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Merge pull request #46 from tuftsceeo/main
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Sync main with dev/nick
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github-actions[bot] authored Dec 20, 2024
2 parents 6b6b255 + a0f0f7b commit ebdfdcd
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2 changes: 0 additions & 2 deletions README.md
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Expand Up @@ -18,11 +18,9 @@ The repository has the following directory tree.
├── README.qmd
├── README.rmarkdown
├── docs
├── file_list.txt
├── firmware
├── hardware
├── overleaf
├── project.Rproj
├── rstudio
└── software

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24 changes: 23 additions & 1 deletion overleaf/README.md
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Expand Up @@ -15,7 +15,29 @@ The repository has the following directory tree.
.
├── README.md
├── README.qmd
└── README.rmarkdown
├── README.rmarkdown
├── StyleAndSettings.sty
├── chapters
│ ├── 00_abstract.tex
│ ├── 01_introduction.tex
│ ├── 02_methods.tex
│ ├── 03_results.tex
│ ├── 04_conclusions.tex
│ ├── 05_biblio_descr.tex
│ ├── 07_appendix_A.tex
│ ├── acknowledgements.tex
│ ├── references.bib
│ └── title.tex
├── habbrv.bst
├── images
│ ├── Tree_example_VIS.jpg
│ ├── dmavt-logo.pdf
│ ├── eth_logo_kurz_pos.pdf
│ ├── ghe-logo-vector.pdf
│ └── small-multiple.png
├── main.tex
├── main.tex.bak
└── unsrtDOI.bst

A short description of the directories can be found below.

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341 changes: 341 additions & 0 deletions overleaf/StyleAndSettings.sty
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% Template created by Jakub Tkaczuk at the Department of Cryogenic Engineering of CEA-Grenoble
% and modified for the Global Health Engineering chair of ETH Zurich
%
% Do not use \usepackage{tocloft} for toc editing. It destroys features of listof.
%
\ProvidesPackage{StyleAndSettings}%
%
%%%%%%%%%%%%%%%%%%%%%%
%% Generic packages %%
%%%%%%%%%%%%%%%%%%%%%%
\usepackage[top=72pt,% 72 pt = 1 inch
bottom=108pt,% 5/4 inch
inner=72pt,% 108pt,% 5/4 inch
outer=54pt% 3/4 inch
]{geometry}% interface to document dimensions
\usepackage[utf8]{inputenc}% translates various standards into LaTeX
\usepackage[T1]{fontenc}% font encoding
\usepackage[english]{babel}% spelling check
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Packages for text and page settings %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{titlesec}% alternative section titles
\usepackage{indentfirst}% indenting the first paragraph in section
\usepackage[toc]{appendix}% appendix editing
\usepackage{lscape}% landscape page
\usepackage{pdflscape}% single page orientation change
\usepackage{setspace}% line spacing
\usepackage{fancyhdr}% extensive control of page headers and footers
\usepackage{color}% foreground and background color management
\usepackage{xcolor}% personalize the font colors
\usepackage{textcomp}% support for text companion fonts
\usepackage{listings}% code formatting
\usepackage{eurosym}% euro symbol
\usepackage{latexsym}% few additional characters
\usepackage{fancyvrb}% sophisticated verbatim text
%
%%%%%%%%%%%%%%%%%%%
%% Math packages %%
%%%%%%%%%%%%%%%%%%%
\usepackage[bitstream-charter]{mathdesign}% font Charter BT
\usepackage{amsmath}% most of the needed math features
\usepackage[makeroom]{cancel}% cancel out symols in math mode
\usepackage{mathtools}% an addition to amsmath
\usepackage{gensymb}% degree symbol
\usepackage{bm}% bold symbols in math
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Figure and Table packages %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx}% figures
\usepackage{float}% force figure placement
\usepackage{subcaption}% analogous to the caption package but for subcaptions
