Merge pull request #225 from andthum/feat/misc/dtrj-lifetimes/compare… #804
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| # 1.) Format and Lint code | |
| # 2.) Test code | |
| # | |
| # See: | |
| # https://docs.github.com/en/actions/guides/building-and-testing-python | |
| # Keep in sync with `test-skip.yml`. | |
| name: "Tests" | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| paths: | |
| - ".github/**" | |
| - "**.py" | |
| - "**.rst" | |
| - "docs/**" | |
| - ".flake8" | |
| - "pyproject.toml" | |
| - "**requirements*.txt" | |
| tags: | |
| - "v[0-9]*" | |
| release: | |
| jobs: | |
| # TODO: The lint job can be removed in favor of pre-commit.ci when all | |
| # files are formatted with black and are compliant with flake8. | |
| lint: | |
| strategy: | |
| matrix: | |
| os: | |
| - "ubuntu-latest" | |
| python-version: | |
| - "3.9" | |
| runs-on: "${{ matrix.os }}" | |
| steps: | |
| - name: "Checkout repository" | |
| uses: "actions/checkout@v4" | |
| - name: "Set up Python ${{ matrix.python-version }}" | |
| uses: "actions/setup-python@v5" | |
| with: | |
| python-version: "${{ matrix.python-version }}" | |
| - name: "Export ${HOME}/.local/bin to ${PATH}" | |
| # Executable Python binaries are usually stored there. | |
| run: 'echo "${HOME}/.local/bin" >> ${GITHUB_PATH}' | |
| - name: "Get pip cache dir" | |
| # pip's cache path depends on the operating system. See | |
| # https://github.com/actions/cache/blob/main/examples.md#python---pip | |
| # This requires pip >=20.1. | |
| id: "pip-cache" | |
| run: | | |
| python -m pip install --user --upgrade pip | |
| echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT} | |
| - name: "Create/Restore cache" | |
| uses: "actions/cache@v4" | |
| with: | |
| path: "${{ steps.pip-cache.outputs.dir }}/**" | |
| key: | | |
| ${{ runner.os }}-${{ matrix.python-version }}-${{ github.job }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ matrix.python-version }} | |
| ${{ runner.os }} | |
| - name: "Install/Upgrade setuptools and wheel" | |
| run: "python -m pip install --user --upgrade setuptools wheel" | |
| - name: "Install/Upgrade packages in requirements-dev.txt" | |
| run: | | |
| python -m pip install \ | |
| --user \ | |
| --upgrade \ | |
| --requirement requirements-dev.txt | |
| - name: "Check code formatting with black" | |
| # TODO: The --include flag should be removed once all files are | |
| # formatted with black. But as long as this is not the case, | |
| # only check those files that are already formatted. | |
| run: | | |
| python -m black ./ --check --diff --color \ | |
| --include \ | |
| docs/source/conf.py \ | |
| misc/*.py \ | |
| src/mdtools/__init__.py \ | |
| src/mdtools/_metadata.py \ | |
| src/mdtools/box.py \ | |
| src/mdtools/dtrj.py \ | |
| src/mdtools/file_handler.py \ | |
| src/mdtools/functions.py \ | |
| src/mdtools/numpy_helper_functions.py \ | |
| src/mdtools/plot.py \ | |
| src/mdtools/run_time_info.py \ | |
| src/mdtools/scipy_helper_functions.py \ | |
| src/mdtools/select.py \ | |
| src/mdtools/statistics.py \ | |
| src/mdtools/structure.py \ | |
| src/mdtools/version.py \ | |
| scripts/discretization/back_jump*.py \ | |
| scripts/discretization/discrete_pos.py \ | |
| scripts/discretization/kaplan_meier*.py \ | |
| scripts/discretization/plot_*.py \ | |
| scripts/discretization/state_lifetime* \ | |
| scripts/dynamics/extract_renewal_events.py \ | |
| scripts/dynamics/lifetime_autocorr*.py \ | |
| scripts/dynamics/msd_layer*.py \ | |
| scripts/dynamics/plot_msd_layer*.py \ | |
| scripts/gmx/*.py \ | |
| scripts/other/*.py \ | |
| scripts/structure/densmap.py \ | |
| scripts/structure/lig_change_at_pos_change_blocks.py \ | |
| scripts/structure/subvolume_charge.py \ | |
| scripts/structure/plot_gmx_densmap.py \ | |
| scripts/structure/rmsd_vs_time.py \ | |
| scripts/templates/*.py \ | |
| *.py | |
| - name: "Lint code and docstrings with flake8" | |
| # Use setup.cfg to configure flake8 | |
| # TODO: The --select flag should be removed once all files are | |
| # revised to be compliant with flake8. But as long as this is | |
| # not the case, select only those error codes that have been | |
| # fixed in all files. | |
| # | |
| # F821 ("undefined name name") gives false positives in | |
| # doctests, because it does not recognize `doctest_global_setup` | |
| # in the Sphinx configuration file `conf.py`. | |
| # | |
