From 6c7b030b056c798d51e81eafed861535116c92f0 Mon Sep 17 00:00:00 2001 From: RLumSK Date: Wed, 6 Nov 2024 15:14:26 +0100 Subject: [PATCH 1/3] Update Copernicus template to 7.9 --- NEWS.md | 4 +- R/copernicus_article.R | 2 +- ....txt => README_copernicus_package_7_9.txt} | 8 +- .../copernicus/skeleton/copernicus.cfg | 17 ++- .../copernicus/skeleton/copernicus.cls | 125 +++++++++++------- man/copernicus_article.Rd | 2 +- 6 files changed, 99 insertions(+), 59 deletions(-) rename inst/rmarkdown/templates/copernicus/resources/{README_copernicus_package_7_8.txt => README_copernicus_package_7_9.txt} (77%) diff --git a/NEWS.md b/NEWS.md index f3c9b6c9e..a35894e7e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,12 @@ # rticles (development version) - Fix `springer_article()` skeleton: It now uses `equal_contribution` in author field (thanks, @nielsbock, #568). -- Updaye `springer_aticle()` template to version 3 (December 2023): +- Update `springer_aticle()` template to version 3 (December 2023): - BREAKING CHANGE: sn-mathphys.bst has been split into Numbered and Author year style namely `sn-mathphys-num.bst` and `sn-mathphys-ay.bst` respectively. Skeleton has been updated. If you have existing article, you need to use `sn-mathphys-num` or `sn-mathphys-ay` option now, instead of `sn-mathphys`. +- Update Copernicus Publications template to version 7.9 from 2024-10-10 (@RLumSK, ). + # rticles 0.27 - `joss_article()` now correctly works as `base_format` for `bookdown::pdf_book()` (thanks, @mlysy, #564). diff --git a/R/copernicus_article.R b/R/copernicus_article.R index 015811607..5bb1f1d3c 100644 --- a/R/copernicus_article.R +++ b/R/copernicus_article.R @@ -13,7 +13,7 @@ #' #' An number of required and optional manuscript sections, e.g. `acknowledgements`, `competinginterests`, or `authorcontribution`, must be declared using the respective properties of the R Markdown header - see skeleton file. #' -#' **Version:** Based on `copernicus_package.zip` in the version 7.8, 18 March 2024, using `copernicus.cls` in version 10.1.11, 03 January. +#' **Version:** Based on `copernicus_package.zip` in the version 7.7, 10 September 2024, using `copernicus.cls` in version 10.1.20, 10 September 2024. #' #' **Copernicus journal abbreviations:** You can use the function `copernicus_journal_abbreviations()` to get the journal abbreviation for all journals supported by the Copernicus article template. #' diff --git a/inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_8.txt b/inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_9.txt similarity index 77% rename from inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_8.txt rename to inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_9.txt index 48ce6c9ae..125643ee3 100644 --- a/inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_8.txt +++ b/inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_9.txt @@ -1,7 +1,7 @@ -File: README_copernicus_package_7_8.txt +File: README_copernicus_package_7_9.txt ------------------------------------------------------------------------- This is a README file for the Copernicus Publications LaTeX Macro Package -copernicus_package.zip in the version 7.8, 18 March 2024 +copernicus_package.zip in the version 7.9, 10 September 2024 ------------------------------------------------------------------------- It consists of several files, each with its separate copyright. This specific archive is collected for journals published by @@ -15,8 +15,8 @@ URL: https://publications.copernicus.org Content: -- copernicus.cls: The LaTeX2e class