Merge pull request #11 from bhklab/katys/add-env-variables

feat: add global environment variables to pixi.toml

Author: strixy16

pixi.toml

@@ -11,6 +11,17 @@ platforms = ["osx-arm64", "linux-64", "win-64", "osx-64"]
 quality = { features = ["quality"], solve-group = "default" }
 docs = { features = ["docs"], solve-group = "default" }
 
+[activation]
+# convenient variables which can be used in scripts
+env.CONFIG = "${PIXI_PROJECT_ROOT}/config"
+env.METADATA = "${PIXI_PROJECT_ROOT}/metadata"
+env.LOGS = "${PIXI_PROJECT_ROOT}/logs"
+env.RAWDATA = "${PIXI_PROJECT_ROOT}/data/rawdata"
+env.PROCDATA = "${PIXI_PROJECT_ROOT}/data/procdata"
+env.RESULTS = "${PIXI_PROJECT_ROOT}/data/results"
+env.SCRIPTS = "${PIXI_PROJECT_ROOT}/workflow/scripts"
+
+
 [dependencies]
 python = ">=3.12"
 ipython = "*"
@@ -33,6 +44,9 @@ readii = ">=1.35.1, <2"
 [target.linux-64.dependencies]
 bioconductor-survcomp = ">=1.56.0,<2"
 
+[tasks]
+example_script = {cmd="python $SCRIPTS/example_script.py"}
+
 ############################################## QUALITY ###############################################
 # Quality includes linting, type checking, and formatting
 [feature.quality.dependencies]

workflow/notebooks/example_notebook.ipynb

@@ -0,0 +1,94 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "442beff9",
+   "metadata": {},
+   "source": [
+    "# Example Notebook\n",
+    "\n",
+    "This is just a quick example showing how to use the template."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "75fde9f9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import logging\n",
+    "\n",
+    "logging.basicConfig(\n",
+    "\tlevel=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s'\n",
+    ")\n",
+    "\n",
+    "logger = logging.getLogger(__name__)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "2d08bd5d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2025-05-09 13:20:53,996 - INFO - PIXI_PROJECT_ROOT: /Users/bhklab/dev/bhklab/testdirs/another-example has 20 files\n",
+      "2025-05-09 13:20:53,997 - INFO - RAWDATA: data/rawdata has 0 files\n",
+      "2025-05-09 13:20:53,998 - INFO - PROCDATA: data/procdata has 0 files\n",
+      "2025-05-09 13:20:53,998 - INFO - SCRIPTS: workflow/scripts has 0 files\n"
+     ]
+    }
+   ],
+   "source": [
+    "import os\n",
+    "from pathlib import Path\n",
+    "\n",
+    "env_dir_variables = [\n",
+    "    'PIXI_PROJECT_ROOT',\n",
+    "    'RAWDATA',\n",
+    "    'PROCDATA',\n",
+    "    'SCRIPTS',\n",
+    "]\n",
+    "\n",
+    "for var in env_dir_variables:\n",
+    "    var_path = Path(os.environ.get(var))\n",
+    "    logger.info(f'{var}: {var_path} has {len(list(var_path.glob(\"*\")))} files')\n",
+    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ac1f9617",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "default",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

workflow/scripts/example_script.py

@@ -0,0 +1,27 @@
+import logging
+import os
+from pathlib import Path
+
+logging.basicConfig(
+	level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s'
+)
+
+logger = logging.getLogger(__name__)
+
+
+def main() -> None:
+	# examples of template defined env variables
+	env_dir_variables = [
+		'RAWDATA',
+		'PROCDATA',
+		'SCRIPTS',
+	]
+
+	for var in env_dir_variables:
+		var_path = Path(os.environ.get(var))
+		logger.info(f'{var}: {var_path} has {len(list(var_path.glob("*")))} files')
+
+
+if __name__ == '__main__':
+	logger.info(f'Starting example script from {Path().cwd()=}')
+	main()