Showing 158 of 158 total issues
First header should be a top level header Open
## Abstract {.page_break_before}- Read upRead up
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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 headerThe first header in the document should be a h1 header:
# Start with a H1 header
## Then use a H2 for subsectionsTrailing spaces Open
1.13. Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN - Read upRead up
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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.
Trailing spaces Open
1.27. ClosedLoop.ai, Austin, TX - Read upRead up
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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.
Trailing spaces Open
1.35. Morgridge Institute for Research, Madison, WI - Read upRead up
- Exclude checks
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
<small><em>- Read upRead up
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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 headerRationale: 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
<small><em>- Read upRead up
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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 headerRationale: 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
Paul-Michael Agapow<sup>1.9</sup>,- Read upRead up
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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 headerRationale: 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
Gail L. Rosen<sup>1.14</sup>,- Read upRead up
- Exclude checks
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 headerRationale: 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
David J. Harris<sup>1.26</sup>,- Read upRead up
- Exclude checks
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 headerRationale: 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
Simina M. Boca<sup>1.31</sup>,- Read upRead up
- Exclude checks
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 headerRationale: 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 continued using the open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/greenelab/deep-review)) [@url:https://github.com/greenelab/deep-review], which was established to write the version 1.0 manuscript.- Read upRead up
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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`Inline HTML Open
<div id="refs"></div>- Read upRead up
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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 headerRationale: 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.
Trailing punctuation in header Open
### Section 6 – Term and Termination.- Read upRead up
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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 headerNote: 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.
Trailing punctuation in header Open
### Will deep learning transform the study of human disease?- Read upRead up
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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 headerNote: 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.
Inline HTML Open
Casey S. Greene<sup>1.2,†</sup>- Read upRead up
- Exclude checks
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 headerRationale: 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
## Methods- Read upRead up
- Exclude checks
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 headerThe first header in the document should be a h1 header:
# Start with a H1 header
## Then use a H2 for subsectionsBare URL used Open
Numerous commentators have described data as the new oil [@url:http://ana.blogs.com/maestros/2006/11/data_is_the_new.html; @url:https://medium.com/twenty-one-hundred/data-is-the-new-oil-a-ludicrous-proposition-1d91bba4f294].- Read upRead up
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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`Bare URL used Open
In CAMEO (which can be interpreted as a fully-automated CASP) [@url:https://www.cameo3d.org], its predicted contacts were also able to fold proteins with a novel fold and only 65--330 sequence homologs.- Read upRead up
- Exclude checks
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`