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

.gitignore

+<<<<<<< HEAD
 /_book/
 /node_modules/
 /book.pdf
 /book.mobi
 /book.epub
 *.svg
+=======
+/_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

SUMMARY.md

@@ -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)

book.json

+{
+  "plugins": [
+    "intopic-toc"
+  ]
+}

quick-start-guides/convert_to_pdf.sh

+#!/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!"

quick-start-guides/get_started_with_git.md

@@ -14,7 +14,7 @@ git reset --hard origin/master (or origin/main)
 ```
 https://stackoverflow.com/a/38784578
 
-## work now! after you have made  changes
+## work now! after you have made changes
 ```
 git add [specify filename]
 ```
@@ -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
+```

quick-start-guides/my.latex

+\PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
+\PassOptionsToPackage{hyphens}{url}
+$if(colorlinks)$
+\PassOptionsToPackage{dvipsnames,svgnames*,x11names*}{xcolor}
+$endif$$if(dir)$$if(latex-dir-rtl)$
+\PassOptionsToPackage{RTLdocument}{bidi}
+$endif$$endif$%
+\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(papersize)$$papersize$paper,$endif$$if(beamer)$ignorenonframetext,$if(handout)$handout,$endif$$if(aspectratio)$aspectratio=$aspectratio$,$endif$$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
+$if(beamer)$
+$if(background-image)$
+\usebackgroundtemplate{%
+\includegraphics[width=\paperwidth]{$background-image$}%
+}
+$endif$
+\usepackage{pgfpages}
+\setbeamertemplate{caption}[numbered]
+\setbeamertemplate{caption label separator}{: }
+\setbeamercolor{caption name}{fg=normal text.fg}
+\beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$
+$for(beameroption)$
+\setbeameroption{$beameroption$}
+$endfor$
+$endif$
+$if(beamerarticle)$
+\usepackage{beamerarticle} % needs to be loaded first
+$endif$
+$if(fontfamily)$
+\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
+$else$
+\usepackage{lmodern}
+$endif$
+$if(linestretch)$
+\usepackage{setspace}
+\setstretch{$linestretch$}
+$endif$
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
+  \usepackage[utf8]{inputenc}
+  \usepackage{textcomp} % provides euro and other symbols
+\else % if luatex or xelatex
+$if(mathspec)$
+  \ifxetex
+    \usepackage{mathspec}
+  \else
+    \usepackage{unicode-math}
+  \fi
+$else$
+  \usepackage{unicode-math}
+$endif$
+  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
+$for(fontfamilies)$
+  \newfontfamily{$fontfamilies.name$}[$fontfamilies.options$]{$fontfamilies.font$}
+$endfor$
+$if(mainfont)$
+    \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
+$endif$
+$if(sansfont)$
+    \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
+$endif$
+$if(monofont)$
+    \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$endif$]{$monofont$}
+$endif$
+$if(mathfont)$
+$if(mathspec)$
+  \ifxetex
+    \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
+  \else
+    \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
+  \fi
+$else$
+  \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
+$endif$
+$endif$
+$if(CJKmainfont)$
+  \ifxetex
+    \usepackage{xeCJK}
+    \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
+  \fi
+$endif$
+$if(luatexjapresetoptions)$
+  \ifluatex
+    \usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset}
+  \fi
+$endif$
+$if(CJKmainfont)$
+  \ifluatex
+    \usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec}
+    \setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
+  \fi
+$endif$
+\fi
+$if(beamer)$
+$if(theme)$
+\usetheme[$for(themeoptions)$$themeoptions$$sep$,$endfor$]{$theme$}
+$endif$
+$if(colortheme)$
+\usecolortheme{$colortheme$}
+$endif$
+$if(fonttheme)$
+\usefonttheme{$fonttheme$}
+$endif$
+$if(mainfont)$
+\usefonttheme{serif} % use mainfont rather than sansfont for slide text
+$endif$
+$if(innertheme)$
+\useinnertheme{$innertheme$}
+$endif$
+$if(outertheme)$
+\useoutertheme{$outertheme$}
+$endif$
+$endif$
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+\usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
+\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+$if(indent)$
+$else$
+\IfFileExists{parskip.sty}{%
+\usepackage{parskip}
+}{% else
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+}
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+$endif$
+$if(colorlinks)$
+\usepackage{xcolor}
+$endif$
+\usepackage{hyperref}
+\hypersetup{
+$if(title-meta)$
+            pdftitle={$title-meta$},
+$endif$
+$if(author-meta)$
+            pdfauthor={$author-meta$},
+$endif$
+$if(keywords)$
+            pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
+$endif$
+$if(colorlinks)$
+            colorlinks=true,
+            linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
+            citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
