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| [gh-actions] | |
| python = | |
| 3.9: py39 | |
| 3.10: py310 | |
| # 3.8: py38, rst_linux, rst_mac, readme, linters, coverage-report, qa | |
| # 3.11: py311, rst_linux, rst_mac, readme, linters, coverage-report, qa | |
| 3.11: py311, rst_linux, rst_mac, readme, coverage-report | |
| # 3.9: py39 | |
| # 3.10: py310 | |
| [tox] | |
| # todo: add back the linters and qa | |
| # envlist = py39, py310, py311, rst_linux, rst_mac, readme, rst, linters, coverage-report, qa | |
| envlist = py39, py310, py311, rst_linux, rst_mac, readme, rst, coverage-report | |
| [testenv] | |
| ; conda_deps = | |
| ; rdkit | |
| ; conda_channels = rdkit | |
| deps = | |
| -r{toxinidir}/requirements_dev.txt | |
| commands = | |
| # coverage run --rcfile=tox.ini -m pytest tests | |
| python -m pip install --upgrade pip | |
| # pip install -r requirements.txt | |
| # pip install . | |
| # coverage run --source=selector --rcfile=tox.ini -m pytest selector selector/test | |
| # python -m pytest --cov-config=.coveragerc --cov=selector --cov-report=xml --color=yes selector/test | |
| python -m pytest --cov-config=.coveragerc --cov=selector --cov-report=xml --color=yes | |
| # pytest --cov-config=.coveragerc --cov=selector/test | |
| # can run it if needed | |
| # coverage report -m | |
| # prevent exit when error is encountered | |
| ignore_errors = true | |
| [testenv:readme] | |
| skip_install = true | |
| deps = | |
| readme_renderer | |
| twine | |
| commands = | |
| python setup.py sdist bdist_wheel | |
| twine check dist/* | |
| [testenv:rst_linux] | |
| platform = | |
| linux | |
| skip_install = true | |
| deps = | |
| doc8 | |
| rstcheck==3.3.1 | |
| commands = | |
| doc8 --config tox.ini doc/ | |
| # ignore code-block related error because | |
| # the Sphinx support in rstcheck is minimal. This results in false positives | |
| # rstcheck uses Docutils to parse reStructuredText files and extract code blocks | |
| # fixme: check updates on the following website in the future | |
| # coala.gitbooks.io/projects/content/en/projects/rstcheck-with-better-sphinx-suppor.html | |
| rstcheck --recursive doc/ --report error \ | |
| --ignore-directives automodule,autoclass,autofunction,bibliography,code-block \ | |
| --ignore-roles cite,mod,class,lineno --ignore-messages code-block | |
| [testenv:rst_mac] | |
| platform = | |
| darwin | |
| skip_install = true | |
| deps = {[testenv:rst_linux]deps} | |
| commands = {[testenv:rst_linux]commands} | |
| [testenv:linters] | |
| deps = | |
| flake8 | |
| flake8-docstrings | |
| flake8-import-order>=0.9 | |
| flake8-colors | |
| pep8-naming | |
| pylint==2.13.9 | |
| # black | |
| bandit | |
| commands = | |
| flake8 selector/ selector/test setup.py | |
| pylint selector --rcfile=tox.ini --disable=similarities | |
| # black -l 100 --check ./ | |
| # black -l 100 --diff ./ | |
| # Use bandit configuration file | |
| bandit -r selector -c .bandit.yml | |
| ignore_errors = true | |
| [testenv:coverage-report] | |
| deps = coverage>=4.2 | |
| skip_install = true | |
| commands = | |
| # coverage combine --rcfile=tox.ini | |
| coverage report | |
| [testenv:qa] | |
| deps = | |
| {[testenv]deps} | |
| {[testenv:linters]deps} | |
| {[testenv:coverage-report]deps} | |
| commands = | |
| {[testenv]commands} | |
| {[testenv:linters]commands} | |
| # {[testenv:coverage-report]commands} | |
| ignore_errors = true | |
| # pytest configuration | |
| [pytest] | |
| addopts = --cache-clear | |
| --showlocals | |
| -v | |
| -r a | |
| --cov-report term-missing | |
| --cov selector | |
| # Do not run tests in the build folder | |
| norecursedirs = build | |
| # flake8 configuration | |
| [flake8] | |
| exclude = | |
| __init__.py, | |
| .tox, | |
| .git, | |
| __pycache__, | |
| build, | |
| dist, | |
| *.pyc, | |
| *.egg-info, | |
| .cache, | |
| .eggs, | |
| _version.py, | |
| max-line-length = 100 | |
| import-order-style = google | |
| ignore = | |
| # E121 : continuation line under-indented for hanging indent | |
| E121, | |
| # E123 : closing bracket does not match indentation of opening bracket’s line | |
| E123, | |
| # E126 : continuation line over-indented for hanging indent | |
| E126, | |
| # E226 : missing whitespace around arithmetic operator | |
| E226, | |
| # E241 : multiple spaces after ‘,’ | |
| # E242 : tab after ‘,’ | |
| E24, | |
| # E704 : multiple statements on one line (def) | |
| E704, | |
