4 files changed, 313 insertions, 0 deletions
diff --git a/tex/preamble-biblatex.tex b/tex/preamble-biblatex.tex
new file mode 100644
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+%% Biblatex settings.
+%%
+%% Since the preamble settings necessary to make the bibliography with
+%% Biblatex is a little long and unclean, and might be used in other places
+%% separately later, it is easier to have it here as a separate file.
+%%
+%% USAGE:
+%%
+%%  - `tex/ref.tex': the file containing Bibtex source of each
+%%     reference. The file suffix doesn't have to be `.bib', this naming
+%%     helps in clearly identifying the files and avoiding places that
+%%     complain about `.bib' files.
+
+
+
+
+
+%% To break up highlighted text (for example texttt when some it is on the
+%% line break) and also to no underline emphasized words (like journal
+%% titles in the references).
+\usepackage[normalem]{ulem}
+
+
+
+
+
+% Basic BibLaTeX settings
+\usepackage[
+    doi=false,
+    url=false,
+    dashed=false,
+    eprint=false,
+    maxbibnames=4,
+    minbibnames=1,
+    hyperref=true,
+    maxcitenames=2,
+    mincitenames=1,
+    style=authoryear,
+    uniquelist=false,
+    backend=biber,natbib]{biblatex}
+\DeclareFieldFormat[article]{pages}{#1}
+\DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
+\addbibresource{./tex/ref.tex}
+\renewbibmacro{in:}{}
+\renewcommand*{\bibfont}{\footnotesize}
+\DefineBibliographyStrings{english}{references = {References}}
+
+%% Include the adsurl field key into those that are recognized:
+\DeclareSourcemap{
+  \maps[datatype=bibtex]{
+    \map{
+      \step[fieldsource=adsurl,fieldtarget=iswc]
+      \step[fieldsource=gbkurl,fieldtarget=iswc]
+    }
+  }
+}
+
+%% Set the color of the doi link to mymg (magenta) and the ads links
+%% to mypurp (or purple):
+\definecolor{mypurp}{cmyk}{0.75,1,0,0}
+\newcommand{\doihref}[2]{\href{#1}{\color{magenta}{#2}}}
+\newcommand{\adshref}[2]{\href{#1}{\color{mypurp}{#2}}}
+\newcommand{\blackhref}[2]{\href{#1}{\color{black}{#2}}}
+
+%% Define a format for the printtext commands in
+%% DeclareBibliographyDriver to make links for the doi, ads link and
+%% arxiv link:
+\DeclareFieldFormat{doilink}{
+  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
+\DeclareFieldFormat{adslink}{
+    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
+\DeclareFieldFormat{arxivlink}{
+  \iffieldundef{eprint}{#1}{\href{http://arxiv.org/abs/\thefield{eprint}}{#1}}}
+
+\DeclareListFormat{doiforbook}{
+  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
+\DeclareFieldFormat{googlebookslink}{
+    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
+
+%% Set the formatting to make the last three values into the
+%% appropriate link. Note that the % signs are necessary. Without
+%% them, the items will be indented.
+\DeclareBibliographyDriver{article}{%
+  \usebibmacro{bibindex}%
+  \usebibmacro{begentry}%
+  \usebibmacro{author/translator+others}%
+  \newunit%
+  \ifdefined\makethesis\printtext{\usebibmacro{title}}\fi%
+  \newunit%
+  \printtext[doilink]{\usebibmacro{journal}}%
+  \addcomma%
+  \printtext[adslink]{\printfield{volume}}%
+  \addcomma%
+  \printtext[arxivlink]{\printfield{pages}}%
+  \addperiod%
+}
+
+\DeclareBibliographyDriver{book}{%
+  \usebibmacro{bibindex}%
+  \usebibmacro{begentry}%
+  \usebibmacro{author/translator+others}%
+  \newunit%
+  \printtext{\usebibmacro{title}}%
+  \addperiod%
+  \addspace%
+  \printlist[doiforbook]{publisher}%
+  \addcomma%
+  \addspace%
+  \printfield[googlebookslink]{edition}%
+  \printtext{ ed.}%
+  \addperiod%
+}
+
+%% In order to have et al. instead of et al.,:
+\renewcommand*{\nameyeardelim}{\addspace}
diff --git a/tex/preamble-necessary.tex b/tex/preamble-necessary.tex
new file mode 100644
index 0000000..debcb4b
--- /dev/null
+++ b/tex/preamble-necessary.tex
@@ -0,0 +1,68 @@
+%% Some (commonly) necessary LaTeX packages.
+%%
+%% These are a set of packages that are commonly necessary in most LaTeX
+%% usages. However, if any are not needed in your work, you can remove them
+%% from here.
+
+
+
+
+
+% Macros for to help in typing, remove them if you don't need them, but
+% this can help as a demo on how you can simply writing of commonly used
+% words that need special formatting (like software names).
+\newcommand{\snsign}{{\small S}/{\small N}}
+\newcommand{\originsoft}{\textsf{ORIGIN}}
+\newcommand{\sextractor}{\textsf{SE\-xtractor}}
+\newcommand{\noisechisel}{\textsf{Noise\-Chisel}}
+\newcommand{\makecatalog}{\textsf{Make\-Catalog}}
+
+
+
+
+
+%% For highlighting updates. When this is set, text marked as \new
+%% will be colored in dark green and text that is marked wtih \tonote
+%% will be marked in dark red.
