Sign upLogin

Ensembl/ensembl-hive

View on GitHub
Star

Showing 446 of 446 total issues

Ordered list item prefix
Open

3. You need to add the analysis to your pipeconfig:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

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.

Line length
Open

  * `same[model]` is needed to ensure that the selected compute nodes all have the same hardware. You may also need something like `select[avx]` to select the nodes that have the [AVX instruction set](http://en.wikipedia.org/wiki/Advanced_Vector_Extensions)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

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.

Ordered list item prefix
Open

8. git checkout master
Severity: Info
Found in docs/release_checklist.md by markdownlint

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.

Line length
Open

It regularly checks the states of both the blackboard and the farm and submits more Workers when needed.
Severity: Info
Found in README.md by markdownlint

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.

Ordered list item prefix
Open

2. Let's now configure a webhook to use with eHive
Severity: Info
Found in docs/Slack_howto.md by markdownlint

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.

Headers should be surrounded by blank lines
Open

Available documentation
Severity: Info
Found in README.md by markdownlint

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.

Line length
Open

    - If you change the schema, meadow, or guest language interfaces, please follow the scheme [for internal versioning in the developer guidelines](https://ensembl-hive.readthedocs.io/en/master/dev/development_guidelines.html#internal-versioning).
Severity: Info
Found in PULL_REQUEST_TEMPLATE.md by markdownlint

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.

Ordered list item prefix
Open

   3. You should be on a page that gives an introduction about WebHooks and
Severity: Info
Found in docs/Slack_howto.md by markdownlint

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.

Ordered list item prefix
Open

      2. Otherwise, click on the "Install" button next to your team name
Severity: Info
Found in docs/Slack_howto.md by markdownlint

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.

Inconsistent indentation for list items at the same level
Open

  * `-q mpi -a openmpi` is needed to tell LSF you will run a job in the MPI/OpenMPI environment
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD005 - Inconsistent indentation for list items at the same level

Tags: bullet, ul, indentation

Aliases: list-indent

This rule is triggered when list items are parsed as being at the same level, but don't have the same indentation:

* Item 1
    * Nested Item 1
    * Nested Item 2
   * A misaligned item

Usually this rule will be triggered because of a typo. Correct the indentation for the list to fix it:

* Item 1
  * Nested Item 1
  * Nested Item 2
  * Nested Item 3

Lists should be surrounded by blank lines
Open

* `warning(message, [True|False])`
Severity: Info
Found in wrappers/README.md by markdownlint

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

  * `span[ptile=4]`, this option specifies the granularity in which LSF will split the jobs/per node. In this example we ask for at least 4 jobs to be executed in the same machine. This might affect queuing times.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

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.

No space after hash on atx style header
Open

###!!!Temporary files!!!
Severity: Info
Found in docs/MPI_howto.md by markdownlint

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

Horizontal rule style
Open

---
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD035 - Horizontal rule style

Tags: hr

Aliases: hr-style

Parameters: style ("consistent", "---", "***", or other string specifying the horizontal rule; default "consistent")

This rule is triggered when inconsistent styles of horizontal rules are used in the document:

---

- - -

***

* * *

****

To fix this, ensure any horizontal rules used in the document are consistent, or match the given style if the rule is so configured:

---

---

Note: by default, this rule is configured to just require that all horizontal rules in the document are the same, and will trigger if any of the horizontal rules are different than the first one encountered in the document. If you want to configure the rule to match a specific style, the parameter given to the 'style' option is a string containing the exact horizontal rule text that is allowed.

Code block style
Open

        module avail
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Lists should be surrounded by blank lines
Open

* `debug`: an unsigned integer indicating the logging level
Severity: Info
Found in wrappers/README.md by markdownlint

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

Unexpected spaces around keyword / parameter equals
Open

    def dataflow(self, output_ids, branch_name_or_code = 1):
Severity: Minor
Found in wrappers/python3/eHive/Process.py by pep8

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):

Whitespace after '('
Open

        self.assertIs( j.param_is_defined('c'), None, '"c"\'s defined-ness is unclear' )
Severity: Minor
Found in wrappers/python3/eHive/Process.py by pep8

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 (80 > 79 characters)
Open

        self.dataflow( { 'partial_product' : self.param('partial_product') }, 1)
Severity: Minor
Found in wrappers/python3/eHive/examples/LongMult/PartMultiply.py by pep8

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
Severity: Info
Found in README.md by markdownlint

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.

Severity
Category
Status
Source
Language