Support new citeproc from Pandoc 2.11

[cderv]

This will close #1915

[jjallaire]

I don't think this full closes #1915 w/o dealing w/ the pandoc_citeproc_convert() function.

[cderv]

Oh yes I know. This is why this is still a draft. Not yet ready to merge. I opened this draft PR to share the work and discuss if necessary.

I should have wrote a little something to comment further...

[jjallaire]

Okay sorry about the itchy GH comment finger....didn't see that is was marked draft!

[cderv]

@JJ following your comment, #1915 (comment):

The manual included in the release bundle (not yet updated on website) give the infos:

Note that pandoc can be used to produce such a YAML metadata section from a BibTeX, BibLaTeX, or CSL JSON bibliography:

pandoc chem.bib -s -t markdown
pandoc chem.json -s -t markdown

pandoc can also be used to produce CSL JSON bibliography from BibTeX, BibLaTeX, or markdown YAML:

pandoc chem.bib -s -t csljson
pandoc chem.yaml -s -t csljson

Running pandoc on a bibliography file with the --citeproc option will create a formatted bibliography in the format of your choice:

pandoc chem.bib -s --citeproc -o chem.html
pandoc chem.bib -s --citeproc -o chem.pdf

There are some differences between the output when converted to YAML:

• a nocite filed is added
• There is no more spaces between fields in the new output
• Oddly, pandoc-citeproc will add a ... at the end of the yaml part. pandoc will add a closing --- - that seems more correct.
• Some fields are not the same. (see issued below for example)

# using this PR
# remotes::install_github("rstudio/rmarkdown#1916")
temp_bib <- tempfile(fileext = ".bib")
knitr::write_bib("bookdown", temp_bib)
#> Warning in utils::citation(..., lib.loc = lib.loc): no date field in DESCRIPTION
#> file of package 'bookdown'
#> Warning in utils::citation(..., lib.loc = lib.loc): could not determine year for
#> 'bookdown' from package DESCRIPTION file
rmarkdown::find_pandoc(cache = FALSE)
#> $version
#> [1] '2.9.2.1'
#> 
#> $dir
#> [1] "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc"
rmarkdown::pandoc_citeproc_convert(temp_bib, type = "yaml")
#>  [1] "---"                                                                         
#>  [2] "references:"                                                                 
#>  [3] "- id: R-bookdown"                                                            
#>  [4] "  type: book"                                                                
#>  [5] "  author:"                                                                   
#>  [6] "  - family: Xie"                                                             
#>  [7] "    given: Yihui"                                                            
#>  [8] "  issued:"                                                                   
#>  [9] "  - year: 2020"                                                              
#> [10] "  title: 'Bookdown: Authoring books and technical documents with r markdown'"
#> [11] "  title-short: Bookdown"                                                     
#> [12] "  note: R package version 0.20.6"                                            
#> [13] "  URL: https://github.com/rstudio/bookdown"                                  
#> [14] ""                                                                            
#> [15] "- id: bookdown2016"                                                          
#> [16] "  type: book"                                                                
#> [17] "  author:"                                                                   
#> [18] "  - family: Xie"                                                             
#> [19] "    given: Yihui"                                                            
#> [20] "  issued:"                                                                   
#> [21] "  - year: 2016"                                                              
#> [22] "  title: 'Bookdown: Authoring books and technical documents with R markdown'"
#> [23] "  title-short: Bookdown"                                                     
#> [24] "  publisher: Chapman; Hall/CRC"                                              
#> [25] "  publisher-place: Boca Raton, Florida"                                      
#> [26] "  note: ISBN 978-1138700109"                                                 
#> [27] "  URL: https://github.com/rstudio/bookdown"                                  
#> [28] "..."
rmarkdown::find_pandoc(cache = FALSE, dir = "C:/Users/chris/Logiciel/pandoc/pandoc-2.11/")
#> $version
#> [1] '2.11'
#> 
#> $dir
#> [1] "C:/Users/chris/Logiciel/pandoc/pandoc-2.11/"
rmarkdown::pandoc_citeproc_convert(temp_bib, type = "yaml")
#>  [1] "---"                                                                
#>  [2] "references:"                                                        
#>  [3] "- author:"                                                          
#>  [4] "  - family: Xie"                                                    
#>  [5] "    given: Yihui"                                                   
#>  [6] "  id: R-bookdown"                                                   
#>  [7] "  issued: 2020"                                                     
#>  [8] "  note: R package version 0.20.6"                                   
#>  [9] "  title: \"Bookdown: Authoring books and technical documents with r"
#> [10] "    markdown\""                                                     
#> [11] "  title-short: Bookdown"                                            
#> [12] "  type: book"                                                       
#> [13] "  url: \"https://github.com/rstudio/bookdown\""                     
#> [14] "- author:"                                                          
#> [15] "  - family: Xie"                                                    
#> [16] "    given: Yihui"                                                   
#> [17] "  id: bookdown2016"                                                 
#> [18] "  issued: 2016"                                                     
#> [19] "  note: ISBN 978-1138700109"                                        
#> [20] "  publisher: Chapman; Hall/CRC"                                     
#> [21] "  publisher-place: Boca Raton, Florida"                             
#> [22] "  title: \"Bookdown: Authoring books and technical documents with R"
#> [23] "    markdown\""                                                     
#> [24] "  title-short: Bookdown"                                            
#> [25] "  type: book"                                                       
#> [26] "  url: \"https://github.com/rstudio/bookdown\""                     
#> [27] "---"                                                                
#> [28] ""

