Bibliography in documentation (data in .json file, scripts checking consistency with DOI mentions in the codebase) #109
Workflow file for this run
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| name: tests | |
| defaults: | |
| run: | |
| shell: bash | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| schedule: | |
| - cron: '0 13 * * 4' | |
| jobs: | |
| precommit: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/[email protected] | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: 3.9 | |
| - run: | | |
| pip install pre-commit | |
| pre-commit clean | |
| pre-commit autoupdate | |
| pre-commit run --all-files | |
| - if: ${{ failure() }} | |
| run: git diff | |
| pylint: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python 3.9 | |
| uses: actions/[email protected] | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| # TODO #1160 https://github.com/pylint-dev/pylint/issues/9099 | |
| pip install "pylint<3.0.0" nbqa | |
| pip install -r tests/devops_tests/requirements.txt | |
| pip install -e ./examples[tests] | |
| pip install -e .[tests] | |
| - run: | | |
| # TODO #682 | |
| pylint --unsafe-load-any-extension=y --disable=fixme,invalid-name,missing-function-docstring,missing-class-docstring,protected-access,duplicate-code $(git ls-files '*.py' | grep -v -e ^examples -e ^tutorials) | |
| - run: | | |
| # TODO #682 | |
| pylint --max-module-lines=550 --unsafe-load-any-extension=y --disable=fixme,too-many-function-args,unsubscriptable-object,consider-using-with,protected-access,too-many-statements,too-many-public-methods,too-many-branches,duplicate-code,invalid-name,missing-function-docstring,missing-module-docstring,missing-class-docstring,too-many-locals,too-many-instance-attributes,too-few-public-methods,too-many-arguments,c-extension-no-member $(git ls-files '*.py' | grep ^examples) | |
| - run: | | |
| # TODO #682 | |
| nbqa pylint --unsafe-load-any-extension=y --disable=fixme,duplicate-code,invalid-name,trailing-whitespace,line-too-long,missing-function-docstring,wrong-import-position,missing-module-docstring,wrong-import-order,ungrouped-imports,no-member,too-many-locals,unnecessary-lambda-assignment $(git ls-files '*.ipynb') | |
| devops: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480 | |
| - run: pip install -r tests/devops_tests/requirements.txt | |
| - env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not test_run_notebooks" tests/devops_tests | |
| zenodo_json: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/[email protected] | |
| - uses: notiz-dev/github-action-json-property@release | |
| with: | |
| path: '.zenodo.json' | |
| prop_path: 'creators' | |
| nojit_and_codecov: | |
| needs: [precommit, pylint, devops, zenodo_json] | |
| runs-on: ubuntu-24.04 | |
| env: | |
| NUMBA_DISABLE_JIT: 1 | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: 3.9 | |
| - name: Generate coverage report | |
| run: | | |
| pip install -e .[tests] | |
| pip install -e ./examples | |
| pip install pytest-cov | |
| pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PySDM | |
| - uses: codecov/[email protected] | |
| with: | |
| fail_ci_if_error: true | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| tests: | |
| needs: [nojit_and_codecov] | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-24.04, macos-13, macos-14, windows-latest] | |
| python-version: ["3.9", "3.12"] | |
| test-suite: ["unit_tests/!(dynamics)", "unit_tests/dynamics/!(collisions)", "unit_tests/dynamics/collisions", "smoke_tests/no_env", "smoke_tests/box", "smoke_tests/parcel_a", "smoke_tests/parcel_b", "smoke_tests/parcel_c", "smoke_tests/parcel_d", "smoke_tests/kinematic_1d", "smoke_tests/kinematic_2d", "tutorials_tests"] | |
| exclude: | |
| - platform: "macos-14" | |
| python-version: "3.9" | |
| - test-suite: "devops_tests" | |
| python-version: "3.9" | |
| # TODO #1406 | |
| - platform: "macos-14" | |
| test-suite: "smoke_tests/box" | |
| - platform: "macos-14" | |
| test-suite: "smoke_tests/parcel_a" | |
| - platform: "macos-14" | |
| test-suite: "smoke_tests/parcel_d" | |
| - platform: "macos-14" | |
| test-suite: "smoke_tests/kinematic_2d" | |
| - platform: "macos-14" | |
| test-suite: "unit_tests/!(dynamics)" | |
| fail-fast: false | |
| runs-on: ${{ matrix.platform }} | |
| timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 30 }} | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: pip install -e . | |
| # sanity check if we do not depend on something from tests extras | |
| - run: python -We -c "import PySDM" | |
| - if: startsWith(matrix.test-suite, 'smoke_tests') || matrix.test-suite == 'tutorials_tests' | |
| run: pip install -e ./examples | |
| # incl. ensuring that the previous pip did not overwrite the package | |
| - run: | | |
| pip install --only-binary :all: -e .[tests] | |
| # install devops_tests for tutorials_tests | |
| - if: matrix.test-suite == 'tutorials_tests' | |
