phables/.github/workflows/testing.yml at develop · Vini2/phables · GitHub

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name: CI

on:
  push:
    branches: [ develop ]
  pull_request:
    branches: [ develop ]


jobs:
  tests:
    name: "Python ${{ matrix.python-version }}"
    runs-on: ${{ matrix.os }}

    defaults:
      run:
        shell: bash -el {0}

    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        # setup.py's python_requires is ">=3.11" (snakemake>=8's own floor --
        # see setup.py's comment on why). This matrix was still 3.9/3.10 despite
        # that, which fails `pip install .` outright on both -- confirmed by
        # reading setup.py, not run against real CI (no Actions access from
        # here). Bumped to match what the package actually supports.
        python-version: ["3.11", "3.12"]

    steps:
      - uses: "actions/checkout@v3"
        with:
          fetch-depth: 0

      # Setup env
      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: phables
          environment-file: build/environment.yml
          python-version: ${{ matrix.python-version }}
          auto-activate-base: false

      - name: "Setup Phables on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
        run: |
          python -m pip install --upgrade pip
          pip install .

      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
        run: |
          # pytest itself + the one real (non-deferred) extra import the test
          # suite needs beyond `pip install .`: tests/test_gene_caller.py calls
          # into workflow/scripts/gene_caller.py directly (not through a
          # Snakemake rule), which needs pyrodigal-gv -- normally supplied at
          # real runtime by envs/genecall.yaml, a per-rule conda env this base
          # CI install never touches. (format_koverage_results.py's own
          # pandas/biopython need is deliberately NOT listed here -- those
          # imports were moved inside main() specifically so
          # test_format_koverage_results.py doesn't need them at all; adding
          # them back here would be masking that, not needing it.)
          pip install pytest pytest-cov pyrodigal-gv
          pytest --cov=./ --cov-report xml --cov-report lcov --cov-append

      - name: Coveralls Parallel
        uses: coverallsapp/github-action@master
        with:
          parallel: true
          github-token: ${{ secrets.github_token }}
          flag-name: run-${{ matrix.test_number }}
          path-to-lcov: "coverage.lcov"

  finish:
    needs: tests
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: ["3.11", "3.12"]
    steps:
    - name: Coveralls Finished
      uses: coverallsapp/github-action@master
      with:
        github-token: ${{ secrets.github_token }}
        parallel-finished: true