CI.yml

name: CI

on:
  push:
    branches: [refactor, main]
    tags: ["*"]
  schedule:
    - cron:  '0 8 * * MON'
  pull_request:
    branches: [refactor, main]
  workflow_dispatch:

env:
  PYTHON_LATEST: "3.11"

jobs:
  pre_commit:
    name: "🅿️ pre-commit"
    runs-on: "ubuntu-latest"
    timeout-minutes: 5
    steps:
      - uses: "actions/checkout@v4"
      - uses: "actions/setup-python@v5"
        with:
          python-version: ${{env.PYTHON_LATEST}}
          cache: pip
      - uses: "pre-commit/action@v3.0.1"

  tests:
    name: "Test Python ${{ matrix.python-version }}"
    runs-on: "ubuntu-latest"
    needs: "pre_commit"
    timeout-minutes: 5
    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "${{ matrix.python-version }}"
          cache: pip
      - name: "Run tests"
        run: |
          set -xe
          python -VV
          python -m site
          python -m pip install -U pip setuptools wheel
          python -m pip install -e ".[tests]"
          coverage run --omit "src/readfish/read_until/*.py,src/readfish/entry_points/targets.py" -pm pytest
      - name: Upload coverage data
        uses: actions/upload-artifact@v4
        with:
          name: my-artifact-${{ matrix.python-version }}
          path: .coverage*
          if-no-files-found: ignore

  merge:
    name: merge
    runs-on: ubuntu-latest
    needs: tests
    steps:
        - name: Merge Artifacts
          uses: actions/upload-artifact/merge@v4
          with:
            name: coverage-data
            pattern: my-artifact-*

  coverage:
    name: Combine coverage
    runs-on: ubuntu-latest
    needs: [tests, merge]

    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PYTHON_LATEST }}
          cache: pip

      - name: Download coverage data
        uses: actions/download-artifact@v4
        with:
          name: coverage-data

      - name: Combine coverage
        run: |
          python -m pip install coverage[toml]
          python -m coverage combine
          python -m coverage report --skip-empty --fail-under=72 --format=markdown >> $GITHUB_STEP_SUMMARY

  build-package:
    name: Build python package
    runs-on: ubuntu-latest
    needs: tests
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PYTHON_LATEST }}
          cache: pip
      - name: Build package
        run: |
          python -m pip install --upgrade pip
          python -m pip install build
          python -m build
      - name: Upload built package
        uses: actions/upload-artifact@v4
        with:
          name: built-package
          path: dist/
          if-no-files-found: error

  build-docs:
    name: Build HTML docs
    runs-on: ubuntu-latest
    needs: "pre_commit"
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PYTHON_LATEST }}
          cache: pip

      - name: Build docs
        run: |
          python -m pip install .[docs]
          cd docs
          make html
      - name: Upload built HTML
        uses: actions/upload-artifact@v4
        with:
          name: html-docs
          path: docs/_build/html
          if-no-files-found: error


  deploy:
    name: Deploy docs and package
    runs-on: ubuntu-latest
    if: startsWith(github.ref, 'refs/tags')
    needs:
      - build-docs
      - build-package
    environment:
      name: PyPI
      url: https://pypi.org/p/readfish
    permissions:
      id-token: write
      contents: write

    steps:
      - name: Download HTML docs
        uses: actions/download-artifact@v4
        with:
          name: html-docs
          path: _build/html
      - name: Download python package
        uses: actions/download-artifact@v4
        with:
          name: built-package
          path: dist

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

      - name: Deploy docs to gh-pages branch
        uses: peaceiris/actions-gh-pages@v4
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: _build/html/