CI_CD_actions.yml

name: Tests

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

jobs:
  pre-commit:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repo
        uses: actions/checkout@v3
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Run pre-commit
        uses: pre-commit/action@v3.0.0

  check-manifest:
    name: Check Manifest
    runs-on: ubuntu-latest
    steps:
      - name: Check out repo
        uses: actions/checkout@v3
      - name: Set up Python 3.10
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Install check manifest
        run: python -m pip install check-manifest 'setuptools>=62.4.0'
      - name: Run check manifest
        run: check-manifest

  docs:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - 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@v4
        with:
          python-version: "3.10"
      - name: Install dependencies
        run: |
          conda install -y pandoc
          python -m pip install -U pip wheel
          python -m pip install .
          python -m pip install -U -r docs/requirements.txt
      - name: Show installed packages
        run: pip freeze
      - name: Build docs
        run: |
          make --directory=docs clean html

  docs-links:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - 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@v4
        with:
          python-version: "3.10"
      - name: Install dependencies
        run: |
          conda install -y pandoc
          python -m pip install -U pip wheel
          python -m pip install .
          python -m pip install -U -r docs/requirements.txt
      - name: Show installed packages
        run: pip freeze
      - name: Check doc links
        run: |
          make --directory=docs clean linkcheck $@ | tee linkcheck-output.txt
          exit ${PIPESTATUS[0]}
      - name: Linkcheck summary
        if: ${{ always() }}
        run: cat linkcheck-output.txt | grep -E "(\(line.*\)|writing output)"

  docs-notebooks:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python 3.10
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Install dependencies
        run: |
          python -m pip install -U pip wheel
          python -m pip install -U -r requirements_dev.txt
          pip install .
      - name: Show installed packages
        run: python -m pip freeze
      - name: Build docs
        run: |
          python -m pytest -vv --nbval docs/source/notebooks

  test:
    runs-on: ${{ matrix.os }}
    needs: [pre-commit, check-manifest]
    strategy:
      matrix:
        os: [ubuntu-latest, windows-latest, macOS-latest]
        python-version: ["3.10", "3.11"]

    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip wheel
          python -m pip install -r requirements_dev.txt
          python -m pip install -e .
      - name: Show installed packages
        run: python -m pip freeze
      - name: Run tests
        run: |
          python -m pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml glotaran

      - name: Codecov Upload
        uses: codecov/codecov-action@v3
        with:
          file: ./coverage.xml

  deploy:
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
    needs: [test, docs, docs-notebooks]
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python 3.10
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Install dependencies
        run: |
          python -m pip install -U pip wheel 'setuptools>=62.4.0'
      - name: Build dist
        run: |
          python setup.py sdist bdist_wheel

      - name: Publish package
        uses: pypa/gh-action-pypi-publish@master
        with:
          user: __token__
          password: ${{ secrets.pypi_pyglotaran_token }}