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

concurrency:
  # Probably overly cautious group naming.
  # Commits to develop/master 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 == 'MDAnalysis/mdanalysis'"
    runs-on: ${{ matrix.os }}
    strategy:
        fail-fast: false
        matrix:
          os: [ubuntu-latest, ]
          python-version: ["3.8", "3.9", "3.10"]
          full-deps: [true, ]
          install_hole: [true, ]
          codecov: [true, ]
          include:
            - name: py311-ubuntu-min
              os: ubuntu-latest
              python-version: "3.11"
              full-deps: false
              install_hole: true
              codecov: false
            - name: macOS_monterey_py39
              os: macOS-12
              python-version: 3.9
              full-deps: true
              install_hole: true
              codecov: true
            - name: macOS_bigsur_py38
              os: macOS-11
              python-version: 3.8
              full-deps: true
              install_hole: true
              codecov: false
            - name: minimal-ubuntu
              os: ubuntu-latest
              python-version: 3.8
              full-deps: false
              install_hole: false
              codecov: true
            - name: numpy_min
              os: ubuntu-latest
              python-version: 3.8
              full-deps: false
              install_hole: false
              codecov: false
              numpy: numpy=1.20.0
            - name: asv_check
              os: ubuntu-latest
              python-version: 3.8
              full-deps: true
              install_hole: false
              codecov: false
              extra-pip-deps: asv
    env:
      CYTHON_TRACE_NOGIL: 1
      MPLBACKEND: agg

    steps:
    - uses: actions/checkout@v3

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

    - name: setup_miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        auto-update-conda: true
        channel-priority: flexible
        channels: conda-forge, bioconda
        add-pip-as-python-dependency: true
        mamba-version: "*"
        architecture: x64

    - name: install_deps
      uses: ./.github/actions/setup-deps
      with:
        mamba: 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-hole: ${{ matrix.install_hole }}
        build-tests: true
        build-docs: false

    - name: run_tests
      if: contains(matrix.name, 'asv_check') != true
      run: |
        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 $numprocs 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: True
        verbose: True


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

    steps:
    - uses: actions/checkout@v3

    - name: setup_miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: 3.8
        auto-update-conda: true
        channel-priority: flexible
        channels: conda-forge, bioconda
        add-pip-as-python-dependency: true
        architecture: x64
        mamba-version: "*"

    - name: install_deps
      uses: ./.github/actions/setup-deps
      with:
        mamba: true
        full-deps: true
        extra-pip-deps: "sphinx sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0 sphinxcontrib-bibtex pybtex pybtex-docutils"

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

    - 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/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


  pylint_check:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - uses: actions/setup-python@v4
      with:
        python-version: 3.8

    - name: install
      run: |
        python -m pip install pylint

    - name: pylint
      env:
        PYLINTRC: package/.pylintrc
      run: |
        pylint package/MDAnalysis && pylint testsuite/MDAnalysisTests


  darker_lint:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash

    steps:
    - uses: actions/checkout@v3
      with:
        fetch-depth: 0

    - uses: actions/setup-python@v4
      with:
        python-version: 3.8

    - name: darker main code
      uses: akaihola/darker@1.5.1
      with:
        version: "@master"
        options: "--check --diff --color"
        src: "./package/MDAnalysis"
        revision: "HEAD^"
        lint: "flake8"

    - name: darker test code
      uses: akaihola/darker@1.5.1
      if: success() || failure()
      with:
        version: "@master"
        options: "--check --diff --color"
        src: "./testsuite/MDAnalysisTests"
        revision: "HEAD^"
        lint: "flake8"


  pypi_check:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: ./package

    steps:
    - uses: actions/checkout@v3

    - uses: actions/setup-python@v4
      with:
        python-version: 3.8

    - name: install_deps
      run: |
        python -m pip install twine "readme-renderer>=34.0"

    - name: build_sdist
      run: |
        pipx run build --sdist

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