made symlink check if the paths are correcly set to shared dir

scripts/actions.sh

@@ -120,32 +120,11 @@ case "$1" in
       # This script creates symbolic links to the shared working directories.
       # 1. Get the path of the private config of the cluster
       # 2. Read the yaml and extract the path of the shared conf
-      # This uses the yq command. It is a python package so uvx (bundled with uv) will donwload and create the right venv
-      export working_dir=$(cat $("$PRIVATE_REPO_PATH"/hpc/platform-env.py hpc-config) | uvx yq .path_shared_working_dir)
-      # Remove quotes
-      export working_dir=$(echo "$working_dir" | sed 's/[\"\x27]//g')
-      # If the working directory does not exist, exit with an error
-      if [ ! -d "$working_dir" ]; then
-        echo "Working directory $working_dir does not exist. Please check the configuration."
-        exit 1
-      fi
-      # Ensure the working directory ends with a slash
-      if [[ "$working_dir" != */ ]]; then
-        working_dir="$working_dir/"
-      fi
-      echo "Working directory: $working_dir"
-      # Create all the links
-      for d in "logs" "models" "output" "plots" "results"
-      do
-        # If the link already exists, do nothing
-        # If a file with the same name exists, skip it
-        if [ -e "$d" ]; then
-          echo "'$d' already exists, skipping. The results in $d will not be linked to the shared working directory."
-          continue
-        fi
-        echo "$d -> $working_dir$d"
-        ln -s "$working_dir$d" "$d"
-      done
+      # A new --fix flag is supported by the Python script to remove incorrect
+      # symlinks automatically; pass it after the command name below.
+      # The Python helper handles config lookup and symlink validation/creation.
+      shift  # consume the "create-links" argument and forward remaining args
+      uv run --no-project python scripts/check_symlinks.py "$@"
     )
     ;;
   create-jupyter-kernel)

scripts/check_symlinks.py

@@ -0,0 +1,102 @@
+#!/usr/bin/env -S uv run
+# /// script
+# dependencies = [ "PyYAML", "GitPython"
+# ]
+# [tool.uv]
+# exclude-newer = "2025-01-01T00:00:00Z"
+# ///
+
+import argparse
+import logging
+import os
+import subprocess
+import sys
+
+import yaml
+
+# parse command-line options
+parser = argparse.ArgumentParser(description="Create symlinks to shared directories")
+parser.add_argument(
+    "--fix",
+    action="store_true",
+    help="automatically remove and recreate any incorrect symlinks",
+)
+args = parser.parse_args()
+
+logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
+logger = logging.getLogger(__name__)
+
+# Change to the repo root directory (parent of scripts/)
+script_dir = os.path.dirname(os.path.abspath(__file__))
+repo_root = os.path.dirname(script_dir)
+os.chdir(repo_root)
+
+# This script creates symbolic links to the shared working directories.
+# 1. Get the path of the private config of the cluster
+# 2. Read the yaml and extract the path of the shared conf
+# This uses the yq command equivalent in Python with PyYAML
+
+# Run the command to get the config file path
+try:
+    result = subprocess.run(
+        ["../WeatherGenerator-private/hpc/platform-env.py", "hpc-config"],
+        capture_output=True,
+        text=True,
+        check=True,
+    )
+    config_file = result.stdout.strip()
+except subprocess.CalledProcessError as e:
+    logger.error(f"Error running platform-env.py: {e}")
+    sys.exit(1)
+
+# Read the YAML file
+try:
+    with open(config_file) as f:
+        data = yaml.safe_load(f)
+    working_dir = data["path_shared_working_dir"]
+except (FileNotFoundError, yaml.YAMLError) as e:
+    logger.error(f"Error reading config file {config_file}: {e}")
+    sys.exit(1)
+
+# Remove quotes
+working_dir = working_dir.strip("\"'").strip()
+
+# If the working directory does not exist, exit with an error
+if not os.path.isdir(working_dir):
+    logger.error(f"Working directory {working_dir} does not exist. Please check the configuration.")
+    sys.exit(1)
+
+# Ensure the working directory ends with a slash
+if not working_dir.endswith("/"):
+    working_dir += "/"
+
+logger.info(f"Working directory: {working_dir}")
+
+# Create all the links
+for d in ["logs", "models", "plots", "results"]:
+    target = working_dir + d
+    # Check if something exists at this path (including broken symlinks)
+    if os.path.islink(d):
+        # It's a symlink - check if it points to the correct target
+        if os.readlink(d) == target and os.path.exists(target):
+            logger.info(f"'{d}' already correctly linked to {target}, skipping.")
+            continue
+        else:
+            logger.warning(f"'{d}' is a symlink BUT IS NOT correctly linked to {target}.")
+            if args.fix:
+                logger.info(f"Removing incorrect symlink '{d}' and recreating it.")
+                os.remove(d)
+                # fall through to create the correct link below
+            else:
+                logger.warning("Run this script with --fix to remove it automatically.")
+                continue
+    elif os.path.exists(d):
+        # It exists but is not a symlink (regular file or directory)
+        logger.warning(
+            f"'{d}' exists as a file/directory (not a symlink), PLEASE REMOVE IT MANUALLY."
+        )
+        continue
+
+    # create link if we didn't continue above
+    logger.info(f"{d} -> {target}")
+    os.symlink(target, d)