additional files and settings for thesis

.gitlab-ci.yml

@@ -7,8 +7,8 @@ pdf:
     - echo "(Branch ${CI_COMMIT_REF_NAME}) ${CI_COMMIT_TIMESTAMP} ${CI_COMMIT_SHA}" > .maindir/tex/current-commit.tex
       # use settings from .latexmkrc
     - latexmk
-      # FIXME: add your name, main file name and output file name
-    - mv out/main.pdf your-name-file.pdf
+      # FIXME: add your name
+    - mv out/thesis.pdf your-name-thesis.pdf
   rules:
     # only on master and only if tex files have changed
     - if: '$CI_COMMIT_REF_NAME == "master"'
@@ -19,5 +19,5 @@ pdf:
   artifacts:
     paths:
       # FIXME: add your name
-    - "your-name-file.pdf"
+    - "your-name-thesis.pdf"
     expire_in: 4 weeks

.latexmkrc

@@ -1,6 +1,6 @@
 # 4 = lualatex, do not know why this magic number, see CTAN repository with latexmkrc examples
 $pdf_mode= 4 ;
-@default_files = ('.maindir/tex/main.tex');
+@default_files = ('.maindir/tex/thesis.tex');
 $out_dir = '.maindir/out';
 # %O: options
 # %S: source file (without argument: main.tex)

README.md

@@ -1,11 +1,46 @@
-# Template
+# FIXME thesis of FIXME name
 
-This is a template for a tex document.
-It combines a lot of details that I (Felix) collected for myself over the years of using LaTeX.
-I hope I documented enough so that you can use it and pick the details that you can use.
+FIXME url, file name from .gitlab-ci.yml [Current version](https://gitlab.mn.tu-dresden.de/api/v4/projects/<project number>/jobs/artifacts/master/raw/<your-name-file.pdf?job=pdf)
+
+## Help
+
+If you want to give me feedback, you are very welcome to do so.
+I am happy of any kind of helpful feedback, including but not limited
+to typos, overcomplicated text, overcomplicated reasoning, proof mistakes,
+new ideas, ...
+
+You can
+
+ * talk to me
+ * write an [e-mail](mailto:FIXME email) with your comments
+ * change something and send me git patch files
+ * change something and create a Merge Request either from your gitlab instance or with write access to the FIXME [Gitlab](FIXME url to repo)
+ * Make comments on the FIXME url (same as above) [pdf](<see top>) and send that to [me](mailto:FIXME email)
+ * Print the pdf and comment on paper and give that to me
+
+## Adviser
+
+FIXME add your advisors
+
+## File structure
+
+The file structure is based on a [LaTeX-template](https://flugit.hilsky.de/flukx/latextemplate) with additions. Top-level directories are
+
+ * **tex** The actual text in `.tex` files are here
+ * **notes** Notes that are not part of the actual master thesis text and are usually not written in LaTeX are here
+ - **scripts** Programs needed for the tex file handling are here
+ - **scripts/.XCompose** a config file, to be put into your home directory and used with a keyboard layout with Compose key (e.g. Neo2, Neoqwertz). Allows to input Unicode symbols.
+ * **out** `latexmk` creates pdfs and temporary files in there, thanks to `.latexmkrc` config file
+ * **.latexmkrc** config file that tells `latexmk` to use `lualatex` and the output directory `out`
+ * **.gitlab-ci.yml** tells the gitlab to compile the current document and supply it via the FIXME url [api](<see top>)
+
+## Create the document
+
+Run the command `latexmk`. If you want to compile only one part, run `latexmk tex/thepart.tex`.
+The product is in `out`.
+
+# Template
 
 See the [technical readme](./technical-readme.md) for some of the used ideas and what to know to use them.
 
