[CI] MDAnalysis self-dependency build fix #332
Workflow file for this run
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| 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 |