.flake8

# Flake8 configuration file.
# Written in INI language.
# See https://flake8.pycqa.org/en/latest/user/configuration.html
#
# Sort all entries alphabetically!
#
# Keep Flake8 plugins in sync with `requirements-dev.txt` and
# `.pre-commit-config.yaml`!


[flake8]
# Print the total number of errors.
count = true
docstring-convention = numpy
# Enable PyFlakes syntax checking of doctests in docstrings.
doctests = true
extend-exclude =
    .build/,
    build/,
    .cache/,
    cache/,
    *.cover,
    cover/,
    .coverage,
    .coverage.*,
    develop-eggs/,
    dist/,
    *.egg,
    *.egg-info/,
    .eggs/,
    eggs/,
    .git,
    .hypothesis/,
    .installed.cfg,
    lib/,
    lib64/,
    .mypy_cache/,
    .nox,
    __pycache__,
    __pypackages__,
    .pytest_cache/,
    .Python,
    .pytype/,
    sdist/,
    .tox,
    wheels/,
    # Virtual Python environments
    *env*/,
    *venv*/,
    *ENV*/,
    *VENV*/,
extend-ignore =
    ### Allow assert statements for consitency checks ###
    # S101: Use of assert detected
    S101,
    ### Allow docstring summaries that are longer than one line ###
    # D205: 1 blank line required between summary line and description
    # D400: First line should end with a period
    D205,
    D400,
    ### Compatibility with black ###
    # E203: whitespace before ':'
    # W503: line break before binary operator
    E203,
    W503,
    ### Bandit ###
    # S404: Consider possible security implications associated with the
    #       subprocess module
    # S603: subprocess call - check for execution of untrusted input
    S404,
    S603,
    ### flake8-bugbear ###
    # B028 No explicit stacklevel keyword argument found.
    B028,
    ### pep8-naming ###
    # N806: variable in function should be lowercase
    # N813: camelcase imported as lowercase
    N806,
    N813,
extend-select =
    ### Compatibility with black ###
    # W504: line break after binary operator
    W504,
# List of glob patterns to include for checks.
filename = *.py
# Number of spaces used for indentation.
indent-size = 4
# Maximum allowed McCabe complexity
max-complexity = 20
# Maximum allowed line length of a comment or docstring.
max-doc-length = 72
# Maximum allowed line length for code.
max-line-length = 79
# Require specific plugins to be installed before running.
require-plugins =
    flake8-bandit,
    flake8-bugbear,
    flake8-builtins,
    flake8-comprehensions,
    flake8-docstrings,
    flake8-isort,
    flake8-logging-format,
    flake8-pytest-style,
    flake8-rst-docstrings,
    pep8-naming,
# Allowed reStructuredText directives.
# See https://github.com/peterjc/flake8-rst-docstrings/pull/16
rst-directives =
    autosummary,
    moduleauthor,
    # reStructuredText admonitions from
    # https://docutils.sourceforge.io/docs/ref/rst/directives.html
    attention,
    caution,
    danger,
    error,
    hint,
    important,
    note,
    tip,
    todo,
    warning,
    # Spinx-specific directives from
    # https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html
    centered,
    code-block,
    codeauthor,
    deprecated,
    glossary,
    highlight,
    hlist,
    index,
    literalinclude,
    math,
    note,
    only,
    productionlist,
    rubric,
    sectionauthor,
    seealso,
    tabularcolumns,
    toctree,
    versionadded,
    versionchanged,
    warning,
    # Spinx-specific domains from
    # https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html
    attribute,
    class,
    classmethod,
    currentmodule,
    data,
    decorator,
    decoratormethod,
    default-domain,
    exception,
    function,
    method,
    module,
    property,
    staticmethod,
    # sphinx.ext.doctest directives from
    # https://www.sphinx-doc.org/en/master/usage/extensions/doctest.html
    doctest,
    testcleanup,
    testcode,
    testoutput,
    testsetup,
# Allowed reStructuredText roles.
# See https://github.com/peterjc/flake8-rst-docstrings/pull/16
rst-roles =
    ref,
    # Self-defined roles:
    bash,
    # reStructuredText Interpreted Text Roles from
    # https://docutils.sourceforge.io/docs/ref/rst/roles.html
    code,
    emphasis,
    literal,
    math,
    pep-reference,
    raw,
    rfc-reference,
    strong,
    subscript,
    superscript,
    title-reference,
    # Spinx-specific roles from
    # https://www.sphinx-doc.org/en/master/usage/restructuredtext/roles.html
    abbr,
    any,
    code,
    command,
    dfn,
    doc,
    download,
    envvar,
    eq,
    file,
    guilabel,
    kbd,
    keyword,
    mailheader,
    makevar,
    manpage,
    math,
    menuselection,
    mimetype,
    newsgroup,
    numref,
    option,
    pep,
    program,
    ref,
    regexp,
    rfc,
    samp,
    term,
    token,
    # Spinx-specific domains from
    # https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html
    attr,
    class,
    const,
    data,
    exc,
    func,
    meth,
    mod,
    obj,
# Allowed reStructuredText roles.
# See https://github.com/peterjc/flake8-rst-docstrings/pull/62
rst-substitutions =
    # Self-defined substitutions:
    dev_guide,
    GNU_GPLv3,
    Git,
    Git_Book,
    GitHub,
    Issue,
    Q&A,
    GCC,
    Lmod,
    Gromacs,
    Python,
    format_specifier,
    PyPI,
    pip,
    virtual_Python_environment,
    venv,
    Black,
    isort,
    Flake8,
    pytest,
    NumPy,
    SciPy,
    matplotlib,
    MDAnalysis,
    MDA_user_guide,
    file-like_object,
    npy_file,
    npz_archive,
    RTD,
    Sphinx,
    RST,
    RST_option_list,
    NumPy_docstring_convention,
    MDA_trj,
    MDA_trjs,
    trajectory_and_topology_formats,
    supported_coordinate_formats,
    supported_topology_formats,
    selection_syntax,
    explanation_of_these_terms,
    MDA_always_guesses_atom_masses,
    shfmt,
    shfmt-py,
    shellcheck,
    shellcheck-py,
    markdownlint,
# Print the source code generating the error/warning in question.
show-source = true
# Count the number of occurrences of each error/warning.
statistics = true