molsysviewer/.github/workflows/CI.yaml at main · uibcdf/molsysviewer · GitHub

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name: CI

on:
  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
  # Existing codes likely still have "master" as the primary branch
  # Both are tracked here to keep legacy and new codes working
  push:
    branches:
      - "main"
    paths-ignore:
      - '**/*.md'
      - '**/*.rst'
      - '**/*.ipynb'
      - '**/*.yml'
      - '**/*.yaml'
      - 'docs/**'
      - 'paper/**'
      - 'examples/**'
      - 'logos/**'
  pull_request:
    branches:
      - "main"
    paths-ignore:
      - '**/*.md'
      - '**/*.rst'
      - '**/*.ipynb'
      - '**/*.yml'
      - '**/*.yaml'
      - 'docs/**'
      - 'paper/**'
      - 'examples/**'
      - 'logos/**'
  schedule:
    # Nightly tests run on master by default:
    #   Scheduled workflows run on the latest commit on the default or base branch.
    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
    - cron: "0 9 * * MON"
  workflow_dispatch:

jobs:
  test:
    name: Test on ${{ matrix.cfg.os }}, Python ${{ matrix.cfg.python-version }}
    if: >
      !(
        (github.event_name == 'push' && contains(github.event.head_commit.message, '[skip ci]'))
        ||
        (github.event_name == 'pull_request' && contains(github.event.pull_request.title, '[skip ci]'))
        ||
        (github.event_name == 'pull_request' && contains(github.event.pull_request.head.ref, 'skip-ci'))
      )
    runs-on: ${{ matrix.cfg.os }}
    strategy:
      fail-fast: false  # do not cancel all in-progress jobs if any job variation fails
      matrix:
        cfg:
          - { os: ubuntu-latest, python-version: "3.10"}
          - { os: ubuntu-latest, python-version: "3.11"}
          - { os: ubuntu-latest, python-version: "3.12"}
          - { os: macos-latest,  python-version: "3.10"}
          - { os: macos-latest,  python-version: "3.11"}
          - { os: macos-latest,  python-version: "3.12"}

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Additional info about the build
      shell: bash
      run: |
        uname -a

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

    - name: Setup conda env
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-file: devtools/conda-envs/test_env.yaml
        environment-name: test
        condarc: |
          channels:
            - uibcdf
            - conda-forge
            - ambermd
          channel_priority: strict

        create-args: >-
          python=${{ matrix.cfg.python-version }}

    - name: Info conda
      shell: bash -l {0}
      run: |
        micromamba activate test
        micromamba info
        micromamba list

    - name: Install package
      shell: bash -l {0}
      run: |
        python -m pip install . --no-deps

    - name: Test import module
      shell: bash -l {0}
      run: |
        echo "::group::Importing module from home directory"
        cd
        pwd
        echo 'import molsysviewer; print("Version of the package: {}".format(molsysviewer.__version__))' | python
        echo "::endgroup::"

    - name: Run tests
      shell: bash -l {0}
      run: |
        export PYTHONPATH=$PYTHONPATH:$(pwd)
        # pytest -n logical -v --cov-config=.coveragerc --cov=molsysviewer --cov-report=xml --junitxml=junit.xml --color=yes
        pytest -v --cov-config=.coveragerc --cov=molsysviewer --cov-report=xml --junitxml=junit.xml --color=yes

    - name: JS unit tests (Node)
      if: matrix.cfg.os == 'ubuntu-latest' && matrix.cfg.python-version == '3.12'
      shell: bash -l {0}
      run: |
        cd molsysviewer/js
        npm ci
        npm run build
        npm run test:js
        npm run coverage:js

    - name: Check coverage
      shell: bash -l {0}
      run: |
        cat ./coverage.xml
        if [ -f molsysviewer/js/coverage-js/lcov.info ]; then
          echo "JS coverage generated"
        fi

    - name: Upload coverage reports to Codecov
      if: matrix.cfg.os == 'ubuntu-latest' && matrix.cfg.python-version == '3.12'
      uses: codecov/codecov-action@v4
      with:
        verbose: true
        file: |
          ./coverage.xml
          ./molsysviewer/js/coverage-js/lcov.info
        flags: unittests
        name: codecov-${{ matrix.cfg.os }}-py${{ matrix.cfg.python-version }}
        token: ${{ secrets.CODECOV_TOKEN }}

    - name: Upload test results to Codecov
      if: matrix.cfg.os == 'ubuntu-latest' && matrix.cfg.python-version == '3.12' && ${{ !cancelled() }}
      uses: codecov/test-results-action@v1
      with:
        token: ${{ secrets.CODECOV_TOKEN }}