Showing 527 of 527 total issues

Line length
Open

      apdot [label="... (RMF::decorator::Atom, RMF::decorator::Particle)" shape=oval URL="\ref RMF::decorator::Atom"];
Severity: Info
Found in doc/MappingToRMF.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.

Line length
Open

| Name                  | Type         | Description                               |

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}
Severity: Info
Found in doc/Developers.md by markdownlint

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"];
Severity: Info
Found in doc/MappingToRMF.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.

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
Severity: Info
Found in doc/MappingToRMF.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

Headers should be surrounded by blank lines
Open

# rmf_frames # {#rmf_frames}
Severity: Info
Found in doc/Executables.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

| `software name`       | string       |  Name of the software used to make the model |

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}

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}
Severity: Info
Found in doc/Library.md by markdownlint

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                       |

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}

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}

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}
Severity: Info
Found in doc/Library.md by markdownlint

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


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}
Severity: Info
Found in doc/FileFormat.md by markdownlint

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.
Severity: Info
Found in doc/MappingToRMF.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.

Line length
Open

| RMF::decorator::Bond            |  RMF::BOND              | bonded {0,1}                       |

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.
Severity: Info
Found in doc/MappingToRMF.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.

Line length
Open

| RMF::decorator::Residue         | RMF::REPRESENTATION     |  index, residue type               |

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 |
Severity: Info
Found in doc/FileFormat.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.

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