Add Wellcome OR latex template

[arnold-c]

To contribute a new article template to this package, please make sure you have done the following things (note that journalname_article below is only an example name):

• This project uses a Contributor Licence Agreement (CLA) that you'll be asked to sign when opening a PR. This is required for a significant pull request (it is fine not to sign it if a PR is only intended to fix a few typos). We use a tool called CLA assistant for that.
  You could also, unless you have done it in any other RStudio's projects before, sign the individual or corporate contributor agreement. You can send the signed copy to jj@rstudio.com.

• Add the journalname_article() function to R/article.R if the output format is simple enough, otherwise create a separate R/journalname_article.R.

• Add the Pandoc LaTeX template inst/rmarkdown/templates/journalname/resources/template.tex.

• Add a skeleton article inst/rmarkdown/templates/journalname/skeleton/skeleton.Rmd.

• Add a description of the template inst/rmarkdown/templates/journalname/template.yaml.

• Please include the document class file (*.cls) if needed, but please do not include standard LaTeX packages (*.sty) that can be downloaded from CTAN. If you are using TinyTeX or TeX Live, you can verify if a package is available on CTAN via tinytex::parse_packages(files = "FILENAME"") (e.g., when FILENAME is plain.bst, it should return "bibtex", which means this file is from a standard CTAN package). Please keep the number of new files absolutely minimal (e.g., do not include PDF output files), and also make examples minimal (e.g., if you need a .bib example, try to only leave one or two bibliography entries in it, and don't include too many items in it without using all of them).

• Update Rd and namespace (could be done by devtools::document()).

• Update NEWS.

• Update README with a link to the newly supported journal. Please add your Github username and the full name of the journal (follow other examples in the list).

• Add a test to tests/testit/test-formats.R by adding a line test_format("journalname"). We try to keep them in alphabetical order.

• Add your name to the list of authors Authors@R in DESCRIPTION. You don't need to bump the package version in DESCRIPTION.

Lastly, please try your best to do only one thing per pull request (e.g., if you want to add two output formats, do them in two separate pull requests), and refrain from making cosmetic changes in the code base: https://yihui.name/en/2018/02/bite-sized-pull-requests/

Thank you!

---

Hi,

I'm afraid I'm relatively inexperienced at both package development and LaTeX, so have adapted the template as much as I can, but am currently running into a problem when I try to knit skeleton.Rmd: Error: 'wellcomeor_article' is not an exported object from 'namespace:rticles'. If anyone can point me in the right direction, that'd be much appreciated, and I can see if the template works as expected.

Thanks,

[CLAassistant]

All committers have signed the CLA.

[cderv]

Thanks for the contribution of this new template.

but am currently running into a problem when I try to knit skeleton.Rmd: Error: 'wellcomeor_article' is not an exported object from 'namespace:rticles'

Did you install the development version of this package (from your branch) ?

Using the Knit button will use the install version. If you are using devtools::load_all() you would need to use command line rmarkdown::render I think

[arnold-c]

Sorry for the delay in response @cderv, and thanks for reminding me to build and install the development version! I'm now getting this issue

Error compiling template "/Users/user/Library/R/x86_64/4.1/library/rticles/rmarkdown/templates/wellcomeor/resources/template.tex" (line 77, column 1):
unexpected end of input
expecting " ", "\t", "$--", "\n", "\r\n", "\r", "$", "${" or "$$"
Error: pandoc document conversion failed with error 5
Execution halted

Looking in both skeleton.Rmd and template.tex I can't see any code that would be causing these issues, but I'm obviously missing something. I've tried removing the majority of the body text in an attempt to see if some of the LaTeX code was causing the error, but this didn't seem to help.

[cderv]

This type of error is thrown by Pandoc when something is not correct regarding syntax in the template. There must be a Pandoc template syntax not correct in the template. It could be an $endif$ missing or any other $ missing around variables.

[cderv]

I have left a few comments.

The CI issue is because a $endfor$ is missing I believe

Also you have some file in this PR the concerns the arxiv template, in the arxiv folder. skeleton.pdf and skeleton.tex ? Why are they here ?
I think they should be removed.

