Updates AMS to V6.1 #444

ConorIA · 2021-10-17T15:59:21Z

Replaces #348 and closes #298

Todos:

I have not made a great effort to make the skeleton article more "RMarkdown-y". I started replacing some of the \section entries with #, but I was having compilation errors, so needed to go back to start.
The AMS template says to use \twocolsig and \twocolcapsule when using twocol mode, but these are giving me undefined control sequence errors. I have commented out my conditional in template.tex, but would like to get the functionality working before this is merged #helpwanted!
The AMS template uses "and" before the final author name. I have used a for loop for authors (yay me), but I am not familair enough to know how to do a "if (i == length(authors)" type of statement to add the "and" before the last author entry. #helpwanted!
I have addressed the for loops, but I had to resort to using a for loop on the last array entry. That doesn't seem to be right, but I can't figure out how to access the values of authors/last. e.g. authors/last.name throws an error and authors/last["name"] returns "true", not "Author Eight".
News not updated yet because this may not make it into main for a while!

Thanks to @eliocamp as much of this was based on his work on the v5 template.

It looks like old releases of pandoc don't play nice with the pipes. For the record:

$ pandoc --version
pandoc 2.11.4
Compiled with pandoc-types 1.22, texmath 0.12.1, skylighting 0.10.2,
citeproc 0.3.0.5, ipynb 0.1.0.1

inst/rmarkdown/templates/ams/resources/template.tex

inst/rmarkdown/templates/ams/skeleton/skeleton.Rmd

cderv

Hi!

Thanks for this and sorry for the delay. Here are a few comment we need to work out.

Overall it would be best in if the skeleton contains more R code examples and Markdown. That would help our test too.

cderv · 2021-11-24T14:12:07Z

R/article.R

@@ -88,9 +88,9 @@ amq_article <- function(
 #'   <https://www.ametsoc.org/ams/index.cfm/publications/authors/journal-and-bams-authors/author-resources/latex-author-info/>.
 #' @export
 #' @rdname article
-ams_article <- function(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")) {
+ams_article <- function(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris", "-auto_identifiers")) {


Just to understand: why do we need to remove this extension here ?

To be honest I'm not sure what my reasoning was. It might be the sort of thing that is obvious if we put it back in and see what results.

cderv · 2021-11-24T14:13:48Z

R/article.R

  pdf_document_format(
-    "ams", keep_tex = keep_tex, md_extensions = md_extensions, ...
+    "ams", keep_tex = keep_tex, md_extensions = md_extensions, citation_package = 'natbib', ...


I think we need to make this also a parameter of the function so that it can be changed.

Previously it was not set - so I don't think natbib was used. Does it need to be used to work now ?

We should try to prevent things breaking if possible and this would change the default citation processing. We need to offer a way to change it.

I understood that natbib is hard-coded in ametsocv6.1.cls

inst/rmarkdown/templates/ams/resources/template.tex

cderv · 2021-11-24T14:35:50Z

inst/rmarkdown/templates/ams/resources/template.tex

-$exauthors.email$
+% Credit to https://stackoverflow.com/a/67609365 for different last-author case.
+\authors{
+$if(authors/allbutlast)$


This syntax allbutlast brings a min Pandoc requirement (at least 2.10) than we need to insure.

cderv · 2021-11-24T15:55:49Z

inst/rmarkdown/templates/ams/skeleton/skeleton.Rmd

-\centerline{(illustration here)}
-\appendcaption{B1}{Here is the appendix figure caption.}
-\end{figure}
+\bibliography{references}


Shouldn't we put this in the template as we usually do with other formats ?

inst/rmarkdown/templates/ams/skeleton/skeleton.Rmd

cderv · 2021-11-24T16:02:11Z

inst/rmarkdown/templates/ams/skeleton/skeleton.Rmd

-plot(1:10)
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(fig.path = "",     # AMS required
+                      out.extra = "",    # To force figure labels


What is the issue exactly ?
fig_caption = TRUE in pdf_document() should be enough to have the caption 🤔

cderv · 2021-11-24T16:02:48Z

inst/rmarkdown/templates/ams/skeleton/skeleton.Rmd

-```{r,echo=FALSE,fig.cap='test the rmd output',fig.align='center',fig.width=3.17}
-plot(1:10)
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(fig.path = "",     # AMS required


If this is required we could probably make that part of the format function 🤔

cderv · 2021-11-24T17:01:24Z

inst/rmarkdown/templates/ams/skeleton/skeleton.Rmd

-Each table must be numbered, provided with a caption, and mentioned specifically in the text. 
-See below (in the .tex document) and at the end of the document for the formatting of a sample table (Table
-\ref{t1}).
+\section{Introduction}