file designed for Copernicus Publications journals. Current Version 10.1.11, 3 January 2024 -- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 18 March 2024 +- copernicus.cls: The LaTeX2e class file designed for Copernicus Publications journals. Current Version 10.1.20, 10 September 2024 +- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 10 September 2024 - copernicus.bst: The bibliographic style file for BibTeX. Current Version 1.6, 20 October 2023 - pdfscreencop.sty / pdfscreen.sty - template.tex: A LaTeX template in journal style. \ No newline at end of file diff --git a/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cfg b/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cfg index 301916a0c..b4c33559b 100644 --- a/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cfg +++ b/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cfg @@ -2,6 +2,7 @@ \newif\ifgtes \DeclareOption{gtes} {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue \@bartrue \gtestrue} \newif\ifdwes \DeclareOption{dwes} {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@twostagejnltrue \@barfalse\dwestrue} \DeclareOption{dwesd} {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@stage@finalfalse \dwestrue} +\newif\ifproofreadingchanges \DeclareOption{proofreadingchanges}{\proofreadingchangestrue\@noreftrue} \newif\ifcopyediting \DeclareOption{copyediting}{\copyeditingtrue\@noreftrue} \newif\ifsmsps \DeclareOption{smsps} { \smspstrue} \newif\ifar \DeclareOption{ar}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@firstbartrue\@twostagejnltrue\artrue} @@ -16,7 +17,7 @@ \newif\ifjbji \DeclareOption{jbji}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\jbjitrue} \newif\ifmr \DeclareOption{mr}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@twostagejnltrue\mrtrue} \DeclareOption{mrd}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@stage@finalfalse\mrtrue} -\newif\ifejm \DeclareOption{ejm}{\@abstractcenteredtrue\@bartrue\ejmtrue} +\newif\ifejm \DeclareOption{ejm}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\ejmtrue} \newif\ifwcd \DeclareOption{wcd}{\@twostagejnltrue\wcdtrue} \DeclareOption{wcdd}{\@stage@finalfalse\wcdtrue} \newif\ifgchron \DeclareOption{gchron}{\@sansseriffacetrue\@sansserifheadertrue\@twostagejnltrue\gchrontrue} @@ -102,6 +103,18 @@ \definecolor{rulecol}{gray}{0.8} \fi \fi +\ifproofreadingchanges% Definition of layout used for proofreading changes document + \def\@journalurl{} + \def\@sentence{\textcolor[rgb]{1,0.58,0.25}{% + Track changes document -- Do not use for proofreading}} + \let\@journalnameabbreviation\@sentence + \if@sansserifface + \definecolor{textcol}{rgb}{0,0,0} + \definecolor{bgcol}{rgb}{1,1,1} + \definecolor{barcol}{gray}{0.8} + \definecolor{rulecol}{gray}{0.8} + \fi +\fi \ifacp%classical \def\@journalname{Atmospheric Chemistry and Physics} @@ -968,7 +981,7 @@ \def\@sentence{Published by Copernicus Publications on behalf of the European mineralogical societies DMG, SEM, SIMP \& SFMC.} \def\@journalurl{www.eur-j-mineral.net} \def\@journallogo{\includegraphics{EJM_Logo.pdf}} - \definecolor{textcol}{rgb}{0.0,0.0,0.0} + \definecolor{textcol}{rgb}{0.075,0.447,0.722} \definecolor{bgcol}{rgb}{1,1,1} \definecolor{rulecol}{rgb}{1.0,1.0,1.0} \fi diff --git a/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls b/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls index d93eb02a3..739f551b8 100644 --- a/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls +++ b/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls @@ -16,7 +16,7 @@ %% ----------------------------------------------------------------- \NeedsTeXFormat{LaTeX2e}[1995/12/01] \ProvidesClass{copernicus} - [2023/12/15 10.1.12 Copernicus papers] + [2024/08/28 10.1.20 Copernicus papers] \frenchspacing \clubpenalty10000 \widowpenalty10000 @@ -157,7 +157,7 @@ \@abstractcenteredfalse \@abstractindentedfalse \fi -\AtEndOfClass{\ifcopyediting\let\@msnumber\relax\fi} +\AtEndOfClass{\ifcopyediting\let\@msnumber\relax\fi\ifproofreadingchanges\let\@msnumber\relax\fi} \LoadClass[fleqn]{article} \AtBeginDocument{\mathindent\z@} \if@stage@final @@ -332,7 +332,7 @@ \fi \fi \@journalnameabbreviation - \ifcopyediting\else\if@noref,\space\@msnumber\else,\space\@pvol, \@fpage\if@nolastpage\else{--\@lpage}\fi\fi, \@pyear\fi} + \ifcopyediting\else\ifproofreadingchanges\else\if@noref,\space\@msnumber\else,\space\@pvol, \@fpage\if@nolastpage\else{--\@lpage}\fi\fi, \@pyear\fi\fi} \def\@journalurlInfo{% %% URL raus, DOI rein; 2020-05-15 \if@preface @@ -463,46 +463,57 @@ {{\runningheaderfont\@sentence}\\ \color[gray]{0.55}\put(0.7,0){\rule[1mm]{\textwidth}{0.1mm}}\\ \textcolor[gray]{0.55}{Your manuscript was typeset and received English language copy-editing.\\ - The resulting file is available for proof-reading in the final journal style.\\ + The resulting file is available for proofreading in the final journal style.\\ The present document is only to review the language changes.}}% \if@bar\@titlebar\fi} \else - \def\@oddhead{% - \parbox[t] - {0.6\textwidth} - {\if@sansserifheader\leavevmode\runningheaderfont\fi - \if@preface - doi:10.5194/\preface@abbrev% - \else - \@journalInfo\\ - %\@journalurlInfo\\ %raus laut Ticket 4529 - https://doi.org/10.5194/% - \if@noref - \@msnumber + \ifproofreadingchanges + \def\@oddhead{% + \parbox[t] + {\textwidth} + {{\runningheaderfont\@sentence}\\ + \color[gray]{0.55}\put(0.7,0){\rule[1mm]{\textwidth}{0.1mm}}\\ + \textcolor[gray]{0.55}{The present document only highlights changes made by Copernicus Publications\\ + based on your comments.\\ + Please do not include your further comments in this PDF file.}}% + \if@bar\@titlebar\fi} + \else + \def\@oddhead{% + \parbox[t] + {0.6\textwidth} + {\if@sansserifheader\leavevmode\runningheaderfont\fi + \if@preface + doi:10.5194/\preface@abbrev% \else - \@journalnameshortlower - -\@pvol-\@fpage-\@pyear + \@journalInfo\\ + %\@journalurlInfo\\ %raus laut Ticket 4529 + https://doi.org/10.5194/% + \if@noref + \@msnumber + \else + \@journalnameshortlower + -\@pvol-\@fpage-\@pyear + \fi \fi - \fi - \ifx\specialp@perstring\@undefined\else-\def\1{Corrigendum}\ifx\specialp@perstring\1corrigendum\else editorial-note\fi\fi - \\ - \@journalcopyright - %\includegraphics[width=1.5cm]{CreativeCommons_Attribution_License.png}% - }% - \hfill - \setbox\z@\hbox{\@journallogo}% - \@tempdima\ht\z@\advance\@tempdima-8\p@\lower\@tempdima\box\z@\\ - \ifangeocom - \textcolor{barcol}{\@ddsidemarginbar}% - %\textcolor{textcol}{\@ddsidemarginrule}% - \textcolor{rulecol}{\@ddsidemarginrule}% - \rlap{\kern9mm\smash{% - \@tempdimc\headsep\advance\@tempdimc\textheight\advance\@tempdimc\footskip - \lower\@tempdimc\hbox{\rotatebox[origin=lB]{90}{\fontsize{15}{15}\usefont{T1}{ma1}{m}{n}AnGeo Communicates}}}}% - \else - \if@bar\@titlebar\fi - \fi} - \fi + \ifx\specialp@perstring\@undefined\else-\def\1{Corrigendum}\ifx\specialp@perstring\1corrigendum\else editorial-note\fi\fi + \\ + \@journalcopyright + %\includegraphics[width=1.5cm]{CreativeCommons_Attribution_License.png}% + }% + \hfill + \setbox\z@\hbox{\@journallogo}% + \@tempdima\ht\z@\advance\@tempdima-8\p@\lower\@tempdima\box\z@\\ + \ifangeocom + \textcolor{barcol}{\@ddsidemarginbar}% + %\textcolor{textcol}{\@ddsidemarginrule}% + \textcolor{rulecol}{\@ddsidemarginrule}% + \rlap{\kern9mm\smash{% + \@tempdimc\headsep\advance\@tempdimc\textheight\advance\@tempdimc\footskip + \lower\@tempdimc\hbox{\rotatebox[origin=lB]{90}{\fontsize{15}{15}\usefont{T1}{ma1}{m}{n}AnGeo Communicates}}}}% + \else + \if@bar\@titlebar\fi + \fi} + \fi\fi \def\@oddfoot{\edit@rnotereminder\runningheaderfont\@sentence\hfil} \else \def\@oddhead{\parbox[t]{0.6\textwidth}{\@manuscriptInfo}} @@ -743,6 +754,7 @@ \parskip\z@ \trivlist\item\relax \textcolor{textcol}{\reset@font\normalsize\if@sansserifface\sffamily\fi\bfseries\abstractname.}% + \subpdfbookmark{\abstractname}{abstract}% \enspace\ignorespaces\@abstr \ifx\second@bstract\@undefined\else\par\vspace{1.7mm}\noindent \second@bstract @@ -795,7 +807,7 @@ \labelsep\z@ \xdef\@indescription{}% \def\makelabel##1{\labelfont##1\hss}}% - \ifnum\corr@cnt=\z@\relax\else\item[{Correspondence:}]\@corresp\fi + \ifnum\corr@cnt=\z@\relax\else\item[{Correspondence:}]\bgroup\hyphenpenalty=\@M\raggedright\@corresp\par\egroup\fi \ifnum\ifx\@published\@undefined\ifx\specialp@perstring\@undefined\if!\@recvd!0\else1\fi\else0\fi\else1\fi=1\relax \item[{Relevant dates:}]% \fi @@ -823,7 +835,7 @@ \ifx\@howtocite\@empty\else\item[{How to cite:}]\@howtocite\fi \ifx\abstractexists\@undefined \else - \item[\abstractname:]\@abstr% + \item[\abstractname:]\subpdfbookmark{\abstractname}{abstract}\@abstr% \ifx\second@bstract\@undefined\else\item[\secabstractname:]\second@bstract\fi \if!\@keyw!\else\item[Keywords:]\@keyw\fi \fi @@ -1153,7 +1165,6 @@ \long\def\abstract{% \immediate\write\@auxout{\string\gdef\string\abstractexists{true}}% \iflanguage{ngerman}{\@abslang}{\iflanguage{german}{\@abslang}{}}% - \subpdfbookmark{\abstractname}{abstract}% \edef\ABS@{\@currenvir}% \toks@{}\ABS@get@body} \let\endabstract\relax @@ -1297,8 +1308,8 @@ \fi \fi \RequirePackage[normalem]{ulem}% -\RequirePackage[T1]{fontenc} -\RequirePackage{textcomp} +\RequirePackage[T3,T1]{fontenc} +\RequirePackage[warn]{textcomp} \if@cop@home \RequirePackage{fontawesome5} \ifluatex @@ -1680,10 +1691,10 @@ \let\curr@corr\relax \@parse@corr#1,,\@nil \ifnum\curr@corr@cnt=\@ne\relax - \edef\curr@corr{\csname curr@corr@1\endcsname}% + \protected@edef\curr@corr{\csname curr@corr@1\endcsname}% \else \ifnum\curr@corr@cnt=\tw@\relax - \edef\curr@corr{% + \protected@edef\curr@corr{% \csname curr@corr@1\endcsname\Authsep \csname curr@corr@2\endcsname}% \else @@ -1691,11 +1702,11 @@ \let\curr@corr\@empty% \loop \advance\@tempcntb\@ne - \expandafter\edef\expandafter\curr@corr\expandafter{\curr@corr\csname curr@corr@\the\@tempcntb\endcsname}% + \expandafter\protected@edef\expandafter\curr@corr\expandafter{\curr@corr\csname curr@corr@\the\@tempcntb\endcsname}% \ifnum\@tempcntb<\numexpr\curr@corr@cnt+\m@ne\relax\relax - \expandafter\edef\expandafter\curr@corr\expandafter{\curr@corr\Authsep}% + \expandafter\protected@edef\expandafter\curr@corr\expandafter{\curr@corr\Authsep}% \repeat - \expandafter\edef\expandafter\curr@corr\expandafter{\curr@corr\Authands\csname curr@corr@\the\curr@corr@cnt\endcsname}% + \expandafter\protected@edef\expandafter\curr@corr\expandafter{\curr@corr\Authands\csname curr@corr@\the\curr@corr@cnt\endcsname}% \fi \fi } @@ -1719,7 +1730,7 @@ #3% \ifx\@tempc\@empty\else\noexpand\nobreakspace\@tempc\fi}% \ifx\curr@corr\@empty\else - \expandafter\expandafter\expandafter\xdef\csname