| # W504 ("line break after binary operator") is turned on in the | |
| # .flake config file but the error code isn't fixed in all | |
| # files, yet. So, ignore it in the CI workflow for now. | |
| # | |
| # The other ignored error codes are copied from the .flake8 | |
| # config file. | |
| run: | | |
| python -m flake8 ./ \ | |
| --select=\ | |
| E1,E2,E3,E4,E9,\ | |
| F4,F7,F63,F82,\ | |
| W1,W2,W3 \ | |
| --extend-ignore=\ | |
| S101,\ | |
| D205,D400,\ | |
| E203,W503,\ | |
| S404,S603,\ | |
| B028,\ | |
| N806,N813,\ | |
| W504,\ | |
| F821 | |
| test: | |
| strategy: | |
| matrix: | |
| # Tests must be run on all target platforms and Python versions. | |
| os: | |
| - "ubuntu-latest" | |
| - "macos-latest" | |
| - "windows-latest" | |
| python-version: | |
| - "3.6" | |
| - "3.7" | |
| - "3.8" | |
| - "3.9" | |
| # Python 3.6 is not supported anymore in the Ubuntu 22.04 runner | |
| # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877 | |
| exclude: | |
| - os: "ubuntu-latest" | |
| python-version: "3.6" | |
| include: | |
| - os: "ubuntu-20.04" | |
| python-version: "3.6" | |
| # Do not cancel in-progress jobs if any matrix job fails | |
| fail-fast: false | |
| runs-on: "${{ matrix.os }}" | |
| steps: | |
| - name: "Checkout repository" | |
| uses: "actions/checkout@v4" | |
| - name: "Set up Python ${{ matrix.python-version }}" | |
| uses: "actions/setup-python@v5" | |
| with: | |
| python-version: "${{ matrix.python-version }}" | |
| - name: "Export ${HOME}/.local/bin to ${PATH}" | |
| # Executable Python binaries are usually stored there. | |
| run: 'echo "${HOME}/.local/bin" >> ${GITHUB_PATH}' | |
| - name: "Get pip cache dir" | |
| # pip's cache path depends on the operating system. See | |
| # https://github.com/actions/cache/blob/main/examples.md#python---pip | |
| # This requires pip >=20.1. | |
| id: "pip-cache" | |
| run: | | |
| python -m pip install --user --upgrade pip | |
| echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT} | |
| - name: "Create/Restore cache" | |
| uses: "actions/cache@v4" | |
| with: | |
| path: | | |
| ${{ steps.pip-cache.outputs.dir }}/** | |
| ./docs/build/** | |
| key: | | |
| ${{ runner.os }}-${{ matrix.python-version }}-${{ github.job }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ matrix.python-version }} | |
| ${{ runner.os }} | |
| - name: "Install/Upgrade setuptools and wheel" | |
| # MDAnalysis requires NumPy (>=1.19.2) for setup (see also | |
| # https://github.com/MDAnalysis/mdanalysis/issues/3374#issuecomment-889189979). | |
| # MDAnalysis <3.0 requires Cython <3.0 (see | |
| # https://github.com/MDAnalysis/mdanalysis/pull/4129 and | |
| # https://github.com/cython/cython/issues/3690). | |
| # Without `python-dev-tools` the installation of MDAnalysis | |
| # fails on MacOS-latest with Python 3.9 while building the wheel | |
| # for MDAnalysis. Strangely, the MDAnalysis wheel is only build | |
| # on this OS-Python combination, whereas other OS-Python | |
| # combinations fetch a pre-build wheel. | |
| run: | | |
| python -m pip install --user --upgrade setuptools wheel | |
| python -m pip install --user --upgrade python-dev-tools | |
| python -m pip install --user "Cython <3.0" | |
| python -m pip install --user "numpy >=1.19.2" | |
| - name: "Test installation of MDTools" | |
| run: | | |
| python -m pip install --user . | |
| python -c "import mdtools" | |
| # Test import of all modules that must be loaded explicitly. | |
| python -c "import mdtools.plot" | |
| - name: "Install/Upgrade requirements to build the documentation" | |
| run: | | |
| python -m pip install --user --upgrade -r docs/requirements-docs.txt | |
| - name: "Test build of the documentation" | |
| run: "make -C ./docs/ html" | |
| - name: "doctest" | |
| # Because the default dtypes of NumPy arrays are different on | |
| # Windows, doctest will detect false failures. See e.g. | |
| # https://stackoverflow.com/questions/36278590/numpy-array-dtype-is-coming-as-int32-by-default-in-a-windows-10-64-bit-machine | |
| if: "${{ runner.os != 'Windows' }}" | |
| run: "make -C ./docs/ doctest" | |
| - name: "linkcheck" | |
| if: "${{ runner.os == 'Linux' && matrix.python-version == '3.9' }}" | |
| run: "make -C ./docs/ linkcheck" | |
| - name: "Install/Upgrade PyTest" | |
| run: "python -m pip install --user --upgrade pytest" | |
| - name: "Test code with pytest" | |
| run: "python -m pytest ./" |