peerj/paper-now

Create, edit and display a journal article, entirely in GitHub

paper-now's Issues

Please add MarkDown support for titles

*Species name* in the article or figure titles are not italicised. They are in the descriptions, and in the titles when using <i>Species name</i>. Please compare the title and topmost figure in my test article with the code here and here.

Display each author's ORCID profile and previous works

Consider moving methods/protocols to a separate page

The methods section of an article, describing the protocols used, can take up a significant portion of the article and often gets in the way of the story - sometimes it is between the introduction and results and sometimes at the end.

Maybe it makes more sense for the methods description to be a separate page, incorporating links to/embedded protocols on external sites.

Fix formatting for math text in table headings

The math text doesn't bold in table headings and rows, and the amount of space that the math box means that it always gets awkwardly typeset in the table. As it stands, it seems like the only options are to either have the equations in tables not be math typeset or have them be a little wonky.

Sorry, I'm just running down some of the issues I've been hitting.

Decide which section to prioritise in the sidebar

For a reader who knows nothing about the article, which sections convey most information about reputation, context and data?

Support for Mathjax?

Mathjax is how mathematics gets rendered on the web (sorry for not opening up the code and taking a look myself).

Should Paper Now article functions & styles be update-able from this template repo?

As long as authors have only one article, authors can of course leave it be a normal fork and merge new template features via GitHub's GUI. But once they/we start the next article, and one after that...? Should each one try git subtree (apparently) or we ask GitHub for some official way to fork a repo multiple times?

Or should Paper Now instances not be updated? If so, for what reasons? Looking forward to your opinions :-)

Automated DOI-only citations

Awesome project! One killer feature would automatically generated citations and bibliographies based on DOIs or pubmed IDs. For example ThinkLab uses the following markdown syntax for a DOI citation:

Sentence in an article section referencing my ThinkLab project [@10.15363/thinklab.4].

Not sure of this feature's feasibility given your current design, but I think this method is the method of the future (see this R package as another example).

Move or eliminate contents menu in print and mobile style

The print and mobile stylesheets have the contents section between the normal sections and the figures. In mobile, it seems like it should be either before or immediately following the abstract. In print, it seems like it should be removed altogether.

Either way, the current position sort of defeats its function.

Generate new article repositories on demand, using paper-now as a template

• Provide an interface for a user to enter their name and email address (for the first Git commit), GitHub username and desired repository name.
• Use that information to generate a new Git repository with a single commit, authored by the user, containing a minimal article scaffold, importable by GitHub's importer (to avoid needing to authenticate with GitHub).

Links from text to figures and references in sidebar

Is there any way to link between a figure/reference mention in the main text to the sidebar? This would be very helpful.

colons in figure titles and/or descriptions break legend

This appears to be a problem of Jekyll parsing the YAML block (returns: Error reading file […].md: (<unknown>): mapping values are not allowed in this context at line […]). Escaping with \: doesn't work. Replacing with : or wrapping in Markdown (*Scale bar: 1µm* or **A:** … **B:** …) both do. In the latter case however, the * then can't be the 1st character after YAML's description:, because it expects an alphanumeric one. What a rabbit hole :-D

Since colons in, as well as panel references at the start of, figure legends are desirable, I'd like to discuss ideas to solve this problem.

• applying the abstract notation with |, newline and two spaces to the figure title and description templates
• adding a note to the readme
• automated escaping of unsupported characters
• other way of paring figure metadata

The first two I could implement & send a pull request.

Generate a table of contents

For long articles with many subheadings, a table of contents gives a useful overview of the article.

Use ServiceWorker's caching API to support offline reading

Document wide TeX macros

Mathematicians who want to write papers often make document wide macros to abbreviate common math forms. For example, in theoretical computer science we like to have lots of upper-case complexity class names, leading to macros like

\newcommand{\SPACE}{\textup{SPACE}} 

So we can write $\SPACE(n^2)$ anywhere in our paper.

I'd like to request this feature in Paper Now. I think it will attract more mathematicians to this publication medium.

Figure headings need more top padding

convert files to a single pdf

I think it would be better if these files can be converted to a single .pdf file.

Make a PDF version of article

Ideally the article could compile into a PDF version as well. Can anyone think of a way to do that?

Describe how to cite the article

paper-now theme not recognized

Hi,

i just cloned the repository and when I try to render the article in gh-pages I get the following error:

I did not change anything in the repo, just cloned it to my organization.

Recommended structure for multiple articles per repo?

Hi – First off, thanks for the work here; really like the template and the philosophy!

I do have one question, however – what do you recommend as a best practice for organizing multiple articles within a single repo? Git submodules? Something else?

I started to modify the structure locally to support multiple articles, but as far as I can tell, Jekyll doesn't support nested collections (e.g., for _figures.yml and _sections.yml)... and I also want to avoid moving too far from this article structure here and creating an accidental fork.

Would love any recommendations or thoughts. And thanks again!

Sidebar headings are too large when in single-column mode

Add Genius as an option for annotation

http://genius.it/peerj.github.io/paper-now

• Disable hypothes.is when on the genius.it domain, as they both perform similar functions.

Prince isn't able to load the imported print stylesheet

Prince has problems loading webcomponents.js, so the print stylesheet isn't being loaded.

Add a version tracker

I am still waiting for the paper-now to arrive to a stable version, so for the moment I wrote an article by hand, see Molecular computers. This made realize that a version tracker would be very useful.
Articles written on the web can be updated; also they can be cited, or there has to be a way to make clear which version is cited, as well as to have a record of the versions.
This can be done by exploiting somehow the history example. Any idea how to make this easy for the reader?

