jupyterlab-biolm 1.0.7__tar.gz

jupyterlab_biolm-1.0.7/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+        node-version: ['18', '20']
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v4
+        with:
+          node-version: ${{ matrix.node-version }}
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install JupyterLab
+        run: |
+          python -m pip install --upgrade pip
+          pip install "jupyterlab>=4.0.0,<5"
+
+      - name: Install Node.js dependencies
+        run: |
+          npm install -g npm
+          npm ci
+
+      - name: Install Python dependencies
+        run: |
+          pip install -e .[dev]
+
+      - name: Build TypeScript
+        run: |
+          npm run clean:lib
+          npm run build:lib
+
+      - name: Build labextension
+        run: |
+          mkdir -p jupyterlab_biolm/labextension
+          JUPYTERLAB_CORE=$(python3 -c "import jupyterlab; import os; print(os.path.join(os.path.dirname(jupyterlab.__file__), 'staging'))")
+          node node_modules/@jupyterlab/builder/lib/build-labextension.js . --core-path "$JUPYTERLAB_CORE"
+
+      - name: Verify labextension files
+        run: |
+          if [ ! -f "jupyterlab_biolm/labextension/package.json" ]; then
+            echo "ERROR: package.json not found in labextension directory"
+            exit 1
+          fi
+          if [ ! -f "jupyterlab_biolm/labextension/static/style.js" ]; then
+            echo "ERROR: style.js not found in labextension/static directory"
+            exit 1
+          fi
+          echo "✅ Labextension files verified"
+
+      - name: Install build dependencies
+        run: |
+          pip install build hatchling hatch-nodejs-version
+
+      - name: Build Python package (includes pre-built extension)
+        run: |
+          python -m build
+
+      - name: Check package contents
+        run: |
+          pip install check-wheel-contents
+          check-wheel-contents dist/*.whl || true
+
+  version:
+    runs-on: ubuntu-latest
+    needs: test
+    # Only run on pushes to main, but skip if it's a release commit (to avoid loops)
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main' && !contains(github.event.head_commit.message, '[skip ci]')
+    permissions:
+      contents: write # Required to push version bumps and tags
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Required for semantic-release to analyze commits
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Configure Git
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run semantic-release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: npx semantic-release
+

jupyterlab_biolm-1.0.7/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]  # Triggers on manual GitHub releases only
+  workflow_dispatch:  # Allow manual triggering
+    inputs:
+      repository:
+        description: 'Repository to publish to (pypi, testpypi, or empty for testpypi)'
+        required: false
+        default: 'testpypi'
+        type: choice
+        options:
+          - testpypi
+          - pypi
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install JupyterLab
+        run: |
+          python -m pip install --upgrade pip
+          pip install "jupyterlab>=4.0.0,<5"
+
+      - name: Install Node.js dependencies
+        run: |
+          npm install -g npm
+          npm ci
+
+      - name: Build TypeScript
+        run: |
+          npm run clean:lib
+          npm run build:lib
+
+      - name: Install Python package (editable)
+        run: |
+          pip install -e .
+
+      - name: Build labextension
+        run: |
+          mkdir -p jupyterlab_biolm/labextension
+          JUPYTERLAB_CORE=$(python3 -c "import jupyterlab; import os; print(os.path.join(os.path.dirname(jupyterlab.__file__), 'staging'))")
+          node node_modules/@jupyterlab/builder/lib/build-labextension.js . --core-path "$JUPYTERLAB_CORE"
+
+      - name: Verify labextension files
+        run: |
+          if [ ! -f "jupyterlab_biolm/labextension/package.json" ]; then
+            echo "ERROR: package.json not found in labextension directory"
+            exit 1
+          fi
+          if [ ! -f "jupyterlab_biolm/labextension/static/style.js" ]; then
+            echo "ERROR: style.js not found in labextension/static directory"
+            exit 1
+          fi
+          echo "✅ Labextension files verified"
+
+      - name: Build Python package (includes pre-built extension)
+        run: |
+          pip install build hatchling hatch-nodejs-version
+          python -m build
+
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+          retention-days: 7
+
+  publish-testpypi:
+    runs-on: ubuntu-latest
+    needs: build
+    if: github.event_name == 'workflow_dispatch' && (github.event.inputs.repository == 'testpypi' || github.event.inputs.repository == '') || github.event_name == 'release' && contains(github.event.release.tag_name, 'rc')
+    environment:
+      name: testpypi
+    permissions:
+      id-token: write  # Required for TestPyPI trusted publishing
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+
+      - name: Publish package to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    runs-on: ubuntu-latest
+    needs: build
+    if: github.event_name == 'release' && !contains(github.event.release.tag_name, 'rc') || github.event_name == 'workflow_dispatch' && github.event.inputs.repository == 'pypi'
+    environment:
+      name: pypi
+    permissions:
+      id-token: write  # Required for PyPI trusted publishing
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+

jupyterlab_biolm-1.0.7/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+coverage/
+htmlcov/
+.tox/
+
+# Jupyter
+.ipynb_checkpoints/
+*.ipynb_checkpoints
+*.ipynb
+.jupyter/
+
+# Node
+node_modules/
+npm-debug.log
+yarn-error.log
+lerna-debug.log
+.yarn/
+.pnp.*
+.yarn/cache
+.yarn/unplugged
+.yarn/build-state.yml
+.yarn/install-state.gz
+
+# TypeScript
+*.tsbuildinfo
+lib/
+
+# Lab extension
+jupyterlab_biolm/labextension/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Environment
+.env
+.venv
+env/
+venv/
+.env.local
+.env.*.local
+
+# Logs
+*.log
+logs/
+
+# Cache
+.cache/
+