run_tests.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: test package

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

env:
  VERMOUTH_TEST_DSSP: mkdssp
  SKIP_GENERATE_AUTHORS: 1
  SKIP_WRITE_GIT_CHANGELOG: 1

jobs:
  build:
    runs-on: ubuntu-20.04
    
    strategy:
      matrix:
       py_version: ["3.9", "3.10", "3.11", "3.12"]
       include:
         - py_version: "3.9"
           WITH_CODECOV: true
         - py_version: "3.10"
           WITH_CODECOV: true
         - py_version: "3.11"
           WITH_CODECOV: true
         - py_version: "3.12"
           WITH_CODECOV: true

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.py_version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.py_version }}
        cache: pip
        cache-dependency-path: |
          **/setup.cfg
          **/requirements-*.txt
          **/pyproject.toml
    - name: Install dependencies part I
      run: |
        sudo apt-get install dssp
        pip install --upgrade setuptools pip
    - name: Install package and requirements
      run: |
        pip install --upgrade .
        pip install -r requirements-tests.txt
        
    - name: Run pytest with codecoverage
      run: |
        coverage run $(which pytest) -vv --hypothesis-show-statistics
        coverage report
        coverage xml 

    - if: ${{ matrix.WITH_CODECOV }}
      name: Upload coverage codecov   
      uses: codecov/codecov-action@v4 
      with:
            token: ${{ secrets.CODECOV_TOKEN }}
            files: ./coverage.xml
            fail_ci_if_error: true
            verbose: true
            
  lint:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3
      uses: actions/setup-python@v5
      with:
        python-version: '3.x'
        cache: pip
        cache-dependency-path: |
          **/setup.cfg
          **/requirements-*.txt
          **/pyproject.toml
    - name: Install dependencies
      run: |
        pip install --upgrade setuptools pip
        pip install --upgrade .
        pip install -r requirements-tests.txt
    - name: Run pylint 
      run: |
         pylint --disable=fixme --fail-under=8.0 vermouth
         pylint --disable=fixme --fail-under=9.0 bin/martinize2 
         
   
  docs:
      runs-on: ubuntu-latest
      
      steps:
      - uses: actions/checkout@v4
      - name: Set up Python 3
        uses: actions/setup-python@v5
        with:
           python-version: '3.x'
           cache: pip
           cache-dependency-path: |
             **/setup.cfg
             **/requirements-*.txt
             **/pyproject.toml
      - name: Install dependencies
        run: |
          pip install --upgrade setuptools pip
          pip install --upgrade .
          pip install -r requirements-docs.txt
          
      - name: Run docs
        run: | 
          mkdir -p doc/source/_static
          sphinx-build -EnW -b html doc/source/ doc/build/html

  deploy:
    needs: [build, lint, docs]
    runs-on: ubuntu-latest
    environment:
      name: testpypi
      url: https://test.pypi.org/p/vermouth
    permissions:
      id-token: write
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-tags: true
        fetch-depth: 0
    - name: Set up Python 3
      uses: actions/setup-python@v5
      with:
        python-version: '3.11'
        cache: pip
        cache-dependency-path: |
          **/setup.cfg
          **/requirements-*.txt
          **/pyproject.toml
    - name: Install dependencies
      run: |
        pip install --upgrade setuptools pip
        pip install --upgrade .
    - name: Install pypa/build
      run: |
        python3 -m pip install build pbr --user
    - name: Build a binary wheel and a source tarball
      run: python3 -m build --sdist --wheel --outdir dist/
    - name: Publish distribution 📦 to PyPI
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        repository-url: https://test.pypi.org/legacy/