From daefdeecb710163b29017b8baa8190ada57746bc Mon Sep 17 00:00:00 2001
From: John Huddleston <huddlej@gmail.com>
Date: Tue, 6 May 2025 16:32:35 -0700
Subject: [PATCH 1/2] Move OpenCV to an optional dependency

Enables a "slim" installation of the package by making OpenCV an
optional dependency. Users can install OpenCV with the new "full"
variant of the package to get support for model fitting. The default
installation will only support forecasting from an existing model. Since
this latter scenario is the most common use case for popcast and
requires a substantially smaller footprint on disk, this default is what
we'll want for environments like the Nextstrain Docker image.
---
 .github/workflows/python-package.yml |  2 +-
 README.md                            | 18 +++++++++++++-----
 pyproject.toml                       |  4 +++-
 src/popcast/fit.py                   |  7 ++++++-
 4 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 3cf8471..2824924 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -27,7 +27,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        python -m pip install .[test]
+        python -m pip install .[full,test]
     - name: Lint with flake8
       run: |
         # stop the build if there are any warnings or errors.
diff --git a/README.md b/README.md
index 6e4832b..9d28163 100644
--- a/README.md
+++ b/README.md
@@ -4,8 +4,16 @@ See the methods of [Huddleston et al. 2020](https://doi.org/10.7554/eLife.60067)
 
 ## Install
 
+For a full installation with the OpenCV package that's required for model fitting, specify the "full" package dependencies.
+
+``` bash
+python -m pip install 'popcast[full]'
+```
+
+For a smaller installation that only supports forecasting with an existing model, omit the optional package dependency.
+
 ``` bash
-python3 -m pip install popcast
+python -m pip install popcast
 ```
 
 ## Usage
@@ -30,7 +38,7 @@ popcast fit \
 ### Install locally
 
 ``` bash
-python3 -m pip install ".[test]"
+python -m pip install '.[full,test]'
 ```
 
 ### Lint and run tests
@@ -52,17 +60,17 @@ cram --shell=/bin/bash tests/
 Install or upgrade publishing tools.
 
 ``` bash
-python3 -m pip install --upgrade build twine
+python -m pip install --upgrade build twine
 ```
 
 Build the distribution packages.
 
 ``` bash
-python3 -m build
+python -m build
 ```
 
 Upload the distribution packages.
 
 ``` bash
-python3 -m twine upload dist/*
+python -m twine upload dist/*
 ```
diff --git a/pyproject.toml b/pyproject.toml
index 5a3b876..20f6fa1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,13 +20,15 @@ classifiers = [
 
 dependencies = [
     "jellyfish >=0.8.2, ==0.*",
-    "opencv-python >=4.5, ==4.*",
     "numpy >=1.17.0, ==1.*",
     "pandas >=1.2.0, ==1.*",
     "scipy >=1.5.4, ==1.*",
 ]
 
 [project.optional-dependencies]
+full = [
+    "opencv-python >=4.5, ==4.*",
+]
 test = [
     "coverage[toml] >=5.2.1, ==5.*",
     "cram >=0.7, ==0.*",
diff --git a/src/popcast/fit.py b/src/popcast/fit.py
index b1b05a5..02c0e6c 100644
--- a/src/popcast/fit.py
+++ b/src/popcast/fit.py
@@ -1,6 +1,5 @@
 """Fit a model for the given data using the requested predictors and evaluate the model by time series cross-validation.
 """
-import cv2
 import json
 import numpy as np
 import pandas as pd
@@ -418,6 +417,12 @@ def _fit(self, coefficients, X, y, use_l1_penalty=True, calculate_optimal_distan
             error between estimated values using the given coefficients and
             input data and the observed values
         """
+        try:
+            import cv2
+        except ImportError:
+            print("Failed to import cv2 package required for model fitting. Install popcast with OpenCV using \"python -m pip install 'popcast[full]'\".", file=sys.stderr)
+            sys.exit(1)
+
         # Estimate target values.
         y_hat = self.predict(X, coefficients)
 

From d858bec97d5723ca9d89bc4e42f1373df8808cad Mon Sep 17 00:00:00 2001
From: John Huddleston <huddlej@gmail.com>
Date: Wed, 7 May 2025 08:49:09 -0700
Subject: [PATCH 2/2] Bump version to reflect major changes

---
 CHANGES.md              | 6 ++++++
 pyproject.toml          | 2 +-
 src/popcast/__init__.py | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index fadf7be..9fa5b2e 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,11 @@
 # Change log
 
+## 2.0.0
+
+### Major changes
+
+- Make [OpenCV](https://pypi.org/project/opencv-python/) an optional dependency, simplifying installation requirements for forecasting from an existing model. This change requires users to specify the "full" package version at installation to get support for model fitting. [#4](https://github.com/blab/popcast/pull/4) (@huddlej)
+
 ## 1.1.0
 
 ### Features
diff --git a/pyproject.toml b/pyproject.toml
index 20f6fa1..d84775d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "popcast"
-version = "1.1.0"
+version = "2.0.0"
 authors = [
   { name="John Huddleston", email="huddlej@gmail.com" },
 ]
diff --git a/src/popcast/__init__.py b/src/popcast/__init__.py
index c94ec09..2301491 100644
--- a/src/popcast/__init__.py
+++ b/src/popcast/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """John Huddleston"""
 __email__ = 'huddlej@gmail.com'
-__version__ = '1.1.0'
+__version__ = '2.0.0'