Showing 158 of 158 total issues
Bare URL used Open
Please attribute by linking to https://github.com/greenelab/deep-review.
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MD034 - Bare URL used
Tags: links, url
Aliases: no-bare-urls
This rule is triggered whenever a URL is given that isn't surrounded by angle brackets:
For more information, see http://www.example.com/.
To fix this, add angle brackets around the URL:
For more information, see <http:></http:>.
Rationale: Without angle brackets, the URL isn't converted into a link in many markdown parsers.
Note: if you do want a bare URL without it being converted into a link, enclose it in a code block, otherwise in some markdown parsers it will be converted:
`http://www.example.com`
Trailing punctuation in header Open
### Section 4 – Sui Generis Database Rights.
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MD026 - Trailing punctuation in header
Tags: headers
Aliases: no-trailing-punctuation
Parameters: punctuation (string; default ".,;:!?")
This rule is triggered on any header that has a punctuation character as the last character in the line:
# This is a header.
To fix this, remove any trailing punctuation:
# This is a header
Note: The punctuation parameter can be used to specify what characters class
as punctuation at the end of the header. For example, you can set it to
'.,;:!'
to allow headers with question marks in them, such as might be used
in an FAQ.
Code block style Open
1. If You Share the Licensed Material (including in modified form), You must:
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Ordered list item prefix Open
4. _arXiv_ ID, cite like `@arxiv:1508.06576v2`.
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MD029 - Ordered list item prefix
Tags: ol
Aliases: ol-prefix
Parameters: style ("one", "ordered"; default "one")
This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').
Example valid list if the style is configured as 'one':
1. Do this.
1. Do that.
1. Done.
Example valid list if the style is configured as 'ordered':
1. Do this.
2. Do that.
3. Done.
Trailing spaces Open
1.2. Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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MD009 - Trailing spaces
Tags: whitespace
Aliases: no-trailing-spaces
Parameters: br_spaces (number; default: 0)
This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.
The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.
Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.
Inline HTML Open
Daniel S. Himmelstein<sup>1.2</sup>,
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MD033 - Inline HTML
Tags: html
Aliases: no-inline-html
This rule is triggered whenever raw HTML is used in a markdown document:
Inline HTML header
To fix this, use 'pure' markdown instead of including raw HTML:
# Markdown header
Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.
Inline HTML Open
Anthony Gitter<sup>1.34,1.35,†</sup>,
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MD033 - Inline HTML
Tags: html
Aliases: no-inline-html
This rule is triggered whenever raw HTML is used in a markdown document:
Inline HTML header
To fix this, use 'pure' markdown instead of including raw HTML:
# Markdown header
Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.
Bare URL used Open
We created an open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/greenelab/deep-review)) [@url:https://github.com/greenelab/deep-review].
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MD034 - Bare URL used
Tags: links, url
Aliases: no-bare-urls
This rule is triggered whenever a URL is given that isn't surrounded by angle brackets:
For more information, see http://www.example.com/.
To fix this, add angle brackets around the URL:
For more information, see <http:></http:>.
Rationale: Without angle brackets, the URL isn't converted into a link in many markdown parsers.
Note: if you do want a bare URL without it being converted into a link, enclose it in a code block, otherwise in some markdown parsers it will be converted:
`http://www.example.com`
Ordered list item prefix Open
4. __Limitations and Disclaimers.__
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MD029 - Ordered list item prefix
Tags: ol
Aliases: ol-prefix
Parameters: style ("one", "ordered"; default "one")
This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').
Example valid list if the style is configured as 'one':
1. Do this.
1. Do that.
1. Done.
Example valid list if the style is configured as 'ordered':
1. Do this.
2. Do that.
3. Done.
Ordered list item prefix Open
3. setting `thumbnail` in `metadata.yaml` to an absolute URL where the image is located.
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MD029 - Ordered list item prefix
Tags: ol
Aliases: ol-prefix
Parameters: style ("one", "ordered"; default "one")
This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').