\usepackage{array}% extensive implementation of array and tabular environments
\usepackage[labelsep=period,%
skip=0.1\baselineskip,%
]{caption}% customize captions in floating environments like figures, tables
\usepackage{longtable}% multipage tables
\usepackage{multirow}% multirow cells in tables
\usepackage{makecell}% line braking in table
\usepackage{tabu, longtable, booktabs}% multipage table editting
\usepackage{siunitx}% aligning decimal points in table
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Bibliography packages %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{csquotes}% advanced facilities for inline and display quotations
\usepackage[style=apa,%
backend=biber,%
natbib=true]{biblatex}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Hyperref is the last package %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[pdfauthor={Author},%
pdftitle={Title},%
pdfsubject={Bachelor Thesis/Semester Project/Master Thesis},%
pdfkeywords={keyword1, keyword2, keyword3},%
pdfproducer={Overleaf},%
pdfcreator={Author},%
linktocpage=true,%
linkcolor=lightblue,%
colorlinks=true,%
citecolor=lightblue,%
urlcolor=lightblue,%
bookmarks=false,%
hypertexnames=true,%
pdfpagelayout=TwoPageRight%
]{hyperref}% hyperlinks
%
%%%%%%%%%%%%%%%%%%%%
%% Reference file %%
%%%%%%%%%%%%%%%%%%%%
%
\addbibresource{./chapters/references.bib}
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Define larger brackets %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\makeatletter%
\newcommand{\Bigger}{\bBigg@{2}}%
\newcommand{\vast}{\bBigg@{3.25}}%
\newcommand{\Vast}{\bBigg@{4.5}}%
%
%%%%%%%%%%%%%%%%%%%%%%%
%% define new colors %%
%%%%%%%%%%%%%%%%%%%%%%%
%
\definecolor{darkblue}{rgb}{0.,0.,0.4}%
\definecolor{lightblue}{HTML}{2c5499}%
\definecolor{greenplot}{HTML}{808000}%
\definecolor{blueplot}{HTML}{0088aa}%
\definecolor{redplot}{HTML}{ff0000}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% set eqref brackets color to lightblue %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\def\eqref#1{\textcolor{lightblue}{(\ref{#1})}}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% define header and footer %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\pagestyle{fancy}%
\renewcommand{\sectionmark}[1]{\markright{#1}}
\renewcommand{\subsectionmark}[1]{}

\fancypagestyle{plain}{%chapter's first page style %
\fancyhf{}%
\fancyfootoffset[OR]{1.85cm}%
\fancyfoot[OR]{%
\leftmark%
\hspace*{0.75cm}%
\rule[-90pt]{1pt}{100pt}%
\hspace*{10pt}%
\begin{minipage}[b]{42pt}%
\normalsize\textbf{\thepage}%
\end{minipage}%
}%
\fancyfootoffset[EL]{1.85cm}%
\fancyfoot[EL]{%
\begin{minipage}[b]{42pt}%
\raggedleft\normalsize\textbf{\thepage}%
\end{minipage}%
\hspace*{10pt}%
\rule[-90pt]{1pt}{100pt}%
\hspace*{0.75cm}%
\MakeUppercase{\chaptername\ \thechapter}%
}%
\renewcommand{\headrulewidth}{0pt}%
\renewcommand{\footrulewidth}{0pt}%
}%
%
\fancypagestyle{mainmatter}{%
\fancyhf{}%
\renewcommand{\headrulewidth}{0pt}%
\fancyfootoffset[OR]{1.85cm}%
\fancyfoot[OR]{%
\leftmark%
\hspace*{0.75cm}%
\rule[-90pt]{1pt}{100pt}%
\hspace*{10pt}%
\begin{minipage}[b]{42pt}%
\normalsize\textbf{\thepage}%
\end{minipage}%
}%
\fancyfootoffset[EL]{1.85cm}%
\fancyfoot[EL]{%
\begin{minipage}[b]{42pt}%
\raggedleft\normalsize\textbf{\thepage}%
\end{minipage}%
\hspace*{10pt}%
\rule[-90pt]{1pt}{100pt}%
\hspace*{0.75cm}%
\MakeUppercase{\chaptername\ \thechapter}%
}%
}%
%
\fancypagestyle{frontmatter}{%
\fancyhf{}%
\renewcommand{\headrulewidth}{0pt}%
\fancyfootoffset[OR]{1.85cm}%
\fancyfoot[OR]{%
\rule[-90pt]{1pt}{100pt}%
\hspace*{10pt}%
\begin{minipage}[b]{42pt}%
\normalsize\textbf{\thepage}%
\end{minipage}%
}%
\fancyfootoffset[EL]{1.85cm}%
\fancyfoot[EL]{%
\begin{minipage}[b]{42pt}%
\raggedleft\normalsize\textbf{\thepage}%
\end{minipage}%
\hspace*{10pt}%
\rule[-90pt]{1pt}{100pt}%
}%
}%
%
\fancypagestyle{backmatter}{%
\fancyhf{}%
\renewcommand{\headrulewidth}{0pt}%
