 74 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 995a6947..4a6a296c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand.
 
 [[package]]
 name = "affine"
@@ -6,6 +6,7 @@ version = "2.4.0"
 description = "Matrices describing affine transformation of the plane"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "affine-2.4.0-py3-none-any.whl", hash = "sha256:8a3df80e2b2378aef598a83c1392efd47967afec4242021a0b06b4c7cbc61a92"},
     {file = "affine-2.4.0.tar.gz", hash = "sha256:a24d818d6a836c131976d22f8c27b8d3ca32d0af64c1d8d29deb7bafa4da1eea"},
@@ -21,6 +22,8 @@ version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
 optional = false
 python-versions = "*"
+groups = ["dev"]
+markers = "sys_platform == \"darwin\""
 files = [
     {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
     {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
@@ -32,6 +35,7 @@ version = "2.6.6"
 description = "An abstract syntax tree for Python with inference support."
 optional = false
 python-versions = "~=3.6"
+groups = ["dev"]
 files = [
     {file = "astroid-2.6.6-py3-none-any.whl", hash = "sha256:ab7f36e8a78b8e54a62028ba6beef7561db4cdb6f2a5009ecc44a6f42b5697ef"},
     {file = "astroid-2.6.6.tar.gz", hash = "sha256:3975a0bd5373bdce166e60c851cfcbaf21ee96de80ec518c1f4cb3e94c3fb334"},
@@ -48,6 +52,7 @@ version = "2.4.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
     {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
@@ -57,8 +62,8 @@ files = [
 six = ">=1.12.0"
 
 [package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=1,<2) ; python_version < \"3\"", "astroid (>=2,<4) ; python_version >= \"3\""]
+test = ["astroid (>=1,<2) ; python_version < \"3\"", "astroid (>=2,<4) ; python_version >= \"3\"", "pytest"]
 
 [[package]]
 name = "atomicwrites"
@@ -66,6 +71,8 @@ version = "1.4.1"
 description = "Atomic file writes."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["dev"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
 ]
@@ -76,6 +83,7 @@ version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "dev"]
 files = [
     {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
     {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
@@ -86,8 +94,8 @@ cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
 dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6) ; platform_python_implementation == \"CPython\" and python_version >= \"3.8\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.8\""]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "autopep8"
@@ -95,6 +103,7 @@ version = "1.5.7"
 description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "autopep8-1.5.7-py2.py3-none-any.whl", hash = "sha256:aa213493c30dcdac99537249ee65b24af0b2c29f2e83cd8b3f68760441ed0db9"},
     {file = "autopep8-1.5.7.tar.gz", hash = "sha256:276ced7e9e3cb22e5d7c14748384a5cf5d9002257c0ed50c0e075b68011bb6d0"},
@@ -110,6 +119,7 @@ version = "0.2.0"
 description = "Specifications for callback functions passed in to an API"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
     {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
@@ -121,6 +131,7 @@ version = "22.12.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
     {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
@@ -156,6 +167,7 @@ version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
     {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
@@ -167,6 +179,7 @@ version = "8.1.7"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "dev"]
 files = [
     {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
     {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
@@ -181,6 +194,7 @@ version = "1.1.1"
 description = "An extension module for click to enable registering CLI commands via setuptools entry-points."
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"},
     {file = "click_plugins-1.1.1-py2.py3-none-any.whl", hash = "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"},
@@ -198,6 +212,7 @@ version = "0.7.2"
 description = "Click params for commmand line interfaces to GeoJSON"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4"
+groups = ["main"]
 files = [
     {file = "cligj-0.7.2-py3-none-any.whl", hash = "sha256:c1ca117dbce1fe20a5809dc96f01e1c2840f6dcc939b3ddbb1111bf330ba82df"},
     {file = "cligj-0.7.2.tar.gz", hash = "sha256:a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27"},
@@ -215,10 +230,12 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["main", "dev"]
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
+markers = {main = "platform_system == \"Windows\"", dev = "platform_system == \"Windows\" or sys_platform == \"win32\""}
 
 [[package]]
 name = "decorator"
@@ -226,6 +243,7 @@ version = "5.1.1"
 description = "Decorators for Humans"
 optional = false
 python-versions = ">=3.5"
+groups = ["dev"]
 files = [
     {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
     {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
@@ -237,13 +255,14 @@ version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
 python-versions = ">=3.5"
+groups = ["dev"]
 files = [
     {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"},
     {file = "executing-2.0.1.tar.gz", hash = "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147"},
 ]
 
 [package.extras]
-tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""]
 
 [[package]]
 name = "fiona"
@@ -251,6 +270,7 @@ version = "1.9.5"
 description = "Fiona reads and writes spatial data files"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "fiona-1.9.5-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:5f40a40529ecfca5294260316cf987a0420c77a2f0cf0849f529d1afbccd093e"},
     {file = "fiona-1.9.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:374efe749143ecb5cfdd79b585d83917d2bf8ecfbfc6953c819586b336ce9c63"},
@@ -300,6 +320,7 @@ version = "3.9.2"
 description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+groups = ["dev"]
 files = [
     {file = "flake8-3.9.2-py2.py3-none-any.whl", hash = "sha256:bf8fd333346d844f616e8d47905ef3a3384edae6b4e9beb0c5101e25e3110907"},
     {file = "flake8-3.9.2.tar.gz", hash = "sha256:07528381786f2a6237b061f6e96610a4167b226cb926e2aa2b6b1d78057c576b"},
@@ -316,6 +337,7 @@ version = "3.0.3"
 description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "greenlet-3.0.3-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:9da2bd29ed9e4f15955dd1595ad7bc9320308a3b766ef7f837e23ad4b4aac31a"},
     {file = "greenlet-3.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d353cadd6083fdb056bb46ed07e4340b0869c305c8ca54ef9da3421acbdf6881"},
@@ -387,10 +409,12 @@ version = "7.0.1"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev"]
 files = [
     {file = "importlib_metadata-7.0.1-py3-none-any.whl", hash = "sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e"},
     {file = "importlib_metadata-7.0.1.tar.gz", hash = "sha256:f238736bb06590ae52ac1fab06a3a9ef1d8dce2b7a35b5ab329371d6c8f5d2cc"},
 ]
+markers = {main = "python_version < \"3.10\""}
 