^{Created on 2020-10-12 by the reprex package (v0.3.0.9001)}

Do we need to get the output of pandoc_citeproc_convert to be the same no matter which pandoc version used ?
I believe we should just provide a wrapper to make the conversion but keep the output as the pandoc binary or pandoc-citeproc binary is doing. That would mean not remove the nocite maybe.

What do you think ?

[jjallaire]

I agree it's fine to keep the nocite in there until we discover there is a reason to remove it.

[CLAassistant]

All committers have signed the CLA.

[jjallaire]

@cderv FYI I wanted to bump the version in DESCRIPTION so I merged master into new-citeproc.

[cderv]

That is good idea ! I forgot to bump it thanks!

This should be ready. Pandoc 2.11+ is now tested and will not use pandoc-citeproc now.

[jjallaire]

@yihui Are you okay if we go ahead and merge this?

[yihui]

@jjallaire Hold on please. There seems to be something wrong with the merge commit c14b967 that you pushed. We lost some commits there. It might be because I deleted 3077b34 and 348ed78 from the master branch (since the latter just reverted the former). Sorry about that, but I guess we have to get rid of c14b967. Are you okay with me doing that? It'll be a force push...

[jjallaire]

That’s fine, I can just add that back after. Sorry about that I had forgotten to push that so it got stale

…

On Mon, Oct 12, 2020 at 5:30 PM Yihui Xie ***@***.***> wrote: @jjallaire <https://github.com/jjallaire> Hold on please. There seems to be something wrong with the merge commit c14b967 <c14b967> that you pushed. We lost some commits there. It might be because I deleted 3077b34 <3077b34> and 348ed78 <348ed78> from the master branch (since the latter just reverted the former). Sorry about that, but I guess we have to get rid of c14b967 <c14b967>. Are you okay with me doing that? It'll be a force push... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1916 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAZPR6XJCARRB7KCD3L353SKNYQ3ANCNFSM4SM2RU2A> .

[yihui]

Okay. The PR looks good to me, and I'll merge it right now. Thanks!

[yihui]

@jjallaire I've restored the master branch, and you may have to clone the repo again.

[jjallaire]

Thx, yes, that took care of it!

…

On Mon, Oct 12, 2020 at 5:42 PM Yihui Xie ***@***.***> wrote: @jjallaire <https://github.com/jjallaire> I've restored the master branch, and you may have to clone the repo again. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1916 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAZPR26TUVBS7R4WB2KGVLSKNZ4LANCNFSM4SM2RU2A> .