ci_cd_pipeline.yml

name: CI/CD Pipeline

on:
  push:
    branches:
      - main
      - "ci-*"
  pull_request:
    branches:
      - main

jobs:
  check_code_quality:
    name: Check Code Quality
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python 3.8
        uses: actions/setup-python@v5
        with:
          python-version: "3.8"

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .[quality]
      - name: Run Ruff code quality checks
        run: |
          ruff check tests src setup.py --output-format=github
          ruff format --check tests src setup.py

  tests:
    needs: check_code_quality
    strategy:
      matrix:
        test: [unit]
        os: [ubuntu-latest, windows-latest]
        python-version: ["3.8", "3.9", "3.10", "3.11"]
    runs-on: ${{ matrix.os }}
    continue-on-error: ${{ matrix.test == 'integration' }}
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install uv --upgrade
          uv pip install --system "biosets[test] @ ."


      - name: Run Tests
        run: |
          mkdir -p reports/${{ matrix.test }}_tests
          python3 -m pytest -m ${{ matrix.test }} -n 2 --dist loadfile -sv ./tests/ --junitxml=reports/${{ matrix.test }}_tests/results.xml

      - name: Upload Unit Test Results
        uses: actions/upload-artifact@v3
        with:
          name: ${{ matrix.test }}-test-reports
          path: reports/${{ matrix.test }}_tests/results.xml