Commit 1cc84bf2 authored by Sabina Köfler's avatar Sabina Köfler
Browse files

Merge branch 'master' of https://gitlab.servus.at/tissue/tissue-research-doc into main

parents d3af67f2 08a26d09
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in 2 minutes and 28 seconds
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/_book/
/node_modules/
/book.pdf
/book.mobi
/book.epub
*.svg
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/_book/
/node_modules/
/book.pdf
/book.mobi
/book.epub
/PDFs/
quick-start-guides/PDFs/
*.aux
*.fls
*.log
*.synctex.gz
*.toc
*.aux
*.out
*.fdb_latexmk
*.pdf
>>>>>>> 08a26d090cefa1a2c071720377dd1be15fd1c4ba
......@@ -6,3 +6,4 @@
* [Quick Start Guide Pannoramic SCAN II](quick-start-guides/quick-start-guide-pannoramic-scan-ii.md)
* [Quick Start Guide TMA Grand Master](quick-start-guides/quick-start-guide-tma-grand-master.md)
* [Get started with git](quick-start-guides/get_started_with_git.md)
{
"plugins": [
"intopic-toc"
]
}
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#!/bin/bash
# First replace all whitespaces from filenames with underscores
replace_whitespaces() {
for f in *\ *; do
mv "$f" "${f// /_}";
done
}
# Create array to store all md files for later
create_filearray () {
mapfile -d $'\0' files < <(find . -iname "*.md" -print0)
}
find_markdown () {
if [ "${#files[@]}" -eq 0 ] ; then
echo -e "No markdown files detected!\n"
exit
else
echo -e "${#files[@]} markdown files detected!\n"
fi
}
# Checks for output directory and creates one if missing
create_outdir_if_not_exists () {
if [ ! -d "$pdf_dir" ]; then
mkdir $pdf_dir
echo -e "Output folder created.\n"
else
echo -e "Selecting existing output folder.\n"
fi
}
# Asks user for the LaTeX engine to be used
select_latex_engine() {
echo -e "LaTeX engines\n------------\n"
PS3=$'\n'"Please choose a LaTeX engine (type 1 for pdflatex): "
select option in pdflatex lualatex xelatex
do
case $option in
pdflatex)
echo -e "\npdflatex engine selected";;
lualatex)
echo -e "\nlualatex engine selected";;
xelatex)
echo -e "\nxelatex";;
*)
echo "Please choose an option";;
esac
break
done
echo
}
construct_filename() {
y="$file" # ./FILENAME.EXTENSION
x="${y%.*}" # ./FILENAME
z="${x##*/}" # FILENAME
pdf_filename="${z}.pdf"
pdf_path="./${pdf_dir}/${pdf_filename}"
}
create_date_string() {
created_date=$(stat -c %y ${pdf_path}) # Get file last modified date and time
IFS=" " read -r a b c <<< "$created_date" # split the string into 3 parts (date time timezone_offset)
file_date="$a" # the first part is the date
ftime="${b%.*}" # the second part is the time (but its too exact, so strip everything after the .)
file_time=${ftime//:} # remove the colons from the time stamp
echo "Constructed date string: $file_date and time string: $file_time"
}
construct_bak_path() {
bak_pdf_filename="${z}_${file_date}-${file_time}.pdf"
bak_pdf_path="./${pdf_dir}/${bak_pdf_filename}"
}
# END functions #
pdf_dir="PDFs"
replace_whitespaces
create_filearray
find_markdown
create_outdir_if_not_exists
select_latex_engine
# # Allow user to add custom LaTeX variables
# echo -n "Would you like to add any LaTeX details(e.g. --variable mainfont:\"Gill Sans\")?: "
# read variable
# Compile documents
echo -e "\nBeginning conversion...\n"
# search1="\[\[_TOC_\]\]"
# search2="## Inhalt"
# # find . -iname "*.md" -o -iname "*.mdown" -o -iname "*.markdown" | while read -r file; do # find -iname finds <pattern> case insensitive
# for file in "${files[@]}"; do
# echo "File:" ${file}
# # remove the line that renders the table of contents in markdown and copy file to /PDFs
# if ! grep -q "$search1" $file; then
# continue
# else
# echo -e "Found search string in $file\n Will make a copy"
# sed "/$search1/d;/$search2/d" $file > ./$pdf_dir/$file
# fi
# done
find ./$pdf_dir -iname "*.md" | while read -r file; do
echo -e "\nFound files to convert $file"
construct_filename #$file
if [ -f "$pdf_path" ]; then
echo -e "File $file was already converted to $pdf_path."
