markdown/html bug in tutorial fixed (#484) #663
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| name: tests+pypi | |
| defaults: | |
| run: | |
| shell: bash | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| schedule: | |
| - cron: '0 13 * * 4' | |
| release: | |
| types: [published] | |
| jobs: | |
| precommit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: "3.10" | |
| - run: | | |
| pip install pre-commit | |
| pre-commit clean | |
| pre-commit autoupdate | |
| pre-commit run --all-files | |
| nojit_and_codecov: | |
| runs-on: ubuntu-latest | |
| env: | |
| NUMBA_DISABLE_JIT: 1 | |
| steps: | |
| - uses: actions/checkout@master | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: 3.9 | |
| - name: Generate coverage report | |
| run: | | |
| pip install -e .[tests] -e ./examples | |
| pip install pytest-cov | |
| pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PyMPDATA | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| verbose: true | |
| pylint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| # TODO #411 https://github.com/pylint-dev/pylint/issues/9099 | |
| pip install "pylint<3.0.0" nbqa | |
| pip install -e .[tests] -e ./examples[tests] | |
| - run: | | |
| pylint --max-module-lines=500 --disable=fixme $(git ls-files '*.py' | grep -v ^examples) | |
| - run: | | |
| # TODO #299 | |
| pylint --disable=fixme --max-module-lines=200 \ | |
| --disable=too-many-locals,too-many-branches,duplicate-code,invalid-name,missing-function-docstring,missing-module-docstring,too-many-arguments,missing-class-docstring,too-many-instance-attributes $(git ls-files '*.py' | grep ^examples) | |
| - run: | | |
| # TODO #299 | |
| nbqa pylint --disable=fixme,trailing-whitespace,wrong-import-position,wrong-import-order,ungrouped-imports \ | |
| --disable=duplicate-code,invalid-name,missing-module-docstring,line-too-long,missing-function-docstring,redefined-outer-name,too-many-arguments,no-member,too-many-locals,cell-var-from-loop,missing-class-docstring $(git ls-files '*.ipynb') | |
| pdoc: | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-latest, macos-latest, windows-latest] | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| persist-credentials: false | |
| - uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: 3.9 | |
| - env: | |
| JUPYTER_PLATFORM_DIRS: 1 | |
| run: | | |
| pip3 install pdoc nbformat | |
| pip install -e . -e ./examples | |
| python - <<EOF | |
| import glob, nbformat | |
| for notebook_path in glob.glob('examples/PyMPDATA_examples/*/*.ipynb'): | |
| with open(notebook_path, encoding="utf8") as fin: | |
| with open(notebook_path + ".badges.md", 'w') as fout: | |
| fout.write(nbformat.read(fin, nbformat.NO_CONVERT).cells[0].source) | |
| EOF | |
| PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PyMPDATA examples/PyMPDATA_examples -t docs/templates --math | |
| - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }} | |
| uses: JamesIves/github-pages-deploy-action@4.1.1 | |
| with: | |
| BRANCH: pdoc | |
| FOLDER: html | |
| CLEAN: true | |
| zenodo_json: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: notiz-dev/github-action-json-property@release | |
| with: | |
| path: '.zenodo.json' | |
| prop_path: 'creators' | |
| tests: | |
| timeout-minutes: 120 | |
| needs: [nojit_and_codecov, pylint, pdoc, precommit, zenodo_json] | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-latest, macos-13, macos-14, windows-latest] | |
| python-version: ["3.9", "3.12"] | |
| exclude: | |
| - platform: macos-14 | |
| python-version: "3.9" | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: | | |
| python -m pip install $PIP_INSTALL_ARGS -e . # to check if usable without test/example dependencies | |
| python -We -c "import PyMPDATA" | |
| python -m pip install $PIP_INSTALL_ARGS -e .[tests] ./examples | |
| # https://github.com/numba/numba/issues/6350#issuecomment-728174860 | |
| - if: startsWith(matrix.platform, 'ubuntu-') | |
