Update Copernicus Publication template to version 6.3 (#432)

Co-authored-by: christophe dervieux <christophe.dervieux@gmail.com>

Author: RLumSK

NEWS.md

@@ -10,9 +10,11 @@
 
 - `bioinformatics_article()` now separates `manuscript_type` (e.g., Applications note, Original article) and `subject_section` (e.g. Genome analysis, Phylogenetics) in template and skeleton (thanks, @stephenturner, #415)
 
+- Update Copernicus Publications template to version 6.3 from 2021-07-08
+
 # rticles 0.20
 
-- `lipics_article()` skeleton now sets option `bookdown.theorem.preamble` to FALSE to work with `bookdown::pdf_book()` and avoid conflicst in theorem environment definition. This requires **bookdown** 0.23 or higher (#392).
+- `lipics_article()` skeleton now sets option `bookdown.theorem.preamble` to FALSE to work with `bookdown::pdf_book()` and avoid conflicts in theorem environment definition. This requires **bookdown** 0.23 or higher (#392).
 
 - `oup_article()` template now largely compatible to that of `elsevier_article()` (thanks, @dmkaplan2000, #403)
 

R/copernicus_article.R

@@ -13,7 +13,7 @@
 #'
 #' 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 6.2, 15 January 2021, using \code{copernicus.cls} in version 9.25.
+#' \strong{Version:} Based on \code{copernicus_package.zip} in the version 6.3, 8 July 2021, using \code{copernicus.cls} in version 9.32, 7 July 2021.
 #'
 #' \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.
 #'

inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_6_2.txt renamed to inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_6_3.txt

@@ -1,7 +1,7 @@
-File: README_copernicus_package_6_2.txt
+File: README_copernicus_package_6_3.txt
 -------------------------------------------------------------------------
 This is a README file for the Copernicus Publications LaTeX Macro Package 
-copernicus_package.zip in the version 6.2, 15 January 2021
+copernicus_package.zip in the version 6.3, 8 July 2021
 -------------------------------------------------------------------------
 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 9.25, 12 January 2021
-- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 15 January 2021
+- copernicus.cls: The LaTeX2e class file designed for Copernicus Publications journals. Current Version 9.32, 7 July 2021
+- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 8 July 2021
 - copernicus.bst: The bibliographic style file for BibTeX. Current Version 1.3, January 2021 
 - pdfscreencop.sty / pdfscreen.sty
 - template.tex: A LaTeX template in journal style.

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

@@ -14,7 +14,7 @@
 
 
 
-%% Journal abbreviations (please use the same for discussion papers and final revised papers)
+%% Journal abbreviations (please use the same for preprints and final revised papers)
 
 
 % Advances in Geosciences (adgeo)

