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

ConorIA · 2021-10-17T18:06:34Z

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

 $endif$
+$for(authors/last)$


I don't think this ought to be a for loop, 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".

I would have tried the same syntax so if it does not work, I think you need a for loop.
I don't see any example in doc: https://pandoc.org/MANUAL.html#pipes

ConorIA · 2021-10-17T18:06:55Z

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

 $endif$
+$for(affiliations/last)$


Again, this probably doesn't need to be a loop.

ConorIA · 2021-10-17T18:08:42Z

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

+$if(statement)$
+%$if(twocol)$\twocolsig$else$\statement$endif$
+$statement$
+$endif$ % FIXME, AMS template says to use twocolsig instead of sig for twocol, but there is no sig, is two col twocolstatement or twocolsig?


I don't know if the AMS folks actually implemented this. I get an undefined control sequence. I also notice that in the example twocol article included in their bundle, the significance statement doesn't actually span two columns. (See "amssamp2V6.1.pdf" in the AMS zip.)

Yes it seems to be commented in there ametsocV6.1.cls class if you look at it. so the command is not defined.

The amssamp2V6.1.tex example does not contain the command.

Probably an issue with AMS article then.

ConorIA · 2021-10-17T18:10:25Z

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

+ - {name: Author Five, current: "Author Five's current affiliation: NCAR, Boulder, Colorado", aff: c} 
+ - {name: Author Six, aff: d} 
+ - {name: Author Seven, aff: d} 
+ - {name: Author Eight, aff: "a,d"}


In the AMS template, Author Eight has two affiliations. I have handled this by quoting the two (otherwise, pandoc thinks this is another array). Would it be better for an additional for loop here? (I think it would be overkill).

You could write like this two

authors: - name: Author Eight aff: a,d

then no quoting is needed. Do we have to show eight authors for the example ?

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 ?

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.

cderv · 2021-11-24T14:19:28Z

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

@@ -1,118 +1,149 @@
-\documentclass[$layout$]{ametsoc}


We probably need to write in the NEWS files to explain the change as there is a new class used.

This will definitely break some old rticles if people update 🤔
I still don't know what the best to be done.

Here layout: will have no more effect

cderv · 2021-11-24T14:19:43Z

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

-\documentclass[$layout$]{ametsoc}
-\usepackage{color}
-\usepackage{hyperref}
-\journal{$journal$}


journal: is no more useful right ?

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 ?

cderv · 2021-11-24T15:59:08Z

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

+ - {name: Author Five, current: "Author Five's current affiliation: NCAR, Boulder, Colorado", aff: c} 
+ - {name: Author Six, aff: d} 
+ - {name: Author Seven, aff: d} 
+ - {name: Author Eight, aff: "a,d"}


You could write like this two

authors: - name: Author Eight aff: a,d

then no quoting is needed. Do we have to show eight authors for the example ?

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.

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

View reviewed changes

cderv requested changes Nov 24, 2021

View reviewed changes

cderv reviewed Nov 24, 2021

View reviewed changes

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

Open

2 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Updates AMS to V6.1 #444

Updates AMS to V6.1 #444

ConorIA commented Oct 17, 2021 •

edited

ConorIA Oct 17, 2021 •

edited

cderv Nov 24, 2021

ConorIA Oct 17, 2021

ConorIA Oct 17, 2021 •

edited

cderv Nov 24, 2021

ConorIA Oct 17, 2021

cderv Nov 24, 2021

cderv left a comment

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv Nov 24, 2021

cderv commented Apr 19, 2023

ConorIA commented Apr 20, 2023

cderv commented Apr 20, 2023

CLAassistant commented Apr 17, 2024 •

edited

		$endif$
		$for(authors/last)$

		$endif$
		$for(affiliations/last)$

Updates AMS to V6.1 #444

Are you sure you want to change the base?

Updates AMS to V6.1 #444

Conversation

ConorIA commented Oct 17, 2021 • edited

Todos:

ConorIA Oct 17, 2021 • edited

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

ConorIA Oct 17, 2021 • edited

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

cderv left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

cderv commented Apr 19, 2023

ConorIA commented Apr 20, 2023

cderv commented Apr 20, 2023

CLAassistant commented Apr 17, 2024 • edited

ConorIA commented Oct 17, 2021 •

edited

ConorIA Oct 17, 2021 •

edited

ConorIA Oct 17, 2021 •

edited

CLAassistant commented Apr 17, 2024 •

edited