Merge pull request #40 from VisLab/indexing_management

Refactoring the actions

Author: VisLab

.github/workflows/black.yaml

@@ -18,16 +18,12 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v6
-        
-      - name: Set up Python
-        uses: actions/setup-python@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.10'
-          
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install codespell tomli
-          
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
+
       - name: Run Codespell
-        run: codespell .
+        run: uvx --with tomli codespell .

.github/workflows/codespell.yaml

@@ -19,45 +19,41 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
-      with:
-        fetch-depth: 0
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
 
-    - name: Set up Python
-      uses: actions/setup-python@v6
-      with:
-        python-version: '3.10'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.10'
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
 
-    - name: Cache dependencies
-      uses: actions/cache@v5
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
+      - name: Create virtual environment
+        run: |
+          uv venv --clear .venv
+          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e .[docs]
+      - name: Install dependencies
+        run: uv pip install -e ".[docs]"
 
-    - name: Configure Git for GitHub Pages
-      run: |
-        git config user.name github-actions
-        git config user.email [email protected]
+      - name: Configure Git for GitHub Pages
+        run: |
+          git config user.name github-actions
+          git config user.email [email protected]
 
-    - name: Build documentation
-      run: |
-        cd docs
-        sphinx-build -b html . _build/html
+      - name: Build documentation
+        run: |
+          sphinx-build -b html docs docs/_build/html
 
-    - name: Setup Pages
-      uses: actions/configure-pages@v5
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
 
-    - name: Upload artifact
-      uses: actions/upload-pages-artifact@v4
-      with:
-        path: ./docs/_build/html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: ./docs/_build/html
 
   #------------------------------------------------
   # Deploy Job: Deploys the built site

.github/workflows/docs.yml

@@ -19,21 +19,24 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v6
 
-      - name: Setup Python
-        uses: actions/setup-python@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: '3.12'
-          cache: 'pip'
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Install dependencies
+      - name: Create virtual environment
         run: |
-          pip install --upgrade pip
-          pip install -e .[docs]
+          uv venv --clear .venv
+          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: uv pip install -e ".[docs]"
 
       - name: Build documentation with Sphinx
         run: |
-          cd docs
-          sphinx-build -b html . _build/html
+          sphinx-build -b html docs docs/_build/html
 
       - name: Link Checker on built documentation
         id: lychee

.github/workflows/links.yml

@@ -18,18 +18,13 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v6
-        
-      - name: Set up Python
-        uses: actions/setup-python@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: '3.12'
-          
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install mdformat==0.7.22 mdformat-myst==0.2.2 mdformat-tables==1.0.0
-          
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
+
       - name: Run mdformat (check only)
-        run: |
-          mdformat --check --wrap no --number docs/
-          mdformat --check --wrap no --number README.md CHANGELOG.md
+        run: uvx --with mdformat-myst mdformat --check --wrap no --number docs/ *.md

.github/workflows/mdformat.yml

@@ -0,0 +1,28 @@
+name: Ruff
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.12"
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
+
+      - name: Run Ruff linter and formatter check
+        run: uvx ruff check . && uvx ruff format --check .

.github/workflows/ruff.yaml

@@ -85,6 +85,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 cover/
 
 
@@ -136,5 +137,11 @@ spec_tests/hed-specification/tests
 spec_tests/hed-examples
 spec_tests/*.json
 
+# Extracted test fixture directories (re-created from zip files during tests)
+tests/data/test_root/
+tests/data/test_root_back1/
+tests/data/test_root_bad/
+tests/data/eeg_ds003645s_hed_remodel/
+
 # GitHub Copilot instructions (project-specific)
 .github/copilot-instructions.md

.gitignore

@@ -54,7 +54,6 @@ dependencies = [
 dev = [
     "ruff>=0.8.0",
     "codespell>=2.2.0",
-    "black[jupyter]>=26.1.0",
     "mdformat>=0.7.0",
     "mdformat-myst>=0.1.5",
 ]
@@ -95,7 +94,7 @@ ignore-words-list = 'te,parms,assertIn'
 [tool.ruff]
 # Target Python 3.10+
 target-version = "py310"
-line-length = 127
+line-length = 120
 
 # Exclude common directories
 exclude = [
@@ -105,6 +104,7 @@ exclude = [
     "__pycache__",
     "build",
     "dist",
+    ".eggs",
     "*.egg-info",
     ".status",
 ]
@@ -152,19 +152,9 @@ max-complexity = 10
 [tool.ruff.lint.isort]
 known-first-party = ["remodeler"]
 
-[tool.black]
-line-length = 127
-target-version = ["py310", "py311", "py312", "py313"]
-exclude = '''
-/(
-    \.git
-  | \.venv
-  | venv
-  | __pycache__
-  | build
-  | dist
-  | \.eggs
-  | .*\.egg-info
-  | \.status
-)/
-'''
+[tool.ruff.format]
+# Match Black defaults
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"

pyproject.toml

@@ -137,7 +137,9 @@ def get_backup_path(self, backup_name, file_name) -> str:
             str:  Full path of the corresponding file in the backup.
 
         """
-        return os.path.realpath(os.path.join(self.backups_path, backup_name, self.BACKUP_ROOT, self.get_file_key(file_name)))
+        return os.path.realpath(
+            os.path.join(self.backups_path, backup_name, self.BACKUP_ROOT, self.get_file_key(file_name))
+        )
 
     def get_file_key(self, file_name):
         file_comp = io_util.get_path_components(self.data_root, file_name) + [os.path.basename(file_name)]
@@ -183,7 +185,9 @@ def _get_backups(self):
                 raise HedFileError("BadBackupPath", f"{backup_root} is not a backup directory.", "")
             if len(os.listdir(backup_root)) != 2:
                 raise HedFileError(
-                    "BadBackupFormat", f"Backup {backup_root} must only contain backup_root and backup_lock.json file.", ""
+                    "BadBackupFormat",
+                    f"Backup {backup_root} must only contain backup_root and backup_lock.json file.",
+                    "",
                 )
             backup_dict, files_not_in_backup, backups_not_in_directory = self._check_backup_consistency(backup)
             if files_not_in_backup:
@@ -216,19 +220,21 @@ def _check_backup_consistency(self, backup_name):
         if not os.path.exists(backup_dict_path):
             raise HedFileError(
                 "BadBackupDictionaryPath",
-                f"Backup dictionary path {backup_dict_path} for backup " f"{backup_name} does not exist so backup invalid",
+                f"Backup dictionary path {backup_dict_path} for backup {backup_name} does not exist so backup invalid",
                 "",
             )
         backup_root_path = os.path.realpath(os.path.join(self.backups_path, backup_name, self.BACKUP_ROOT))
         if not os.path.isdir(backup_root_path):
             raise HedFileError(
                 "BadBackupRootPath",
-                f"Backup root path {backup_root_path} for {backup_name} " f"does not exist so backup invalid",
+                f"Backup root path {backup_root_path} for {backup_name} does not exist so backup invalid",
                 "",
             )
         with open(backup_dict_path, "r") as fp:
             backup_dict = json.load(fp)
-        backup_paths = {os.path.realpath(os.path.join(backup_root_path, backup_key)) for backup_key in backup_dict.keys()}
+        backup_paths = {
+            os.path.realpath(os.path.join(backup_root_path, backup_key)) for backup_key in backup_dict.keys()
+        }
         file_paths = set(io_util.get_file_list(backup_root_path))
         files_not_in_backup = list(file_paths.difference(backup_paths))
         backups_not_in_directory = list(backup_paths.difference(file_paths))