greenelab/deep-review

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Trailing punctuation in header
Open

### Section 2 – Scope.
Severity: Info
Found in LICENSE.md by markdownlint

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

2. setting `thumbnail` in `metadata.yaml` to a path, relative to the repository root, where the image file is located.
Severity: Info
Found in USAGE.md by markdownlint

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

1.3. Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

1.7. Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

1.10. Princess Margaret Cancer Centre, Toronto, ON, Canada  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

1.11. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

1.23. Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

    Amr M. Alexandari<sup>1.19</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

    Marwin H.S. Segler<sup>1.30</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

8. Any other compact identifier supported by <https://identifiers.org>.
Severity: Info
Found in USAGE.md by markdownlint

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

In a famous and early example, scientists from Google demonstrated that a neural network "discovered" that cats, faces, and pedestrians were important components of online videos [@url:http://research.google.com/archive/unsupervised_icml2012.html] without being told to look for them.
Severity: Info
Found in content/02.intro.md by markdownlint

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

1.20. Toyota Technological Institute at Chicago, Chicago, IL  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

1.21. Department of Computer Science, Trinity University, San Antonio, TX  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

1.24. Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA  
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

<sup>⚄</sup> --- Author order for version 2.0 is currently randomized [with each new build](https://github.com/greenelab/deep-review/pull/997).<br>
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

    Jinbo Xu<sup>1.20</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

    David J. Harris<sup>1.26</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

    S. Joshua Swamidass<sup>1.32</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

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

## The impact of deep learning in treating disease and developing new treatments
Severity: Info
Found in content/05.treat.md by markdownlint

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 spaces
Open

One of the molecules was chosen for further testing and showed promising results in a cancer cell line and mouse model [@tag:Zhavoronkov2019_drugs]. 
Severity: Info
Found in content/05.treat.md by markdownlint

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.

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