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
      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
      - "renovate/**" # branches Renovate creates
    paths-ignore:
      - "docs/**"
      - "CHANGELOG.md"
  pull_request:
    paths-ignore:
      - "docs/**"
      - "CHANGELOG.md"
      # ignore github workflows except for the current one
      - ".github/**"
      - "!.github/workflows/pytest.yml"
  release:
    types: [published]
  workflow_dispatch:
    inputs:
      nextflow-version:
        description: "Nextflow version to test against"
        required: false
        default: "latest-stable"

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

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

jobs:
  # create a test matrix based on all python files in /tests
  list_tests:
    name: Get test file matrix
    runs-on: "ubuntu-latest"
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
        name: Check out source-code repository

      - name: List tests
        id: list_tests
        run: |
          echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
    outputs:
      tests: ${{ steps.list_tests.outputs.tests }}

  test:
    name: Run ${{matrix.test}} with Python ${{ matrix.python-version }} and Nextflow ${{ matrix.nextflow-version }}
    needs: list_tests
    runs-on:
      - runs-on=${{ github.run_id }}-run-test
      - runner=4cpu-linux-x64
    strategy:
      matrix:
        # On PRs to main test with 3.10 and 3.14, otherwise just 3.10
        python-version: ${{ github.base_ref == 'main' && fromJson('["3.10", "3.14"]') || fromJson('["3.10"]') }}
        test: ${{ fromJson(needs.list_tests.outputs.tests).test }}
        # On push/release test both NF versions, otherwise just 25.10.4
        # Note: python×nextflow must stay ≤2 with 88 tests to stay under GitHub's 256-config limit
        nextflow-version: ${{ (github.event_name == 'push' || github.event_name == 'release') && fromJson('["25.10.4", "latest-stable"]') || fromJson('["25.10.4"]') }}
      fail-fast: false # run all tests even if one fails
    steps:
      - name: go to subdirectory and change nextflow workdir
        run: |
          mkdir -p pytest
          cd pytest
          export NXF_WORK=$(pwd)

      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
        name: Check out source-code repository

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
        with:
          python-version: ${{ matrix.python-version }}
          token: ${{ secrets.GITHUB_TOKEN }}

      - name: Install uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --all-extras

      - name: Set up Apptainer
        if: ${{ startsWith(matrix.test, 'pipelines/download/') }}
        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
        with:
          version: ${{ github.event.inputs.nextflow-version || matrix.nextflow-version }}

      - name: Install nf-test
        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
        with:
          version: 0.9.5
          install-fast-diff: true

      - name: move coveragerc file up
        run: |
          mv .github/.coveragerc .

      - name: Test with pytest
        id: pytest
        run: |
          uv run python -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.coveragerc --durations=0 -n logical && exit_code=0|| exit_code=$?
          # don't fail if no tests were collected, e.g. for test_licence.py
          if [ "${exit_code}" -eq 5 ]; then
            echo "No tests were collected"
            exit 0
          elif [ "${exit_code}" -ne 0 ]; then
            echo "Tests failed with exit code ${exit_code}"
            exit 1
          fi

      - name: Generate coverage XML
        if: always()
        run: |
          uv run coverage xml --rcfile=.coveragerc

      - name: Upload coverage to Codecov
        if: always()
        uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6
        with:
          files: ./coverage.xml
          flags: python-${{ matrix.python-version }}
          env_vars: MATRIX_TEST
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
          MATRIX_TEST: ${{ matrix.test }}

      - name: remove slashes from test name
        run: |
          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
          echo "test=${test}" >> $GITHUB_ENV

      - name: Store snapshot report
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
        if: always() && contains(matrix.test, 'test_create_app') && steps.pytest.outcome == 'failure'
        with:
          include-hidden-files: true
          name: Snapshot Report ${{ env.test }}
          path: ./snapshot_report.html