Mdpi update

[mps9506]

This is a fresh pull request with the newest version of the mdpi template circa 2022-12 (PR #381 seemed to stall out and was already outdated). There are numerous updates to the yaml header to make better use of the mdpi.cls and template file.
Also fixes #502

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How to contribute a new output format ?

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). Unless you have done it in any other RStudio / Posit projects before, sign the individual or corporate contributor agreement as appropriate. You can send the signed copy to contribute@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.

• Document your function using roxygen2. Markdown syntax is supported. Refer to https://roxygen2.r-lib.org/articles/rd-formatting.html for formatting references.

• 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!

[rempsyc]

There is a MDPI special issue deadline next Thursday. It would be awesome if this PR could be merged before then :-)

[cderv]

Thanks a lot for this PR. Sorry for the delay. I am going back on rticles now.

I have a few comments and questions.

If you don't have time anymore on this, I can understand. I'll do the change myself if so. Please do tell me.

Thank you

[cderv]

I understand the change, though I wonder if we shouldn't mix both.

It seemed useful to not rely of the order of classoption but use named field in YAML for the expected option by mdpi.cls

We can do both either from root yaml or ven something more targeted to format function

output:
  mdpi_article:
    journal: ... 

Just curious if you think that letting classoption be free is really best for users.

[mps9506]

Having the open classoption felt more consistent with what I saw in other templates so I adopted it. I think I agree that using named fields makes sense here.

[cderv]

We can do both

• Named field to make it easier for authors, and insure correct order
• classoption for further customization

We could do

journal: sports
type: article
status: submit
classoption:
  - moreauthors # use when multiple author
  - pdftex # use when using latex_engine pdflatex
output: mdpi_article

Or set everything under mdpi_article directly, not sure which is better.

We could probably also handle moreauthors and pdftex insertion from R format function, by (1) checking if multiple authors in yaml header and (2) checking latex_engine value

Does it sounds helpful ?

I am also fine with leaving classoption free. Easier to maintain, but more responsability for authors who need to know.

[mps9506]

moreauthors and pdftex are now set by the format function so are not needed in the yaml header. journal, type, and status are named fields. classoption is no longer needed in this case.

[mps9506]

@cderv I'll work on the changes.

[cderv]

Awesome. Do not hesitate to tell me if you need me to help or if I should do it instead.

[cderv]

Thanks for the work @mps9506 ! I'll review it now.

As stated in the PR template, can you be sure to sign the CLA document and send it to the email ?

Thank you

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). Unless you have done it in any other RStudio / Posit projects before, sign the individual or corporate contributor agreement as appropriate. You can send the signed copy to contribute@rstudio.com.

[cderv]

Thanks - this is really good PR !

I'll do a few tweaks myself, and then merge once you have confirmed me you sent the CLA document.

Thank you again !

[cderv]

@mps9506 do you have aslo these warnings locally ?

Warning: Package fancyhdr Warning: \headheight is too small (12.0pt):
Warning: (fancyhdr) Make it at least 20.0pt, for example:
Warning: (fancyhdr) \setlength{\headheight}{20.0pt}.
Warning: (fancyhdr) You might also make \topmargin smaller to compensate:
Warning: (fancyhdr) \addtolength{\topmargin}{-8.0pt}.
Warning: Package fancyhdr Warning: \headheight is too small (12.0pt):
Warning: (fancyhdr) Make it at least 16.18796pt, for example:
Warning: (fancyhdr) \setlength{\headheight}{16.18796pt}.
Warning: (fancyhdr) You might also make \topmargin smaller to compensate:
Warning: (fancyhdr) \addtolength{\topmargin}{-4.18796pt}.

Is this by default with their template ?

[mps9506]

@cderv Those warnings are issues in mdpi cls or template file. I get them when compiling the template directly in TexLive. I'll send over the CLA shortly.

[cderv]

Those warnings are issues in mdpi cls or template file.

ok good to know. Hopefully they'll fix them

[cderv]

All good now. Just waiting for confirmation of the CLA and then I'll merge

[mps9506]

@cderv I sent over the CLA. Just a note that the repository template file for contributors has the contribute@rstudio.com address while the actual CLA form indicates to send it to jj@posit.co. I copied both since I was unsure.

[cderv]

Oh thanks. I'll check that. Merging now then !

Thanks a lot for the work on this !