 [package.dependencies]
 zipp = ">=0.5"
@@ -398,7 +422,7 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3) ; python_version < \"3.9\"", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\"", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "ipython"
@@ -406,6 +430,7 @@ version = "8.12.3"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "ipython-8.12.3-py3-none-any.whl", hash = "sha256:b0340d46a933d27c657b211a329d0be23793c36595acf9e6ef4164bc01a1804c"},
     {file = "ipython-8.12.3.tar.gz", hash = "sha256:3910c4b54543c2ad73d06579aa771041b7d5707b033bd488669b4cf544e3b363"},
@@ -445,6 +470,7 @@ version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
 optional = false
 python-versions = ">=3.8.0"
+groups = ["dev"]
 files = [
     {file = "isort-5.13.2-py3-none-any.whl", hash = "sha256:8ca5e72a8d85860d5a3fa69b8745237f2939afe12dbf656afbcb47fe72d947a6"},
     {file = "isort-5.13.2.tar.gz", hash = "sha256:48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109"},
@@ -459,6 +485,7 @@ version = "0.18.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "jedi-0.18.2-py2.py3-none-any.whl", hash = "sha256:203c1fd9d969ab8f2119ec0a3342e0b49910045abe6af0a3ae83a5764d54639e"},
     {file = "jedi-0.18.2.tar.gz", hash = "sha256:bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612"},
@@ -478,6 +505,7 @@ version = "3.1.3"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
     {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
@@ -495,6 +523,7 @@ version = "1.10.0"
 description = "A fast and thorough lazy object proxy."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "lazy-object-proxy-1.10.0.tar.gz", hash = "sha256:78247b6d45f43a52ef35c25b5581459e85117225408a4128a3daf8bf9648ac69"},
     {file = "lazy_object_proxy-1.10.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:855e068b0358ab916454464a884779c7ffa312b8925c6f7401e952dcf3b89977"},
@@ -541,6 +570,7 @@ version = "2.1.4"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "MarkupSafe-2.1.4-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:de8153a7aae3835484ac168a9a9bdaa0c5eee4e0bc595503c95d53b942879c84"},
     {file = "MarkupSafe-2.1.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e888ff76ceb39601c59e219f281466c6d7e66bd375b4ec1ce83bcdc68306796b"},
@@ -610,6 +640,7 @@ version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
 python-versions = ">=3.5"
+groups = ["dev"]
 files = [
     {file = "matplotlib-inline-0.1.6.tar.gz", hash = "sha256:f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304"},
     {file = "matplotlib_inline-0.1.6-py3-none-any.whl", hash = "sha256:f1f41aab5328aa5aaea9b16d083b128102f8712542f819fe7e6a420ff581b311"},
@@ -624,6 +655,7 @@ version = "0.6.1"
 description = "McCabe checker, plugin for flake8"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
     {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
@@ -635,6 +667,7 @@ version = "10.2.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "more-itertools-10.2.0.tar.gz", hash = "sha256:8fccb480c43d3e99a00087634c06dd02b0d50fbf088b380de5a41a015ec239e1"},
     {file = "more_itertools-10.2.0-py3-none-any.whl", hash = "sha256:686b06abe565edfab151cb8fd385a05651e1fdf8f0a14191e4439283421f8684"},
@@ -646,6 +679,7 @@ version = "1.0.7"
 description = "MessagePack serializer"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "msgpack-1.0.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:04ad6069c86e531682f9e1e71b71c1c3937d6014a7c3e9edd2aa81ad58842862"},
     {file = "msgpack-1.0.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:cca1b62fe70d761a282496b96a5e51c44c213e410a964bdffe0928e611368329"},
@@ -711,6 +745,7 @@ version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
 optional = false
 python-versions = ">=3.5"
+groups = ["dev"]
 files = [
     {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
     {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
@@ -722,6 +757,7 @@ version = "0.3.1"
 description = "Transition packgage for pynvim"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "neovim-0.3.1.tar.gz", hash = "sha256:a6a0e7a5b4433bf4e6ddcbc5c5ff44170be7d84259d002b8e8d8fb4ee78af60f"},
 ]
@@ -735,6 +771,7 @@ version = "1.24.4"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "numpy-1.24.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c0bfb52d2169d58c1cdb8cc1f16989101639b34c7d3ce60ed70b19c63eba0b64"},
     {file = "numpy-1.24.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:ed094d4f0c177b1b8e7aa9cba7d6ceed51c0e569a5318ac0ca9a090680a6a1b1"},
@@ -772,6 +809,7 @@ version = "23.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
     {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
@@ -783,6 +821,7 @@ version = "0.8.3"
 description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "parso-0.8.3-py2.py3-none-any.whl", hash = "sha256:c001d4636cd3aecdaf33cbb40aebb59b094be2a74c556778ef5576c175e19e75"},
     {file = "parso-0.8.3.tar.gz", hash = "sha256:8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0"},
@@ -798,6 +837,7 @@ version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
     {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
@@ -809,6 +849,8 @@ version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
 optional = false
 python-versions = "*"
+groups = ["dev"]
+markers = "sys_platform != \"win32\""
 files = [
     {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"},
     {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"},
@@ -823,6 +865,7 @@ version = "0.7.5"
 description = "Tiny 'shelve'-like database with concurrency support"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "pickleshare-0.7.5-py2.py3-none-any.whl", hash = "sha256:9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56"},
     {file = "pickleshare-0.7.5.tar.gz", hash = "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca"},
@@ -834,6 +877,7 @@ version = "4.1.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "platformdirs-4.1.0-py3-none-any.whl", hash = "sha256:11c8f37bcca40db96d8144522d925583bdb7a31f7b0e37e3ed4318400a8e2380"},
     {file = "platformdirs-4.1.0.tar.gz", hash = "sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420"},
@@ -849,6 +893,7 @@ version = "0.13.1"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["dev"]
 files = [
     {file = "pluggy-0.13.1-py2.py3-none-any.whl", hash = "sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"},
     {file = "pluggy-0.13.1.tar.gz", hash = "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0"},
@@ -863,6 +908,7 @@ version = "3.0.43"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
+groups = ["dev"]
 files = [
     {file = "prompt_toolkit-3.0.43-py3-none-any.whl", hash = "sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6"},
     {file = "prompt_toolkit-3.0.43.tar.gz", hash = "sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d"},
@@ -877,6 +923,8 @@ version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
 optional = false
 python-versions = "*"
+groups = ["dev"]
+markers = "sys_platform != \"win32\""
 files = [
     {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"},
     {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
@@ -888,6 +936,7 @@ version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "pure_eval-0.2.2-py3-none-any.whl", hash = "sha256:01eaab343580944bc56080ebe0a674b39ec44a945e6d09ba7db3cb8cec289350"},
     {file = "pure_eval-0.2.2.tar.gz", hash = "sha256:2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3"},
@@ -902,6 +951,7 @@ version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["dev"]
 files = [
     {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
     {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
@@ -913,6 +963,7 @@ version = "2.7.0"
 description = "Python style guide checker"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["dev"]
 files = [
     {file = "pycodestyle-2.7.0-py2.py3-none-any.whl", hash = "sha256:514f76d918fcc0b55c6680472f0a37970994e07bbb80725808c17089be302068"},
     {file = "pycodestyle-2.7.0.tar.gz", hash = "sha256:c389c1d06bf7904078ca03399a4816f974a1d590090fecea0c63ec26ebaf1cef"},
@@ -924,6 +975,7 @@ version = "6.3.0"
 description = "Python docstring style checker"
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "pydocstyle-6.3.0-py3-none-any.whl", hash = "sha256:118762d452a49d6b05e194ef344a55822987a462831ade91ec5c06fd2169d019"},
     {file = "pydocstyle-6.3.0.tar.gz", hash = "sha256:7ce43f0c0ac87b07494eb9c0b462c0b73e6ff276807f204d6b53edc72b7e44e1"},
@@ -933,7 +985,7 @@ files = [
 snowballstemmer = ">=2.2.0"
 
