galaxyproject/gxformat2 (opens in new tab)

name: Deploy
on: [push, pull_request]
jobs:
  build_packages:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6
        with:
          persist-credentials: false
      - uses: actions/setup-python@v6
        with:
          python-version: '3.14'
          cache: pip
      - name: Install requirements
        run: |
          python3 -m pip install build twine
      - name: Create and check sdist and wheel packages
        run: make dist
      - uses: actions/upload-artifact@v6
        with:
          name: packages
          path: dist/
  pypi-publish:
    needs: [build_packages]
    name: Upload release to PyPI
    runs-on: ubuntu-latest
    permissions:
      id-token: write
    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'galaxyproject'
    steps:
      - uses: actions/download-artifact@v7
        with:
          name: packages
          path: dist
      - name: Publish to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1

name: Java CI
on: [push, pull_request]
jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v6
      with:
        persist-credentials: false
    - name: Set up Python
      uses: actions/setup-python@v6
      with:
        python-version: '3.9'
        cache: pip
    - name: Install Python dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install -r requirements.txt -r dev-requirements.txt
    - name: Run Python tests to generate workflow examples.
      run: |
        pytest tests/test_lint.py tests/test_cytoscape.py
    - name: Set up JDK
      uses: actions/setup-java@v5
      with:
        distribution: 'temurin'
        java-version: '25'
        cache: 'maven'
    - name: Run Java maven (mvn) tests for generated workflow examples.
      run: |
        cd java
        mvn -B test --file pom.xml

name: Publish gxformat2 Docs
on: [push, pull_request]
concurrency:
  group: docs-${{ github.ref }}
  cancel-in-progress: true
jobs:
  deploy:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v6
      with:
        persist-credentials: false
    - name: Set up Python
      uses: actions/setup-python@v6
      with:
        python-version: '3.13'
        cache: pip
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install -r requirements.txt -r dev-requirements.txt
    - name: Build docs
      run: |
        USE_VENV=0 SKIP_JAVA=1 SKIP_TYPESCRIPT=1 bash build_schema.sh
    - name: Deploy Docs
      if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
      uses: JamesIves/github-pages-deploy-action@releases/v4
      with:
        folder: dist/schema

name: Python CI
on: [push, pull_request]
concurrency:
  group: tox-${{ github.ref }}
  cancel-in-progress: true
jobs:
  build:
    runs-on: ubuntu-latest

    strategy:
      max-parallel: 4
      matrix:
        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']

    steps:
    - uses: actions/checkout@v6
      with:
        persist-credentials: false
    - name: Clone IWC
      if: matrix.python-version == '3.13'
      uses: actions/checkout@v6
      with:
        repository: galaxyproject/iwc
        ref: main
        path: iwc
        persist-credentials: false
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.python-version }}
        allow-prereleases: true
        cache: pip
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip setuptools
        pip install tox tox-gh-actions
    - name: Test with tox
      run: tox
      env:
        GXFORMAT2_TEST_IWC_DIRECTORY: ${{ matrix.python-version == '3.13' && 'iwc' || '' }}

name: TypeScript Continuous integration tests

on: [push, pull_request]

concurrency:
  group: build-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:

  CI:
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: ./typescript
    steps:
      - uses: actions/checkout@v6
        with:
          persist-credentials: false
      - uses: actions/setup-node@v6
        with:
          node-version: '20'
          cache: 'npm'
          cache-dependency-path: typescript/package-lock.json
      - run: node --version
      - run: npm install
      - run: npm test
      - name: Upload coverage to Codecov
        if: github.repository_owner == 'galaxyproject'
        uses: codecov/codecov-action@v5
        with:
          directory: ./typescript
          fail_ci_if_error: true
          flags: unittests
          token: ${{ secrets.CODECOV_TOKEN }}