Example valid list if the style is configured as 'one':
1. Do this.
1. Do that.
1. Done.
Example valid list if the style is configured as 'ordered':
1. Do this.
2. Do that.
3. Done.
Fenced code blocks should be surrounded by blank lines Open
```
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MD031 - Fenced code blocks should be surrounded by blank lines
Tags: code, blank_lines
Aliases: blanks-around-fences
This rule is triggered when fenced code blocks are either not preceded or not followed by a blank line:
Some text
```
Code block
```
```
Another code block
```
Some more text
To fix this, ensure that all fenced code blocks have a blank line both before and after (except where the block is at the beginning or end of the document):
Some text
```
Code block
```
```
Another code block
```
Some more text
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse fenced code blocks that don't have blank lines before and after them.
Trailing spaces Open
1.26. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
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MD009 - Trailing spaces
Tags: whitespace
Aliases: no-trailing-spaces
Parameters: br_spaces (number; default: 0)
This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.
The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.
Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.
Inline HTML Open
Paul-Michael Agapow<sup>1.9</sup>,
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MD033 - Inline HTML
Tags: html
Aliases: no-inline-html
This rule is triggered whenever raw HTML is used in a markdown document:
Inline HTML header
To fix this, use 'pure' markdown instead of including raw HTML:
# Markdown header
Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.
Inline HTML Open
Wei Xie<sup>1.13</sup>,
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MD033 - Inline HTML
Tags: html
Aliases: no-inline-html
This rule is triggered whenever raw HTML is used in a markdown document:
Inline HTML header
To fix this, use 'pure' markdown instead of including raw HTML:
# Markdown header
Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.
Inline HTML Open
Srinivas C. Turaga<sup>1.24</sup>,
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MD033 - Inline HTML
Tags: html
Aliases: no-inline-html
This rule is triggered whenever raw HTML is used in a markdown document:
Inline HTML header
To fix this, use 'pure' markdown instead of including raw HTML:
# Markdown header
Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.
First header should be a top level header Open
## Discussion
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MD002 - First header should be a top level header
Tags: headers
Aliases: first-header-h1
Parameters: level (number; default 1)
This rule is triggered when the first header in the document isn't a h1 header:
## This isn't a H1 header
### Another header
The first header in the document should be a h1 header:
# Start with a H1 header
## Then use a H2 for subsections
Trailing punctuation in header Open
### Section 7 – Other Terms and Conditions.
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MD026 - Trailing punctuation in header
Tags: headers
Aliases: no-trailing-punctuation
Parameters: punctuation (string; default ".,;:!?")
This rule is triggered on any header that has a punctuation character as the last character in the line:
# This is a header.
To fix this, remove any trailing punctuation:
# This is a header
Note: The punctuation parameter can be used to specify what characters class
as punctuation at the end of the header. For example, you can set it to
'.,;:!'
to allow headers with question marks in them, such as might be used
in an FAQ.
Ordered list item prefix Open
9. For references that do not have any of the above persistent identifiers, the citation key does not need to include a prefix.
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MD029 - Ordered list item prefix
Tags: ol
Aliases: ol-prefix
Parameters: style ("one", "ordered"; default "one")
This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').
Example valid list if the style is configured as 'one':
1. Do this.
1. Do that.
1. Done.
Example valid list if the style is configured as 'ordered':
1. Do this.
2. Do that.
3. Done.
Inline HTML Open
> **Open collaborative writing with Manubot**<br>
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MD033 - Inline HTML
Tags: html
Aliases: no-inline-html
This rule is triggered whenever raw HTML is used in a markdown document:
Inline HTML header
To fix this, use 'pure' markdown instead of including raw HTML:
# Markdown header
Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.
Lists should be surrounded by blank lines Open
* New sections on natural language processing in healthcare, cryo-electron microscopy, and MHC-peptide binding.
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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