| run: pip install -r tests/devops_tests/requirements.txt | |
| # https://github.com/numba/numba/issues/6350#issuecomment-728174860 | |
| - if: startsWith(matrix.platform, 'ubuntu-') | |
| run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV | |
| - name: Run pytest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NUMBA_OPT: 1 | |
| run: | | |
| shopt -s extglob | |
| pytest --durations=10 --timeout=900 --timeout_method=thread -p no:unraisableexception -We tests/${{ matrix.test-suite }} | |
| # - if: ${{ failure() }} | |
| # uses: mxschmitt/action-tmate@v3 | |
| # with: | |
| # limit-access-to-actor: true | |
| examples-setup: | |
| needs: [nojit_and_codecov] | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-24.04, macos-13, windows-latest] | |
| python-version: ["3.9", "3.12"] | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: | | |
| echo pip_user_site=$(python -c "import sysconfig; print(sysconfig.get_path('purelib'))") >> $GITHUB_ENV | |
| echo toml_ci_md5=$(cat pyproject.toml setup.py examples/pyproject.toml examples/setup.py tests/devops_tests/requirements.txt .github/workflows/tests.yml \ | |
| | python -c "import hashlib;print(hashlib.md5(open(0,'rb').read()).hexdigest())") >> $GITHUB_ENV | |
| - uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: ${{ env.pip_user_site }} | |
| key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }} | |
| lookup-only: true | |
| - if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| python -m pip uninstall -y jupyterlab-server # https://github.com/pypa/pip/issues/6275 | |
| python -m pip install -e . -e ./examples | |
| python -m pip install -r tests/devops_tests/requirements.txt | |
| - if: steps.cache.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{ env.pip_user_site }} | |
| key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }} | |
| examples: | |
| needs: [examples-setup] | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-24.04, macos-13, windows-latest] | |
| python-version: ["3.9", "3.12"] | |
| test-suite: [ "chemistry_freezing", "isotopes", "condensation_a", "condensation_b", "condensation_c", "coagulation", "breakup", "multi-process_a", "multi-process_b", "multi-process_c", "multi-process_d", "multi-process_e"] | |
| fail-fast: false | |
| runs-on: ${{ matrix.platform }} | |
| timeout-minutes: 35 | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: | | |
| echo pip_user_site=$(python -c "import sysconfig; print(sysconfig.get_path('purelib'))") >> $GITHUB_ENV | |
| echo toml_ci_md5=$(cat pyproject.toml setup.py examples/pyproject.toml examples/setup.py tests/devops_tests/requirements.txt .github/workflows/tests.yml \ | |
| | python -c "import hashlib;print(hashlib.md5(open(0,'rb').read()).hexdigest())") >> $GITHUB_ENV | |
| - run: | | |
| rm -rf $pip_user_site | |
| - id: cache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| fail-on-cache-miss: true | |
| path: ${{ env.pip_user_site }} | |
| key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }} | |
| # https://github.com/numba/numba/issues/6350#issuecomment-728174860 | |
| - if: startsWith(matrix.platform, 'ubuntu-') | |
| run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV | |
| - if: startsWith(matrix.platform, 'ubuntu-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b') | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libegl1 libopengl0 ghostscript | |
| wget -nv "https://paraview.org/paraview-downloads/download.php?submit=Download&version=v5.13&type=binary&os=Linux&downloadFile=ParaView-5.13.1-egl-MPI-Linux-Python3.10-x86_64.tar.gz" -O paraview.tar.gz | |
| tar xzf paraview.tar.gz | |
| echo `pwd`/`dirname ParaView*/bin/pvpython` >> $GITHUB_PATH | |
| - if: startsWith(matrix.platform, 'macos-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b') | |
| run: | | |
| brew install --cask paraview | |
| echo `dirname /Applications/ParaView-*.app/Contents/bin/pvpython | head -1` >> $GITHUB_PATH | |
| brew install ghostscript | |
| - if: startsWith(matrix.platform, 'windows-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b') | |
| run: | | |
| curl "https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.13&type=binary&os=Windows&downloadFile=ParaView-5.13.1-Windows-Python3.10-msvc2017-AMD64.msi" -o paraview.msi | |
| msiexec //i paraview.msi //quiet //qn //norestart | |
| echo "C:\\Program Files\\ParaView 5.13.1\\bin\\" >> $GITHUB_PATH | |
| - if: matrix.test-suite == (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b') | |
| run: | | |
| pvpython --version | |
| pvpython -c "from paraview import simple" | |
| - env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| python -m pytest --durations=10 -v -p no:unraisableexception -We tests/examples_tests/test_tests_completeness.py | |
| python -m pytest --durations=10 -v -p no:unraisableexception -We tests/examples_tests/test_run* --suite ${{ matrix.test-suite }} |