From 4483a81c4254596dd2fa977e7a2faf6f28a7ac6f Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sat, 18 Jan 2020 00:57:43 +0000
Subject: First set of customizations done

The unnecessary parts were removed and the project now runs.
---
 paper.tex | 136 +++-----------------------------------------------------------
 1 file changed, 5 insertions(+), 131 deletions(-)

(limited to 'paper.tex')

diff --git a/paper.tex b/paper.tex
index 10c9910..0b92607 100644
--- a/paper.tex
+++ b/paper.tex
@@ -56,17 +56,7 @@
 %% Project abstract and keywords.
 \includeabstract{
 
-  You have completed the reproducible paper template and are ready to
-  configure and implement it for your own research. This template contains
-  almost all the elements that you will need in a research project
-  containing the downloading of raw data and necessary software, building
-  the software, and processing the data with the software in a
-  highly-controlled environment. It then allows including the results in
-  plots and producing the final report, including this abstract, figures
-  and bibliography. If you design your project with this template's
-  infra-structure in your work, don't forget to add a notice and clearly
-  let the readers know that your work is reproducible. If this template
-  proves useful in your research, please cite \citet{gnuastro}.
+  To be filled.
 
   \vspace{0.25cm}
 
@@ -84,117 +74,8 @@
 
 
 %% Start of main body.
-\section{Congratulations!}
-Congratulations on running the raw template project! You can now follow the
-checklist in the \texttt{README.md} file to customize this template to your
-exciting research project.
-
-Just don't forget to \emph{never} use numbers or fixed strings (for example
-database urls like \url{\wfpctwourl}) directly within your \LaTeX{}
-source. Read them directly from your configuration files, or processing
-outputs, and import them into \LaTeX{} as macros through the
-\texttt{tex/build/macros/project.tex} file (created after running the
-project). See the several existing examples within the template for a
-demonstration. For some recent real-world examples, the reproducible
-project sources 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.
-
-Figure \ref{delete-me} shows a simple plot as a demonstration of creating
-plots within \LaTeX{} (using the {\small PGFP}lots package). The minimum
-value in this distribution is $\deletememin$, and $\deletememax$ is the
-maximum. Take a look into the \LaTeX{} source and you'll see these numbers
-are actually macros that were calculated from the same dataset (they will
-change if the dataset, or function that produced it, changes).
-
-The individual {\small PDF} file of Figure \ref{delete-me} is available
-under the \texttt{tex/tikz/} directory of your build directory. You can use
-this PDF file in other contexts (for example in slides showing your
-progress or after publishing the work). If you want to directly use the
-{\small PDF} file in the figure without having to let {\small T}i{\small
-  KZ} decide if it should be remade or not, you can also comment the
-\texttt{makepdf} macro at the top of this \LaTeX{} source file.
-
-\begin{figure}[t]
-  \includetikz{delete-me}
-
-  \captionof{figure}{\label{delete-me} A very basic $X^2$ plot for
-    demonstration.}
-\end{figure}
-
-Figure \ref{delete-me-demo} is another demonstration of showing images
-(datasets) using PGFPlots. It shows a small crop of an image from the
-Wide-Field Planetary Camera 2, on board the Hubble Space Telescope from
-1993 to 2009. This cropped image is one of the sample FITS files from the
-FITS file standard
-webpage\footnote{\url{https://fits.gsfc.nasa.gov/fits_samples.html}}. Just
-as another basic reporting of measurements on this dataset within the paper
-without using numbers in the \LaTeX{} source, the mean is
-$\deletemewfpctwomean$ and the median is $\deletemewfpctwomedian$. The
-skewness in the histogram of Figure \ref{delete-me-demo}(b) explains this
-difference between the mean and median. The dataset was prepared for
-demonstration here with Gnuastro's \textsf{Convert\-Type} program and the
-histogram and basic statstics were generated with Gnuastro's
-\textsf{Statistics} program.
-
-{\small PGFP}lots\footnote{\url{https://ctan.org/pkg/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 project. There are
-high-level language libraries like Matplotlib which also generate
-plots. However, the problem is that they require many dependencies (Python,
-Numpy and etc). Installing these dependencies from source, is not easy and
-will harm the reproducibility of your paper. Note that after several years,
-the binary files of these high-level libraries, that you easily install
-today, will no longer be available in common repositories. Therefore
-building the libraries from source is the only option to reproduce your
-results.
-
-Furthermore, since {\small PGFP}lots is built by \LaTeX{} it respects all
-the properties of your text (for example line width and fonts and
-etc). Therefore 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}}.
-
-This template also defines two \LaTeX{} macros that allow you to mark text
-within your document as \emph{new} and \emph{notes}. For example, \new{this
-  text has been marked as \texttt{new}.} \tonote{While this one is marked
-  as \texttt{tonote}.} If you comment the line (by adding a `\texttt{\%}'
-at the start of the line or simply deleting the line) that defines
-\texttt{highlightchanges}, then the one that was marked \texttt{new} will
-become black (totally blend in with the rest of the text) and the one
-marked \texttt{tonote} will not be in the final PDF. You can thus use
-\texttt{highlightchanges} to easily make copies of your research for
-existing coauthors (who are just interested in the new parts or notes) and
-new co-authors (who don't want to be distracted by these issues in their
-first time reading).
-
-\begin{figure}[t]
-  \includetikz{delete-me-demo}
-
-  \captionof{figure}{\label{delete-me-demo} (a) An example image of the
-    Wide-Field Planetary Camera 2, on board the Hubble Space Telescope from
-    1993 to 2009. This is one of the sample images from the FITS standard
-    webpage, kept as examples for this file format. (b) Histogram of pixel
-    values in (a).}
-\end{figure}
-
-
-
-\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
-template. Until then, we would be grateful if you could cite the first
-paper that used the early versions of this template: \citet{gnuastro}.
-
-After publication, don't forget to upload all the necessary data, software
-source code and the project's source to a long-lasting host like Zenodo
-(\url{https://zenodo.org}).
+\section{Introduction}
+
 %% End of main body.
 
 
@@ -202,15 +83,8 @@ source code and the project's source to a long-lasting host like Zenodo
 
 
 \section{Acknowledgements}
-\new{Please include the following two paragraphs in the Acknowledgement
-  section of your paper. This reproducible paper template was developed in
-  parallel with Gnuastro, so it benefited from the same grants. If you
-  don't use Gnuastro in your final/customized project, please remove it
-  from the paragraph below, only mentioning the reproducible paper
-  template.}
-
-This research was partly done using GNU Astronomy Utilities (Gnuastro,
-ascl.net/1801.009), and the reproducible paper template
+
+This research was partly done with the reproducible paper template
 \projectversion. Work on Gnuastro and the reproducible paper template has
 been funded by the Japanese Ministry of Education, Culture, Sports,
 Science, and Technology (MEXT) scholarship and its Grant-in-Aid for
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