tests.yml

#schema: https://github.com/softprops/github-actions-schemas/blob/master/workflow.json
name: "Test"

on:
  push:
    branches: [main, dev]
  pull_request:
    branches: [main, dev]
  workflow_dispatch:


permissions:
  id-token: write
  actions: write
  contents: read
  packages: write


env:
  ANNOY_COMPILER_ARGS: "-DANNOYLIB_MULTITHREADED_BUILD,-mno-avx512f"

jobs:
  pre_job:
    continue-on-error: true
    runs-on: ubuntu-latest
    # Map a step output to a job output
    outputs:
      should_skip: ${{ steps.skip_check.outputs.should_skip }}
      paths_result: ${{ steps.skip_check.outputs.paths_result }}
    steps:
      - id: skip_check
        uses: fkirc/skip-duplicate-actions@v5
        if: ${{ !github.event.act }}
        with:
          concurrent_skipping: "same_content_newer"
          skip_after_successful_duplicate: "true"
          do_not_skip: '["workflow_dispatch"]'
          paths_filter: |
            python:
              paths:
                - 'pyproject.toml'
                - 'poetry.lock'
                - 'src/pixelator/**'
                - 'tests/**'
              paths_ignore:
                - 'tests/**/*.md'

  test:
    name: Test - python ${{ matrix.py }}
    if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip
    runs-on: ubuntu-latest
    needs: [pre_job]
    strategy:
      fail-fast: false
      matrix:
        py:
          - "3.11"
          - "3.10"

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python environment - ${{ matrix.py }}
        uses: ./.github/actions/setup-python
        with:
          python-version: ${{ matrix.py }}

      - uses: supplypike/setup-bin@v3
        with:
          uri: 'https://opengene.org/fastp/fastp'
          name: 'fastp'
          version: '0.23.2'

      - name: Generate tox env for python version
        uses: actions/github-script@v6
        id: set_tox_env
        with:
          script: |
            const pythonVersion = "${{ matrix.py }}"
            const toxEnv = "py" + pythonVersion.replace(/\./g, '')
            core.setOutput("tox_env", toxEnv)

      - name: Install dependencies
        run: |
          python -m pip install --user pipx
          python -m pipx ensurepath
          pipx install poetry
          pip install tox
          poetry self add poetry-plugin-export
          poetry export --output dev_requirements.txt --quiet --no-interaction --no-ansi --without-hashes --with dev
          pip install -r dev_requirements.txt
          pip install -e .

      - name: Run test suite on local python version
        run: tox -e ${{ steps.set_tox_env.outputs.tox_env }} --current-env

  test-coverage:
    name: "Check the test coverage"
    runs-on: ubuntu-latest
    needs:
      - pre_job
    if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Set up Python environment
        uses: ./.github/actions/setup-python
        with:
          python-version: "3.11"

      - name: Create dependencies file
        run: |
          pip install poetry
          poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev
          pip install -r requirements.txt

      - name: Run test suite
        run: |
          pytest --cov=src/

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v3
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

  test-workflow:
    name: Test small workflow - ${{ matrix.case }}
    runs-on: ubuntu-latest
    needs: [ pre_job ]
    strategy:
      fail-fast: false
      matrix:
        case:
          - mpx_v1
          - mpx_v2

    if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python environment
        uses: ./.github/actions/setup-python
        with:
          python-version: "3.11"

      - uses: supplypike/setup-bin@v3
        with:
          uri: 'https://opengene.org/fastp/fastp'
          name: 'fastp'
          version: '0.23.2'

      - name: Install dependencies
        run: |
          pip install poetry
          poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev
          pip install -r requirements.txt

      - name: Run workflow tests
        run: |
          pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG