JMLR MLOSS revision: capabilities docs, uv migration, paper sync

.github/workflows/code-quality.yml

@@ -2,171 +2,69 @@ name: Code Quality
 
 on:
   push:
-    branches: [ main, dev/jmlr, feature/gpu_fix ]
+    branches: [main]
   pull_request:
-    branches: [ main, dev/jmlr, feature/gpu_fix ]
+    branches: [main]
 
 jobs:
-  code-quality:
+  lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
-
-    - name: Cache pip dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-quality-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-quality-
-          ${{ runner.os }}-pip-
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e ".[dev, security, linting]"
-      # pip install ruff mypy bandit safety
-
-    - name: Check code formatting with Black
-      run: |
-        black --check --diff torchsom/ tests/
-
-    - name: Check import sorting with isort
-      run: |
-        isort --check-only --diff torchsom/ tests/
-
-    - name: Lint with Ruff
-      run: |
-        ruff check torchsom/ tests/ --output-format=github
-
-    - name: Type checking with MyPy
-      run: |
-        mypy torchsom/ --ignore-missing-imports --strict
-      # mypy torchsom/
-      continue-on-error: true
-
-    - name: Check for security issues with Bandit (library code)
-      run: |
-        bandit -r torchsom/ -f json -o bandit-report-library.json --skip B101,B311,B601
-      continue-on-error: true
-
-    - name: Check for security issues with Bandit (tests)
-      run: |
-        bandit -r tests/ -f json -o bandit-report-tests.json --skip B101,B311,B601
-      continue-on-error: true
-
-    # - name: Check for known security vulnerabilities
-    #   run: |
-    #     safety check --json --output safety-report.json
-    #   continue-on-error: true
-
-    - name: Upload security reports
-      uses: actions/upload-artifact@v4
-      if: always()
-      with:
-        name: security-reports
-        path: |
-          bandit-report-library.json
-          bandit-report-tests.json
-        # safety-report.json
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Sync dependencies
+        run: uv sync --extra linting
+
+      - name: Ruff format check
+        run: uv run ruff format --check torchsom/ tests/
+
+      - name: Ruff lint
+        run: uv run ruff check torchsom/ tests/ --output-format=github
+
+      - name: Type checking with mypy
+        run: uv run mypy torchsom/ --ignore-missing-imports
+        continue-on-error: true
 
   docstring-quality:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
-
-    - name: Cache pip dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-quality-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-quality-
-          ${{ runner.os }}-pip-
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e ".[dev, docs]"
-      # pip install pydocstyle interrogate
-
-    - name: Check docstring style
-      run: |
-        pydocstyle torchsom/ --convention=google
-      continue-on-error: true
-
-    - name: Check docstring coverage
-      run: |
-        interrogate torchsom/ --verbose --ignore-init-method --ignore-magic --ignore-module --fail-under=80
-      continue-on-error: true
-
-  complexity-analysis:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
-
-    - name: Cache pip dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-quality-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-quality-
-          ${{ runner.os }}-pip-
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e ".[dev, linting]"
-      # pip install radon
-
-    - name: Analyze code complexity
-      run: |
-        radon cc torchsom/ --show-complexity --min B
-        radon mi torchsom/ --show --min B
-      continue-on-error: true
-
-  check-dependencies:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Sync dependencies
+        run: uv sync --extra docs
+
+      - name: Docstring coverage
+        run: uv run interrogate torchsom/ --verbose --ignore-init-method --ignore-magic --ignore-module --fail-under=80
+        continue-on-error: true
+
+  complexity:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
-
-    - name: Cache pip dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-quality-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-quality-
-          ${{ runner.os }}-pip-
-
-    - name: Install pip-tools
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e ".[security]"
-      # pip install pip-tools
-
-    - name: Check for dependency conflicts
-      run: |
-        pip-compile pyproject.toml --dry-run --verbose
-      continue-on-error: true
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Sync dependencies
+        run: uv sync --extra linting
+
+      - name: Complexity analysis
+        run: |
+          uv run radon cc torchsom/ --show-complexity --min B
+          uv run radon mi torchsom/ --show --min B
+        continue-on-error: true

