From 30733df5d30e150a26d53173d14bf941f179f6f5 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Tue, 27 Feb 2018 14:48:02 +0100
Subject: 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.
---
 paper.tex | 86 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 84 insertions(+), 2 deletions(-)

(limited to 'paper.tex')

diff --git a/paper.tex b/paper.tex
index d42cd7c..b0250b3 100644
--- a/paper.tex
+++ b/paper.tex
@@ -14,7 +14,7 @@
 %% report, while keeping modularity in the preambles.
 \input{tex/pipeline.tex}
 \input{tex/preamble-style.tex}
-%\input{tex/preamble-biblatex.tex}
+\input{tex/preamble-biblatex.tex}
 \input{tex/preamble-pgfplots.tex}
 \input{tex/preamble-necessary.tex}
 
@@ -32,6 +32,88 @@
 
 \maketitle
 
-Data were taken from \url{\websurvey}.
 
+
+%% Begin the multi-column environment. A `*' means that all extra empty
+%% space is added in the last column.
+\begin{multicols}{2}
+
+
+
+%% -------- Delete this ---------
+\section{Congratulations!}
+Congratulations on running the reproduction pipeline! You can now follow
+the checklist in the \texttt{README.md} file to customize this pipeline to
+your exciting research project.
+
+Just don't forget to \emph{never} use any numbers or fixed strings (for
+example database urls like \url{\websurvey}) directly within your \LaTeX{}
+source. Read them directly from your configuration files or outputs of the
+programs as part of the reproduction pipeline and import them into \LaTeX{}
+as macros through the \texttt{tex/pipeline.tex} file. See the several
+examples within the pipeline for a demonstration. For some recent
+real-world examples, the reproduction pipelines for Sections 4 and 7.3 of
+\citet{bacon17} are available at
+\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}\footnote{\url{https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes}},
+or
+\href{https://doi.org/10.5281/zenodo.1163746}{zenodo.1163746}\footnote{\url{https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry}}. Working
+in this way, will let you focus clearly on your science and not have to
+worry about fixing this or that number/name in the text.
+
+Just as a demonstration of creating plots within \LaTeX{} (using the
+PGFPlots package), in Figure \ref{deleteme} we show a plot of
+\deletemenum{} random points that were generated by this pipeline using the
+text manipulation program {\small AWK} (which is not the best random number
+generator, but just used here to generate some values). The minimum value
+in this distribution is $\deletememin$ and $\deletememax$ is the maximum.
+
+The {\small PDF} file of Figure \ref{deleteme} is available in the
+directory \texttt{\bdir/tex/build/tikz} and can be used in other contexts
+(for example slides). If you want to directly use the PDF file in the
+figure without having to let TiKZ decide if it should be remade or not, you
+can also comment the \texttt{makepdf} macro at the top of this \LaTeX{}
+source file.
+
+PGFPlots is a great tool to build the plots within \LaTeX{} and removes the
+necessity to add further dependencies (to create the plots) to your
+reproduction pipeline. High-level language libraries like Matplotlib do
+exist to also generate plots. However, bare in mind that they require many
+dependencies (Python, Numpy and etc). Installing these dependencies from
+source (after several years when the binaries are no longer available in
+common repositories), is not easy and will harm the reproducibility of your
+paper.
+
+\begin{Figure}
+  \includetikz{delete-me}
+
+  \captionof{figure}{\label{deleteme} A random set of values plotted as a
+    demonstration of how to generate plots within LaTeX.}
+\end{Figure}
+
+Furthermore, since PGFPlots is built by \LaTeX{} it respects all the
+properties of your text (for example line width and fonts and etc), so the
+final plot blends in your paper much more nicely. It also has a wonderful
+manual\footnote{\url{http://mirrors.ctan.org/graphics/pgf/contrib/pgfplots/doc/pgfplots.pdf}}.
+
+
+\section{Notice and citations}
+To encourage other scientists to publish similarly reproducible papers,
+please add a notice close to the start of your paper or in the end of the
+abstract clearly mentioning that your work is fully reproducible.
+
+For the time being, we haven't written a specific paper only for this
+reproduction pipeline, so until then, we would be grateful if you could
+cite the first paper that used the first version of this pipeline:
+\citet{ai15}.
+
+After publication, don't forget to upload all the necessary data, software
+source code and the reproduction pipeline to a long-lasting host like
+Zenodo (\url{https://zenodo.org/}).
+
+%% ------------------------------
+
+
+
+\printbibliography
+\end{multicols}
 \end{document}
-- 
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