 To customize it for you, search for FIXME and todo and TODO in all documents and add your name or other information.
-
-In the branch `thesis` you find a version of the template that additionally includes a bunch of settings and files for writing a (master) thesis.

notes/.maindir

@@ -0,0 +1 @@
+..

notes/how-to-read.md

@@ -0,0 +1,13 @@
+# How to read mathematical papers
+
+- first pass: Abstract, Section titles, grobes strukturelles Verständnis. Keine Beweise. Quellen anschauen um es mit anderem einzuordnen
+  - das mit den Quellen ist schwierig, wenn man noch keine Ahnung hat
+- second pass: Lese Beweise schnell. Notizen, was für später interessant sein könnte anzuschauen
+- third pass: in detail
+  - Beispiele überlegen
+  - Voraussetzungen weglassen und schauen, wo es kaputt geht
+
+## Sources
+http://eprints.maths.manchester.ac.uk/2484/1/reading.pdf
+https://math.stackexchange.com/questions/13460/how-to-read-a-mathematical-paper
+http://blizzard.cs.uwaterloo.ca/keshav/home/Papers/data/07/paper-reading.pdf

notes/paper-notes/.maindir

@@ -0,0 +1 @@
+../..

scripts/pre-commit

@@ -0,0 +1,136 @@
+#!/bin/bash
+
+set -e
+
+# If we have a STDIN, use it, otherwise get one
+if tty >/dev/null 2>&1; then
+    TTY=$(tty)
+else
+    TTY=/dev/tty
+fi
+
+IFS=$'\n'
+
+# http://djm.me/ask
+ask() {
+    while true; do
+
+        if [ "${2:-}" = "Y" ]; then
+            prompt="Y/n/c(hange)"
+            default=Y
+        elif [ "${2:-}" = "N" ]; then
+            prompt="y/N/c(hange)"
+            default=N
+        else
+            prompt="y/n/c(hange)"
+            default=
+        fi
+
+        # Ask the question (not using "read -p" as it uses stderr not stdout)
+        echo -n "$1 [$prompt] "
+
+        # Read the answer
+        read REPLY < "$TTY"
+
+        # Default?
+        if [ -z "$REPLY" ]; then
+            REPLY=$default
+        fi
+
+        # Check if the reply is valid
+        case "$REPLY" in
+            c*|C*) ./.maindir/scripts/repairgitlabmathmd.sh ; return 1 ;;
+            Y*|y*) return 0 ;;
+            N*|n*) return 1 ;;
+        esac
+
+    done
+}
+
+check_file() {
+    local file="$1"
+    local match_pattern="$2"
+
+    local file_changes_with_context=$(git diff -U999999999 -p --cached --color=always -- "${file}")
+
+    # From the diff, get the green lines starting with '+' and including '$match_pattern'
+    local matched_additions=$(echo "$file_changes_with_context" | grep -C1 $'^\e\\[32m\+.*'"$match_pattern")
+
+    if [ -n "$matched_additions" ]; then
+        echo -e "\n$file additions match '$match_pattern':\n"
+
+        for matched_line in $matched_additions
+        do
+            echo "$matched_line"
+        done
+
+        if ask "Include this in your commit?"; then
+            echo 'Including'
+        else
+            echo "Not committing, because $file matches $match_pattern"
+            exit 1
+        fi
+    fi
+}
+
+# Actual hook logic:
+
+for file in $(git diff --cached -p --name-status | cut -c3-); do
+  case "${file}" in
+    *.md) echo "check file ${file}"
+      check_file "${file}" '[^`]\$[^$`]\+\$' ;;
+  esac
+done
+exit
+
+# ------------
+# from pre-commit.sample
+# ------------
+
+# A hook script to verify what is about to be committed.
+# Called by "git commit" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+	against=HEAD
+else
+	# Initial commit: diff against an empty tree object
+	against=$(git hash-object -t tree /dev/null)
+fi
+
+# If you want to allow non-ASCII filenames set this variable to true.
+allownonascii=$(git config --type=bool hooks.allownonascii)
+
+# Redirect output to stderr.
+exec 1>&2
+
+# Cross platform projects tend to avoid non-ASCII filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$allownonascii" != "true" ] &&
+	# Note that the use of brackets around a tr range is ok here, (it's
+	# even required, for portability to Solaris 10's /usr/bin/tr), since
+	# the square bracket bytes happen to fall in the designated range.
+	test $(git diff --cached --name-only --diff-filter=A -z $against |
+	  LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
+then
+	cat <<\EOF
+Error: Attempt to add a non-ASCII file name.
+
+This can cause problems if you want to work with people on other platforms.
+
+To be portable it is advisable to rename the file.
+
+If you know what you are doing you can disable this check using:
+
+  git config hooks.allownonascii true
+EOF
+	exit 1
+fi
+
+# If there are whitespace errors, print the offending file names and fail.
+exec git diff-index --check --cached $against --
+

