fix the Cite link in URL footer

[avallecam]

The default Cite link in the footer currently links to a 404 path:
https://github.com/epiverse-trace/research-compendium/blob/main/CITATION

We have a CITATION.cff on the root, but the .cff extension is not recognized by the template Cite link.

The Cite link is generated by {varnish} in the footer:
https://github.com/carpentries/varnish/blob/c59c9ed79746d6d490486f0ebd3245f9edeb7f3a/inst/pkgdown/templates/footer.html#L21

The git-novice lesson citation relies on the other citation files identifiable by GitHub:

• only one human-readable CITATION file,
• has the "Cite this repository" label on GitHub, without a visible .cff file,
• But it does not produce the APA and BibTeX outputs in the citation prompts.

Before the identification of this issue, we created CITATION files with these steps (we recommend steps 1-3 in the training material of this repo):

1. Fill contributors' data in DESCRIPTION file.

2. Create from the DESCRIPTION file a CITATION.cff with:

cffr::cff_write(dependencies = FALSE)

3. Create from the CITATION.cff file a inst/CITATION file with:

cffr::write_citation(x = "CITATION.cff", file = "./inst/CITATION")

4. Use the ./inst/CITATION for a human-readable output it in the README:

research-compendium/README.Rmd

Lines 48 to 51 in 8ae2bf0

	```{r,echo=FALSE}
	readCitationFile(file = "inst/CITATION")
	```

This is problematic for the template for two reasons:

• It is not located in the root folder,
• and if we write it in the root, the output is generated in bibTeX format, which compared to a carpentries reference, is not human-readable:

research-compendium/inst/CITATION

Lines 1 to 4 in 8ae2bf0

	bibentry(bibtype = "Misc",
	key = "epiresearchcompendium",
	year = 2023,

To adapt this for the template,

5. Create manually a CITATION file in the root with the output of:

readCitationFile(file = "inst/CITATION")

This will be as readable as in the README

research-compendium/README.md

Lines 46 to 49 in 8ae2bf0

	#>
	#> Valle A, Tamayo C, Azam J (2023). "research-compendium: Improve Your
	#> Code For Epidemic Analysis With R."
	#>

Include a Please cite as: on top according to reference: https://github.com/swcarpentry/git-novice/blob/main/CITATION

6. Add to gitignore the inst/CITATION file to avoid redundancy in the online repo. This is a useful transition file to knit the README.

The output of these steps are:

• CITATION.cff file: to get the "Cite this repository" label with APA and BibTeX outputs.
• inst/CITATION file: to generate a human-readable file with utils::readCitationFile() to include in README. --> removed in step 6.
• CITATION file: to fill the Cite link for the workbench template. This is visible in the footer of the URL and generated from code.

[avallecam]

Read the citation section suggestions from this lesson https://carpentries.github.io/lesson-development-training/aio.html#readme

[avallecam]

We can also evaluate this arrangement:

• Only one in the root folder: keep the CITATION file only.
  • This is human-readable and
  • generates a "Cite this repository" link in the About section.
• in the inst/ folder, keep the CITATION file in bibtex format
• in README,
  • keep the readCitationFile output, and
  • refer to both files for citation formats: CITATION for APA, inst/CITATION for bibtex.
• gitignore the .cff and use it to generate the citation from the DESCRIPTION file.

[Bisaloo]

Update on this: the workbench now supports CFF out of the box.