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doc/FileFormat.md

Summary

Maintainability
Test Coverage

Line length
Open

RMF::decorator::Colored, RMF::decorator::Ball etc. See [Decorators](\ref decoratorsattributes) for
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.

Lists should be surrounded by blank lines
Open

- most biological molecules have a natural hierarchical structure
Severity: Info
Found in doc/FileFormat.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

Lists should be surrounded by blank lines
Open

- low resolution and multiresolution structures are then more natural
Severity: Info
Found in doc/FileFormat.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

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

|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.

Line length
Open

Note that the file stayed in RAM for these operations (hence the identical buffer and to disk times).
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.

Header style
Open

# Benchmarks # {#benchmarks}
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

is the type for the single data with an \c s on the end, eg \c Floats for a list of \c Float
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.

Line length
Open

Container](https://avro.apache.org/docs/1.7.5/spec.html#Object+Container+Files). If
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.

Lists should be surrounded by blank lines
Open

- a \ref decoratorsattributes "category" such as \ref physics "physics",
Severity: Info
Found in doc/FileFormat.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

Multiple consecutive blank lines
Open
Severity: Info
Found in doc/FileFormat.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.

Line length
Open

|RMF::FloatsKey | std::vector<RMF::FloatKey> | a RMF::Key used to identify a list of floating points value associated with a node in the RMF hierarchy |
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.

Lists should be surrounded by blank lines
Open

- The RMF::decorator::Particle and RMF::decorator::RigidParticle coordinates
Severity: Info
Found in doc/FileFormat.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

Header style
Open

# Examples # {#example_files}
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.

Multiple consecutive blank lines
Open
Severity: Info
Found in doc/FileFormat.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.

Line length
Open

|RMF::Floats | std::vector<RMF::Float> | the type used to pass a list of floating point values. It looks like an \c std::vector in \c C++ and a \c list in \c Python |
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.

Headers must start at the beginning of the line
Open

 # Attributes # {#attribute}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD023 - Headers must start at the beginning of the line

Tags: headers, spaces

Aliases: header-start-left

This rule is triggered when a header is indented by one or more spaces:

Some text

  # Indented header

To fix this, ensure that all headers start at the beginning of the line:

Some text

# Header

Rationale: Headers that don't start at the beginning of the line will not be parsed as headers, and will instead appear as regular text.

Line length
Open

values. These are passed as \c std::vector like lists in \c C++ and \c lists in \c Python.
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.

Multiple top level headers in the same document
Open

# On disk format # {#on_disk}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Line length
Open

|RMF::FloatKey | RMF::ID<RMF::FloatTraits> | a RMF::Key used to identify a floating point value associated with a node in the RMF hierarchy |
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.

Multiple top level headers in the same document
Open

# Inheritance of properties # {#inheritance}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Multiple top level headers in the same document
Open

# Frames # {#frames}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Lists should be surrounded by blank lines
Open

- geometric markup such as segments, surfaces, balls, colors which can
Severity: Info
Found in doc/FileFormat.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

Lists should be surrounded by blank lines
Open

- RMF::decorator::Colored is inherited. That is, a node that is not an
Severity: Info
Found in doc/FileFormat.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

Header style
Open

# Inheritance of properties # {#inheritance}
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.

Header style
Open

# Frames # {#frames}
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.

Header style
Open

# On disk format # {#on_disk}
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.

Multiple top level headers in the same document
Open

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

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Lists should be surrounded by blank lines
Open

- molecular structures stored hierarchically. These structures need
Severity: Info
Found in doc/FileFormat.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

Lists should be surrounded by blank lines
Open

- it reduces redundancy (eg the residue type is only stored once, as is
Severity: Info
Found in doc/FileFormat.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

Lists should be surrounded by blank lines
Open

- most software uses a hierarchy of some sort to represent structures at
Severity: Info
Found in doc/FileFormat.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

Lists should be surrounded by blank lines
Open

- `create`: create a RMF file with a hierarchy with 45000 particles
Severity: Info
Found in doc/FileFormat.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

Multiple consecutive blank lines
Open
Severity: Info
Found in doc/FileFormat.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.

Lists should be surrounded by blank lines
Open

- [simple pdb](simple.pdb.txt)
Severity: Info
Found in doc/FileFormat.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

Lists should be surrounded by blank lines
Open

- bonds
Severity: Info
Found in doc/FileFormat.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

Header style
Open

# Adding custom data to an RMF # {#adding}
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.

Multiple top level headers in the same document
Open

# Examples # {#example_files}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Multiple top level headers in the same document
Open

# Benchmarks # {#benchmarks}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Line length
Open

|RMF::FloatsTraits | RMF::FloatsTraits | a traits classes to tell HDF5 how to read and write one or more lists of 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.

Multiple top level headers in the same document
Open

# The RMF Hierarchy # {#hierarchy}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Multiple top level headers in the same document
Open

# Adding custom data to an RMF # {#adding}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Lists should be surrounded by blank lines
Open

- feature information about parts of the structures, such as how well it
Severity: Info
Found in doc/FileFormat.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

Header style
Open

# Overview #
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

In addition, an arbitrary length list of any of the above can be stored. The type for that
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.

Lists should be surrounded by blank lines
Open

- [3U7W pdb](3U7W.pdb.txt)
Severity: Info
Found in doc/FileFormat.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

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