scripts/repairgitlabmathmd.sh

@@ -0,0 +1,21 @@
+#! /usr/bin/env sh
+# gitlab marks math with $`  `$. I often forget the backticks
+# so this script should add them
+this=$(readlink -f "$0")
+here=$(dirname "${this}")
+echo "${this} in ${here}"
+cd "${here}"
+for i in $(find .maindir/notes -type f -name "*.md")
+  # -type f means regular file. Without it, the symbolic links are changed to regular files by sed
+  do
+    sed -i 's#\([^`]\|^\)\$\([^$`]\+\)\$#\1\$`\2`\$#g' "${i}"
+    # \(      # the symbol in front of the math is captured (-> \1)
+    #   [^`]  # if it is `, then we are looking at text behind a math env, so it should not be matched
+    #   |^    # but it is OK if there is nothing but the beginning of the line ( | = or )
+    # \)
+    # \$      # without \, the $ is a special symbol for the beginning of a line
+    # \(      # the actual math content needs to be captured
+    #   [^$`]\+  # sed regexp is greedy, taking the end of the math until the end of the last math in the line if we didn't forbid $ and ` (if the content has `, then it's already fine)
+    # \)
+    # \$     # the closing $
+  done

tex/abstract.tex

@@ -0,0 +1,17 @@
+%! TEX program = lualatex
+
+\input{.maindir/tex/header/preamble-section}
+% inputs the preamble only if necessary
+\docStart
+
+\begin{abstract}
+  TODO Here an abstract which is a short summary.
+\end{abstract}
+
+\begin{otherlanguage}{ngerman}
+  \begin{abstract}
+    Hier nochmal der gleiche Text in Deutsch.
+  \end{abstract}
+\end{otherlanguage}
+
+\docEnd

tex/bibliography.bib

@@ -1,2 +1,11 @@
 % the bib file with the bibiliography entries
 % use doitex.gitlab.io/ to get the entries based on the dois
+@article{nice-image,
+  author        = {Joshi, Gargi and Okeyoshi, Kosuke and Mitsumata, Tetsu and Kaneko, Tatsuo},
+  doi           = {10.1016/j.jcis.2019.03.062},
+  journal       = {Journal of Colloid and Interface Science},
+  pages         = {184--191},
+  title         = {Micro-deposition control of polysaccharides on evaporative {air-LC} interface to design quickly swelling hydrogels},
+  volume        = {546},
+  year          = {2019},
+}

tex/declaration.tex

@@ -0,0 +1,13 @@
+\section*{Declaration}
+\thispagestyle{empty}
+I hereby confirm that the present master thesis on \emph{\topic} submitted on \submissiondate\ under supervision of \advisor\ is solely my own work and that if any text passages or diagrams from books or other sources have been copied or used, all references have been acknowledged and fully cited. Only the quoted sources have been used.
+%Hiermit erkläre ich, dass ich die am \datum\ eingereichte Bachelorarbeit zum Thema
+%\emph{\thema} unter Betreuung von \betreuer\ selbstständig erarbeitet,
+%verfasst und Zitate kenntlich gemacht habe. Andere als die angegebenen Hilfsmittel
+%wurden von mir nicht benutzt.
+
+\bigskip \bigskip \bigskip \bigskip \bigskip
+
+FIXME place Dresden, \submissiondate\ \hfill Signature
+
+\normalsize

tex/header/preamble.tex

@@ -2,9 +2,13 @@
 
 \IfFileExists{.maindir/tex/current-commit.tex}{
 \documentclass[%
+  twoside,%
+  abstract=true,%
   headheight=27.2pt
 ]{scrartcl}}{
 \documentclass[%
+  twoside,%
+  abstract=true,%
 ]{scrartcl}
 }
 \usepackage{geometry}

tex/introduction.tex

@@ -0,0 +1,8 @@
+%! TEX program = lualatex
+
+\input{.maindir/tex/header/preamble-section}
+% inputs the preamble only if necessary
+\docStart
+\section{Introduction} \label{sec:introduction}
+
+\docEnd

tex/main.tex

@@ -1,12 +0,0 @@
-%! TEX program = lualatex
-\input{.maindir/tex/header/preamble-section}
-\docStart
-\title{FIXME Dokumententitel}
-\author{FIXME}
-\maketitle
-% use \textinput as described in /header and _TEMPLATE
-\begin{appendices}
-  % \textinput{some-appendix-section}
-\end{appendices}
-% use \textinput as described in /header and _TEMPLATE
-\docEnd

