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: "3.12"
      - 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
    outputs:
      file-path: ${{ steps.path.outputs.file-path }}
    steps:
      - uses: actions/checkout@v4
      - 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 build
          yarn install

      - name: Build JS
        run: yarn run vite build
      - name: Build package
        run: python -m build

      - name: Get file name
        id: path

        run: echo "file-path=$(cd dist && find . -type f -name cobramod-*.whl)" >> "$GITHUB_OUTPUT"

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


  unittest:
    needs: [build]
    strategy:
      max-parallel: 1
      matrix:
        os: [ ubuntu-latest, macos-latest, windows-latest ]
        python-version: [ "3.10", "3.11", "3.12" ]
    runs-on: ${{ matrix.os}}
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - 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

      - name: Install tox
        run: python -m pip install tox-gh>=1.2

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

      - name: Setup test suite
        run: tox -vv --notest --installpkg ${{ needs.build.outputs.file-path }}

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

      - name: Upload coverage reports to Codecov
        if: ${{ ( matrix.python-version == '3.12' ) && ( runner.os == 'Linux' ) }}
        uses: codecov/codecov-action@v4.0.1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}

  publish-to-pypi:
    needs: [unittest]
    name: >-
      Publish Python 🐍 distribution 📦 to PyPI
    if: github.event.pull_request.merged == true && github.event_name != 'schedule'
    runs-on: ubuntu-latest
    environment:
      name: pypi
      url: https://pypi.org/p/cobramod
    permissions:
      id-token: write

    steps:
    - name: Download all the dists
      uses: actions/download-artifact@v4
      with:
        name: cobramod-dist
        path: |
          dist 

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

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

    - name: Publish distribution 📦 to PyPI
      uses: pypa/gh-action-pypi-publish@release/v1