.flake8

# Can't yet be moved to the pyproject.toml due to https://github.com/PyCQA/flake8/issues/234
[flake8]
max-line-length = 88
ignore = # module imported but unused -> required for Scanpys API
         F401,
         # line break before a binary operator -> black does not adhere to PEP8
         W503,
         # line break occured after a binary operator -> black does not adhere to PEP8
         W504,
         # line too long -> we accept long comment lines; black gets rid of long code lines
         E501,
         # whitespace before : -> black does not adhere to PEP8
         E203,
         # missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
         E231,
         # module level import not at top of file -> required to circumvent circular imports for Scanpys API
         E402,
         # continuation line over-indented for hanging indent -> black does not adhere to PEP8
         E126,
         # E266 too many leading '#' for block comment -> Scanpy allows them for comments into sections
         E262,
         # inline comment should start with '# ' -> Scanpy allows them for specific explanations
         E266,
         # Do not assign a lambda expression, use a def -> Scanpy allows lambda expression assignments,
         E731,
         # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
         E741
 per-file-ignores =
    # F811 Redefinition of unused name from line, does not play nice with pytest fixtures
    tests/test*.py: F811
    # F821 Undefined name, can't import AnnData or it'd be a circular import
    anndata/compat/_overloaded_dict.py: F821
    # E721 comparing types, but we specifically are checking that we aren't getting subtypes (views)
    anndata/tests/test_readwrite.py: E721
exclude =
    .git,
    __pycache__,
    build,
    docs/_build,
    dist,