tex/thanks.tex

@@ -0,0 +1,12 @@
+%! TEX program = lualatex
+
+\input{.maindir/tex/header/preamble-section}
+% inputs the preamble only if necessary
+\docStart
+
+\section*{Acknowledgements}
+- Betreuer
+- Korrekturlesende
+- Institutionen, die Quellen unkompliziert zur Verfügung gestellt haben
+
+\docEnd

tex/thesis.tex

@@ -0,0 +1,22 @@
+%! TEX program = lualatex
+\input{.maindir/tex/header/preamble-section}
+\docStart
+\title{FIXME thesis}
+\author{FIXME name}
+
+\textinput{title-page}
+% \textinput{abstract} % included in title-page
+\tableofcontents
+
+\listoftheorems[title={List of theorems, definitions, examples}]
+
+\newpage
+\textinput{introduction}
+\textinput{usageexamples}
+\newpage
+\begin{appendices}
+  % \textinput{some-appendix-section}
+\end{appendices}
+\newpage
+\textinput{declaration}
+\docEnd

tex/title-page.tex

@@ -0,0 +1,69 @@
+%! TEX program = lualatex
+
+\input{.maindir/tex/header/preamble-section}
+% inputs the preamble only if necessary
+
+\newcommand*{\name}{FIXME}
+\newcommand*{\firstname}{FIXME}
+\newcommand*{\birthday}{FIXME}
+\newcommand*{\birthplace}{FIXME}
+\newcommand*{\place}{Dresden}
+\newcommand*{\advisor}{FIXME}
+\newcommand*{\institute}{Institute of FIXME}
+\newcommand*{\topic}{FIXME}
+\newcommand*{\submissiondate}{FIXME-FIXME-FIXME}
+
+\docStart
+
+\newgeometry{margin=3cm}
+\thispagestyle{empty}
+
+\begin{center}
+  % FIXME: your university
+{\Large Technische Universität Dresden\  \ \textbullet\ \ Faculty of Physics}
+
+\vskip 2cm
+
+{\bfseries\Huge\topic}
+
+\vskip 2cm
+
+{\LARGE
+FIXME:Masters Thesis \\[\bigskipamount]
+for the attainment of the academic degree of\\[\bigskipamount]
+\bfseries{\itshape FIXME:Master of Science  (M.Sc.)}\\[\bigskipamount]
+}
+
+\vskip 2cm
+
+presented by
+\\[\bigskipamount]
+% textsc should make it cursive but I that gives an error due to missing font and why should it be?
+% \textsc{\firstname\ } \MakeUppercase{\name}
+\firstname~\MakeUppercase{\name}
+\\[\bigskipamount]
+(born \birthday\ in \birthplace)
+\\[\bigskipamount]
+Submission date: \submissiondate
+\\[\bigskipamount]
+supervised by \advisor\ (\institute)
+\end{center}
+
+\clearpage
+
+\textinput{abstract}
+
+\vfill
+
+DONOTFIXME: use a free licence. The world is better if knowledge is shared!
+This work is licensed under a Attribution-ShareAlike 4.0 International License.
+The whole license can be found under \url{https://creativecommons.org/licenses/by-sa/4.0/legalcode}.
+
+The \LaTeX-code can be found under FIXME \url{your repo url}. Feedback is welcomed. The author can be reached via FIXME \url{your e-mail-address}.
+%\newpage
+\clearpage
+% \pagenumbering{roman}
+\restoregeometry
+\newpage
+
+\docEnd