corresp-\the\corr@cnt\expandafter\endcsname\expandafter{\@tempd\noexpand\space(\curr@corr)}% + \expandafter\expandafter\expandafter\protected@xdef\csname corresp-\the\corr@cnt\expandafter\endcsname\expandafter{\@tempd\noexpand\space(\curr@corr)}% \fi \expandafter\expandafter\expandafter\author\expandafter\expandafter\expandafter [\expandafter\@tempa\expandafter]\expandafter{\@tempd}} @@ -2237,8 +2248,19 @@ \fi \DeclareMathAlphabet{\mathbbs}{U}{BOONDOX-ds}{m}{n} \DeclareMathAlphabet{\mathblackbold}{U}{dsrom}{m}{n} -\let\ltx@mathbb\mathbb +\def\cop@zavm@symb#1{% + \mathord{\mathchoice + {\mbox{\fontsize{\tf@size}{\tf@size}\usefont{U}{zavm}{m}{it}\symbol{#1}}} + {\mbox{\fontsize{\tf@size}{\tf@size}\usefont{U}{zavm}{m}{it}\symbol{#1}}} + {\mbox{\fontsize{\sf@size}{\sf@size}\usefont{U}{zavm}{m}{it}\symbol{#1}}} + {\mbox{\fontsize{\ssf@size}{\ssf@size}\usefont{U}{zavm}{m}{it}\symbol{#1}}}% + }} +\def\coppa{\cop@zavm@symb{162}} +\def\Koppa{\cop@zavm@symb{163}} +\def\koppa{\cop@zavm@symb{164}} + +\let\ltx@mathbb\mathbb \def\mathbb#1{% \sbox\z@{\@tempcnta 0#1}% \ifdim\wd\z@>\z@\relax @@ -3081,6 +3103,9 @@ \DeclareUnicodeCharacter{200B}{{\unskip\;\color{red}\vrule \@width1ex \@height1ex}} \fi \fi + +\def\invbreve#1{\def\x##1{\fontencoding{T3}\selectfont\textroundcap{{\fontencoding{T1}\selectfont##1}}}\ifmmode \x{$#1$}\else\x{#1}\fi} + \endinput %% %% End of file `copernicus.cls'. diff --git a/man/copernicus_article.Rd b/man/copernicus_article.Rd index 6e5a8eb59..d121f028c 100644 --- a/man/copernicus_article.Rd +++ b/man/copernicus_article.Rd @@ -61,7 +61,7 @@ This was adapted from An number of required and optional manuscript sections, e.g. \code{acknowledgements}, \code{competinginterests}, or \code{authorcontribution}, must be declared using the respective properties of the R Markdown header - see skeleton file. -\strong{Version:} Based on \code{copernicus_package.zip} in the version 7.8, 18 March 2024, using \code{copernicus.cls} in version 10.1.11, 03 January. +\strong{Version:} Based on \code{copernicus_package.zip} in the version 7.7, 10 September 2024, using \code{copernicus.cls} in version 10.1.20, 10 September 2024. \strong{Copernicus journal abbreviations:} You can use the function \code{copernicus_journal_abbreviations()} to get the journal abbreviation for all journals supported by the Copernicus article template. From 9d71ac35d26b827f1533ba2ea122bc843ba4bcac Mon Sep 17 00:00:00 2001 From: RLumSK Date: Wed, 6 Nov 2024 15:17:22 +0100 Subject: [PATCH 2/3] Add PR ID --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index a35894e7e..a64984542 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,7 +5,7 @@ - BREAKING CHANGE: sn-mathphys.bst has been split into Numbered and Author year style namely `sn-mathphys-num.bst` and `sn-mathphys-ay.bst` respectively. Skeleton has been updated. If you have existing article, you need to use `sn-mathphys-num` or `sn-mathphys-ay` option now, instead of `sn-mathphys`. -- Update Copernicus Publications template to version 7.9 from 2024-10-10 (@RLumSK, ). +- Update Copernicus Publications template to version 7.9 from 2024-10-10 (@RLumSK, #577). # rticles 0.27 From 6850ed82cf47588cbdf005a69b052f41c06005f5 Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Mon, 16 Dec 2024 10:31:27 +0100 Subject: [PATCH 3/3] Bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f04abe255..588af3897 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: rticles Title: Article Formats for R Markdown -Version: 0.27.8 +Version: 0.27.9 Authors@R: c( person("JJ", "Allaire", , "jj@posit.co", role = "aut"), person("Yihui", "Xie", , "xie@yihui.name", role = "aut",