+            urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
+$else$
+            pdfborder={0 0 0},
+$endif$
+            breaklinks=true}
+\urlstyle{same}  % don't use monospace font for urls
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+$if(geometry)$
+\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$endif$
+$if(beamer)$
+\newif\ifbibliography
+$endif$
+$if(listings)$
+\usepackage{listings}
+\newcommand{\passthrough}[1]{#1}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+$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
+$else$
+% 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)$
+\setbeamertemplate{part page}{
+\centering
+\begin{beamercolorbox}[sep=16pt,center]{part title}
+  \usebeamerfont{part title}\insertpart\par
+\end{beamercolorbox}
+}
+\setbeamertemplate{section page}{
+\centering
+\begin{beamercolorbox}[sep=12pt,center]{part title}
+  \usebeamerfont{section title}\insertsection\par
+\end{beamercolorbox}
+}
+\setbeamertemplate{subsection page}{
+\centering
+\begin{beamercolorbox}[sep=8pt,center]{part title}
+  \usebeamerfont{subsection title}\insertsubsection\par
+\end{beamercolorbox}
+}
+\AtBeginPart{
+  \frame{\partpage}
+}
+\AtBeginSection{
+  \ifbibliography
+  \else
+    \frame{\sectionpage}
+  \fi
+}
+\AtBeginSubsection{
+  \frame{\subsectionpage}
+}
+$endif$
+$endif$
+$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}{}}
+$endif$
+\setlength{\emergencystretch}{3em}  % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+$if(numbersections)$
+\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(beamer)$
+$else$
+$if(subparagraph)$
+$else$
+% Redefines (sub)paragraphs to behave more like sections
+\ifx\paragraph\undefined\else
+\let\oldparagraph\paragraph
+\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+\let\oldsubparagraph\subparagraph
+\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+$endif$
+$endif$
+$if(pagestyle)$
+\pagestyle{$pagestyle$}
+$endif$
+
+% set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
+
+$for(header-includes)$
+$header-includes$
+$endfor$
+$if(lang)$
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
+$if(babel-newcommands)$
+  $babel-newcommands$
+$endif$
+\else
+  % load polyglossia as late as possible as it *could* call bidi if RTL lang (e.g. Hebrew or Arabic)
+  \usepackage{polyglossia}
+  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
+$for(polyglossia-otherlangs)$
+  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
+$endfor$
+\fi
+$endif$
+$if(dir)$
+\ifxetex
+  % load bidi as late as possible as it modifies e.g. graphicx
+  \usepackage{bidi}
+\fi
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \TeXXeTstate=1
+  \newcommand{\RL}[1]{\beginR #1\endR}
+  \newcommand{\LR}[1]{\beginL #1\endL}
+  \newenvironment{RTL}{\beginR}{\endR}
+  \newenvironment{LTR}{\beginL}{\endL}
+\fi
+$endif$
+$if(natbib)$
+\usepackage[$natbiboptions$]{natbib}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(biblatex)$
+\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
+$for(bibliography)$
+\addbibresource{$bibliography$}
+$endfor$
+$endif$
+
+$if(title)$
+\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
+$endif$
+$if(subtitle)$
+\providecommand{\subtitle}[1]{}
+\subtitle{$subtitle$}
+$endif$
+$if(author)$
+\author{$for(author)$$author$$sep$ \and $endfor$}
+$endif$
+$if(institute)$
+\providecommand{\institute}[1]{}
+\institute{$for(institute)$$institute$$sep$ \and $endfor$}
+$endif$
+\date{$date$}
+$if(beamer)$
+$if(titlegraphic)$
+\titlegraphic{\includegraphics{$titlegraphic$}}
+$endif$
+$if(logo)$
+\logo{\includegraphics{$logo$}}
+$endif$
+$endif$
+
+\renewcommand{\contentsname}{Inhalt}
+
+\begin{document}
+$if(title)$
+$if(beamer)$
+\frame{\titlepage}
+$else$
+\maketitle
+$endif$
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+$endif$
+
+$for(include-before)$
+$include-before$
+
+$endfor$
+$if(toc)$
+$if(beamer)$
+\begin{frame}
+\tableofcontents[hideallsubsections]
+\end{frame}
+$else$
+{
+$if(colorlinks)$
+\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
+$endif$
+\setcounter{tocdepth}{$toc-depth$}
+\tableofcontents
+}
+$endif$
+$endif$
+$if(lot)$
+\listoftables
+$endif$
+$if(lof)$
+\listoffigures
+$endif$
+$body$
+
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+$if(book-class)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+$if(beamer)$
+\begin{frame}[allowframebreaks]{$biblio-title$}
+\bibliographytrue
+$endif$
+\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+$if(beamer)$
+\end{frame}
+$endif$
+
+$endif$
+$endif$
+$if(biblatex)$
+$if(beamer)$
+\begin{frame}[allowframebreaks]{$biblio-title$}
+\bibliographytrue
+\printbibliography[heading=none]
+\end{frame}
+$else$
+\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
+$endif$
+
+$endif$
+$for(include-after)$
+$include-after$
+
+$endfor$
+\end{document}