gh-ci.yaml

name: GH Actions CI
'on':
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
      - develop
  schedule:
    # Weekly tests at midnight on Sundays run on main 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 0 * * 0

concurrency:
  # Specific group naming so CI is only cancelled
  # within same PR or on merge to main
  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
  cancel-in-progress: true

defaults:
  run:
    shell: bash -l {0}

jobs:
  environment-config:
    runs-on: ubuntu-latest
    outputs:
      stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
      python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }}
    steps:
      - uses: actions/setup-python@v4
        with:
          python-version: '3.11'

      - id: get-compatible-python
        uses: MDAnalysis/mdanalysis-compatible-python@main
        with:
          release: latest

  main-tests:
    if: github.repository == 'Becksteinlab/zarrtraj'
    needs: environment-config
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os:
          - macOS-latest
          - ubuntu-latest
          - windows-latest
        python-version: ["3.10", "3.11", "3.12"]
        mdanalysis-version:
          - latest
          - develop

    steps:
      - uses: actions/checkout@v4

      - name: Build information
        run: |
          uname -a
          df -h
          ulimit -a

      # More info on options: https://github.com/conda-incubator/setup-miniconda
      - name: Install conda dependencies
        uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: ${{ matrix.python-version }}
          environment-file: devtools/conda-envs/test_env.yaml
          add-pip-as-python-dependency: true
          architecture: x64

          channels: defaults

          activate-environment: zarrtraj-test
          auto-update-conda: true
          auto-activate-base: false
          show-channel-urls: true
          # Need this to ensure miniconda installed
          # if not already on MacOS
          miniconda-version: latest

      - name: Install MDAnalysis version
        uses: MDAnalysis/install-mdanalysis@main
        with:
          version: ${{ matrix.mdanalysis-version }}
          install-tests: true
          installer: conda
          shell: bash -l {0}

      - name: Install package
        run: |
          python --version
          python -m pip install .  --no-deps

      - name: Python information
        run: |
          which python
          which pip
          pip list
          conda info
          conda list

      - name: Run tests
        run: |
          pytest -v -x --cov=zarrtraj --cov-report=xml --color=yes zarrtraj/tests/

      - name: codecov
        if: github.repository == 'Becksteinlab/zarrtraj' && github.event_name !=
          'schedule'
        uses: codecov/codecov-action@v4.0.1
        with:
          file: coverage.xml
          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
          verbose: true
          token: ${{ secrets.CODECOV_TOKEN }}
          slug: Becksteinlab/zarrtraj

      

  pylint_check:
    if: github.repository == 'Becksteinlab/zarrtraj'
    needs: environment-config
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ needs.environment-config.outputs.stable-python-version }}

      - name: Install Pylint
        run: |
          which pip
          which python
          pip install pylint mdanalysis

      - name: Run Pylint
        env:
          PYLINTRC: .pylintrc
        run: |
          pylint zarrtraj

  pypi_check:
    if: github.repository == 'Becksteinlab/zarrtraj'
    needs: environment-config
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ needs.environment-config.outputs.stable-python-version }}

      - name: Install dependencies
        run: |
          pip install pipx twine

      - name: Build package
        run: |
          python -m pipx run build --sdist

      - name: Check package build
        run: |
          DISTRIBUTION=$(ls -t1 dist/zarrtraj-*.tar.gz | head -n 1)
          test -n "${DISTRIBUTION}" || { echo "no distribution dist/zarrtraj-*.tar.gz found"; exit 1; }
          echo "twine check $DISTRIBUTION"
          twine check $DISTRIBUTION