+\ifdefined\highlightchanges
+\newcommand{\new}[1]{\textcolor{green!60!black}{#1}}
+\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}}
+\else
+\newcommand{\new}[1]{\textcolor{black}{#1}}
+\newcommand{\tonote}[1]{{}}
+\fi
+
+
+
+
+
+% Better than verbatim for displaying typed text.
+\usepackage{alltt}
+
+
+
+
+
+% For arithmetic opertions within LaTeX
+\usepackage[nomessages]{fp}
+
+
+
+
+
+%To add a code font to the text:
+\usepackage{courier}
+
+
+
+
+
+%To add some enumerating styles
+\usepackage{enumerate}
+
+
+
+
+
+%Including images if necessary
+\usepackage{graphicx}
diff --git a/tex/preamble-pgfplots.tex b/tex/preamble-pgfplots.tex
new file mode 100644
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--- /dev/null
+++ b/tex/preamble-pgfplots.tex
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+%% PGFPlots settings.
+%%
+%% PGFPlots is a package in (La)TeX for making plots internally. It fits
+%% nicely with the purpose of a reproduction pipeline. But it isn't
+%% mandatory. Therefore if needed, you can just uncomment the line that
+%% includes this file in the top LaTeX source (`paper.tex').
+
+
+
+
+
+% For a tikz environment:
+\usepackage{tikz}
+\usetikzlibrary{external}
+\tikzexternalize
+
+\tikzsetexternalprefix{\bdir/tex/tikz/}
+
+%% Uncomment the following lines for EPS and PS images. Note that you
+%% still have to use pdflatex and also add a `[dvips]' option to
+%% graphicx.
+
+%\tikzset{external/system call={rm -f "\image".eps "\image".ps
+%"\image".dvi; latex \tikzexternalcheckshellescape -halt-on-error
+%-interaction=batchmode -jobname "\image" "\texsource";
+%dvips -o "\image".ps "\image".dvi;
+%ps2eps "\image.ps"}}
+
+%For drawing plots:
+\usepackage{pgfplots}
+\pgfplotsset{compat=newest}
+\usepgfplotslibrary{groupplots}
+\pgfplotsset{axis line style={thick}, tick style={semithick}}
diff --git a/tex/preamble-style.tex b/tex/preamble-style.tex
new file mode 100644
index 0000000..ae7ce92
--- /dev/null
+++ b/tex/preamble-style.tex
@@ -0,0 +1,97 @@
+%% General paper's style settings.
+%%
+%% This preamble can be completely ignored when including this TeX file in
+%% another style. This is done because this LaTeX build is meant to be an
+%% initial/internal phase or part of a larger effort, so it has a basic
+%% style defined here as a preamble. To ignore it, uncomment or delete the
+%% respective line in `paper.tex'.
+
+
+
+%% Print size
+\usepackage[a4paper, includeheadfoot, body={18.7cm, 24.5cm}]{geometry}
+
+
+
+
+%% Set the distance between the columns if two columns:
+\setlength{\columnsep}{0.75cm}
+
+
+
+
+
+% To allow figures to take up more space on the top of the page:
+\renewcommand{\topfraction}{.99}
+\renewcommand{\bottomfraction}{.7}
+\renewcommand{\textfraction}{.05}
+\renewcommand{\floatpagefraction}{.99}
+\renewcommand{\dbltopfraction}{.99}
+\renewcommand{\dblfloatpagefraction}{.99}
+\setcounter{topnumber}{1}
+\setcounter{bottomnumber}{0}
+\setcounter{totalnumber}{2}
+\setcounter{dbltopnumber}{1}
+
+
+
+%% Color related settings:
+\usepackage{xcolor}
+\color{black}                   % Text color
+\definecolor{DarkBlue}{RGB}{0,0,90}
+
+
+% figure and figure* ordering correction:
+\usepackage{fixltx2e}
+
+
+
+%% For editing the caption appearence. The `setspace' package defines
+%% the `stretch' variable. `abovecaptionskip' is the distance between
+%% the figure and the caption.
+\usepackage{setspace, caption}
+\captionsetup{font=small, labelfont={color=DarkBlue,bf}, skip=1pt}
+\captionsetup[figure]{font={stretch=1, small}}
+\setlength{\abovecaptionskip}{3pt plus 1pt minus 1pt}
+
+
+
+%% To make the footnotes align:
+\usepackage[hang]{footmisc}
+\setlength\footnotemargin{10pt}
+
+
+
+%For including time in the title:
+\usepackage{datetime}
+
+
+
+%To make links to webpages and include document information in the
+%properties of the PDF
+\usepackage[
+  colorlinks,
+  urlcolor=blue,
+  citecolor=blue,
+  linkcolor=blue,
+  linktocpage]{hyperref}
+\renewcommand\UrlFont{\rmfamily}
+
+
+
+% Basic Document information
+\hypersetup
+{
+    pdfauthor={Mohammad Akhlaghi},
+    pdfsubject={MUSE detected objects},
+    pdftitle={Broadband HST photometry of MUSE detected objects},
+    pdfkeywords={Mohammad, Akhlaghi, photometry, MUSE, HST}
+}
+
+
+
+% Title
+\title{A nice title for your research project}
+\date{\small Reproduction pipeline \pipelineversion{}
+      and Gnuastro \gnuastroversion\\on \today, \currenttime}
+\author{Your name here.}