gh-ci.yaml

name: GH Actions CI
on:
  push:
    branches:
      - develop
  pull_request:
    branches:
      - develop
  workflow_dispatch:

concurrency:
  # Probably overly cautious group naming.
  # Commits to develop will cancel each other, but PRs will only cancel
  # commits within the same PR
  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
  cancel-in-progress: true

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

jobs:
  main_tests:
    if: "github.repository == 'yuxuanzhuang/mdanalysis'"
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    strategy:
        fail-fast: false
        matrix:
          os: [self-hosted, ]
          python-version: ["3.10", "3.11", "3.12"]
          full-deps: [true, ]
          codecov: [true, ]
          include:
            - name: macOS_monterey_py311
              os: macOS-12
              python-version: "3.12"
              full-deps: true
              codecov: true
            - name: macOS_14_arm64_py312
              os: macOS-14
              python-version: "3.12"
              full-deps: false
              codecov: true
            - name: numpy_min
              os: ubuntu-latest
              python-version: "3.10"
              full-deps: false
              codecov: true
              numpy: numpy=1.23.2
            - name: asv_check
              os: ubuntu-latest
              python-version: "3.10"
              full-deps: true
              codecov: false
              extra-pip-deps: asv
    env:
      CYTHON_TRACE_NOGIL: 1
      MPLBACKEND: agg

    steps:
    - uses: actions/checkout@v4

    - name: setup_os
      uses: ./.github/actions/setup-os
      with:
        os-type: ${{ matrix.os }}

    - name: remove_old_micromamba
      run: |
        rm -rf $HOME/micromamba
        rm -rf $HOME/micromamba-bin

    - name: setup_micromamba
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-name: mda
        create-args: >-
          python=${{ matrix.python-version }}
          pip
        # using jaime's shim to avoid pulling down the cudatoolkit
        condarc: |
          channels:
            - jaimergp/label/unsupported-cudatoolkit-shim
            - conda-forge
            - bioconda

    - name: install_deps
      uses: ./.github/actions/setup-deps
      with:
        micromamba: true
        full-deps: ${{ matrix.full-deps }}
        # in most cases will just default to empty, i.e. pick up max version from other deps
        numpy: ${{ matrix.numpy }}
        extra-pip-deps: ${{ matrix.extra-pip-deps }}

    - name: build_srcs
      uses: ./.github/actions/build-src
      with:
        build-tests: true
        build-docs: false
        # The standard mdanalysis deployment is to build with the
        # oldest supported numpy version and then use whatever new
        # numpy version we want at runtime. To do this we ensure
        # that we use build isolation
        isolation: true

    - name: check_deps
      run: |
        micromamba list
        pip list

    - name: run_tests
    
      if: contains(matrix.name, 'asv_check') != true
      run: |
        export OPENBLAS_NUM_THREADS=1
        export GOTO_NUM_THREADS=1
        export OMP_NUM_THREADS=1
        export MKL_NUM_THREADS=1

        export PYTEST_XDIST_AUTO_NUM_WORKERS=2

        PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
        if [ ${{ matrix.codecov }} = "true" ]; then
          PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"
        fi
        echo $PYTEST_FLAGS
        pytest -n auto --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS

    - name: run_asv
      if: contains(matrix.name, 'asv_check')
      run: |
        cd benchmarks
        time python -m asv check -E existing

    - name: codecov
      if: matrix.codecov
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: coverage.xml
        fail_ci_if_error: False
        verbose: True


  build_docs:
    if: "github.repository == 'yuxuanzhuang/mdanalysis'"
    runs-on: ubuntu-latest
    timeout-minutes: 15
    env:
      CYTHON_TRACE_NOGIL: 1
      MPLBACKEND: agg

    steps:
    - uses: actions/checkout@v4

    - name: setup_micromamba
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-name: mda
        create-args: >-
          python=3.10
          pip
        # using jaime's shim to avoid pulling down the cudatoolkit
        condarc: |
          channels:
            - jaimergp/label/unsupported-cudatoolkit-shim
            - conda-forge
            - bioconda

