Showing 272 of 273 total issues
Trailing whitespace Open
count, docs = r_manager.get_kinlaw_by_rxn(substrates, products, dof=dof,
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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 (111 > 79 characters) Open
species='homo sapiens', projection="{'kegg_meta.gene_ortholog': 0, 'kegg_meta._id': 0, '_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.
Line too long (98 > 79 characters) Open
type=str, default='default value of opt-arg-1', help='Description of opt-arg-3')),
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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 (119 > 79 characters) Open
org_format (:obj:`str`, optional): format of species identifier (tax_id or tax_name). Defaults to 'tax_id'.
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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 (153 > 79 characters) Open
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.
Too many blank lines (2) Open
class get_distinct():
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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 (82 > 79 characters) Open
p_manager_new = query_manager.Manager().protein_manager(database="datanator-test")
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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 (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.
Trailing whitespace Open
return list(kinlaw_ids)
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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 (87 > 79 characters) Open
docs = r_manager.get_info_by_entryid(entry_id, target_organism=target_organism,
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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 (85 > 79 characters) Open
return r_manager.collection.count_documents({'parameter.observed_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 (115 > 79 characters) Open
return path_match.group('extended_path').replace('/', '.') if path_match.group('extended_path') else ''
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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
No newline at end of file Open
return result
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Trailing blank lines are superfluous.
Okay: spam(1)
W391: spam(1)\n
However the last line should end with a new line (warning W292).
Line too long (93 > 79 characters) Open
tax_field(:obj:`str`, optional): Field containing taxon information in documents.
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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 (86 > 79 characters) Open
includes=includes, excludes=excludes)
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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.
Too many blank lines (2) Open
class gene_ranked_by_ko:
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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
No newline at end of file Open
return manager.page(_from=_from, size=size)
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Trailing blank lines are superfluous.
Okay: spam(1)
W391: spam(1)\n
However the last line should end with a new line (warning W292).
Line too long (80 > 79 characters) Open
count, docs = r_manager.get_kinlaw_by_rxn(substrates, products, dof=dof,
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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
skip=_from, limit=size)
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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)