pombo-lab/gamtools

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Unexpected spaces around keyword / parameter equals
Open

    ext_modules = cythonize(extensions, language_level = "3"),
Severity: Minor
Found in setup.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Line too long (81 > 79 characters)
Open

    window_in_region = np.logical_and( #pylint: disable=assignment-from-no-return
Severity: Minor
Found in lib/gamtools/segregation.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (2)
Open

    return [c for c in segregation_table.index.get_level_values(0).unique()
Severity: Minor
Found in lib/gamtools/segregation.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Indentation contains tabs
Open

       ]
Severity: Minor
Found in setup.py by pep8

On new projects, spaces-only are strongly recommended over tabs.

Okay: if True:\n    return
W191: if True:\n\treturn

FIXME found
Open

notes=FIXME,XXX,TODO
Severity: Minor
Found in .pylintrc by fixme

XXX found
Open

notes=FIXME,XXX,TODO
Severity: Minor
Found in .pylintrc by fixme

TODO found
Open

    # TODO: Convert from interactions csv back into a matrix
Severity: Minor
Found in lib/gamtools/matrix.py by fixme

TODO found
Open

    # TODO: Handle split interactions where one half is permuted past the
Severity: Minor
Found in lib/gamtools/enrichment.py by fixme

TODO found
Open

notes=FIXME,XXX,TODO
Severity: Minor
Found in .pylintrc by fixme

TODO found
Open

        # TODO: Allow specification of which chromosomes to generate matrices
Severity: Minor
Found in lib/gamtools/pipeline.py by fixme

TODO found
Open

    # TODO: Check that this file doesn't exist
Severity: Minor
Found in lib/gamtools/enrichment.py by fixme

TODO found
Open

    # TODO: Fix passing additional arguments to py.test
Severity: Minor
Found in lib/gamtools/main.py by fixme

TODO found
Open

    #TODO: Refactor this function
Severity: Minor
Found in lib/gamtools/bias.py by fixme
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