.github/workflows/docs.yml

@@ -2,30 +2,25 @@ name: Build and Deploy Docs
 
 on:
   push:
-    branches: [main, dev/jmlr, feature/gpu_fix]
+    branches: [main]
 
 jobs:
   build-and-deploy:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
       - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
+        run: uv python install 3.12
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e '.[dev, docs]'
-        # pip install -e '.[dev]'
-        # pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints
+      - name: Sync dependencies
+        run: uv sync --extra dev --extra docs
 
       - name: Build docs
-        run: |
-          cd docs
-          make html
+        run: uv run sphinx-build -b html docs/source/ docs/build/html
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3

.github/workflows/release.yml

@@ -3,7 +3,7 @@ name: Release
 on:
   push:
     tags:
-      - 'v*'
+      - "v*"
 
 jobs:
   test-before-release:
@@ -19,72 +19,60 @@ jobs:
       id-token: write
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
 
-    - name: Cache pip dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-release-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-release-
-          ${{ runner.os }}-pip-
+      - name: Set up Python
+        run: uv python install 3.12
 
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build twine commitizen pygithub
+      - name: Sync release dependencies
+        run: uv sync --extra release
 
-    - name: Generate CHANGELOG
-      run: |
-        if git log $(git describe --tags --abbrev=0)..HEAD --oneline | grep -q .; then
-          cz changelog
-        else
-          echo "No new commits"
-        fi
+      - name: Generate CHANGELOG
+        run: |
+          if git log $(git describe --tags --abbrev=0)..HEAD --oneline | grep -q .; then
+            uv run cz changelog
+          else
+            echo "No new commits"
+          fi
 
-    - name: Commit updated CHANGELOG.md
-      run: |
-        git config user.name "github-actions[bot]"
-        git config user.email "github-actions[bot]@users.noreply.github.com"
-        git add CHANGELOG.md
-        git commit -m "chore: update changelog for $GITHUB_REF_NAME" || echo "No changes to commit"
-        git push origin HEAD:main
+      - name: Commit updated CHANGELOG.md
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add CHANGELOG.md
+          git commit -m "chore: update changelog for $GITHUB_REF_NAME" || echo "No changes to commit"
+          git push origin HEAD:main
 
-    - name: Build package
-      run: |
-        python -m build
+      - name: Build package
+        run: uv build
 
-    - name: Check package
-      run: |
-        twine check dist/*
+      - name: Check package
+        run: uv run twine check dist/*
 
-    - name: Extract changelog
-      id: changelog
-      run: |
-        echo "RELEASE_NOTES<<EOF" >> $GITHUB_ENV
-        sed -n '/## \['"$GITHUB_REF_NAME"'\]/,/^## \[/{/^## \[/b;p}' CHANGELOG.md >> $GITHUB_ENV
-        echo "EOF" >> $GITHUB_ENV
+      - name: Extract changelog
+        id: changelog
+        run: |
+          echo "RELEASE_NOTES<<EOF" >> $GITHUB_ENV
+          sed -n '/## \['"$GITHUB_REF_NAME"'\]/,/^## \[/{/^## \[/b;p}' CHANGELOG.md >> $GITHUB_ENV
+          echo "EOF" >> $GITHUB_ENV
 
-    - name: Create Release with changelog notes
-      uses: actions/create-release@v1.1.4
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-        tag_name: ${{ github.ref_name }}
-        release_name: Release ${{ github.ref }}
-        body: ${{ env.RELEASE_NOTES }}
-        draft: false
-        prerelease: false
+      - name: Create Release
+        uses: actions/create-release@v1.1.4
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref_name }}
+          release_name: Release ${{ github.ref }}
+          body: ${{ env.RELEASE_NOTES }}
+          draft: false
+          prerelease: false
 
-    - name: Publish to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}