ci.yaml

name: Python CI

on: [ push, pull_request ]

env:
  TERM: screen-256color

jobs:
  cog_check_job:
    runs-on: ubuntu-latest
    name: check conventional commit compliance
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          # pick the pr HEAD instead of the merge commitonly if it's a PR, otherwise use the default
          ref: ${{ github.event.pull_request.head.sha || github.sha }}

      - name: Conventional commit check
        uses: cocogitto/cocogitto-action@v3
        with:
          check-latest-tag-only: true
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        python-version: [ 3.8 ]
        os: [ ubuntu-latest, macos-latest ]
    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: ${{ matrix.python-version }}
          miniforge-variant: Mambaforge
          channels: conda-forge,bioconda,defaults
          channel-priority: strict
          activate-environment: tbpore
          environment-file: environment.yaml
          auto-update-conda: true
      - name: Install project
        shell: bash -l {0}
        run: |
          mamba install python=${{ matrix.python-version }}
          just install
      - name: Check formatting
        shell: bash -l {0}
        run: just check-fmt
      - name: Lint
        shell: bash -l {0}
        run: just lint
      - name: Test and generate coverage report with pytest
        shell: bash -l {0}
        run: just test-ci
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          file: ./coverage.xml
          flags: unittests
          fail_ci_if_error: false
          token: ${{ secrets.CODECOV_TOKEN }}