| # W503 : line break occurred before a binary operator | |
| W503, | |
| # W504 : Line break occurred after a binary operator | |
| W504, | |
| # D202: No blank lines allowed after function docstring | |
| D202, | |
| # E203: Whitespace before ':' | |
| E203, | |
| # E731: Do not assign a lambda expression, use a def | |
| E731, | |
| # D401: First line should be in imperative mood: 'Do', not 'Does' | |
| D401, | |
| per-file-ignores = | |
| # F401: Unused import | |
| # this is used to define the data typing | |
| selector/utils.py: F401, | |
| # E1101: rdkit.Chem has no attribute xxx | |
| # D403: first word of the first line should be properly capitalized | |
| selector/feature.py: E1101, D403 | |
| # doc8 configuration | |
| [doc8] | |
| # Ignore target directories and autogenerated files | |
| ignore-path = doc/_build/, build/, selector.egg-info/, selector.egg-info, .*/, doc/intro_about.rst | |
| # File extensions to use | |
| extensions = .rst, .txt | |
| # Maximal line length should be 100 | |
| max-line-length = 100 | |
| # Disable some doc8 checks: | |
| # D000: Check RST validity (cannot handle the "linenos" directive) | |
| # D002: Trailing whitespace | |
| # D004: Found literal carriage return | |
| # Both D002 and D004 can be problematic in Windows platform, line ending is `\r\n`, | |
| # but in Linux and MacOS, it's "\n" | |
| # Known issue of doc8, https://bugs.launchpad.net/doc8/+bug/1756704 | |
| # ignore = D000,D002,D004 | |
| ignore = D000 | |
| # pylint configuration | |
| [MASTER] | |
| # This is a known issue of pylint with recognizing numpy members | |
| # https://github.com/PyCQA/pylint/issues/779 | |
| # https://stackoverflow.com/questions/20553551/how-do-i-get-pylint-to-recognize-numpy-members | |
| extension-pkg-whitelist=numpy | |
| [FORMAT] | |
| # Maximum number of characters on a single line. | |
| max-line-length=100 | |
| [MESSAGES CONTROL] | |
| # disable pylint warnings | |
| disable= | |
| # attribute-defined-outside-init (W0201): | |
| # Attribute %r defined outside __init__ Used when an instance attribute is | |
| # defined outside the __init__ method. | |
| W0201, | |
| # too-many-instance-attributes (R0902): | |
| # Too many instance attributes (%s/%s) Used when class has too many instance | |
| # attributes, try to reduce this to get a simpler (and so easier to use) | |
| # class. | |
| R0902, | |
| # too many branches (R0912) | |
| R0912, | |
| # too-many-arguments (R0913): | |
| # Too many arguments (%s/%s) Used when a function or method takes too many | |
| # arguments. | |
| R0913, | |
| # Too many local variables (r0914) | |
| R0914, | |
| # Too many statements (R0915) | |
| R0915, | |
| # fixme (W0511): | |
| # Used when a warning note as FIXME or XXX is detected. | |
| W0511, | |
| # bad-continuation (C0330): | |
| # Wrong hanging indentation before block (add 4 spaces). | |
| C0330, | |
| # wrong-import-order (C0411): | |
| # %s comes before %s Used when PEP8 import order is not respected (standard | |
| # imports first, then third-party libraries, then local imports) | |
| C0411, | |
| # arguments-differ (W0221): | |
| # Parameters differ from %s %r method Used when a method has a different | |
| # number of arguments than in the implemented interface or in an overridden | |
| # method. | |
| W0221, | |
| # unecessary "else" after "return" (R1705) | |
| R1705, | |
| # Value XX is unsubscriptable (E1136). this is a open issue of pylint | |
| # https://github.com/PyCQA/pylint/issues/3139 | |
| E1136, | |
| # Used when a name doesn't doesn't fit the naming convention associated to its type | |
| # (constant, variable, class…). | |
| C0103, | |
| # Unnecessary pass statement | |
| W0107, | |
| # Module 'rdkit.Chem' has no 'ForwardSDMolSupplier' member (no-member) | |
| E1101, | |
| # todo: fix this one later and this is a temporary solution | |
| # E0401: Unable to import xxx (import-error) | |
| E0401, | |
| # R1721: Unnecessary use of a comprehension | |
| R1721, | |
| # I1101: Module xxx has no yyy member (no-member) | |
| I1101, | |
| # R0903: Too few public methods (too-few-public-methods) | |
| R0903, | |
| # R1702: Too many nested blocks (too-many-nested-blocks) | |
| R1702, | |
| [SIMILARITIES] | |
| min-similarity-lines=5 | |
| # coverage configuration | |
| [run] | |
| branch = True | |
| parallel = True | |
| source = selector | |
| [paths] | |
| source = | |
| selector | |
| .tox/*/lib/python*/site-packages/selector | |
| .tox/pypy*/site-packages/selector | |