inst/rmarkdown/templates/copernicus/skeleton/copernicus.cfg

@@ -1,7 +1,7 @@
 \newif\ifprp             \DeclareOption{prp}     {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue                  \@bartrue \prptrue}
 \newif\ifgtes            \DeclareOption{gtes}    {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue                  \@bartrue \gtestrue}
 \newif\ifcopyediting     \DeclareOption{copyediting}{\copyeditingtrue\@noreftrue}
-\newif\ifpolf  \DeclareOption{polf}{\@sansseriffacetrue\@sansserifheadertrue\polftrue}
+\newif\ifpolf  \DeclareOption{polf}{\@sansseriffacetrue\@sansserifheadertrue\@bartrue\polftrue}
 \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}
@@ -35,7 +35,8 @@
 \newif\ifasr  \DeclareOption{asr}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\asrtrue}
 \newif\ifms  \DeclareOption{ms}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\mstrue}
 \newif\ifjsss  \DeclareOption{jsss}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\jssstrue}
-\newif\ifhgss  \DeclareOption{hgss}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\hgsstrue}
+\newif\ifhgss  \DeclareOption{hgss}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@twostagejnltrue\hgsstrue}
+            \DeclareOption{hgssd}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@stage@finalfalse\hgsstrue}
 \newif\ifgh  \DeclareOption{gh}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\ghtrue}
 \newif\ifesurf  \DeclareOption{esurf}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@twostagejnltrue\esurftrue}
             \DeclareOption{esurfd}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@stage@finalfalse\esurftrue}
@@ -593,12 +594,24 @@
   \def\@journalnameshortlower{hgss}
   \def\@journalstartyear{2010}
   \def\@sentence{Published by Copernicus Publications.}
-  \def\@journalurl{www.hist-geo-space-sci.net}
-  \def\@journallogo{\includegraphics{HGSS_Logo.pdf}}
-  \definecolor{textcol}{rgb}{0.0,0.443,0.706}
-  \definecolor{bgcol}{rgb}{1,1,1}
-  \definecolor{barcol}{rgb}{1.0,1.0,1.0}
-  \definecolor{rulecol}{rgb}{0.0,0.443,0.706}
+  \if@stage@final
+    \def\@journalurl{www.hist-geo-space-sci.net}
+    \def\@journallogo{\includegraphics{HGSS_Logo.pdf}}
+    \definecolor{textcol}{rgb}{0.0,0.443,0.706}
+    \definecolor{bgcol}{rgb}{1,1,1}
+    \definecolor{barcol}{rgb}{1.0,1.0,1.0}
+    \definecolor{rulecol}{rgb}{0.0,0.443,0.706}
+  \else
+    \def\@journalurl{https://hgss.copernicus.org/preprints/preprints.html}
+    \def\@journallogo{\includegraphics{HGSSD_Logo.pdf}}
+    \def\@sentenceDiscussion{This preprint is/has been under review for the journal History of Geo- and Space Sciences (HGSS). Please refer to the corresponding final paper in HGSS if available.}
+    \if@cop@home
+      \definecolor{journalname}{rgb}{1.0,1.0,1.0}
+      \definecolor{buttonbackground}{rgb}{1.0,1.0,1.0}
+      \definecolor{paneltext}{rgb}{1.0,1.0,1.0}
+      \definecolor{buttontext}{rgb}{1.0,1.0,1.0}
+    \fi
+  \fi
 \fi
 \ifjsss%classical
   \def\@journalname{Journal of Sensors and Sensor Systems}
@@ -1027,7 +1040,7 @@
   \def\@journalnameshort{JBJI}
   \def\@journalnameshortlower{jbji}
   \def\@journalstartyear{2016}
-  \def\@sentence{Published by Copernicus Publications on behalf of of EBJIS and MSIS.}
+  \def\@sentence{Published by Copernicus Publications on behalf of EBJIS and MSIS.}
   \def\@journalurl{https://jbji.copernicus.org/}
   \def\@journallogo{\includegraphics{JBJI_Logo.pdf}}
   \definecolor{textcol}{rgb}{0.161,0.337,0.361}
@@ -1040,7 +1053,7 @@
   \def\@journalnameabbreviation{Polarforschung}
   \def\@journalnameshort{POLF}
   \def\@journalnameshortlower{polf}
-  \def\@journalstartyear{2021}
+  \def\@journalstartyear{1931}
   \def\@sentence{Published by Copernicus Publications on behalf of the Deutsche Gesellschaft für Polarforschung e.V.}
   \def\@journalurl{https://polf.copernicus.org}
   \def\@journallogo{\includegraphics{POLF_Logo.pdf}}

inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls

@@ -16,7 +16,7 @@
 %% -----------------------------------------------------------------
 \NeedsTeXFormat{LaTeX2e}[1995/12/01]
 \ProvidesClass{copernicus}
-    [2021/01/12 9.25 Copernicus papers]
+    [2021/07/07 9.32 Copernicus papers]
 \frenchspacing
 \clubpenalty10000
 \widowpenalty10000
@@ -437,8 +437,9 @@
              \fi
              \ifx\specialp@perstring\@undefined\else-\def\1{Corrigendum}\ifx\specialp@perstring\1corrigendum\else editorial-note\fi\fi
              \\
-             \@journalcopyright\\[1mm]
-             \includegraphics[width=1.5cm]{CreativeCommons_Attribution_License.png}}%
+             \@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@\\
@@ -1032,7 +1033,6 @@
     \fi
   \fi
 }
-
 \if@stage@final
   \ifnum\if@abstractcentered1\else\if@abstractindented1\else0\fi\fi=1\relax%modern oder indented
     \long\def\abstract{%
@@ -1184,6 +1184,30 @@
   \RequirePackage{fontawesome5}
   \RequirePackage{fontawesome}
 \fi
+\usepackage{upquote}%% #7510
+\usepackage{regexpatch}
+\def\active@text@prime{\ifin@texttt\textquotesingle\else'\fi}
+\def\active@math@prime{^\bgroup\prim@s}
+\newif\ifin@texttt
+\regexpatchcmd{\pr@m@s}{\'}{\cA\'}{}{}
+\xapptocmd{\ttfamily}{\in@texttttrue}{}{}
+\begingroup\lccode`\~=`\'
+\lowercase{\endgroup\protected\def~}{%
+  \ifmmode
+    \expandafter\active@math@prime
+  \else
+    \expandafter\active@text@prime
+  \fi}
+\AtBeginDocument{\catcode`\'=\active}
+\ifx\xmltexversion\@undefined
+\begingroup
+\obeylines\obeyspaces%
+\gdef\@resetactivechars{%
+\def^^M{\@activechar@info{EOL}\space}%
+\def {\@activechar@info{space}\space}%
+}%
+\endgroup
+\fi
 \ifx\xmltexversion\@undefined
   \RequirePackage[utf8]{inputenc}
   \def\strip@x#1x#2\@nil{#1}%
@@ -1201,6 +1225,7 @@
 \def\@tempa{french}\ifx\bbl@main@language\@tempa
   \StandardLayout
   %% Switch to quotation marks with additional horizontal spacing
+  \let\update@frenchlists\relax
   \bbl@frenchguillemets
   \global\let\flqq\og \global\let\frqq\fg
   \ifx\xmltexversion\@undefined\else
@@ -2200,7 +2225,7 @@
   \fi
 \fi
 %% some of the following commands are only active if \@cop@hometrue
-\def\texlicencestatement#1{\gdef\@texlicencestatement{#1}}%
+\def\texlicencestatement#1#2{\gdef\@texlicencestatement{#1}\gdef\@texlicencelogo{#2}}%
   \def\@texlicencestatement{\CopernicusError{Please add \string\texlicencestatement}{You must provide the licence statement before \string\maketitle"}}
 \def\received#1{\if@cop@home\def\@recvd{#1}\fi}        \def\@recvd{}%+1,+2,+d
 \def\pubdiscuss#1{\if@cop@home\def\@pubdiscuss{#1}\fi} \def\@pubdiscuss{}%+1,+2,-d -- twostagejnltrue
@@ -2584,18 +2609,24 @@
 \fi
 \def\iftwocol#1#2{\if@twocolumn#1\else #2\fi}
 \let\hack\@firstofone
+\let\notforhtml\@firstofone
 \newcommand\@journalname{Journalname}
 \newcommand\@journalnameabbreviation{J. Name}
 \newcommand\@journalnameshort{JN}
 \newcommand\@journalnameshortlower{jn}
 \newcommand\@journalurl{www.jn.net}
 \newcommand\@journalpublisher{Copernicus Publications}
 \newcommand\@journalcopyright{%
-  \copyright\ Author(s)\ \@cyear. %
+  %\copyright\ Author(s)\ \@cyear. %
   \if!\@texlicencestatement!%
     \CopernicusError{\string\texlicencestatement{} must have content}{Say, e.g., "\string\texlicencestatement{CC Attribution 4.0 License.}"}%
   \else
     \@texlicencestatement
+    \if!\@texlicencelogo!\else
+      \def\@optarg{width=1.5cm}%
+      \\[1mm]
+      \expandafter\expandafter\expandafter\includegraphics\expandafter\expandafter\expandafter[\expandafter\@optarg\expandafter]\expandafter{\@texlicencelogo}
+    \fi
   \fi}
 \newcommand\@journalstartyear{2013}
 \newcommand\@journallogo{Journallogo}