A second question, not related, but I'm not sure if it is worthy for an issue: it would be good to design the article to be easily visible on phones. Is that the case for paper-now?

Remove the "unresolved" attribute from the body element

Pros:

• The article will be readable even if the research-article web component fails to load.

Cons:

• The article is visible without the full layout/styles until the web components have finished loading.

Capture and display author contributions

Description

In the article metadata, describe the contributions made by each author.

An array of contributions, each as plain text, perhaps with identifiers from a standard set of roles.

Related links

• SCoRO, the Scholarly Contributions and Roles Ontology

not a programmer / Peer J looks great

Not a programmer, Really interested in how this works. Can this be expanded beyond Peer J.

Add sections?

Hello Alf!

I think paper-now is a great idea, congratulations! I tried to add more sections to those previously included in the folder, but unfortunately the page doesn't build correctly. I also changed sections.html to include the new files but it didn't work. Any suggestions?

Here's my repo if you want to check out the mess I did: https://github.com/danilofreire/invalid-votes

Thanks! :)

Add various other things to print style sheet

It seems like the author affiliations, funding, contributions, acknowledgements, and corresponding author annotations should be added to the print style sheet.

Consider supporting name parts for authors

Breaking names into given name, family name, etc

Pros:

• Useful for downstream citation formats that insist on using initials.

Cons:

• Adds complication.

Add anchor indicators next to headings

In the same way as GitHub shows a clickable icon next to each heading, make it easy to link to each section.

Each heading already has an id (derived from the text), but the icon will need to be added with JS.

Could use section IDs instead of heading IDs, instead.

Add support/examples for footnotes

In one example, superscript references in one section need to be linked to notes in another section.

Hide links to annotation tools when in an annotation tool

When annotating an article in hypothes.is or Genius, there's no need to link to hypothes.is or Genius.

Set a rel="canonical" meta tag and hide the annotation links if the current URL isn't the canonical URL?

Allow comments on the article

Proposal: if annotation: hypothesis is set in the configuration, add the hypothes.is annotation interface:

<script src="https://hypothes.is/embed.js"></script>

Internally reference citations

It would be really nice to internally reference citations that get automagically formatted. For example, the latex internal references.

For that matter, having internal references to sections and subsections would be nice as well.

d3.js animations as data

Is it possible to have data in the form of d3.js (say) animations? I want to use paper-now for an article about artificial chemistry which HAS to contain data like in the demos from here http://chorasimilarity.github.io/chemlambda-gui/dynamic/demos.html

Show the owner/guarantor/corresponding author

Background:

• Authorship and Contributorship (BMJ)
• Authorship and Accountability (The Lancet)

Load data from external sources

If the article has a DOI, load comments/reviews/metrics/annotations from external sources that have APIs.

• PubMed Commons (no API yet, could use http://www.macropus.org/2015/pubmed-commons/?pmid={pmid})
• Publons
• PubPeer (requires an API key)
• hypothes.is (waiting for CORS header)
• Twitter + other metrics via Altmetric
• CrossRef (waiting for counts to be added to the API)
• Mendeley (not currently possible)
• Zotero?

Incorporate citation style?

Hello!

Awesome project :-) I wasn't sure if or how some kind of automatic citation styling can be included, so I tweaked one to meet the examples in _sections. It should at least make copy & pasting the final bibliography into 06-references.md.

Cheers!

Abstract should be a self-contained <article>

As the abstract can be syndicated elsewhere, it should be marked up as a self-contained <article> with its own hierarchy of headings.

This will probably mean giving it a separate abstract.md file, instead of treating it as one of the standard sections.

Consider moving figures into the main body of the article

Instead of having figures in the sidebar, they could be distributed at appropriate places in the article.

Pros:

• No need to click on a figure reference to show the figure in the sidebar.
• The full-size figure can be viewed without opening a modal window (perhaps even the interactive version rather than a preview).

Cons:

• Figures take up more room in the article body.
• Figures may not be positioned next to all the places that reference them, making it more difficult to correlate the text with a figure.

Theorem environments

Pretty much every mathematics paper has special support for a Theorem/proof environment that tracks labels. In LaTeX, one typically uses the following to set up the theorem environments

\usepackage{amsthm}
\newtheorem{theorem}{Theorem}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{propn}[theorem]{Proposition}
\newtheorem{conjecture}[theorem]{Hypothesis}
\newtheorem{lemma}[theorem]{Lemma}

The option describes the numbering system (not that important), and after defining these one can produce a theorem/proof like

\begin{theorem} \label{theoremlabel}
Theorem statement
\end{theorem}

\begin{proof}
... 
\end{proof}

And the result is almost always like this

Theorem: Theorem statement.
Proof. ...
[right-aligned tombstone]

I would be interested to see a way to include theorems/proofs (etc) in the same way that figures are included, as separate files that can be referenced with hash labels. And then one could do something like folding/expanding proof text on demand to make a paper easer to leaf through.

Add links to annotation tools

Rather than loading annotation tools inline, provide links to https://genius.it{url} and https://via.hypothes.is/h/{url}.

Licence Section

As the Contribution Section, referenced by http://dictionary.casrai.org/Contributor_Roles, it would be interesting a Licence Section or link, as referenced on http://dictionary.casrai.org/Licence_Types