Showing 272 of 273 total issues
Line too long (109 > 79 characters) Open
result = mm_manager.db_obj['metabolite_concentrations'].find_one(filter=query, projection={'_id': 0})
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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.
Missing whitespace after ':' Open
return ey_manager.get_conc_from_inchi(inchi_key, inchi_key=True, projection={'_id':0, 'concentrations': 1})
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Each comma, semicolon or colon should be followed by whitespace.
Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]
Line too long (139 > 79 characters) Open
docs = dist_manager.arrange_distance_objs(docs, target_species=target_species, tax_field='species_name', org_format='tax_name')
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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.
Blank line contains whitespace Open
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Trailing whitespace is superfluous.
The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.
Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n \n bang = 12
Line too long (107 > 79 characters) Open
# for doc in p_manager.db_obj['uniprot'].aggregate(pipeline, hint="modifications.reference_1"):
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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.
Line too long (130 > 79 characters) Open
docs = dist_manager.arrange_distance_objs(docs, target_species=species, tax_field='taxon_name', org_format='tax_name')
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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.
Line too long (101 > 79 characters) Open
obj_name(:obj:`str`, optional): name of the object containing taxon distance information.
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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.
Line too long (102 > 79 characters) Open
dist = manager.get_canon_common_ancestor_fast(name, target_species, org_format=org_format)
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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.
Line too long (96 > 79 characters) Open
(:obj:`list` of :obj:`Obj`): List of documents that have the taxon_distance objects.
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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.
Line too long (94 > 79 characters) Open
def get(inchikey, threshold=0.6, target_species='homo sapiens', taxon_distance=False):
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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.
Line too long (118 > 79 characters) Open
doc = mm_manager.db_obj['metabolite_concentrations'].find_one({'InChI_Key': inchikey}, projection=projection)
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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.
Trailing whitespace Open
# return doc['total']
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Trailing whitespace is superfluous.
The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.
Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n \n bang = 12
Line too long (80 > 79 characters) Open
version=datanator_rest_api.__version__)),
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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.
Line too long (92 > 79 characters) Open
return '{}.{}{}'.format(get_controller_name(), get_path_name(), get_function_name())
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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.
Continuation line under-indented for visual indent Open
target_species, org_format='tax_id',
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Continuation lines indentation.
Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.
When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
as a continuation line.
Okay: a = (\n)
E123: a = (\n )
Okay: a = (\n 42)
E121: a = (\n 42)
E122: a = (\n42)
E123: a = (\n 42\n )
E124: a = (24,\n 42\n)
E125: if (\n b):\n pass
E126: a = (\n 42)
E127: a = (24,\n 42)
E128: a = (24,\n 42)
E129: if (a or\n b):\n pass
E131: a = (\n 42\n 24)
Line too long (87 > 79 characters) Open
docs = mc_manager.get_similar_concentrations(inchikey, threshold=threshold)
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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.
Blank line contains whitespace Open
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Trailing whitespace is superfluous.
The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.
Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n \n bang = 12
Too many blank lines (2) Open
class num_obs_abundances():
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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
Line too long (87 > 79 characters) Open
pipeline = pipelines.Pipeline().aggregate_total_array_length("observation")
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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.
Continuation line under-indented for visual indent Open
tax_field='species_name', obj_name='taxon_distance'):
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Continuation lines indentation.
Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.
When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
as a continuation line.
Okay: a = (\n)
E123: a = (\n )
Okay: a = (\n 42)
E121: a = (\n 42)
E122: a = (\n42)
E123: a = (\n 42\n )
E124: a = (24,\n 42\n)
E125: if (\n b):\n pass
E126: a = (\n 42)
E127: a = (24,\n 42)
E128: a = (24,\n 42)
E129: if (a or\n b):\n pass
E131: a = (\n 42\n 24)