create_date_string
construct_bak_path
echo "Constructing back up path: $bak_pdf_path"
mv $pdf_path $bak_pdf_path
echo -e "\nExisting file was moved to ${bak_pdf_path}\n"
else
echo -e "File $file not the same as $pdf_path."
fi
echo -e "\nContinuing with new file creation\n"
pandoc -s --toc --template=my.latex -f gfm "$file" --pdf-engine=$option -o "$pdf_path" # could add --variable font-family:sans-serif $variable
echo -e "File created\n"
done
echo -e "\nAll files complete!"
......@@ -49,3 +49,11 @@ then
```
git push
```
## automatically close an open issue when pushing a commit
```
git commit -m "Sort more efficiently" -m "Closes #[INSERT_ISSUE_NO]]"
```
```
git push
```
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\PassOptionsToPackage{RTLdocument}{bidi}
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$if(beamer)$
$if(background-image)$
\usebackgroundtemplate{%
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$endif$
\usepackage{pgfpages}
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\usecolortheme{$colortheme$}
$endif$
$if(fonttheme)$
\usefonttheme{$fonttheme$}
$endif$
$if(mainfont)$
\usefonttheme{serif} % use mainfont rather than sansfont for slide text
$endif$
$if(innertheme)$
\useinnertheme{$innertheme$}
$endif$
$if(outertheme)$
\useoutertheme{$outertheme$}
$endif$
$endif$
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(indent)$
$else$
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
$if(colorlinks)$
\usepackage{xcolor}
$endif$
\usepackage{hyperref}
\hypersetup{
$if(title-meta)$
pdftitle={$title-meta$},
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pdfauthor={$author-meta$},
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$endif$
breaklinks=true}
\urlstyle{same} % don't use monospace font for urls
$if(verbatim-in-note)$
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$endif$
$if(geometry)$
\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
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$if(listings)$
\usepackage{listings}
\newcommand{\passthrough}[1]{#1}
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$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
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$if(highlighting-macros)$
$highlighting-macros$
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$if(tables)$
\usepackage{longtable,booktabs}
$if(beamer)$
\usepackage{caption}
% These lines are needed to make table captions work with longtable:
\makeatletter
\def\fnum@table{\tablename~\thetable}
\makeatother
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% Fix footnotes in tables (requires footnote package)
\IfFileExists{footnote.sty}{\usepackage{footnote}\makesavenoteenv{longtable}}{}
$endif$
$endif$
$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
$endif$
$if(beamer)$
% Prevent slide breaks in the middle of a paragraph:
\widowpenalties 1 10000
\raggedbottom
$if(section-titles)$
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}
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\centering
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}
\setbeamertemplate{subsection page}{
\centering
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\usebeamerfont{subsection title}\insertsubsection\par
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}
\AtBeginPart{
\frame{\partpage}
}
\AtBeginSection{
\ifbibliography
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}
\AtBeginSubsection{
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$endif$
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$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
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% set default figure placement to htbp
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\def\fps@figure{htbp}
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$if(lang)$
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
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$if(babel-newcommands)$
$babel-newcommands$
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\else
% load polyglossia as late as possible as it *could* call bidi if RTL lang (e.g. Hebrew or Arabic)
\usepackage{polyglossia}
\setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
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% load bidi as late as possible as it modifies e.g. graphicx
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# Quick Start Guide Pannoramic SCAN II
<!-- the following 2 lines need to be removed before pdf creation - see issue #5 -->
## Inhalt
[[_TOC_]]
## Prinzip
Das Pannoramic SCAN II wurde entwickelt, um biologische Proben und Präparate (typischerweise histologische Schnitte) mit Hilfe von Durchlicht zu digitalisieren.
Der Pannoramic SCAN II wurde entwickelt, um biologische Proben und Präparate (typischerweise histologische Schnitte) mit Hilfe von Durchlicht zu digitalisieren.