gh-ci-cron.yaml

name: GH Actions Cron CI
on:
  schedule:
    # 3 am Tuesdays and Fridays
    - cron: "0 3 * * 2,5"
  workflow_dispatch:
  # Uncomment when you need to test on a PR
  pull_request:
    branches:
      - develop


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}

env:
  CYTHON_TRACE_NOGIL: 1
  MPLBACKEND: agg

jobs:
  # a pip only, minimal deps install w/ scipy & numpy nightly upstream wheels
  numpy_and_scipy_dev:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ubuntu-latest
    timeout-minutes: 60

    steps:
    - uses: actions/checkout@v4

    - name: setup_os
      uses: ./.github/actions/setup-os
      with:
        os-type: "ubuntu"

    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    # minimally install nightly wheels & core deps
    - name: nightly_wheels
      run: |
        # Nightlies: add in networkx and matplotlib because we can
        python -m pip install --pre -U --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
            scipy           \
            numpy           \
            networkx        \
            matplotlib      \
        # Base deps
        python -m pip install        \
            "cython>=0.28"           \
            packaging                \
            "setuptools>69.4"        \
            wheel                    \
            "griddataformats>=0.4.0" \
            "mmtf-python>=1.0"      \
            "joblib>=0.12"           \
            "tqdm>=4.43.0"           \
            threadpoolctl            \
            fasteners                \
            mda-xdrlib               \
            pytest                   \
            pytest-xdist             \
            pytest-timeout
        # deps that depend on MDA
        python -m pip install --no-deps \
            waterdynamics   \
            pathsimanalysis \
            mdahole2

    - name: pre_install_list_deps
      run: python -m pip list

    - name: build_srcs
      run: |
        python -m pip install --no-build-isolation -v -e ./package
        python -m pip install --no-build-isolation -v -e ./testsuite

    - name: post_install_list_deps
      run: python -m pip list

    - name: run_tests
      run: |
        pytest --timeout=200 -n auto testsuite/MDAnalysisTests --durations=50 -W error::FutureWarning


  # Issue #3442
  native_march:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ubuntu-latest
    timeout-minutes: 60

    steps:
    - uses: actions/checkout@v4

    - name: setup_os
      uses: ./.github/actions/setup-os
      with:
        os-type: "ubuntu"

    - name: setup_micromamba
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-name: mda
        create-args: >-
          python=3.11
          pip
        condarc: |
          channels:
            - jaimergp/label/unsupported-cudatoolkit-shim
            - conda-forge
            - bioconda

    - name: install_deps
      uses: ./.github/actions/setup-deps
      with:
        micromamba: true
        full-deps: true

    - name: set_extra_flags
      run: |
        sed -i "s/#extra_cflags =/extra_cflags = -march=native -mtune=native/g" package/setup.cfg
        cat package/setup.cfg

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

    - name: run_tests
      run: |
        pytest --timeout=200 -n auto testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50


  old_ubuntu_macos:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-20.04, macos-12]

    steps:
    - uses: actions/checkout@v4

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

    - name: setup_micromamba
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-name: mda
        create-args: >-
          python=3.10
          pip
        condarc: |
          channels:
            - jaimergp/label/unsupported-cudatoolkit-shim
            - conda-forge
            - bioconda

    - name: install_deps
      uses: ./.github/actions/setup-deps
      with:
        micromamba: true
        full-deps: true

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

    - name: run_tests
      run: |
        pytest --timeout=200 -n auto testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50


  # Issue 1727
  pip-only-develop:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ubuntu-latest
    timeout-minutes: 60
    strategy:
        fail-fast: false
        matrix:
          python-version: ["3.10", "3.11", "3.12"]
    steps:
    - uses: actions/checkout@v4

    - name: setup_os
      uses: ./.github/actions/setup-os
      with:
        os-type: "ubuntu"

    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: pip install mdanalysis
      run: |
        cd package && pip install .

    - name: pip install mdanalysistests
      run: |
        cd testsuite && pip install .

    - name: install_pip_extras
      run: |
        pip install pytest-xdist pytest-timeout

    - name: check env
      run: pip list

    - name: run_tests
      run: |
        pytest --timeout=200 -n auto testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
        
  # Issue 4208
  conda-latest-release:
    # A set of runner to check that the latest conda release works as expected
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    strategy:
        fail-fast: false
        matrix:
          # Stick to macos-13 because some of our
          # optional depss don't support arm64 (i.e. macos-14)
          os: [ubuntu-latest, macos-13]
          python-version: ["3.9", "3.10", "3.11", "3.12"]
    steps:
    - uses: actions/checkout@v4

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

    - 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: true

    - name: install_mdanalysis
      run: |
          micromamba install mdanalysis mdanalysistests

    - name: run_tests
      run: |
          pytest --timeout=200 -n auto --pyargs MDAnalysisTests
          
  pypi-latest-release:
    # A set of runner to check that the latest conda release works as expected
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    strategy:
        fail-fast: false
        matrix:
          os: [ubuntu-latest, macos-latest, macos-14, windows-latest]
          python-version: ["3.9", "3.10", "3.11", "3.12"]
          wheels: ['true', 'false']
          exclude:
          - os: "macos-14"
            python-version: "3.9"
    steps:
      # Checkout to have access to local actions (i.e. setup-os)
    - uses: actions/checkout@v4

      # We need this here in order to make sure we assign the correct compiler (i.e. clang for macos)
    - name: setup_os
      uses: ./.github/actions/setup-os
      with:
        os-type: ${{ matrix.os }}

    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: install_mdanalysis
      shell: bash
      run: |
          # If wheels is False we build directly from source so we use the --no-binary flag
          # to avoid pulling down wheels for MDAnalysis (which are already precompiled)
          if [ "${{ matrix.wheels }}" == "false" ]; then
            INSTALL_FLAGS="-vvv --no-binary"
          fi
          pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout

    - name: run_tests
      shell: bash
      run: |
          pytest --timeout=200 -n auto --pyargs MDAnalysisTests