Default PDF now uses PGFPlots and BibLaTeX

Making plots and including references are integral parts of a scientific
paper. Therefore to demonstrate how cleanly they can be used within the
pipeline, they are now used to produce the final PDF.

To use PGFPlots a random dataset is made (using AWK's random function) and
is plotted using PGFPlots. The minimum and maximum values of the dataset
are also included in the text to further show how such calculations can go
into the macros and text.

For the references, the NoiseChisel paper was added as a reference to cite
when using this pipeline along with the MUSE UDF paper I, which uses this
pipeline for two sections. Following this discussion, citation is also
discussed in `README.md` and the NoiseChisel paper is also added as a
published work with a reproduction pipeline.

5 files changed, 68 insertions, 2 deletions

diff --git a/tex/delete-me.tex b/tex/delete-me.tex
new file mode 100644
index 0000000..495333a
--- /dev/null
+++ b/tex/delete-me.tex
@@ -0,0 +1,17 @@
+%% PGFPlots code to plot a random set of numbers as demo
+
+\begin{tikzpicture}
+
+  %% Settings of the plotted axis
+  \begin{axis}[
+      width=\linewidth,
+      xlabel=Counter,
+      ylabel=Random value,
+    ]
+
+    %% A particular plot.
+    \addplot+[scatter, only marks]
+    table {\bdir/tex/delete-me/data.txt};
+
+  \end{axis}
+\end{tikzpicture}
diff --git a/tex/preamble-biblatex.tex b/tex/preamble-biblatex.tex
index 757f007..869d3d5 100644
--- a/tex/preamble-biblatex.tex
+++ b/tex/preamble-biblatex.tex
@@ -40,7 +40,7 @@
     backend=biber,natbib]{biblatex}
 \DeclareFieldFormat[article]{pages}{#1}
 \DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
-\addbibresource{./tex/ref.tex}
+\addbibresource{tex/references.tex}
 \renewbibmacro{in:}{}
 \renewcommand*{\bibfont}{\footnotesize}
 \DefineBibliographyStrings{english}{references = {References}}
diff --git a/tex/preamble-pgfplots.tex b/tex/preamble-pgfplots.tex
index c2a7f14..78937a7 100644
--- a/tex/preamble-pgfplots.tex
+++ b/tex/preamble-pgfplots.tex
@@ -37,8 +37,12 @@
 %% figures. These numbers can be hard to manage and they will also depend
 %% on order in the final PDF, so it will be very buggy to manage them.
 \newcommand{\includetikz}[1]{%
+  \ifdefined\makepdf%
     \tikzsetnextfilename{#1}%
     \input{tex/#1.tex}%
+  \else
+    \includegraphics[width=\linewidth]{\bdir/tex/build/tikz/#1.pdf}
+  \fi
 }
 
 
diff --git a/tex/preamble-style.tex b/tex/preamble-style.tex
index d794ac1..228cd10 100644
--- a/tex/preamble-style.tex
+++ b/tex/preamble-style.tex
@@ -128,7 +128,7 @@
 
 
 % Title, author, pipeline info and date as they appear on the output PDF.
-\title{THE TITLE OF THIS PROJECT}
+\title{THE TITLE OF YOUR PROJECT}
 \author{YOUR NAME, COLLEAGE1 NAME, ETC}
 \date{\small Reproduction pipeline \pipelineversion{}
       and Gnuastro \gnuastroversion\\on \today, \currenttime}
diff --git a/tex/references.tex b/tex/references.tex
new file mode 100644
index 0000000..b3998a2
--- /dev/null
+++ b/tex/references.tex
@@ -0,0 +1,45 @@
+@ARTICLE{bacon17,
+   author = {{Bacon}, R. and {Conseil}, S. and {Mary}, D. and {Brinchmann}, J. and
+	{Shepherd}, M. and {Akhlaghi}, M. and {Weilbacher}, P.~M. and
+	{Piqueras}, L. and {Wisotzki}, L. and {Lagattuta}, D. and {Epinat}, B. and
+	{Guerou}, A. and {Inami}, H. and {Cantalupo}, S. and {Courbot}, J.~B. and
+	{Contini}, T. and {Richard}, J. and {Maseda}, M. and {Bouwens}, R. and
+	{Bouch{\'e}}, N. and {Kollatschny}, W. and {Schaye}, J. and
+	{Marino}, R.~A. and {Pello}, R. and {Herenz}, C. and {Guiderdoni}, B. and
+	{Carollo}, M.},
+    title = "{The MUSE Hubble Ultra Deep Field Survey. I. Survey description, data reduction, and source detection}",
+  journal = {A\&A},
+archivePrefix = "arXiv",
+   eprint = {1710.03002},
+ keywords = {galaxies: distances and redshifts, galaxies: high-redshift, cosmology: observations, methods: data analysis, techniques: imaging spectroscopy, galaxies: formation},
+     year = 2017,
+    month = nov,
+   volume = 608,
+      eid = {A1},
+    pages = {A1},
+      doi = {10.1051/0004-6361/201730833},
+   adsurl = {http://adsabs.harvard.edu/abs/2017A\%26A...608A...1B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
+@ARTICLE{ai15,
+   author = {{Akhlaghi}, M. and {Ichikawa}, T.},
+    title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
+  journal = {ApJS},
+archivePrefix = "arXiv",
+   eprint = {1505.01664},
+ primaryClass = "astro-ph.IM",
+ keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric},
+     year = 2015,
+    month = sep,
+   volume = 220,
+      eid = {1},
+    pages = {1},
+      doi = {10.1088/0067-0049/220/1/1},
+   adsurl = {http://adsabs.harvard.edu/abs/2015ApJS..220....1A},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}