Showing 446 of 446 total issues
Lists should be surrounded by blank lines Open
1. You first need to choose the channel eHive will write too. Although
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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
These tasks (we call them Jobs) are claimed and processed by "Worker bees" or just Workers - autonomous processes
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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
* **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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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
Both are extensively used by the Ensembl project and are regularly updated. The LSF meadow supports workloads reaching thousands of parallel jobs.
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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
| :--------------------------------------- | ------------- | ----| --------------- |
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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
| Job limiter and resource management | Not available | Yes | Yes |
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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
documentation](https://rawgit.com/Ensembl/ensembl-hive/version/2.4/wrappers/python3/doxygen/index.html) and
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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
####If your compute environment uses [Module ](http://modules.sourceforge.net/)
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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.
Header style Open
###!!!Temporary files!!!
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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.
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.
Line length Open
First of all, your institution / compute-farm provider may have documentation on this topic. Please refer to them for implementation details (intranet-only links: [EBI](http://www.ebi.ac.uk/systems-srv/public-wiki/index.php/EBI_Good_Computing_Guide), [Sanger institute](http://mediawiki.internal.sanger.ac.uk/index.php/How_to_run_MPI_jobs_on_the_farm))
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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.
Code block style Open
sub resource_classes {
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Code block style Open
module load openmpi-x86_64
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Code block style Open
{ -logic_name => 'MPI_app',
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Code block style Open
sub worker_temp_directory_name {
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Ordered list item prefix Open
5. Check all of the above into "master" branch
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MD029 - Ordered list item prefix
Tags: ol
Aliases: ol-prefix
Parameters: style ("one", "ordered"; default "one")
This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').
Example valid list if the style is configured as 'one':
1. Do this.
1. Do that.
1. Done.
Example valid list if the style is configured as 'ordered':
1. Do this.
2. Do that.
3. Done.
Lists should be surrounded by blank lines Open
* a wrapper that GuestProcess will launch, which will in turn run the
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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
XXX found Open
3. -url $ehive_url job_id XXX. The reference to an existing job from which the parameters will be pulled. It is
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FIXME found Open
die "Job with dbID='$job_id' is already in progress, cannot run"; # FIXME: try GC first, then complain
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FIXME found Open
# FIXME: move the decision making completely to the API side and so avoid the potential race condition.
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