 [package.extras]
-toml = ["tomli (>=1.2.3)"]
+toml = ["tomli (>=1.2.3) ; python_version < \"3.11\""]
 
 [[package]]
 name = "pyflakes"
@@ -941,6 +993,7 @@ version = "2.3.1"
 description = "passive checker of Python programs"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["dev"]
 files = [
     {file = "pyflakes-2.3.1-py2.py3-none-any.whl", hash = "sha256:7893783d01b8a89811dd72d7dfd4d84ff098e5eed95cfa8905b22bbffe52efc3"},
     {file = "pyflakes-2.3.1.tar.gz", hash = "sha256:f5bc8ecabc05bb9d291eb5203d6810b49040f6ff446a756326104746cc00c1db"},
@@ -952,13 +1005,14 @@ version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
     {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
 ]
 
 [package.extras]
-plugins = ["importlib-metadata"]
+plugins = ["importlib-metadata ; python_version < \"3.8\""]
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -967,6 +1021,7 @@ version = "2.9.6"
 description = "python code static checker"
 optional = false
 python-versions = "~=3.6"
+groups = ["dev"]
 files = [
     {file = "pylint-2.9.6-py3-none-any.whl", hash = "sha256:2e1a0eb2e8ab41d6b5dbada87f066492bb1557b12b76c47c2ee8aa8a11186594"},
     {file = "pylint-2.9.6.tar.gz", hash = "sha256:8b838c8983ee1904b2de66cce9d0b96649a91901350e956d78f289c3bc87b48e"},
@@ -985,6 +1040,7 @@ version = "0.4.0"
 description = "A Flake8 plugin for the Python Language Server"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "pyls-flake8-0.4.0.tar.gz", hash = "sha256:630cec96e494c0f3bffa381451d71a05f46b4f4e6d9b897ad6377e81cc4f8f70"},
     {file = "pyls_flake8-0.4.0-py2.py3-none-any.whl", hash = "sha256:ca8051e53ee0e06e621abfa7bdc72c9a7f56d5bede51fa7c17caba166b7101a2"},
@@ -1000,6 +1056,7 @@ version = "0.2.2"
 description = "Isort plugin for python-lsp-server"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "pyls-isort-0.2.2.tar.gz", hash = "sha256:2192bd2203db00459f85eb329521feba58af63075d2dd10a051a4eccd000bba0"},
 ]
@@ -1014,6 +1071,7 @@ version = "0.1.11"
 description = "Extended refactoring capabilities for Python LSP Server using Rope."
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "pylsp-rope-0.1.11.tar.gz", hash = "sha256:48aadf993dafa5e8fca1108b4a5431314cf80bc78cffdd56400ead9c407553be"},
     {file = "pylsp_rope-0.1.11-py3-none-any.whl", hash = "sha256:71fb08dc6ead9a69202f2e7c5f7bbc5ada037a0f0722d7eb2d1f8cac2c9a18af"},
@@ -1033,6 +1091,7 @@ version = "0.5.0"
 description = "Python client for Neovim"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "pynvim-0.5.0-py2.py3-none-any.whl", hash = "sha256:2ac197ef0cdfff53719184a45c33cfb7cef88d1c9bf7f0525c21b3239cb5365f"},
     {file = "pynvim-0.5.0.tar.gz", hash = "sha256:e80a11f6f5d194c6a47bea4135b90b55faca24da3544da7cf4a5f7ba8fb09215"},
@@ -1052,6 +1111,7 @@ version = "3.1.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
+groups = ["main"]
 files = [
     {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
     {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
@@ -1066,6 +1126,7 @@ version = "5.4.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.5"
+groups = ["dev"]
 files = [
     {file = "pytest-5.4.3-py3-none-any.whl", hash = "sha256:5c0db86b698e8f170ba4582a492248919255fcd4c79b1ee64ace34301fb589a1"},
     {file = "pytest-5.4.3.tar.gz", hash = "sha256:7979331bfcba207414f5e1263b5a0f8f521d0f457318836a7355531ed1a4c7d8"},
@@ -1091,6 +1152,7 @@ version = "1.1.0"
 description = "Black plugin for the Python LSP Server"
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "python-lsp-black-1.1.0.tar.gz", hash = "sha256:4f665aca0fd1611f9e2a4c1ea09de8809810bbe5013eeee5dfb8796c90a12d4c"},
     {file = "python_lsp_black-1.1.0-py3-none-any.whl", hash = "sha256:1d2a9eb1f46c28cb994b22bfd1463a90d4779ad314d12db65d91940b0f1bd137"},
@@ -1110,6 +1172,7 @@ version = "1.1.2"
 description = "JSON RPC 2.0 server library"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "python-lsp-jsonrpc-1.1.2.tar.gz", hash = "sha256:4688e453eef55cd952bff762c705cedefa12055c0aec17a06f595bcc002cc912"},
     {file = "python_lsp_jsonrpc-1.1.2-py3-none-any.whl", hash = "sha256:7339c2e9630ae98903fdaea1ace8c47fba0484983794d6aafd0bd8989be2b03c"},
@@ -1127,6 +1190,7 @@ version = "1.2.4"
 description = "Python Language Server for the Language Server Protocol"
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "python-lsp-server-1.2.4.tar.gz", hash = "sha256:007278c4419339bd3a61ca6d7eb8648ead28b5f1b9eba3b6bae8540046116335"},
     {file = "python_lsp_server-1.2.4-py3-none-any.whl", hash = "sha256:a163907c83ba7bae6b45a9bc9e407b7001fbed7c7561d032a5fd355ae6fae42c"},
@@ -1167,6 +1231,7 @@ version = "1.3.1"
 description = "Python tool configuration"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pytoolconfig-1.3.1-py3-none-any.whl", hash = "sha256:5d8cea8ae1996938ec3eaf44567bbc5ef1bc900742190c439a44a704d6e1b62b"},
     {file = "pytoolconfig-1.3.1.tar.gz", hash = "sha256:51e6bd1a6f108238ae6aab6a65e5eed5e75d456be1c2bf29b04e5c1e7d7adbae"},
@@ -1189,6 +1254,7 @@ version = "1.3.9"
 description = "Fast and direct raster I/O for use with Numpy and SciPy"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "rasterio-1.3.9-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:04247da9f4002587ac2bec967c3a72f63fc0e6654101c06850bae3d8131b700d"},
     {file = "rasterio-1.3.9-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c9edce37b70f4cd4be5d3f5d314877e3130aeebb612120405cd28f83fe200865"},
@@ -1225,12 +1291,12 @@ setuptools = "*"
 snuggs = ">=1.4.1"
 
 [package.extras]
-all = ["boto3 (>=1.2.4)", "ghp-import", "hypothesis", "ipython (>=2.0)", "matplotlib", "numpydoc", "packaging", "pytest (>=2.8.2)", "pytest-cov (>=2.2.0)", "shapely", "sphinx", "sphinx-rtd-theme"]
+all = ["boto3 (>=1.2.4)", "ghp-import", "hypothesis", "ipython (>=2.0)", "matplotlib", "numpydoc", "packaging", "pytest (>=2.8.2)", "pytest-cov (>=2.2.0)", "shapely ; python_version < \"3.12\"", "sphinx", "sphinx-rtd-theme"]
 docs = ["ghp-import", "numpydoc", "sphinx", "sphinx-rtd-theme"]
 ipython = ["ipython (>=2.0)"]
 plot = ["matplotlib"]
 s3 = ["boto3 (>=1.2.4)"]
-test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest (>=2.8.2)", "pytest-cov (>=2.2.0)", "shapely"]
+test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest (>=2.8.2)", "pytest-cov (>=2.2.0)", "shapely ; python_version < \"3.12\""]
 
