python-ci.yml

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name: "Python CI"

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

permissions: write-all

defaults:
  run:
    working-directory: ./

jobs:
  pylint:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
      - uses: actions/checkout@v4
      - uses: ./.github/actions/python_build

      - name: Run pylint
        run: |
          pylint --rcfile pyproject.toml mevolib
          pylint --rcfile pyproject.toml tests

  mypy:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
      - uses: actions/checkout@v4
      - uses: ./.github/actions/python_build

      - name: Run mypy
        run: |
          mypy --config-file pyproject.toml mevolib
          mypy --config-file pyproject.toml tests

  black:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
      - uses: actions/checkout@v4
      - uses: ./.github/actions/python_build

      - name: Run black
        run: |
          black --config pyproject.toml --check .

  pytest:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
      - uses: actions/checkout@v4
      - uses: ./.github/actions/python_build

      - name: Install dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y fasttree raxml mafft muscle clustalo

      - name: Run pytest with coverage
        continue-on-error: true
        run: |
          coverage run -m pytest --junitxml=./reports/test-results-${{ matrix.python-version }}.xml
          coverage xml -o ./reports/coverage/coverage.xml
          genbadge coverage -i ./reports/coverage/coverage.xml -o ./reports/coverage/coverage-badge.svg
          coverage report -m

      - name: Archive code coverage results
        uses: actions/upload-artifact@v4
        with:
          name: code-coverage-report
          path: ./tests/inference_init_tmp_dir

      - name: Add coverage reports
        uses: xportation/junit-coverage-report@main
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          junit-path: ./reports/unit/test-results-${{ matrix.python-version }}.xml
          coverage-path: ./reports/coverage/coverage.xml

      - name: Upload badge as artifact
        uses: actions/upload-artifact@v4
        with:
          name: badge
          path: ./reports/coverage/coverage-badge.svg
          if-no-files-found: error

      - name: Commit badge
        continue-on-error: true
        env:
          BADGE: ./reports/coverage/coverage-badge.svg
        run: |
          git config --local user.email "action@github.com"
          git config --local user.name "GitHub Action"
          git add "${BADGE}"
          git commit -m "Add/Update badge"

      - name: Push badge commit
        uses: ad-m/github-push-action@master
        if: ${{ success() }}
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: badges