test-build-and-publish.yml

name: Test build and publish Cobramod to PyPI
on:
  workflow_dispatch:

  schedule:
    - cron: "0 5 * * 1"

  pull_request:
    types: [ opened, synchronize, reopened, closed ]
    branches:
      - master

jobs:
  lint-format:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: 3.7
      - name: Install dependencies
        run: python -m pip install tox
      - name: Linter
        run: python -m tox -e lint
      - name: Format
        run: python -m tox -e format

  types:
    needs: [ lint-format ]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [ "3.10", "3.11", "3.12" ]
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: python -m pip install tox
      - name: Run type-checking
        run: python -m tox -e types

  build:
    needs: [ types ]
    runs-on: ubuntu-latest
    steps:
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"
          cache: "pip"

      - name: Set up JS & build js
        uses: actions/setup-node@v4
        with:
          node-version: 20

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip setuptools wheel twine build
          yarn install

      - name: Build JS
        run: yarn run vite build
      - name: Build package
        run: python -m build
      - name: Archive package as artifact
        uses: actions/upload-artifact@v4
        with:
          name: cobramod-dist
          path: |
            dist


  unittest:
    needs: [build]
    strategy:
      matrix:
        os: [ ubuntu-latest, macos-latest, windows-latest ]
        python-version: [ "3.10", "3.11", "3.12" ]
    runs-on: ${{ matrix.os}}
    steps:
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip"

      - name: Display Python version
        run: python -c "import sys; print(sys.version)"

      - name: Download package as artifact
        uses: actions/download-artifact@v4
        with:
          name: cobramod-dist
          path: |
            dist

      - name: Install CobraMod & dependencies from wheel
        run: pip install ./dist/cobramod-*.whl

      - name: Install tox
        run: python -m pip install tox

      - name: Setup test suite
        run: tox -vv --notest

      - name: Credentials
        run: echo "${{ secrets.BIOCYC_USER }}\n${{ secrets.BIOCYC_PASS }}" >> credentials.txt

      - name: Run test suite
        run: tox --skip-pkg-install -e py

  build-publish:
    needs: [unittest]
    name: Build and publish the package to PyPI
    if: github.event.pull_request.merged == true && github.event_name != 'schedule'
    runs-on: ubuntu-latest

    steps:
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: "3.10"
        cache: "pip"

    - name: Download package as artifact
      uses: actions/download-artifact@v4
      with:
        name: cobramod-dist
        path: |
          dist    

    - name: Check the package
      run: twine check dist/*

    - name: Publish to PyPI
      env:
        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
      run:
        twine upload --non-interactive dist/*