| run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV | |
| - env: | |
| NUMBA_OPT: 1 | |
| run: | | |
| python -m pytest --durations=10 -p no:unraisableexception -We tests/unit_tests | |
| python -m pytest --durations=10 -p no:unraisableexception -We -k "not test_timing_3d" tests/smoke_tests | |
| - env: | |
| NUMBA_OPT: 3 | |
| run: | | |
| python -m pytest --durations=10 -p no:unraisableexception -We -k "test_timing_3d" tests/smoke_tests | |
| examples: | |
| needs: [pylint, precommit] | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-latest, macos-13, macos-14, windows-latest] | |
| python-version: ["3.9", "3.12"] | |
| fail-fast: false | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: python -m pip install $PIP_INSTALL_ARGS -e .[tests] ./examples | |
| - run: python -m pip install $PIP_INSTALL_ARGS -r tests/devops_tests/requirements.txt | |
| - if: matrix.platform == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get install libblitz0-dev libboost-thread-dev libboost-date-time-dev libboost-system-dev libboost-iostreams-dev libboost-timer-dev libboost-filesystem-dev | |
| git clone https://github.com/igfuw/libmpdataxx.git | |
| cd libmpdataxx/libmpdata++ | |
| mkdir build | |
| cd build | |
| cmake .. | |
| sudo make install | |
| cd ../../../ | |
| rm -rf libmpdataxx | |
| - uses: julia-actions/setup-julia@v2 | |
| - run: julia --version | |
| # https://github.com/numba/numba/issues/6350#issuecomment-728174860 | |
| - if: matrix.platform == 'ubuntu-latest' | |
| run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV | |
| - env: | |
| NUMBA_OPT: 1 | |
| run: python -m pytest --durations=10 -p no:unraisableexception -We tests/devops_tests/test_notebooks.py | |
| - if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'}} | |
| run: | | |
| mkdir -p /home/runner/work/_temp/_github_home/figures | |
| rm /tmp/pytest-of-runner/pytest-current/test_run_notebooks_examples_Pycurrent | |
| mv /tmp/pytest-of-runner/pytest-current/test_run_notebooks_examples_*/fig_4.svg /home/runner/work/_temp/_github_home/figures | |
| mv /tmp/pytest-of-runner/pytest-current/test_run_notebooks_examples_*/advection_diffusion.gif /home/runner/work/_temp/_github_home/figures | |
| # - if: ${{ failure() }} | |
| # uses: mxschmitt/action-tmate@v3 | |
| # with: | |
| # limit-access-to-actor: true | |
| - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'}} | |
| uses: eine/tip@master | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| files: | | |
| /github/home/figures/*.svg | |
| /github/home/figures/*.gif | |
| devops: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480 | |
| - run: pip install -r tests/devops_tests/requirements.txt | |
| - run: pip install -e . -e ./examples | |
| - env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not run_notebooks" tests/devops_tests | |
| dist: | |
| strategy: | |
| matrix: | |
| package-dir: [".", "examples"] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| needs: [tests, examples, devops] | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480 | |
| - uses: actions/setup-python@v5.2.0 | |
| with: | |
| python-version: "3.10" | |
| - run: pip install twine build | |
| - run: | | |
| unset CI | |
| cd ${{ matrix.package-dir }} | |
| python -m build 2>&1 | tee build.log | |
| exit `fgrep -v "warning: no previously-included files matching" buid.log | fgrep -i warning | wc -l` | |
| twine check --strict dist/* | |
| exit `tar tzf dist/*.tar.gz | fgrep ".ipynb" | wc -l` | |
| cd .. | |
| - if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| uses: pypa/gh-action-pypi-publish@release/v1.12 | |
| with: | |
| attestations: false | |
| repository_url: https://test.pypi.org/legacy/ | |
| packages-dir: ${{ matrix.package-dir }}/dist | |
| - if: startsWith(github.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@release/v1.12 | |
| with: | |
| attestations: false | |
| packages-dir: ${{ matrix.package-dir }}/dist | |