We would need to change to Markdown before merging

Suggested change

\section{Introduction}

# Introduction

If we are lazy to do it manually, we can probably convert the tex file body using Pandoc directly

cderv · 2021-11-24T17:11:46Z

R/article.R

@@ -88,9 +88,9 @@ amq_article <- function(
 #'   <https://www.ametsoc.org/ams/index.cfm/publications/authors/journal-and-bams-authors/author-resources/latex-author-info/>.
 #' @export
 #' @rdname article
-ams_article <- function(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")) {
+ams_article <- function(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris", "-auto_identifiers")) {
  pdf_document_format(


We need to put a Pandoc requirement before running the function here - the test are failing because of this mainly

rmarkdown::pandoc_available('2.10', TRUE)

cderv · 2023-04-19T09:44:39Z

@ConorIA do you plan to keep working on this or should I take over ?

Maybe AMS has also update to a newer version than 6.1.

Enquiring about the status of this PR following my latest review

ConorIA · 2023-04-20T13:10:54Z

Hi @cderv, sorry to have been unresponsive to your very detailed review. I find myself very short on free time these days, and haven't been writing much after finishing my thesis last fall. I would be happy to have you take over.

The good news is that v6.1 is still the current AMS template https://www.ametsoc.org/index.cfm/ams/publications/author-information/latex-author-info/

cderv · 2023-04-20T14:51:07Z

Thanks for the feedback - I'll add that to my list then. Thanks for your contribution

CLAassistant · 2024-04-17T19:36:43Z

All committers have signed the CLA.

cderv · 2024-11-27T18:49:24Z

I did solve some of the conflict, but my last review did not get reply. I'll see if I can finish the work without the information of choice you made. It's been some time, so you may not remember why anyway.

ConorIA · 2024-11-28T01:35:52Z

Hi @cderv . Sorry for my lack of responsiveness. It sure has been a while since I opened this PR. To be honest, I'm not sure that there was much thinking in my work. It was mostly about hacking the new template into the old example and trying to make it work. Certainly not up to the quality. I will take a look at your review comments, but as I noted in 2023. I don't think I'll be the one to get this PR over the finish line. I not longer use R in my day-to-day, nor am I in academia anymore. Just rusty skills and pleasant memories at this point! Sorry about that.

and document

eliocamp and others added 4 commits October 17, 2021 10:16

Cherry-pick @eliocamp

beec027

Uses xelatex in the AMS skeleton

5f12f3a

Update for v6.1

7f65495

Default to twocol=FALSE

e9cd1a1

ConorIA changed the title ~~Updates AMS to V5~~ Updates AMS to V6.1 Oct 17, 2021

Cleanup changes to

5e580d8

ConorIA force-pushed the ams61 branch from 4fd6cb0 to 5e580d8 Compare October 17, 2021 16:06

ConorIA added 2 commits October 17, 2021 13:11

Redocument article.Rd

9df3228

Fix last-entry cases for author and affiliation loops

c36f847

ConorIA commented Oct 17, 2021

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cderv requested changes Nov 24, 2021

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cderv mentioned this pull request Nov 29, 2021

Updates AMS to V5 #348

Closed

cderv self-assigned this Apr 20, 2023

cderv added the WIP label Apr 20, 2023

cderv mentioned this pull request Nov 2, 2023

Pandoc 3.1.7 new citeproc for LaTeX breaks some formats #550

Closed

2 tasks

Merge branch 'main' into ams61

664ce6e

cderv added 4 commits November 29, 2024 18:17

check for old argument unsupported and warn

29e34d2

Set pandoc requirment and add warning about new tempalte

3cc1fd7

Check various metadata

3352213

rewrite the new for loop for auhtor

944c15a

cderv added 16 commits November 29, 2024 18:18

rewrite affiliation as YAML

0bd2da5

Move article function to its own file

93c3121

and document

set bibliography in the right place

4521383

Add missing part in template for Pandoc

3aa21ec

mention doc on abstract

f013c2a

Use markdown in the template for most part

5409113

Update bibliography file

ef268a7

Add a lua filter to help write expected AMS syntax

3b10ab5

fix filter

4cd9f70

fix affiliation

5ff8ffd

re-document

801be50

Adapt test and fix citation package to natbib

3021031

Fix merge problem

d16e04a

Re document

f4550da

Trigger warning immediately

e75fe96

Bump version

4ffd088

cderv merged commit fe7347d into rstudio:main Dec 6, 2024
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Updates AMS to V6.1 #444

Updates AMS to V6.1 #444

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Updates AMS to V6.1 #444

Updates AMS to V6.1 #444

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