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
Pipeline #1688 passed with stage
in 2 minutes and 28 seconds
<<<<<<< HEAD
/_book/ /_book/
/node_modules/ /node_modules/
/book.pdf /book.pdf
/book.mobi /book.mobi
/book.epub /book.epub
*.svg *.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
...@@ -6,3 +6,4 @@ ...@@ -6,3 +6,4 @@
* [Quick Start Guide Pannoramic SCAN II](quick-start-guides/quick-start-guide-pannoramic-scan-ii.md) * [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) * [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"
]
}
img/focus_levels.png

130 Bytes

img/open_profile.png

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img/settings.png

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img/settings02.png

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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!"
...@@ -14,7 +14,7 @@ git reset --hard origin/master (or origin/main) ...@@ -14,7 +14,7 @@ git reset --hard origin/master (or origin/main)
``` ```
https://stackoverflow.com/a/38784578 https://stackoverflow.com/a/38784578
## work now! after you have made changes ## work now! after you have made changes
``` ```
git add [specify filename] git add [specify filename]
``` ```
...@@ -49,3 +49,11 @@ then ...@@ -49,3 +49,11 @@ then
``` ```
git push git push
``` ```
## automatically close an open issue when pushing a commit
```
git commit -m "Sort more efficiently" -m "Closes #[INSERT_ISSUE_NO]]"
```
```
git push
```
\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=$biblio-title$]$endif$
$endif$
$endif$
$for(include-after)$