 [[package]]
 name = "rope"
@@ -1238,6 +1304,7 @@ version = "1.12.0"
 description = "a python refactoring library..."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "rope-1.12.0-py3-none-any.whl", hash = "sha256:01f06624159e6b2ec9b94412d519e8877a19eeabe392f469c36f7236df05d443"},
     {file = "rope-1.12.0.tar.gz", hash = "sha256:93a1bb991fbf0426e8d415102d1c092ccc42e826ce9a42c4d61ce53d7786d9d9"},
@@ -1257,6 +1324,7 @@ version = "0.8.3"
 description = "R-Tree spatial index for Python GIS"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "Rtree-0.8.3-py2-none-any.whl", hash = "sha256:8526431aa15d8cea1c07b451ce853b62b1da4cf6b74c07810aba5b81d12efe66"},
     {file = "Rtree-0.8.3-py3-none-any.whl", hash = "sha256:a9e67386073f93f22449f396d5993dfe479335169c376f3f7fb04a396391f0dc"},
@@ -1272,6 +1340,7 @@ version = "69.0.3"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev"]
 files = [
     {file = "setuptools-69.0.3-py3-none-any.whl", hash = "sha256:385eb4edd9c9d5c17540511303e39a147ce2fc04bc55289c322b9e5904fe2c05"},
     {file = "setuptools-69.0.3.tar.gz", hash = "sha256:be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78"},
@@ -1279,71 +1348,16 @@ files = [
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
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-    {file = "Shapely-1.8.5.post1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:78fb9d929b8ee15cfd424b6c10879ce1907f24e05fb83310fc47d2cd27088e40"},
-    {file = "Shapely-1.8.5.post1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:89164e7a9776a19e29f01369a98529321994e2e4d852b92b7e01d4d9804c55bf"},
-    {file = "Shapely-1.8.5.post1-cp39-cp39-win32.whl", hash = "sha256:8e59817b0fe63d34baedaabba8c393c0090f061917d18fc0bcc2f621937a8f73"},
-    {file = "Shapely-1.8.5.post1-cp39-cp39-win_amd64.whl", hash = "sha256:e9c30b311de2513555ab02464ebb76115d242842b29c412f5a9aa0cac57be9f6"},
-    {file = "Shapely-1.8.5.post1.tar.gz", hash = "sha256:ef3be705c3eac282a28058e6c6e5503419b250f482320df2172abcbea642c831"},
-]
-
-[package.extras]
-all = ["numpy", "pytest", "pytest-cov"]
-test = ["pytest", "pytest-cov"]
-vectorized = ["numpy"]
-
 [[package]]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["main", "dev"]
 files = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -1355,6 +1369,7 @@ version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
     {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
@@ -1366,6 +1381,7 @@ version = "1.4.7"
 description = "Snuggs are s-expressions for Numpy"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "snuggs-1.4.7-py3-none-any.whl", hash = "sha256:988dde5d4db88e9d71c99457404773dabcc7a1c45971bfbe81900999942d9f07"},
     {file = "snuggs-1.4.7.tar.gz", hash = "sha256:501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b"},
@@ -1384,6 +1400,7 @@ version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
     {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
@@ -1403,6 +1420,7 @@ version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["dev"]
 files = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
@@ -1414,6 +1432,7 @@ version = "2.0.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
@@ -1425,6 +1444,7 @@ version = "5.14.1"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "traitlets-5.14.1-py3-none-any.whl", hash = "sha256:2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74"},
     {file = "traitlets-5.14.1.tar.gz", hash = "sha256:8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e"},
@@ -1440,6 +1460,8 @@ version = "4.9.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
+markers = "python_version < \"3.10\""
 files = [
     {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
     {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
@@ -1451,6 +1473,7 @@ version = "5.9.0"
 description = "Ultra fast JSON encoder and decoder for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "ujson-5.9.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ab71bf27b002eaf7d047c54a68e60230fbd5cd9da60de7ca0aa87d0bccead8fa"},
     {file = "ujson-5.9.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:7a365eac66f5aa7a7fdf57e5066ada6226700884fc7dce2ba5483538bc16c8c5"},
@@ -1525,6 +1548,7 @@ version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
     {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
@@ -1536,6 +1560,7 @@ version = "1.12.1"
 description = "Module for decorators, wrappers and monkey patching."
 optional = false
 python-versions = "*"
+groups = ["dev"]
 files = [
     {file = "wrapt-1.12.1.tar.gz", hash = "sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"},
 ]
@@ -1546,6 +1571,7 @@ version = "0.40.2"
 description = "A formatter for Python code"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "yapf-0.40.2-py3-none-any.whl", hash = "sha256:adc8b5dd02c0143108878c499284205adb258aad6db6634e5b869e7ee2bd548b"},
     {file = "yapf-0.40.2.tar.gz", hash = "sha256:4dab8a5ed7134e26d57c1647c7483afb3f136878b579062b786c9ba16b94637b"},
@@ -1562,16 +1588,18 @@ version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev"]
 files = [
     {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
     {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
+markers = {main = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\"", "pytest-ruff"]
 
 [metadata]
-lock-version = "2.0"
+lock-version = "2.1"
 python-versions = "^3.8"
-content-hash = "07a6a34a534ac6229a9dba81e4fcd47d39017999aa311c40f443bb1811f476e7"
+content-hash = "7d6da9988fc2582ebfed8a651c76f4badbd1c008b259f43f4df90c469240a52f"
diff --git a/pyproject.toml b/pyproject.toml
index 50309d63..f1cb99d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,6 @@ Fiona = "^1.9"
 jinja2 = "^3.0"
 numpy = "^1.16"
 rasterio = "^1.0"
-shapely = "^1.6"
 rtree = "^0.8"
 
 [tool.poetry.dev-dependencies]
diff --git a/pythia/io.py b/pythia/io.py
index 6663f4c4..110be715 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -4,8 +4,6 @@
 import fiona
 import numpy.ma as ma
 import rasterio
-from shapely.geometry import Point, MultiPoint
-from shapely.ops import nearest_points
 from pythia.gis import euclidean_distance
 
 import pythia.functions

From ebaee24ba992fcd5f1b5ecb01d7c7180c83b70ce Mon Sep 17 00:00:00 2001
From: "Nathan P. Bombana" <nathan.pbombana@gmail.com>
Date: Sun, 27 Apr 2025 20:06:09 -0300
Subject: [PATCH 100/105] perf: add a lookup map for exact matches on the
 ``io.py/find_closest_vector_coords``.

