greenelab/deep-review

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Trailing spaces
Open

Current heuristics of synthesizability, such as the synthetic accessibility score, are based on a relatively limited domain of chemical data and are too restrictive, so better models of synthesizability should help in this area [@doi:10.1021/acs.jcim.0c00174]. 
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.

Header levels should only increment by one level at a time
Open

### Using Creative Commons Public Licenses
Severity: Info
Found in LICENSE.md by markdownlint

MD001 - Header levels should only increment by one level at a time

Tags: headers

Aliases: header-increment

This rule is triggered when you skip header levels in a markdown document, for example:

# Header 1

### Header 3

We skipped out a 2nd level header in this document

When using multiple header levels, nested headers should increase by only one level at a time:

# Header 1

## Header 2

### Header 3

#### Header 4

## Another Header 2

### Another Header 3

Trailing punctuation in header
Open

### Section 1 – Definitions.
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.

Fenced code blocks should be surrounded by blank lines
Open

    ```yaml
Severity: Info
Found in USAGE.md by markdownlint

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.

Inline HTML
Open

*PLOS Computational Biology* (2019-06-24) <https://doi.org/c7np><br>
Severity: Info
Found in USAGE.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.

Trailing spaces
Open

1.26. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL  
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

1.34. Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI  
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

<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.7.2/css/all.css">
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

    Alexandr A. Kalinin<sup>1.4</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

    Brian T. Do<sup>1.5</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

    Gregory P. Way<sup>1.2</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

    Stephen Woloszynek<sup>1.14</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

    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.

First header should be a top level header
Open

## Discussion
Severity: Info
Found in content/06.discussion.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

Code block style
Open

    1. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
Severity: Info
Found in LICENSE.md by markdownlint

Code block style
Open

    1. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
Severity: Info
Found in LICENSE.md by markdownlint

Ordered list item prefix
Open

2. A single reference is cited many times.
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`

Lists should be surrounded by blank lines
Open

* New sections on natural language processing in healthcare, cryo-electron microscopy, and MHC-peptide binding.

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

First header should be a top level header
Open

## Authors
Severity: Info
Found in content/00.front-matter.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
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