python-app.yml

# This workflow installs Python dependencies, runs tests and lints with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: microbiorust-py python tests

on:
  push:
    branches: [ "main" ]
    paths:
      - 'microbiorust-py/**'
  pull_request:
    branches: [ "main" ]
    paths:
      - 'microbiorust-py/**'

permissions:
  contents: read

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
  cancel-in-progress: true

jobs:
  build:
    name: Build and Test (Python)
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
      with:
        persist-credentials: false
    - name: Set up Python 3.12
      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
      with:
        python-version: "3.12"
        cache: 'pip'
        cache-dependency-path: 'microbiorust-py/pyproject.toml'

    - name: Set up Rust stable
      run: rustup toolchain install stable

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install maturin ruff pytest
        pip install ./microbiorust-py

    - name: Lint with ruff
      run: |
        # stop the build for critical errors (E9, F63, F7, F82 equivalents)
        ruff check microbiorust-py/ --select E9,F63,F7,F82 --output-format=full
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        ruff check microbiorust-py/ --exit-zero --line-length=127

    - name: Test with pytest
      run: |
        pytest -v
      working-directory: microbiorust-py/tests