\fancyfootoffset[OR]{1.85cm}%
\fancyfoot[OR]{%
\leftmark%
\hspace*{0.75cm}%
\rule[-90pt]{1pt}{100pt}%
\hspace*{10pt}%
\begin{minipage}[b]{42pt}%
\normalsize\textbf{\thepage}%
\end{minipage}%
}%
\fancyfootoffset[EL]{1.85cm}%
\fancyfoot[EL]{%
\begin{minipage}[b]{42pt}%
\raggedleft\normalsize\textbf{\thepage}%
\end{minipage}%
\hspace*{10pt}%
\rule[-90pt]{1pt}{100pt}%
}%
}%
%
\renewcommand{\chaptermark}[1]{\markboth{\MakeUppercase{\quad{#1}}}{}}%
\renewcommand{\sectionmark}[1]{\markright{\MakeUppercase{\thesection\quad{#1}}}}%
%
%%%%%%%%%%%%%%%%%%%%
%% figure editing %%
%%%%%%%%%%%%%%%%%%%%
%
\renewcommand{\floatpagefraction}{.8}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% redefine chapter, section, subsection title displaying %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\titleformat{\chapter}{\huge\scshape}{\thechapter}{1em}{}%
\titleformat{\section}{\LARGE}{\thesection}{1em}{}%
\titleformat{\subsection}{\Large}{\thesubsection}{1em}{}%
\titleformat{\subsubsection}{\large}{\thesubsubsection}{1em}{}%
%
%%%%%%%%%%%%%%%%%%
%% text editing %%
%%%%%%%%%%%%%%%%%%
%
%\setlength\parindent{0pt}% zero indentation in the whole document
\onehalfspacing% 1.5 x spacing
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% enumerate and itemize options %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\newenvironment{tight_enumerate}{
\begin{enumerate}
\setlength{\itemsep}{0pt}
\setlength{\parskip}{0pt}
}{\end{enumerate}}
%
\newenvironment{tight_itemize}{
\begin{itemize}
\setlength{\itemsep}{0pt}
\setlength{\parskip}{0pt}
}{\end{itemize}}
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% define blank page and blank page subs %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\def\blankpage{\clearpage\thispagestyle{empty}\null\clearpage}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% edit the toc style and numbering %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\AtBeginDocument{\addtocontents{toc}{\protect\thispagestyle{plain}}}%
% \setcounter{tocdepth}{4}% set toc depth
% \setcounter{secnumdepth}{4}% set toc numbering depth
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% edit the bibliography spacing %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\let\OLDthebibliography\thebibliography
\renewcommand\thebibliography[1]{
\OLDthebibliography{#1}
\setlength{\parskip}{2pt}
\setlength{\itemsep}{0pt plus 0.3ex}
}
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% define absolute path to images %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\graphicspath{{./images/}}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Declare authoryear as a hyperlink to bibliography entry %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\DeclareFieldFormat{citehyperref}{%
\DeclareFieldAlias{bibhyperref}{noformat}% Avoid nested link
\bibhyperref{#1}}
%
\DeclareFieldFormat{textcitehyperref}{%
\DeclareFieldAlias{bibhyperref}{noformat}% Avoid nested links
\bibhyperref{%
#1%
\ifbool{cbx:parens}%
{\bibcloseparen\global\boolfalse{cbx:parens}}%
{}}}%
%
\savebibmacro{cite}%
\savebibmacro{textcite}%
%
\renewbibmacro*{cite}{%
\printtext[citehyperref]{%
\restorebibmacro{cite}%
\usebibmacro{cite}}}%
%
\renewbibmacro*{textcite}{%
\ifboolexpr{%
( not test {\iffieldundef{prenote}} and%
test {\ifnumequal{\value{citecount}}{1}} )%
or%
( not test {\iffieldundef{postnote}} and%
test {\ifnumequal{\value{citecount}}{\value{citetotal}}} )%
}%
{\DeclareFieldAlias{textcitehyperref}{noformat}}%
{}%
\printtext[textcitehyperref]{%
\restorebibmacro{textcite}%
\usebibmacro{textcite}}}%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Make "et al." italic in bibliography entry %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\DefineBibliographyStrings{english}{%
andothers = {\mkbibemph{et\addabbrvspace al\adddot}}%
}%
%
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