Showing 446 of 446 total issues
Spaces inside link text Open
####If your compute environment uses [Module ](http://modules.sourceforge.net/)
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MD039 - Spaces inside link text
Tags: whitespace, links
Aliases: no-space-in-links
This rule is triggered on links that have spaces surrounding the link text:
[ a link ](http://www.example.com/)
To fix this, remove the spaces surrounding the link text:
[a link](http://www.example.com/)
Line length Open
or claim some more. When a Worker discovers that its predefined time is up or that there are no more Jobs to do,
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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.
Lists should be surrounded by blank lines Open
* **LOCAL**. A simple meadow that submits jobs locally via `system()` (i.e. `fork()`). It is inherently limited by the specification of the machine beekeeper is running on.
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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
Line length Open
| Post-mortem inspection of resource usage | Not available | Yes | Not implemented |
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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.
Unordered list indentation Open
- Do not modify code without testing for regression.
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MD007 - Unordered list indentation
Tags: bullet, ul, indentation
Aliases: ul-indent
Parameters: indent (number; default 2)
This rule is triggered when list items are not indented by the configured number of spaces (default: 2).
Example:
* List item
* Nested list item indented by 3 spaces
Corrected Example:
* List item
* Nested list item indented by 2 spaces
Rationale (2 space indent): indenting by 2 spaces allows the content of a nested list to be in line with the start of the content of the parent list when a single space is used after the list marker.
Rationale (4 space indent): Same indent as code blocks, simpler for editors to implement. See http://www.cirosantilli.com/markdown-styleguide/#indented-lists for more information.
In addition, this is a compatibility issue with multi-markdown parsers, which require a 4 space indents. See http://support.markedapp.com/discussions/problems/21-sub-lists-not-indenting for a description of the problem.
Unexpected spaces around keyword / parameter equals Open
def dataflow(self, output_ids, branch_name_or_code = 1):
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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 length Open
- Review the [development guidelines](https://ensembl-hive.readthedocs.io/en/master/dev/development_guidelines.html#ehive-development-in-a-nutshell) for eHive; remember in particular:
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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
7. On the "version/x.y" branch in README.md file substitute the occurences of "HEAD" in the URLs by "version/x.y" (for rawgit) and commit it.
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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
- Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
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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 too long (221 > 79 characters) Open
self.__send_message('DATAFLOW', {'output_ids': output_ids, 'branch_name_or_code': branch_name_or_code, 'params': {'substituted': self.__params.param_hash, 'unsubstituted': self.__params.unsubstituted_param_hash}})
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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.
Multiple consecutive blank lines Open
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MD012 - Multiple consecutive blank lines
Tags: whitespace, blank_lines
Aliases: no-multiple-blanks
This rule is triggered when there are multiple consecutive blank lines in the document:
Some text here
Some more text here
To fix this, delete the offending lines:
Some text here
Some more text here
Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.
Whitespace before ')' Open
self.assertIs( j.param_is_defined('d'), False, '"d" is not defined (it doesn\'t exist)' )
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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
- If you change the database schema, please follow the instructions [for schema changes in the developer guidelines](https://ensembl-hive.readthedocs.io/en/master/dev/development_guidelines.html#schema-changes).
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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
sub_tasks = [ { 'digit': _ } for _ in set(str(b_multiplier)).difference('01') ]
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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
>If you have already compiled your code and know how to enable the use of multiple threads / cores, this case should be very straightforward. It basically consists in defining the proper resource class in your pipeline. We also include some tips on how to compile code under MPI environment, but be aware that will vary across systems.
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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.
Header style Open
####Otherwise, follow the recommended usage in your institute
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MD003 - Header style
Tags: headers
Aliases: header-style
Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")
This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:
# ATX style H1
## Closed ATX style H2 ##
Setext style H1
===============
Be consistent with the style of header used in a document:
# ATX style H1
## ATX style H2
The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:
Setext style H1
===============
Setext style H2
---------------
### ATX style H3
Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.
Line length Open
If you have access to Intel compilers, we strongly recommend you to try compiling your code with it and checking for performance improvements.
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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.
Blank line at end of file Open
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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 length Open
Here again, once the environment is properly set up, we only have to define the correct resource class and comand lines in Hive.
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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
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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.