The following report originates from running this function twice per pixel on Tanzania 10x10 km grid:

BEFORE (4ad13a605fbfe83b00f6ffc3e9914d521daa698a) ->
Performance counter stats for 'python -X perf -m pythia --clean-work-dir --setup test2/pythia-config.json' (3 runs):

      4,435,650.67 msec task-clock                       #   27.544 CPUs utilized               ( +-  0.39% )
           220,607      context-switches                 #   49.735 /sec                        ( +-  3.27% )
            13,995      cpu-migrations                   #    3.155 /sec                        ( +-  0.83% )
           222,164      page-faults                      #   50.086 /sec                        ( +-  0.21% )
22,727,605,668,167      instructions                     #    1.28  insn per cycle
                                                  #    0.28  stalled cycles per insn     ( +-  0.06% )
17,736,864,542,617      cycles                           #    3.999 GHz                         ( +-  0.39% )
 6,306,883,751,606      stalled-cycles-frontend          #   35.56% frontend cycles idle        ( +-  0.86% )
 4,876,195,822,590      branches                         #    1.099 G/sec                       ( +-  0.06% )
    41,536,653,902      branch-misses                    #    0.85% of all branches             ( +-  1.52% )

           161.038 +- 0.870 seconds time elapsed  ( +-  0.54% )

AFTER ->
Performance counter stats for 'python -X perf -m pythia --clean-work-dir --setup test2/pythia-config.json' (3 runs):

        919,616.65 msec task-clock                       #   26.100 CPUs utilized               ( +-  0.14% )
           143,583      context-switches                 #  156.134 /sec                        ( +-  4.34% )
             8,313      cpu-migrations                   #    9.040 /sec                        ( +-  5.51% )
           259,900      page-faults                      #  282.618 /sec                        ( +-  0.11% )
 6,434,303,689,973      instructions                     #    1.75  insn per cycle
                                                  #    0.12  stalled cycles per insn     ( +-  0.01% )
 3,674,947,238,272      cycles                           #    3.996 GHz                         ( +-  0.14% )
   750,853,165,462      stalled-cycles-frontend          #   20.43% frontend cycles idle        ( +-  0.51% )
 1,430,992,318,806      branches                         #    1.556 G/sec                       ( +-  0.01% )
     7,936,273,176      branch-misses                    #    0.55% of all branches             ( +-  1.64% )

            35.234 +- 0.108 seconds time elapsed  ( +-  0.31% )
---
 pythia/io.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/pythia/io.py b/pythia/io.py
index 110be715..ace368b9 100644
--- a/pythia/io.py
+++ b/pythia/io.py
@@ -4,6 +4,8 @@
 import fiona
 import numpy.ma as ma
 import rasterio
+from functools import cache
+from typing import Any, Dict, Tuple
 from pythia.gis import euclidean_distance
 
 import pythia.functions
@@ -77,6 +79,27 @@ def get_shp_profile(f):
     pass
 
 
+@cache
+def index_points_ids(file: str, id_field: str) -> Dict[Tuple[float, float], Any]:
+    """
+    Create a mapping of (lon, lat) coordinates to feature IDs from a GIS file.
+
+    :param file: Path to the GIS file (e.g., Shapefile, GeoJSON).
+    :param id_field: Property field name whose values are mapped to coordinates.
+    :returns: A dictionary with (longitude, latitude) keys and `id_field` values.
+    """
+    coords_map = {}
+    with fiona.open(file, "r") as source:
+        for feature in source:
+            if feature["geometry"]["type"] == "MultiPoint":
+                for coords in feature["geometry"]["coordinates"]:
+                    coords_map[(coords[0], coords[1])] = feature["properties"][id_field]
+            if feature["geometry"]["type"] == "Point":
+                coords = feature["geometry"]["coordinates"]
+                coords_map[(coords[0], coords[1])] = feature["properties"][id_field]
+    return coords_map
+
+
 def extract_vector_coords(f):
     points = []
     with fiona.open(f, "r") as source:
@@ -101,6 +124,10 @@ def find_vector_coords(f, lng, lat, a):
 
 
 def find_closest_vector_coords(f, lng, lat, a):
+    lookup = index_points_ids(f, a)[(lng, lat)]
+    if lookup is not None:
+        return lookup
+
     closest_id = None
     with fiona.open(f, "r") as source:
         closest_distance = sys.float_info.max

From 8d162b6502a88a85e609cf9a0d5c714470ffe08f Mon Sep 17 00:00:00 2001
From: Felipe <felipemarostega.ff@gmail.com>
Date: Mon, 28 Apr 2025 18:18:54 -0300
Subject: [PATCH 101/105] fix: fix get_vector_resolution inferring the y
 resolution to zero

---
 pythia/rescale.py | 77 ++++++++++++++++++++++++++++++++---------------
 1 file changed, 52 insertions(+), 25 deletions(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index 1a848da2..c23a5928 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -15,35 +15,61 @@ def get_raster_resolution(file_path):
     with rasterio.open(file_path, 'r') as raster:
         return [round(raster.profile['transform'][0], 6), round(raster.profile['transform'][4], 6)]
 
