ci.yml

name: tests

on:
  push:
    # # Avoid using all the resources/limits available by checking only
    # # relevant branches and tags. Other branches can be checked via PRs.
    branches:
      - "main"
      - "*"
    tags: ["v[0-9]*", "[0-9]+.[0-9]+*"] # Match tags that resemble a version
  pull_request: # Run in every PR
  workflow_dispatch: # Allow manually triggering the workflow
  schedule:
    # Run roughly every 15 days at 00:00 UTC
    # (useful to check if updates on dependencies break the package)
    - cron: "0 0 1,16 * *"

permissions:
  contents: read

concurrency:
  group: >-
    ${{ github.workflow }}-${{ github.ref_type }}-
    ${{ github.event.pull_request.number || github.sha }}
  cancel-in-progress: true

jobs:
  prepare:
    runs-on: ubuntu-latest
    outputs:
      wheel-distribution: ${{ steps.wheel-distribution.outputs.path }}
    steps:
      - uses: actions/checkout@v3
        with: { fetch-depth: 0 } # deep clone for setuptools-scm
      - uses: actions/setup-python@v4
        id: setup-python
        with: { python-version: "3.11" }
      - name: Run static analysis and format checkers
        run: pipx run pre-commit run --all-files --show-diff-on-failure
      - name: Build package distribution files
        run: >-
          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
          tox -e clean,build
      - name: Record the path of wheel distribution
        id: wheel-distribution
        run: echo "path=$(ls dist/*.whl)" >> $GITHUB_OUTPUT
      - name: Store the distribution files for use in other stages
        # `tests` and `publish` will use the same pre-built distributions,
        # so we make sure to release the exact same package that was tested
        uses: actions/upload-artifact@v3
        with:
          name: python-distribution-files
          path: dist/
          retention-days: 1

  download_big_testdata:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Download test data
        run: >-
          pip install requests && python tests/specific_analyses/e03_download_intraassay_zenodo_zip.py
      - name: Store the test data for use in other stages
        uses: actions/upload-artifact@v3
        with:
          name: example_data
          path: example_data/
          retention-days: 1

  # Starting point from: https://coderefinery.github.io/documentation/gh_workflow/
  docs:
    runs-on: ubuntu-latest
    needs:
      - prepare
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        id: setup-python
        with:
          python-version: "3.11"
      - name: Retrieve pre-built distribution files
        uses: actions/download-artifact@v3
        with: { name: python-distribution-files, path: dist/ }
      - name: Run tests
        run: >-
          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
          tox -e docs
      - name: Deploy to GitHub Pages
        uses: peaceiris/actions-gh-pages@v3
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: docs/_build/html

  test:
    needs:
      - prepare
      - download_big_testdata
    strategy:
      matrix:
        python:
          - "3.8" # oldest Python supported by PSF
          - "3.11" # newest Python that is stable
        platform:
          - ubuntu-latest
          # - macos-latest  # graphviz would not install (2023-12-08)
          - windows-latest
    runs-on: ${{ matrix.platform }}
    steps:
      - uses: actions/checkout@v3
      # https://github.com/marketplace/actions/setup-graphviz
      - name: Setup Graphviz
        uses: ts-graphviz/setup-graphviz@v1
      - uses: actions/setup-python@v4
        id: setup-python
        with:
          python-version: ${{ matrix.python }}
      # https://docs.github.com/en/actions/using-workflows/storing-workflow-data-as-artifacts#passing-data-between-jobs-in-a-workflow
      - name: Retrieve pre-built distribution files
        uses: actions/download-artifact@v3
        with: { name: python-distribution-files, path: dist/ }
      - name: Retrieve downloaded big test files
        uses: actions/download-artifact@v3
        with: { name: example_data, path: example_data/ }
      - name: Run tests
        run: >-
          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
          tox -e coverage_githubCI --installpkg '${{ needs.prepare.outputs.wheel-distribution }}' -- -rFEx --durations 10 --color yes
      - name: Generate coverage report
        run: pipx run coverage lcov -o coverage.lcov
      - name: Upload partial coverage report
        uses: coverallsapp/github-action@master
        with:
          path-to-lcov: coverage.lcov
          github-token: ${{ secrets.GITHUB_TOKEN }}
          flag-name: ${{ matrix.platform }} - py${{ matrix.python }}
          parallel: true

  finalize:
    needs: test
    runs-on: ubuntu-latest
    steps:
      - name: Finalize coverage report
        uses: coverallsapp/github-action@master
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          parallel-finished: true

  # publish:
  #   needs: finalize
  #   if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }}
  #   runs-on: ubuntu-latest
  #   permissions:
  #     contents: write
  #   steps:
  #     - uses: actions/checkout@v3
  #     - uses: actions/setup-python@v4
  #       with: {python-version: "3.11"}
  #     - name: Retrieve pre-built distribution files
  #       uses: actions/download-artifact@v3
  #       with: {name: python-distribution-files, path: dist/}
  #     - name: Publish Package
  #       env:
  #         # TODO: Set your PYPI_TOKEN as a secret using GitHub UI
  #         # - https://pypi.org/help/#apitoken
  #         # - https://docs.github.com/en/actions/security-guides/encrypted-secrets
  #         TWINE_REPOSITORY: pypi
  #         TWINE_USERNAME: __token__
  #         TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
  #       run: pipx run tox -e publish