python-package.yml

# 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: Testing Linux

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v4
        with:
          python-version: "3.10"
          cache: pip
          cache-dependency-path: pyproject.toml

      - uses: pre-commit/action@v3.0.1

  test:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]
        split: [1, 2, 3, 4, 5, 6]


    steps:
    - name: Check out repo
      uses: actions/checkout@v4

    - name: Set up micromamba
      uses: mamba-org/setup-micromamba@main

    - name: Create mamba environment
      run: |
        micromamba create -n lobpy python=${{ matrix.python-version }} --yes

    - name: Install uv
      run: micromamba run -n lobpy pip install uv

    - name: Install LobsterPy and dependencies
      run: |
        micromamba activate lobpy
        uv pip install --upgrade pip
        uv pip install --editable '.[tests,featurizer]'

    - name: Test with pytest and coverage
      # run this locally to update tests durations
      # pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./tests/test_data/.pytest-split-durations --store-durations
      env:
        MPLBACKEND: Agg  # non-interactive backend for matplotlib
      run: |
        micromamba activate lobpy
        pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 6 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations

    - name: Upload coverage
      if: matrix.python-version == '3.10'
      uses: actions/upload-artifact@v4
      with:
        name: coverage-${{ matrix.python-version }}-${{ matrix.split }}
        include-hidden-files: true
        overwrite: false
        path: ./.coverage

    - name: Upload test durations artifact
      if: matrix.python-version == '3.10'
      uses: actions/upload-artifact@v3
      with:
        name: test-durations-${{ matrix.python-version }}-${{ matrix.split }}
        include-hidden-files: true
        path: ./tests/test_data/.pytest-split-durations

  coverage:
      needs: test
      runs-on: ubuntu-latest
      steps:
        - uses: actions/checkout@v4
        - name: Set up Python 3.10
          uses: actions/setup-python@v4
          with:
            python-version: '3.10'

        - name: Install Coverage
          run: |
           python -m pip install coverage[toml]

        - name: Download coverage artifacts
          continue-on-error: true
          uses: actions/download-artifact@v4
          with:
           pattern: coverage-3.10-*

        - name: Run coverage
          continue-on-error: true
          run: |
            coverage combine coverage*/.coverage*
            coverage report --show-missing

        - name: Upload coverage reports to Codecov
          uses: codecov/codecov-action@v4.0.1
          with:
            token: ${{ secrets.CODECOV_TOKEN }}
            slug: JaGeo/LobsterPy

  commit-durations:
    if: github.repository_owner == 'JaGeo' && github.ref == 'refs/heads/main'
    needs: test
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile

    steps:

    - name: Check out repo
      uses: actions/checkout@v4
    - name: Set up micromamba
      uses: mamba-org/setup-micromamba@main
    - name: Create mamba environment
      run: |
          micromamba create -n lobpy_test python=3.10 --yes
    - name: Install uv
      run: micromamba run -n lobpy_test pip install uv
    - name: Install lobsterpy and dependencies
      run: |
          micromamba activate lobpy_test
          uv pip install --upgrade pip
          uv pip install -e .[tests,featurizer]

    - name: Download test duration artifacts
      uses: actions/download-artifact@v4

    - name: Compute average of test durations
      run: |
        micromamba activate lobpy_test
        python3 .github/scripts/average_test_durations.py
        rm -rf test-durations-*

    - name: Create Pull Request to push consolidated test durations
      uses: peter-evans/create-pull-request@v7
      with:
        commit-message: update test durations
        title: Update test durations file
        body: Auto updated test durations file
        branch: update-test-durations
        delete-branch: true
        base: main

  docs:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v3

      - uses: actions/setup-python@v4
        with:
          python-version: "3.10"
          cache: pip
          cache-dependency-path: pyproject.toml

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .[docs,featurizer]

      - name: Build
        run: sphinx-build -W docs _build