-
 def get_vector_resolution(file_path):
     with fiona.open(file_path, 'r') as src:
         min_x_dist, min_y_dist = None, None
-        if src[0]['geometry']['type'] == 'Polygon':
-            x_min, y_min, x_max, y_min = None, None
-            for coords in src[0]['geometry']['coordinates']:
-                if x_min is None or coords[0] < x_min:
-                    x_min = coords[0]
-                if x_max is None or x_max < coords[0]:
-                    x_max = coords[0]
-                if y_min is None or coords[1] < y_min:
-                    y_min = coords[1]
-                if y_max is None or y_max < coords[1]:
-                    y_max = coords[1]
-            x_dist = x_max - x_min
-            y_dist = y_max - y_min
-            return (x_dist, y_dist)
+        
+        points = [feature['geometry']['coordinates'] for feature in src]
+
+        for i in range(len(points) - 1):
+            x1, y1 = points[i]
+            x2, y2 = points[i + 1]
+
+            x_diff = abs(x2 - x1)
+            y_diff = abs(y2 - y1)
+
+            if x_diff > 0:
+                if min_x_dist is None or x_diff < min_x_dist:
+                    min_x_dist = x_diff
+            if y_diff > 0:
+                if min_y_dist is None or y_diff < min_y_dist:
+                    min_y_dist = y_diff
+
+        if (min_x_dist not in (None, 0)) and (min_y_dist not in (None, 0)): #if min_x_dist is not None and min_y_dist is not None:
+            #return [round(min_x_dist, 6), round(min_y_dist, 6)] # acredito que o problema seja que o valor de y é tao pequeno que usando o round com 6 casas ele vira 0
+            return [(min_x_dist), (min_y_dist)]
         else:
-            for i in range(len(src) - 1):
-                x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i + 1]['geometry']['coordinates'][0])
-                y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i + 1]['geometry']['coordinates'][1])
-                if 0 < x_dist:
-                    if min_x_dist is None or x_dist < min_x_dist:
-                        min_x_dist = x_dist
-                if 0 < y_dist:
-                    if min_y_dist is None or y_dist < min_y_dist:
-                        min_y_dist = y_dist
-            return [round(min_x_dist, 6), round(min_y_dist, 6)]
+            return None, None
+
+
+# def get_vector_resolution(file_path):
+#     with fiona.open(file_path, 'r') as src:
+#         min_x_dist, min_y_dist = None, None
+#         if src[0]['geometry']['type'] == 'Polygon':
+#             x_min, y_min, x_max, y_max = None, None, None, None
+#             for coords in src[0]['geometry']['coordinates']:
+#                 if x_min is None or coords[0] < x_min:
+#                     x_min = coords[0]
+#                 if x_max is None or x_max < coords[0]:
+#                     x_max = coords[0]
+#                 if y_min is None or coords[1] < y_min:
+#                     y_min = coords[1]
+#                 if y_max is None or y_max < coords[1]:
+#                     y_max = coords[1]
+#             x_dist = x_max - x_min
+#             y_dist = y_max - y_min
+#             return (x_dist, y_dist)
+#         else:
+#             for i in range(len(src) - 1):
+#                 x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i + 1]['geometry']['coordinates'][0]) #is the x value of the geometry point 
+#                 y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i + 1]['geometry']['coordinates'][1]) #is the y value of the geometry point 
+#                 if 0 < x_dist:
+#                     if min_x_dist is None or x_dist < min_x_dist:
+#                         min_x_dist = x_dist
+#                 if 0 < y_dist:
+#                     if min_y_dist is None or y_dist < min_y_dist:
+#                         min_y_dist = y_dist
+#            return [round(min_x_dist, 6), round(min_y_dist, 6)]
 
 
 def change_raster_resolution(file_path, scale_factor, config, dst_path=None, need_val_scaling=False):
@@ -109,6 +135,7 @@ def change_raster_resolution(file_path, scale_factor, config, dst_path=None, nee
     return dst_path
 
 
+
 def change_vector_resolution(file_path, scale_factor, config, current_res, dst_path=None):
     """
     Rescale the original file by a defined factor.

From 70274363f02361932657fc1b784d0a7d3ac26d25 Mon Sep 17 00:00:00 2001
From: Felipe <felipemarostega.ff@gmail.com>
Date: Wed, 30 Apr 2025 22:42:48 -0300
