improving docstring (and definition?!) of mean free path in diffusion kinetics #1145

Workflow file for this run

.github/workflows/tests+artifacts+pypi.yml at df15976

	name: tests+artifacts+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@v1
	with:
	python-version: 3.8
	- run: \|
	pip install pre-commit
	pre-commit clean
	pre-commit autoupdate
	pre-commit run --all-files
	- if: ${{ failure() }}
	run: git diff

	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@master
	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
	- if: github.event_name == 'push' && github.ref == 'refs/heads/main'
	uses: codecov/codecov-action@v2
	with:
	fail_ci_if_error: true
	verbose: true

	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@v2
	with:
	python-version: 3.9
	- run: \|
	pip install pdoc3
	pip install -e .
	pip install -e examples
	python -We -m pdoc --html PySDM examples/PySDM_examples
	python -We .github/workflows/pdoc_index_workaround.py
	- 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

	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@v2
	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 pdoc3 # (pdoc3 for checking the .github/workflows/pdoc_index_workaround.py)
	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')

	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:
	needs: [pylint, pdoc, nojit_and_codecov, precommit, zenodo_json]
	strategy:
	matrix:
	platform: [ubuntu-latest, macos-12, windows-latest]
	python-version: ["3.8", "3.11"]
	test-suite: ["unit_tests", "smoke_tests/no_env", "smoke_tests/box", "smoke_tests/parcel", "smoke_tests/kinematic_1d", "smoke_tests/kinematic_2d", "tutorials_tests"]
	exclude:
	- test-suite: "devops_tests"
	python-version: "3.8"
	fail-fast: false
	runs-on: ${{ matrix.platform }}
	timeout-minutes: 90
	steps:
	- uses: actions/checkout@v2
	with:
	submodules: recursive
	fetch-depth: 0
	- uses: actions/setup-python@v1
	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"

	- run: \|
	pip install -e ./examples
	pip install -e .[tests]

	# ensure previous pip did not overwrite the package
	- run: \|
	pip install -e .

	# https://github.com/numba/numba/issues/6350#issuecomment-728174860
	- if: startsWith(matrix.platform, 'ubuntu-')
	run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV

	# install devops_tests for tutorials_tests
	- if: matrix.test-suite == 'tutorials_tests'
	run: pip install -r tests/devops_tests/requirements.txt

	- env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: pytest --durations=10 --timeout=900 --timeout_method=thread -p no:unraisableexception -We tests/${{ matrix.test-suite }}

	# - if: ${{ failure() }}
	# uses: mxschmitt/action-tmate@v3
	# with:
	# limit-access-to-actor: true

	examples:
	needs: [pylint, precommit]
	strategy:
	matrix:
	platform: [ubuntu-22.04, macos-12, windows-latest]
	python-version: ["3.8", "3.11"]
	test-suite: [ "aqueous_chemistry", "freezing", "condensation", "coagulation", "breakup", "multi-process", "isotopes"]
	fail-fast: false
	runs-on: ${{ matrix.platform }}
	steps:
	- uses: actions/checkout@v2
	with:
	submodules: recursive
	fetch-depth: 0
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- run: \|
	python -m pip install --upgrade --user pip
	- run: \|
	python -m pip install -e . ./examples
	python -m 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

	- if: startsWith(matrix.platform, 'ubuntu-')
	run: \|
	sudo apt-get update
	sudo apt-get install python3-paraview
	- if: startsWith(matrix.platform, 'macos-')
	run: \|
	brew install --cask paraview
	echo `dirname /Applications/ParaView-*.app/Contents/bin/pvpython \| head -1` >> $GITHUB_PATH
	- if: matrix.platform != 'windows-latest'
	run: pvpython --version

	- 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 }}

	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
	- env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not test_run_notebooks" tests/devops_tests

	package:
	strategy:
	matrix:
	packages-dir: [".", "examples"]
	fail-fast: false
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	with:
	submodules: recursive
	fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480
	- uses: actions/setup-python@v2
	with:
	python-version: "3.11"

	- run: pip install twine build

	- run: \|
	unset CI
	cd ${{ matrix.packages-dir }}
	python -m build 2>&1 \| tee build.log
	exit `fgrep -i warning build.log \| grep -v impl_numba/warnings.py \| grep -v "no previously-included files matching" \| wc -l`
	twine check --strict dist/*

	- uses: actions/upload-artifact@v2
	with:
	path: ${{ matrix.packages-dir}}/dist
	name: dist

	pkg_install_check:
	strategy:
	matrix:
	platform: [ubuntu-latest, macos-latest, windows-latest]
	python-version: ["3.8", "3.11"]
	runs-on: ${{ matrix.platform }}
	needs: [package]
	steps:
	- uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v2
	with:
	name: dist
	path: dist
	- run: pip install dist/*.whl
	- run: python -c "import PySDM; print(PySDM.__version__)"
	- run: python -c "import PySDM_examples; print(PySDM_examples.__version__)"

	publish:
	runs-on: ubuntu-latest
	needs: [tests, examples, devops, package, pkg_install_check]
	permissions:
	id-token: write
	steps:
	- uses: actions/download-artifact@v2
	with:
	name: dist
	path: dist

	- if: github.event_name == 'push' && github.ref == 'refs/heads/main'
	uses: pypa/gh-action-pypi-publish@unstable/v1
	with:
	repository_url: https://test.pypi.org/legacy/
	packages-dir: dist

	- if: startsWith(github.ref, 'refs/tags')
	uses: pypa/gh-action-pypi-publish@unstable/v1
	with:
	packages-dir: dist

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improving docstring (and definition?!) of mean free path in diffusion kinetics #1145

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improving docstring (and definition?!) of mean free path in diffusion kinetics #1145

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