Merge pull request #7 from samsrabin/add-testing

Add testing of relink.py

Author: jedwards4b

.github/workflows/pytest.yml

@@ -0,0 +1,51 @@
+name: Run Tests
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+      fail-fast: false
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+
+    - name: Run tests
+      run: |
+        pytest tests/ -v
+
+    - name: Run tests with coverage
+      if: matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
+      run: |
+        pip install pytest-cov
+        pytest tests/ --cov=. --cov-report=xml --cov-report=term
+
+    - name: Upload coverage reports
+      if: success() && matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: false
+      continue-on-error: true

.gitignore

@@ -0,0 +1 @@
+__pycache__

relink.py

@@ -1,6 +1,15 @@
+"""
+Finds files owned by a specific user in a source directory tree,
+deletes them, and replaces them with symbolic links to the same
+relative path in a target directory tree.
+"""
+
 import os
-import shutil
 import pwd
+import argparse
+
+DEFAULT_SOURCE_ROOT = '/glade/campaign/cesm/cesmdata/cseg/inputdata/'
+DEFAULT_TARGET_ROOT = '/glade/campaign/collections/gdex/data/d651077/cesmdata/inputdata/'
 
 def find_and_replace_owned_files(source_dir, target_dir, username):
     """
@@ -25,10 +34,10 @@ def find_and_replace_owned_files(source_dir, target_dir, username):
 
     print(f"Searching for files owned by '{username}' (UID: {user_uid}) in '{source_dir}'...")
 
-    for dirpath, dirnames, filenames in os.walk(source_dir):
+    for dirpath, _, filenames in os.walk(source_dir):
         for filename in filenames:
             file_path = os.path.join(dirpath, filename)
-            
+
             # Use os.stat().st_uid to get the file's owner UID
             try:
                 if os.path.islink(file_path):
@@ -38,14 +47,14 @@ def find_and_replace_owned_files(source_dir, target_dir, username):
                 file_uid = os.stat(file_path).st_uid
             except FileNotFoundError:
                 continue # Skip if file was deleted during traversal
-            
+
             if file_uid == user_uid:
                 print(f"Found owned file: {file_path}")
 
                 # Determine the relative path and the new link's destination
                 relative_path = os.path.relpath(file_path, source_dir)
                 link_target = os.path.join(target_dir, relative_path)
-                
+
                 # Check if the target file actually exists
                 if not os.path.exists(link_target):
                     print(f"Warning: Corresponding file not found in '{target_dir}' for '{file_path}'. Skipping.")
@@ -73,14 +82,41 @@ def find_and_replace_owned_files(source_dir, target_dir, username):
                     os.rename(link_name+".tmp", link_name)
                     print(f"Error creating symlink for {link_name}: {e}. Skipping.")
 
+def parse_arguments():
+    """
+    Parse command-line arguments.
+
+    Returns:
+        argparse.Namespace: Parsed arguments containing source_root
+                            and target_root.
+    """
+    parser = argparse.ArgumentParser(
+        description=(
+            'Find files owned by a user and replace them with symbolic links to a target directory.'
+        )
+    )
+    parser.add_argument(
+        '--source-root',
+        default=DEFAULT_SOURCE_ROOT,
+        help=(
+            f'The root of the directory tree to search for files (default: {DEFAULT_SOURCE_ROOT})'
+        )
+    )
+    parser.add_argument(
+        '--target-root',
+        default=DEFAULT_TARGET_ROOT,
+        help=(
+            f'The root of the directory tree where files should be moved to '
+            f'(default: {DEFAULT_TARGET_ROOT})'
+        )
+    )
+
+    return parser.parse_args()
+
 if __name__ == '__main__':
     # --- Configuration ---
-    # Replace these with your actual directories and username
-    source_root = '/glade/campaign/cesm/cesmdata/cseg/inputdata/'
-    target_root = '/glade/campaign/collections/gdex/data/d651077/cesmdata/inputdata/'
+    args = parse_arguments()
     my_username = os.environ['USER']
 
     # --- Execution ---
-    find_and_replace_owned_files(source_root, target_root, my_username)
-    
-
+    find_and_replace_owned_files(args.source_root, args.target_root, my_username)

tests/README.md

@@ -0,0 +1 @@
+Test using `pytest` from this dir or repo top-level.

tests/__init__.py

@@ -0,0 +1 @@
+"""Tests package for inputdataTools."""

tests/conftest.py

@@ -0,0 +1,13 @@
+"""
+Pytest configuration and shared fixtures for relink tests.
+"""
+
+import os
+
+import pytest
+
+
+@pytest.fixture(scope="session")
+def workspace_root():
+    """Return the root directory of the workspace."""
+    return os.path.dirname(os.path.dirname(os.path.abspath(__file__)))