I did not do a thorough review yet but can you also fill the template with some missing pieces required by Pandoc ?
At least

rticles/inst/rmarkdown/templates/acm/resources/template.tex

Lines 60 to 97 in 2e0a3d0

	% Pandoc syntax highlighting
	$if(highlighting-macros)$
	$highlighting-macros$
	$endif$
	% Pandoc citation processing
	$if(csl-refs)$
	\newlength{\csllabelwidth}
	\setlength{\csllabelwidth}{3em}
	\newlength{\cslhangindent}
	\setlength{\cslhangindent}{1.5em}
	% for Pandoc 2.8 to 2.10.1
	\newenvironment{cslreferences}%
	{$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
	\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
	{\par}
	% For Pandoc 2.11+
	\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
	{% don't indent paragraphs
	\setlength{\parindent}{0pt}
	% turn on hanging indent if param 1 is 1
	\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
	% set entry spacing
	\ifnum #2 > 0
	\setlength{\parskip}{#2\baselineskip}
	\fi
	}%
	{}
	\usepackage{calc} % for calculating minipage widths
	\newcommand{\CSLBlock}[1]{#1\hfill\break}
	\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
	\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
	\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
	$endif$
	$for(header-includes)$
	$header-includes$
	$endfor$

After theses changes I'll test further the template and check if everything is there.

[arnold-c]

Thanks @cderv. I've added the Pandoc requirements you linked, along with your other suggestions, and removed the arXiv files that accidentally were made when I was examining the template.

It is no longer throwing the Pandoc error, but I am now getting the following error

! Undefined control sequence.
<argument> ...sed on Wellcome Open Research \href 
                                                  {https://www.overleaf.com/...
l.62 Latex template}}

l.62 refers to

\emph{Text based on Wellcome Open Research
\href{https://www.overleaf.com/project/6131911644b635ad3aaa4cb2}{Overleaf
Latex template}}

When removing _Text based on Wellcome Open Research [Overleaf Latex template](https://www.overleaf.com/project/6131911644b635ad3aaa4cb2)_ from skeleton.Rmd, I instead get the following error:

! Undefined control sequence.
l.60 \hypertarget
                 {introduction}{% 

Which refers to:

\hypertarget{introduction}{%
\section{Introduction}\label{introduction}}

Thanks

[cderv]

Interesting. I think you get this from again missing part from the template for Pandoc requirement.

First

\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}

This package seems missing and required to use \href command.

then

\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

required by Pandoc for creating specific list style

Those must be added in the template.

After that, there may be other issue. I get something about font but i'll wait for you to try as I am not sure of my env.

[arnold-c]

I've updated the template and it now produces a pdf. The only remaining issues I couldn't figure out is how to disable link coloring (setting it using hypersetup{} didn't seem to work), and the author affiliation number isn't correct and doesn't allow for multiple authors. I tried to copy across code from the OUP template, which allows for it, but couldn't get it to work I'm afraid. I also get font warning, but it seems like that is also an warning on the Overleaf template, so I don't think it's too much of an issue that should be fixed on our end.

Warning message:
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 53.

[cderv]

I couldn't figure out is how to disable link coloring

It is possible this is something produced by Pandoc. Did you try opting out using the variables ?
https://pandoc.org/MANUAL.html#links

Something like

colorlinks: false

in the YAML header ?

the author affiliation number isn't correct and doesn't allow for multiple authors.

This can be tricky and require to modify the template. Several formats have different trick for this kind of thing.
I could try to have a look. That would be helpful if you know what syntax it should look like in the .tex output ?
We could then adapt as template for Pandoc.

Thanks

[cderv]

Hey !

What is the status on this PR ?

I reviewed it as is after merging changes from the main branch to be up to date.

Overall it looks good ! Small questions and feedback before we can merge.

Thanks !

[cderv]

Hi,

thanks a lot for the feedback. We are preparing a releasing so this is good news if we can merge this.

Based on your feedback, and my previous work this past two weeks on rticles I did more comment. Instead of just making them and pushing, I made them as suggestion so that you can validate if that is ok to you.

My aim is for the template to be closest to Pandoc's one so that features work and it is easy to update.

Please, have a look (below and above) and confirm or not my sugestion. Once I'll have your ok, I'll commit and merge everything.

Tests are now passing - some contents where missing.

[arnold-c]

All look good to me so I just went ahead and committed the suggestions. Thanks

[cderv]

Thanks @arnold-c !

There were also the discussion box above my last comment 😅 sorry for that, Github have separated them from the other. Can you validate those too ?

Especially this one: #436 (comment)

Thanks

[arnold-c]

Sorry about that. I've just gone through and confirmed it all works as expected after those suggestions (I think I got them all)

[cderv]

Awesome that is great !

We are ready to roll then. Thank you for this PR and you're availability to make the necessary changes!

[cderv]

We must just redocument following new arguments in function. I'll do that tommorow and merge it.