tex/usageexamples.tex

@@ -0,0 +1,94 @@
+%! TEX program = lualatex
+
+\input{.maindir/tex/header/preamble-section}
+% inputs the preamble only if necessary
+\docStart
+% do not use \input nor \begin{document nor \end{document}
+
+\section{TeX-Beispiele} \label{sec:tex_beispiele}
+{ % diese Klammer 1 sorgt dafür, dass mein Editor den Inhalt einrückt und in eine Zeile zusammenfasst und ich sie nur bei Bedarf aufklappe
+  % dadurch gibt es mehr Übersicht. Ohne die Klammer kann der Editor das nicht, weil \section kein Ende hat
+  \begin{definition}[Beispiel-Definition] \label{def:beispiel_definition}
+    This is basic definition.
+    Since definitions have no special markup to separate it from the rest of the text, there is a little symbol at the end.
+  \end{definition} % end definition of Beispiel-Definition
+  \begin{example}[Explanation example] \label{ex:explanation_example}
+    After a definition you need an example to illustrate your idea.    
+  \end{example}
+  \begin{lemma}[Beispiel-Lemma] \label{thm:beispiel_lemma}
+    Every important theorem needs a preparation lemma.
+    The label starts with thm: for all kinds of theorem-like environments
+    because one might call it lemma now but theorem or proposition later.
+  \end{lemma} % end lemma Beispiel-Lemma
+  \begin{proof} % of lemma Beispiel-Lemma
+    And every lemma needs a proof.
+  \end{proof} % of lemma Beispiel-Lemma
+  \begin{theorem}[Beispiel-Satz] \label{thm:beispiel_satz}
+    This is the important theorem.
+  \end{theorem} % end theorem Beispiel-Satz
+  \begin{proof} % of theorem Beispiel-Satz
+    It has a proof. It refers to \cref{thm:beispiel_lemma}.
+    cref adds the information that it is a lemma automatically.
+    If you change it into a proposition, cref makes sure
+    that it becomes a proposition everywhere.
+    Originally cref writes lemma while Cref writes Lemma.
+    But a setting for this document always uses capital letters.
+  \end{proof} % of theorem Beispiel-Satz
+  \begin{note}[Little remark]  \label{note:little_remark}
+    After a theorem one might add a remark, also called note. 
+  \end{note} % end note Little remark
+  \subsection{Smaller TeX example} \label{sec:smaller_tex_example}
+  {
+    There can be subsections.
+    \subsubsection{Even smaller TeX example} \label{sec:even_smaller_tex_example}
+    {
+      And subsubsections.
+
+      \paragraph{and paragraphs}. \label{sec:and_paragraphs}
+      {
+        They are also numbered. Felix likes it this way.
+        With a number they can also be referenced.
+
+        Now we use a citation.
+        \textcite{nice-image} include nice images in their work.
+        If we do not want to name the authors, we can refer to the work
+        \parencite[Sec.~1][]{nice-image} without the names.
+        Bridging gaps in is also nice \parencite[][3]{nice-image}.
+        Do not use parencite at the begin of a sentence.
+      }
+    }
+  }
+  Commonly used abbreviations include \ie and \eg
+  and their begin-of-sentence versions \Ie and \Eg.
+  Those makros handle the space behind them correctly, even
+  with punctuation and whitespace.
+
+  Words that are introduced should be highlighted.
+  Use \newTerm{new Word} for this. Then you can change the way of highlighting
+  easily later in tex/header/stdmath.sty.
+  Similarly for non-new but important words you can use \imp{something important}.
+
+  Some math makros need mentioning.
+  \begin{align*}
+    2ℤ &:= \setDef{x ∈ ℤ}{2 \,|\, x} \\
+    ℤ &= \Union_{i ∈ \{1, -1\}} iℕ \\
+    \intertext{You can use unicode with NeoQwertz and Compose key and .XCompose config file}
+    ια&πσβλαξ \\
+    f &⫶ A → B (⫶ \text{typed with Compose - d - p as in Doppelpunkt,} → \text{ for \textbackslash{}to}) \\
+    ⟨ψ, φ⟩ &\text{For braket with automatic resizing} \\
+    3 &⸨ \sum_{i = 1}^10 i ⸩ = 165 ⸨\text{ and } ⸩ \text{ with Compose - l - k and Compose - r - k } \\
+      &\text{ as in linke Klammer, rechte Klammer for parenthesis that resize} \\
+  \text{Here } Σ& \text{ is a greek letter, so } \sum \text{ should be used for sums. Same with } Π\\
+    ⇔⇐⇒↦& \text{ should not be forgotten.  Much shorter than } \implies, \impliedby, \iff, \mapsto.
+  \end{align*}
+  Also look in .maindir/scripts/.XCompose for many more symbols.
+} % hier endet Klammer 1
+
+% write the text here
+% for including a tikz picture, place it in the directory tikz and
+% use \tikzinput{tikzpicture}
+% for including another tex (text) file, place it in the directory
+% tex and use \textinput{textfile}
+% for including some other file use \maininput{file/path/relative/to/main/repodir}
+
+\docEnd