feat(codebase): added utils folder from TRTools to core

.devcontainer.json

@@ -18,20 +18,32 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "mamba env create -n core -f dev-env.yml && conda run -n core poetry install",
+	"postCreateCommand": "mamba env create -n core -f dev-env.yml && conda run -n core poetry config virtualenvs.in-project true && conda run -n core poetry install",
 
 	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
-			"extensions": ["ms-python.python"],
+			"extensions": [
+				"ms-python.python",
+				"ms-vscode.live-server",
+				"ms-python.black-formatter"
+			],
 			"settings": {
+				"python.analysis.typeCheckingMode": "strict",
 				"python.condaPath": "/opt/conda/condabin/conda",
-				"python.defaultInterpreterPath": "/opt/conda/envs/core/bin/python",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
-				"python.venvFolders": ["/home/vscode/.cache/pypoetry/virtualenvs"],
+				"python.venvPath": "/workspaces/core/.venv",
+				"python.defaultInterpreterPath": "/workspaces/core/.venv/bin/python",
+				"python.testing.pytestArgs": [
+					"tests"
+				],
+				"python.testing.pytestEnabled": true,
+				"python.testing.unittestEnabled": false,
 				"terminal.integrated.environmentChangesRelaunch": true,
-				"terminal.integrated.hideOnStartup": "always"
+				"editor.defaultFormatter": "ms-python.black-formatter",
+				"terminal.integrated.hideOnStartup": "always",
+				"files.eol": "\n"
 			}
 		}
 	}

.github/workflows/tests.yml

@@ -22,7 +22,8 @@ jobs:
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
           # - { python: "3.11", os: "windows-latest", session: "tests" }
-          - { python: "3.8", os: "macos-latest", session: "tests" }
+          - { python: "3.9", os: "macos-13", session: "tests" }
+          - { python: "3.11", os: "macos-latest", session: "tests" }
           - { python: "3.8", os: "ubuntu-latest", session: "size" }
           - { python: "3.8", os: "ubuntu-latest", session: "coverage" }
 
@@ -86,7 +87,7 @@ jobs:
         run: |
           export NOXSESSION=tests
           # check that code coverage is not lower than specific percent
-          nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=93
+          nox --verbose --python=${{ matrix.python }} -- --cov-fail-under=92.5
 
       - name: Run tests with nox
         if: matrix.session == 'tests' || matrix.session == 'lint'

core/genotypes.py

@@ -13,12 +13,8 @@
 from pysam import VariantFile
 from cyvcf2 import VCF, Variant
 
-try:
-    import trtools.utils.tr_harmonizer as trh
-except ModuleNotFoundError:
-    from . import tr_harmonizer as trh
-
 from .data import Data
+from . import tr_harmonizer as trh
 
 
 class Genotypes(Data):

core/logging.py

@@ -0,0 +1,46 @@
+from __future__ import annotations
+import logging
+
+
+def getLogger(name: str = None, level: str = "ERROR", exact_time=False):
+    """
+    Retrieve a Logger object
+
+    Parameters
+    ----------
+    name : str, optional
+        The name of the logging object
+    level : str, optional
+        The level of verbosity for the logger
+    """
+    if name is None:
+        name = ""
+    else:
+        name = "." + name
+
+    # create logger
+    logger = logging.getLogger("core" + name)
+    logger.setLevel(level)
+
+    # create console handler and set level to debug
+    ch = logging.StreamHandler()
+    ch.setLevel(level)
+
+    # create formatter
+    db_time = (
+        ("|%(asctime)s" + (".%(msecs)03d" if exact_time else ""))
+        if level == "DEBUG"
+        else ""
+    )
+    formatter = logging.Formatter(
+        fmt="[%(levelname)8s" + db_time + "] %(message)s (%(filename)s:%(lineno)s)",
+        datefmt="%H:%M:%S",
+    )
+
+    # add formatter to ch
+    ch.setFormatter(formatter)
+
+    # add ch to logger
+    logger.addHandler(ch)
+
+    return logger