    - name: install_deps
      uses: ./.github/actions/setup-deps
      with:
        micromamba: true
        full-deps: true
        extra-pip-deps: "docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils"
        extra-conda-deps: "mdanalysis-sphinx-theme>=1.3.0"

    - name: build_srcs
      uses: ./.github/actions/build-src
      with:
        build-tests: true
        build-docs: true
        isolation: true

    - name: doctests
      if: github.event_name == 'pull_request'
      continue-on-error: true
      run: |
        cd package && sphinx-build -b doctest --keep-going ./doc/sphinx/source ./doc/html

    - name: deploy_docs
      if: github.event_name != 'pull_request'
      env:
        GH_USER: github-actions
        GH_EMAIL: "github-action@users.noreply.github.com"
        GH_REPOSITORY: "github.com/${{ github.repository }}.git"
        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        URL: https://docs.mdanalysis.org

      run: |
        # set up environment variables
        # cannot execute bash to make variables in env section
        # export URL for the Python script $UPDATE_JSON
        export URL
        export VERSION=$(cd package/MDAnalysis; python -c 'import version; print(version.__version__)')
        UPDATE_JSON=$(pwd)/maintainer/update_json_stubs_sitemap.py
        BRANCH="${GITHUB_REF#refs/heads/}"

        # the below turns off non-blocking as it causes large writes to stdout to fail
        # (see https://github.com/travis-ci/travis-ci/issues/4704)
        # commented out as this is not a problem with gh-actions
        # python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
        cd package/doc/html/

        # move docs into version subfolder
        mkdir ../${VERSION} && mv * ../${VERSION} && mv ../${VERSION} $VERSION

        # set up git
        REV=$(git rev-parse --short HEAD)
        git init
        git config user.name $GH_USER
        git config user.email $GH_EMAIL
        git remote add upstream "https://${GH_USER}:${GH_TOKEN}@${GH_REPOSITORY}"
        git fetch --depth 50 upstream $BRANCH gh-pages
        git reset upstream/gh-pages

        # redirects and copies
        mkdir latest
        python $UPDATE_JSON
        touch .
        touch .nojekyll

        git add -A ${VERSION}/
        git add .nojekyll versions.json *.xml *.html index.html latest

        for dirname in dev stable documentation_pages ; do
          if [ -d $dirname ]; then git add $dirname; fi
        done

        # check for anything to commit
        # https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes
        git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs for version ${VERSION} from branch ${BRANCH} with sphinx at ${REV}"
        git push -q upstream HEAD:gh-pages


  sdist_check_and_build:
    if: "github.repository == 'yuxuanzhuang/mdanalysis'"
    runs-on: ubuntu-latest
    timeout-minutes: 30

    steps:
    - uses: actions/checkout@v4

    - uses: actions/setup-python@v4
      with:
        python-version: 3.11

    - name: install_deps
      run: |
        python -m pip install -U pip pipx wheel build
        python -m pip install twine "readme-renderer>=34.0" pytest-xdist pytest-timeout

    - name: build_package_sdist
      run: |
        pipx run build --sdist --outdir dist package

    - name: build_testsuite_sdist
      run: |
        pipx run build --sdist --outdir dist testsuite

    - name: check_package_build
      run: |
        DISTRIBUTION=$(ls -t1 dist/mdanalysis-*.tar.gz | head -n1)
        test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysis-*.tar.gz found"; exit 1; }
        twine check $DISTRIBUTION

    - name: check_testsuite_build
      run: |
        DISTRIBUTION=$(ls -t1 dist/mdanalysistests-*.tar.gz | head -n1)
        test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysisTests-*.tar.gz found"; exit 1; }
        twine check $DISTRIBUTION

    - name: install sdist
      working-directory: ./dist
      run: |
        ls -a .
        python -m pip install mdanalysis-*.tar.gz
        python -m pip install mdanalysistests-*.tar.gz

    - name: run tests
      working-directory: ./dist
      run: python -m pytest --timeout=200 -n auto --pyargs MDAnalysisTests