Showing 446 of 446 total issues
Headers should be surrounded by blank lines Open
PipeConfig file defines Analyses and dependency rules of the pipeline
- Read upRead up
- Exclude checks
MD022 - Headers should be surrounded by blank lines
Tags: headers, blank_lines
Aliases: blanks-around-headers
This rule is triggered when headers (any style) are either not preceded or not followed by a blank line:
# Header 1
Some text
Some more text
## Header 2
To fix this, ensure that all headers have a blank line both before and after (except where the header is at the beginning or end of the document):
# Header 1
Some text
Some more text
## Header 2
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse headers that don't have a blank line before, and will parse them as regular text.
Whitespace before ':' Open
'take_time' : 0
- Read upRead up
- Exclude checks
Avoid extraneous whitespace.
Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.
Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })
E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x
Line too long (84 > 79 characters) Open
self.__created_worker_temp_directory = self.__read_message()['response']
- Read upRead up
- Exclude checks
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 length Open
and generally an Analysis can be viewed as a "base class" for the Jobs that belong to it.
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Trailing spaces Open
---
- Read upRead up
- Exclude checks
MD009 - Trailing spaces
Tags: whitespace
Aliases: no-trailing-spaces
Parameters: br_spaces (number; default: 0)
This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.
The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.
Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.
Line length Open
* Dataflow rules define how data that flows out of an Analysis can be used to trigger creation of Jobs in other Analyses
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Whitespace before ')' Open
self.assertIs( j.param('b'), None, '"b" is None' )
- Read upRead up
- Exclude checks
Avoid extraneous whitespace.
Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.
Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })
E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x
Line length Open
'24Gb_16_core_job' => { 'LSF' => '-n 16 -M24000 -R"select[mem>24000] span[hosts=1] rusage[mem=24000]"' },
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Line length Open
The table below lists the capabilities of each meadow, and whether they are available and implemented:
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Whitespace after '(' Open
self.assertIs( j.param_required('a'), 3, '"a" is 3' )
- Read upRead up
- Exclude checks
Avoid extraneous whitespace.
Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.
Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })
E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x
Line length Open
>This case requires a bit more attention, so please be very careful in including / loading the right libraries / modules.
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Expected 2 blank lines, found 1 Open
class CompleteEarlyException(Exception):
- Read upRead up
- Exclude checks
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 length Open
into a separate software tool and is used in many projects both in Genome Campus, Cambridge and outside.
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Whitespace before ':' Open
'take_time' : 0,
- Read upRead up
- Exclude checks
Avoid extraneous whitespace.
Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.
Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })
E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x
Line length Open
* `-q mpi -a openmpi` is needed to tell LSF you will run a job in the MPI/OpenMPI environment
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Expected 2 blank lines, found 1 Open
class DigitFactory(eHive.BaseRunnable):
- Read upRead up
- Exclude checks
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 (84 > 79 characters) Open
self.__send_message_and_wait_for_OK('PARAM_DEFAULTS', self.param_defaults())
- Read upRead up
- Exclude checks
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.
Lists should be surrounded by blank lines Open
* what should be automatically done with a Job if it needs more memory/time,
- Read upRead up
- Exclude checks
MD032 - Lists should be surrounded by blank lines
Tags: bullet, ul, ol, blank_lines
Aliases: blanks-around-lists
This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:
Some text
* Some
* List
1. Some
2. List
Some text
To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):
Some text
* Some
* List
1. Some
2. List
Some text
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.
Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:
* This is
not okay
* This is
okay
No space after hash on atx style header Open
###The Hive bit
- Read upRead up
- Exclude checks
MD018 - No space after hash on atx style header
Tags: headers, atx, spaces
Aliases: no-missing-space-atx
This rule is triggered when spaces are missing after the hash characters in an atx style header:
#Header 1
##Header 2
To fix this, separate the header text from the hash character by a single space:
# Header 1
## Header 2
Too many blank lines (2) Open
def fetch_input(self):
- Read upRead up
- Exclude checks
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