Subject: [PATCH 102/105] fix: fix get_vector_resolution not considering
 polygon shapes

---
 pythia/rescale.py | 81 ++++++++++++++++++-----------------------------
 1 file changed, 30 insertions(+), 51 deletions(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index c23a5928..fe5e3696 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -18,58 +18,37 @@ def get_raster_resolution(file_path):
 def get_vector_resolution(file_path):
     with fiona.open(file_path, 'r') as src:
         min_x_dist, min_y_dist = None, None
-        
-        points = [feature['geometry']['coordinates'] for feature in src]
-
-        for i in range(len(points) - 1):
-            x1, y1 = points[i]
-            x2, y2 = points[i + 1]
-
-            x_diff = abs(x2 - x1)
-            y_diff = abs(y2 - y1)
-
-            if x_diff > 0:
-                if min_x_dist is None or x_diff < min_x_dist:
-                    min_x_dist = x_diff
-            if y_diff > 0:
-                if min_y_dist is None or y_diff < min_y_dist:
-                    min_y_dist = y_diff
-
-        if (min_x_dist not in (None, 0)) and (min_y_dist not in (None, 0)): #if min_x_dist is not None and min_y_dist is not None:
-            #return [round(min_x_dist, 6), round(min_y_dist, 6)] # acredito que o problema seja que o valor de y é tao pequeno que usando o round com 6 casas ele vira 0
-            return [(min_x_dist), (min_y_dist)]
+        if src[0]['geometry']['type'] == 'Polygon':
+            x_min, y_min, x_max, y_max = None, None, None, None
+            for coords in src[0]['geometry']['coordinates']:
+                if x_min is None or coords[0] < x_min:
+                    x_min = coords[0]
+                if x_max is None or x_max < coords[0]:
+                    x_max = coords[0]
+                if y_min is None or coords[1] < y_min:
+                    y_min = coords[1]
+                if y_max is None or y_max < coords[1]:
+                    y_max = coords[1]
+            x_dist = x_max - x_min
+            y_dist = y_max - y_min
+            return (x_dist, y_dist)
         else:
-            return None, None
-
-
-# def get_vector_resolution(file_path):
-#     with fiona.open(file_path, 'r') as src:
-#         min_x_dist, min_y_dist = None, None
-#         if src[0]['geometry']['type'] == 'Polygon':
-#             x_min, y_min, x_max, y_max = None, None, None, None
-#             for coords in src[0]['geometry']['coordinates']:
-#                 if x_min is None or coords[0] < x_min:
-#                     x_min = coords[0]
-#                 if x_max is None or x_max < coords[0]:
-#                     x_max = coords[0]
-#                 if y_min is None or coords[1] < y_min:
-#                     y_min = coords[1]
-#                 if y_max is None or y_max < coords[1]:
-#                     y_max = coords[1]
-#             x_dist = x_max - x_min
-#             y_dist = y_max - y_min
-#             return (x_dist, y_dist)
-#         else:
-#             for i in range(len(src) - 1):
-#                 x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i + 1]['geometry']['coordinates'][0]) #is the x value of the geometry point 
-#                 y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i + 1]['geometry']['coordinates'][1]) #is the y value of the geometry point 
-#                 if 0 < x_dist:
-#                     if min_x_dist is None or x_dist < min_x_dist:
-#                         min_x_dist = x_dist
-#                 if 0 < y_dist:
-#                     if min_y_dist is None or y_dist < min_y_dist:
-#                         min_y_dist = y_dist
-#            return [round(min_x_dist, 6), round(min_y_dist, 6)]
+            points = [feature['geometry']['coordinates'] for feature in src]
+            for i in range(len(points) - 1):
+                x1, y1 = points[i]
+                x2, y2 = points[i + 1]
+                x_diff = abs(x2 - x1)
+                y_diff = abs(y2 - y1)
+                if x_diff > 0:
+                    if min_x_dist is None or x_diff < min_x_dist:
+                        min_x_dist = x_diff
+                if y_diff > 0:
+                    if min_y_dist is None or y_diff < min_y_dist:
+                        min_y_dist = y_diff
+            if (min_x_dist not in (None, 0)) and (min_y_dist not in (None, 0)): 
+                return [(min_x_dist), (min_y_dist)]
+            else:
+                return None, None
 
