Showing 158 of 158 total issues
Bare URL used Open
[@url:http://hazyresearch.github.io/snorkel/blog/weak_supervision.html].
- 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`
Trailing punctuation in header Open
### Section 3 – License Conditions.
- Read upRead up
- Exclude checks
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.
Trailing spaces Open
1.3. Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- 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.
Trailing spaces Open
1.6. Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH
- 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.
Trailing spaces Open
1.18. Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA
- 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.
Headers should be surrounded by blank lines Open
##}
- Read upRead up
- Exclude checks
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.
Inline HTML Open
S. Joshua Swamidass<sup>1.32</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 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.
Ordered list item prefix Open
2. The [`pandoc-manubot-cite` filter](https://github.com/manubot/manubot#pandoc-filter) automatically retrieves the bibliographic metadata for citation keys.
- Read upRead up
- Exclude checks
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
1.25. National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD
- 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>
- 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 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
Michael M. Hoffman<sup>1.10,1.11,1.12</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 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
The resulting dataset [@url:https://nihcc.app.box.com/v/ChestXray-NIHCC] consisted of 112,120 frontal-view chest X-ray images from 30,805 patients, and each image was associated with one or more *text-mined* (weakly-labeled) pathology categories (e.g. pneumonia and cardiomegaly) or "no finding" otherwise.
- 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`
Inline HTML Open
Zhiyong Lu<sup>1.25</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 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
Blindly tested in the latest CASP competition (i.e. CASP12 [@url:http://www.predictioncenter.org/casp12/rrc_avrg_results.cgi]), RaptorX-Contact ranked first in F₁ score on free-modeling targets as well as the whole set of targets.
- 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`
Inline HTML Open
Yanjun Qi<sup>1.17</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 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.
Ordered list item prefix Open
2. __Waiver.__ To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose.
- Read upRead up
- Exclude checks
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.
Bare URL used Open
+ **HTML manuscript** at https://greenelab.github.io/deep-review/
- 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`
Trailing spaces Open
The following YAML shows the supported key–value pairs for an author:
- 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.
Ordered list item prefix Open
3. The [`pandoc-citeproc` filter](https://github.com/jgm/pandoc-citeproc/blob/master/man/pandoc-citeproc.1.md) renders in-text citations and generates styled references.
- Read upRead up
- Exclude checks
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
```yaml
- Read upRead up
- Exclude checks
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.