Showing 158 of 158 total issues
First header should be a top level header Open
## Conclusions- 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 subsectionsBare 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].- 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`First header should be a top level header Open
## References {.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 subsectionsFirst header should be a top level header Open
## The impact of deep learning in treating disease and developing new treatments- 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
We note in passing that Jensen (2018) [@doi:10.1039/C8SC05372C] and Yoshikawa et al. (2019) [@doi:10.1246/cl.180665] have both demonstrated genetic algorithms that are competitive with deep learning approaches. - 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
- 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.
Ordered list item prefix Open
7. Wikidata Items, cite like `@wikidata:Q50051684`.- Read upRead up
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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
2. setting `thumbnail` in `metadata.yaml` to a path, relative to the repository root, where the image file is located.- Read upRead up
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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
1.23. Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC - 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.
Inline HTML Open
Jinbo Xu<sup>1.20</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
Dave DeCaprio<sup>1.27</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
Laura K. Wiley<sup>1.29</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.
Trailing spaces Open
Progress on overcoming both of these shortcomings is proceeding on many fronts, and we believe the future of deep learning for molecular design is quite bright.- 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.
Code block style Open
1. automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or- Exclude checks
Trailing spaces Open
1.11. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada - 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
1.14. Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA - 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.
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>- 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
Enrico Ferrero<sup>1.8</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
Evan M. Cofer<sup>1.21,1.22</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
<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.)- 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.