revert changes since it was last working, because having trouble with…

… includes argument
FredHutch · Jul 4, 2024 · ffb22d5 · ffb22d5
1 parent 0a367b9
commit ffb22d5
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Showing 5 changed files with 301 additions and 128 deletions.
diff --git a/R/template.R b/R/template.R
@@ -262,11 +262,10 @@ visc_pdf_document <- function(latex_engine = "pdflatex",
                               ...) {
 
   if (rmarkdown::pandoc_version() < '3.1.7') {
-    csl_refs_preamble <- find_resource("visc_report", "csl_refs_old.tex")
+    template <- find_resource("visc_report", "template_with_old_csl_refs.tex")
   } else {
-    csl_refs_preamble <- find_resource("visc_report", "csl_refs_new.tex")
+    template <- find_resource("visc_report", "template.tex")
   }
-  template <- find_resource("visc_report", "visc_latex_template.tex")
 
   logo_path_scharp <- find_resource("visc_report", "SCHARP_logo.png")
   logo_path_fh <- find_resource("visc_report", "FredHutch_logo.png")
@@ -296,7 +295,6 @@ visc_pdf_document <- function(latex_engine = "pdflatex",
       "-V", paste0("logo_path_fh=", logo_path_fh),
       "-V", paste0("logo_path_visc=", logo_path_visc)
     ),
-    includes = rmarkdown::includes(in_header = csl_refs_preamble),
     ...)
 }
 

diff --git a/inst/rmarkdown/templates/visc_report/resources/csl_refs_new.tex b/inst/rmarkdown/templates/visc_report/resources/csl_refs_new.tex
diff --git a/inst/rmarkdown/templates/visc_report/resources/csl_refs_old.tex b/inst/rmarkdown/templates/visc_report/resources/csl_refs_old.tex
diff --git a/..._report/resources/visc_latex_template.tex → ...plates/visc_report/resources/template.tex b/..._report/resources/visc_latex_template.tex → ...plates/visc_report/resources/template.tex
@@ -1,17 +1,20 @@
 \documentclass[11pt]{article}
-
+%\usepackage{etex}
+%\reserveinserts{28}
 \usepackage{lastpage}
 \usepackage[hmargin=2cm, top=2.7cm, bottom=3.5cm, footskip=0.5cm]{geometry}
 \usepackage{url}
 \usepackage[maxfloats=50]{morefloats}
 \usepackage{parskip}
+%\usepackage[citestyle=authoryear-comp,natbib=true]{biblatex}
 \usepackage{pdflscape}
 \usepackage[absolute]{textpos}
 \usepackage{rotating} %for xtable sideways
 \usepackage{verbatim}
 \usepackage{longtable}
 \usepackage{multirow}
 \usepackage{lipsum}
+%\usepackage[acronym,nomain]{glossaries}
 \usepackage{fancyhdr, graphicx, lastpage, ifthen, lscape}
 \usepackage[dvipsnames, table]{xcolor}
 \usepackage{soul}
@@ -211,12 +214,11 @@
 \setlength{\footskip}{56pt}
 \pagestyle{fancy}
 \setlength{\parindent}{0pt}
-
-
+%\makeglossaries
 \begin{document}
 \sloppy
 
-% get current date into insertdate
+%get current date into insertdate
 \makeatletter
 \let\insertdate\@date
 \makeatother
@@ -225,7 +227,7 @@
 \newcommand{\blandscape}{\begin{landscape}}
 \newcommand{\elandscape}{\end{landscape}}
 
-% To and From Section
+%begin To and From Section
 \makeatletter
 \newcommand\tabfill[1]{%
   \dimen@\linewidth
@@ -235,6 +237,7 @@
     \leftskip=2em\hspace*{-2em}#1\ifhmode\strut\fi}%
 }
 \makeatother
+
 \vspace{0.1cm}
 \begin{flushleft}
 \begin{tabbing}
@@ -255,18 +258,20 @@
 
 \vspace{2cm}
 
+%begin contents section
 $if(toc)$
 \tableofcontents
 $endif$
 
-% change color of header and footer text to gray
+%change color of header and footer text to gray
 \makeatletter
 \patchcmd{\@fancyhead}{\rlap}{\color{gray}\rlap}{}{}
 \patchcmd{\headrule}{\hrule}{\color{gray}\hrule}{}{}
 \patchcmd{\@fancyfoot}{\rlap}{\color{gray}\rlap}{}{}
 \patchcmd{\footrule}{\hrule}{\color{gray}\hrule}{}{}
 \makeatother
 
+
 $if(includesummary)$
 \begin{abstract}
 $summary$
@@ -289,7 +294,9 @@
 $else$
 \fancyhead[L]{\em VISC Report}
 $endif$
+%\printglossaries
 
 $body$
 \label{LastPageOfBackMatter}~
 \end{document}
+