test.yml

name: "Tests"

on:
  push:
    tags:
      - v**
    branches-ignore:
      - "dependabot/**"
      - "sourcery/**"
      - "pre-commit-ci-update-config"
  pull_request:

jobs:
  pre-commit:
    name: Pre-commit
    runs-on: ubuntu-latest
    steps:
      - name: Check out repo
        uses: actions/checkout@v4

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

      - name: Run pre-commit
        uses: pre-commit/action@v3.0.1

  docs:
    name: Build Docs
    runs-on: ubuntu-latest
    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Setup conda
        uses: s-weigand/setup-conda@v1
        with:
          conda-channels: conda-forge
          activate-conda: false

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

      - name: Install dependencies
        run: |
          conda install -y pandoc
          python -m pip install -U pip wheel
          python -m pip install ".[docs]"

      - name: Show installed dependencies
        run: pip freeze

      - name: Build docs
        run: make --directory=docs clean html

  docs-link:
    name: Check Doc Links
    runs-on: ubuntu-latest
    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Setup conda
        uses: s-weigand/setup-conda@v1
        with:
          conda-channels: conda-forge
          activate-conda: false

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

      - name: Install dependencies
        run: |
          conda install -y pandoc
          python -m pip install -U pip wheel
          python -m pip install ".[docs]"

      - name: Show installed dependencies
        run: pip freeze

      - name: Build docs
        run: make --directory=docs clean linkcheck

  test:
    name: Test pyglotaran stable
    runs-on: ${{ matrix.os }}
    needs: [pre-commit, docs]
    strategy:
      matrix:
        os: [ubuntu-latest, windows-latest, macOS-latest]
        python-version: ["3.10", "3.11"]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install -U pip wheel
          python -m pip install -r requirements_pinned.txt
          python -m pip install -U ".[test]"

      - name: Run tests
        run: python -m pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests

      - name: Codecov Upload
        continue-on-error: true
        uses: codecov/codecov-action@v4
        with:
          file: ./coverage.xml
          name: ${{ matrix.os }}-py${{ matrix.python-version }}
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

  test-pyglotaran-dev:
    name: Test pyglotaran dev
    runs-on: ubuntu-latest
    needs: [pre-commit, docs]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

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

      - name: Install dependencies
        run: |
          python -m pip install -U pip wheel
          python -m pip install -r requirements_pinned.txt
          python -m pip install -U ".[test]"
          python -m pip install git+https://github.com/glotaran/pyglotaran

      - name: Show installed dependencies
        run: pip freeze

      - name: Run tests
        run: python -m pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests

      - name: Codecov Upload
        continue-on-error: true
        uses: codecov/codecov-action@v4
        with:
          file: ./coverage.xml
          name: test-pyglotaran-dev
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

  test-min-versions:
    name: Test dependency min versions
    runs-on: ubuntu-latest
    needs: [pre-commit, docs]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

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

      - name: Install dependencies
        run: |
          python -m pip install -U pip wheel
          python -m pip install -r .github/requirements_min.txt
          python -m pip install -e ".[test]"

      - name: Show installed dependencies
        run: pip freeze

      - name: Run tests
        run: python -m pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests

      - name: Codecov Upload
        continue-on-error: true
        uses: codecov/codecov-action@v4
        with:
          file: ./coverage.xml
          name: test-min-versions
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

  deploy:
    name: Deploy to PyPi
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
    needs: [test, test-pyglotaran-dev, test-min-versions]
    permissions:
      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"

      - name: Install dependencies
        run: python -m pip install -U hatch

      - name: Build dist
        run: hatch build

      - name: Publish package
        uses: pypa/gh-action-pypi-publish@v1.10.1
        with:
          print-hash: true
          attestations: true