pytest.yml

name: Python tests
# This workflow is triggered on pushes and PRs to the repository.
# Only run if we changed a Python file
on:
  push:
    branches:
      - dev
    paths-ignore:
      - "docs/**"
      - "CHANGELOG.md"
  pull_request:
    paths-ignore:
      - "docs/**"
      - "CHANGELOG.md"
  release:
    types: [published]

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

jobs:
  setup:
    runs-on: ["ubuntu-latest"]
    strategy:
      matrix:
        python-version: ["3.8", "3.11"]
        runner: ["ubuntu-latest"]
        include:
          - python-version: "3.8"
            runner: "ubuntu-20.04"

    steps:
      - name: Check conditions
        id: conditions
        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"

    outputs:
      python-version: ${{ matrix.python-version }}
      runner: ${{ matrix.runner }}
      run-tests: ${{ steps.conditions.outputs.run-tests }}

  test:
    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
    needs: setup
    if: ${{ needs.setup.outputs.run-tests}}
    runs-on: ${{ needs.setup.outputs.runner }}
    steps:
      - uses: actions/checkout@v4
        name: Check out source-code repository

      - name: Set up Python ${{ needs.setup.outputs.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ needs.setup.outputs.python-version }}
          cache: "pip"

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip -r requirements-dev.txt
          pip install -e .

      - name: Downgrade git to the Ubuntu official repository's version
        if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
        run: |
          sudo apt update
          sudo apt remove -y git git-man
          sudo add-apt-repository --remove ppa:git-core/ppa
          sudo apt install -y git
      - name: Get current date
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "latest-everything"

      - name: Cache nf-test installation
        id: cache-software
        uses: actions/cache@v3
        with:
          path: |
            /usr/local/bin/nf-test
            /home/runner/.nf-test/nf-test.jar
          key: ${{ runner.os }}-nftest-${{ env.date }}

      - name: Install nf-test
        if: steps.cache-software.outputs.cache-hit != 'true'
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash
          sudo mv nf-test /usr/local/bin/

      - name: Test with pytest
        run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core

      - uses: codecov/codecov-action@v1
        name: Upload code coverage report
        with:
          if: success()
          token: ${{ secrets.CODECOV_TOKEN }}