Merge branch 'feature/test-notebooks-ci' of https://github.com/selmanozleyen/squidpy into feature/test-notebooks-ci

Author: selmanozleyen

.run_notebooks.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import argparse
+import glob
+import os
+import subprocess
+import sys
+
+EPILOG = """
+Examples:
+  python .run_notebooks.py docs/notebooks
+  python .run_notebooks.py /path/to/notebooks --kernel my-kernel
+"""
+
+
+def main() -> None:
+    # Set up argument parser
+    parser = argparse.ArgumentParser(
+        description="Run Jupyter notebooks in specified directories using jupytext",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog=EPILOG,
+    )
+
+    parser.add_argument("base_directory", help="Base directory containing notebook subdirectories")
+
+    parser.add_argument(
+        "-k", "--kernel", default="squidpy", help="Jupyter kernel to use for execution (default: squidpy)"
+    )
+
+    parser.add_argument(
+        "--dry-run", action="store_true", help="Show which notebooks would be run without executing them"
+    )
+
+    args = parser.parse_args()
+
+    # Base directory for notebooks
+    base_dir = args.base_directory
+
+    # Define notebook directories or patterns
+    notebook_patterns = [
+        f"{base_dir}/examples/tools/*.ipynb",
+        f"{base_dir}/examples/plotting/*.ipynb",
+        f"{base_dir}/examples/image/*.ipynb",
+        f"{base_dir}/examples/graph/*.ipynb",
+        # f"{base_dir}/tutorials/*.ipynb"  # don't include because it contains many external modules
+    ]
+
+    # Initialize a list to hold valid notebook paths
+    valid_notebooks = []
+
+    # Gather all valid notebook files from the patterns
+    print("Gathering notebooks...")
+    for pattern in notebook_patterns:
+        for nb_path in glob.glob(pattern):
+            if os.path.isfile(nb_path):  # Check if the file exists
+                valid_notebooks.append(nb_path)  # Add to the list of valid notebooks
+
+    # Check if we have any notebooks to run
+    if len(valid_notebooks) == 0:
+        print("No notebooks found to run.")
+        sys.exit(1)
+
+    # Echo the notebooks that will be run for clarity
+    print("Preparing to run the following notebooks:")
+    for nb in valid_notebooks:
+        print(f"  {nb}")
+
+    # If dry run, exit here
+    if args.dry_run:
+        print(f"\nDry run complete. Would execute {len(valid_notebooks)} notebooks with kernel '{args.kernel}'.")
+        return
+
+    # Initialize a flag to track the success of all commands
+    all_success = True
+
+    # Execute all valid notebooks
+    print(f"\nExecuting notebooks with kernel '{args.kernel}'...")
+    for nb in valid_notebooks:
+        print(f"Running {nb}")
+        try:
+            subprocess.run(["jupytext", "-k", args.kernel, "--execute", nb], check=True)
+        except subprocess.CalledProcessError:
+            print(f"Failed to run {nb}")
+            all_success = False
+
+    # Check if any executions failed
+    if not all_success:
+        print("One or more notebooks failed to execute.")
+        sys.exit(1)
+
+    print("All notebooks executed successfully.")
+
+
+if __name__ == "__main__":
+    main()