Showing 527 of 527 total issues
Line length Open
apdot [label="... (RMF::decorator::Atom, RMF::decorator::Particle)" shape=oval URL="\ref RMF::decorator::Atom"];
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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
| Name | Type | Description |
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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
# Avro # {#avrocpp}
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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
copy_1 [label="Copy 1 (RMF::decorator::ReferenceFrame)" shape=folder URL="\ref RMF::decorator::ReferenceFrame"];
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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
- each PDB chain is a node that is a child of the root and stores data using the RMF::decorator::Chain decorator
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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
Headers should be surrounded by blank lines Open
# rmf_frames # {#rmf_frames}
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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
| `software name` | string | Name of the software used to make the model |
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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
## Attributes ## {#physicsattributes}
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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
# Parallel I/O # {#parallel}
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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
| RMF::decorator::FilterProvenance | RMF::PROVENANCE | filter threshold, filter frames |
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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
## Attributes ## {#sequenceattributes}
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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.
Multiple headers with the same content Open
## Decorators ## {#provenancedecorators}
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MD024 - Multiple headers with the same content
Tags: headers
Aliases: no-duplicate-header
Parameters: allowdifferentnesting (boolean; default false)
This rule is triggered if there are multiple headers in the document that have the same text:
# Some text
## Some text
To fix this, ensure that the content of each header is different:
# Some text
## Some more text
Rationale: Some markdown parses generate anchors for headers based on the header name, and having headers with the same content can cause problems with this.
If the parameter allow_different_nesting
is set to true
, header duplication
under different nesting is allowed, like it usually happens in change logs:
# Change log
## 2.0.0
### Bug fixes
### Features
## 1.0.0
### Bug fixes
Header style Open
# Invariants # {#invariants}
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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.
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.
Header style Open
# The RMF Hierarchy # {#hierarchy}
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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
This page outlines how one would go about storing various types of data in RMF files. Much of what it says is merely suggestions, and is not mandatory.
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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
| RMF::decorator::Bond | RMF::BOND | bonded {0,1} |
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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
If the PDB file has more than one model, all with the same structure, the models should be stored as frames in the RMF file.
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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
| RMF::decorator::Residue | RMF::REPRESENTATION | index, residue type |
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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
|RMF::FloatTraits | RMF::FloatTraits | a traits classes to tell HDF5 how to read and write one or more floating point values |
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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.