 
 def change_raster_resolution(file_path, scale_factor, config, dst_path=None, need_val_scaling=False):

From 6edec703c17deb25eb6d4f743a68c95fd0eee03c Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Wed, 7 May 2025 16:39:48 -0400
Subject: [PATCH 103/105] Added documentation for debugging

---
 pythia/rescale.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index 1a848da2..11ec842f 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -16,9 +16,12 @@ def get_raster_resolution(file_path):
         return [round(raster.profile['transform'][0], 6), round(raster.profile['transform'][4], 6)]
 
 
+# Decides that a vector file is desired
 def get_vector_resolution(file_path):
     with fiona.open(file_path, 'r') as src:
         min_x_dist, min_y_dist = None, None
+
+        # Check if the geometry is a polygon or points
         if src[0]['geometry']['type'] == 'Polygon':
             x_min, y_min, x_max, y_min = None, None
             for coords in src[0]['geometry']['coordinates']:
@@ -33,16 +36,21 @@ def get_vector_resolution(file_path):
             x_dist = x_max - x_min
             y_dist = y_max - y_min
             return (x_dist, y_dist)
+        
+        # Otherwise the file contains many separate points
         else:
             for i in range(len(src) - 1):
+                # Calculate the x and y distances between the two points
                 x_dist = abs(src[i]['geometry']['coordinates'][0] - src[i + 1]['geometry']['coordinates'][0])
                 y_dist = abs(src[i]['geometry']['coordinates'][1] - src[i + 1]['geometry']['coordinates'][1])
+                
+                # Record minimum & non-zero resolutions
                 if 0 < x_dist:
                     if min_x_dist is None or x_dist < min_x_dist:
                         min_x_dist = x_dist
                 if 0 < y_dist:
                     if min_y_dist is None or y_dist < min_y_dist:
-                        min_y_dist = y_dist
+                        min_y_dist = y_dist # <- 0,083333 is the desired value here
             return [round(min_x_dist, 6), round(min_y_dist, 6)]
 
 

From 8b14366ea09c19fbd8074c34e55185f84159eeaf Mon Sep 17 00:00:00 2001
From: Virginia Covert <66711984+VirginiaBee47@users.noreply.github.com>
Date: Thu, 5 Jun 2025 16:18:10 -0400
Subject: [PATCH 104/105] Update issue templates

---
 .github/ISSUE_TEMPLATE/improvement-task.md | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 .github/ISSUE_TEMPLATE/improvement-task.md

diff --git a/.github/ISSUE_TEMPLATE/improvement-task.md b/.github/ISSUE_TEMPLATE/improvement-task.md
new file mode 100644
index 00000000..956fcc60
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/improvement-task.md
@@ -0,0 +1,20 @@
+---
+name: Improvement Task
+about: Suggest an idea for this project
+title: "[TASK]"
+labels: ''
+assignees: felipe-mf, VirginiaBee47
+
+---
+
+# Task Title
+
+Description: Task Description
+
+
+Measurement Criteria: 
+- Criterion #1
+- Criterion #2
+
+Timeline:
+- List dates of past progress and planned future updates.

From d517f50bbc1531e2e807b7dd6c281df41c2db7fa Mon Sep 17 00:00:00 2001
From: Virginia Covert <virginiacovert454@gmail.com>
Date: Thu, 14 Aug 2025 14:46:51 -0400
Subject: [PATCH 105/105] Removed formatting in rescale script.

---
 pythia/rescale.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pythia/rescale.py b/pythia/rescale.py
index fe5e3696..591e8e16 100644
--- a/pythia/rescale.py
+++ b/pythia/rescale.py
@@ -37,8 +37,8 @@ def get_vector_resolution(file_path):
             for i in range(len(points) - 1):
                 x1, y1 = points[i]
                 x2, y2 = points[i + 1]
-                x_diff = abs(x2 - x1)
-                y_diff = abs(y2 - y1)
+                x_diff = abs(x2 - x1)  # Can we add a round() here and...
+                y_diff = abs(y2 - y1)  # here?
                 if x_diff > 0:
                     if min_x_dist is None or x_diff < min_x_dist:
                         min_x_dist = x_diff