ci.yaml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: python_package

on:
  push:
    branches: [ master, dev ]
  pull_request:
    branches: [ master, dev ]

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        python-version: [ "3.11", "3.12", "3.13" , "3.14" ]
        os: [ ubuntu-latest, macos-latest ]

    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
      - name: Install the latest version of uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          enable-cache: true

      - name: Install Python ${{ matrix.python-version }}
        run: uv python install ${{ matrix.python-version }}

      - name: Install dependencies
        run:  make install-ci

      - name: Check formatting with black and isort
        run:  make check-fmt

      - name: Lint with flake8
        run:  make lint

      - name: Test and generate coverage report with pytest
        run:  |
              # have to do this as use of tmpdir in tests changes directory
              covg_report="$(pwd)/coverage.xml"
              uv run pytest --cov=snakefmt --cov-report=xml:$covg_report --cov-branch tests/

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@3f20e214133d0983f9a10f3d63b0faf9241a3daa # v6.0.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: ./coverage.xml
          flags: unittests