%% Copyright (C) 2018-2020 Mohammad Akhlaghi %% See the end of the file for license conditions. \documentclass[10pt, twocolumn]{article} %% This is a convenience variable if you are using PGFPlots to build plots %% within LaTeX. If you want to import PDF files for figures directly, you %% can use the standard `\includegraphics' command. See the definition of %% `\includetikz' in `tex/preamble-pgfplots.tex' for where the files are %% assumed to be if you use `\includetikz' when `\makepdf' is not defined. \newcommand{\makepdf}{} %% When defined (value is irrelevant), `\highlightchanges' will cause text %% in `\tonote' and `\new' to become colored. This is useful in cases that %% you need to distribute drafts that is undergoing revision and you want %% to hightlight to your colleagues which parts are new and which parts are %% only for discussion. \newcommand{\highlightchanges}{} %% Necessary LaTeX preambles to include for relevant functionality. We want %% to start this file as fast as possible with the actual body of the %% paper, while keeping modularity in the preambles. \input{tex/src/preamble-style.tex} \input{tex/src/preamble-header.tex} \input{tex/src/preamble-biblatex.tex} \input{tex/src/preamble-pgfplots.tex} \input{tex/src/preamble-necessary.tex} %% Title and author information. For a more fine-grained control of the %% headers including author name, or paper info, see %% `tex/src/preamble-header.tex'. Note that if you plan to use a journal's %% LaTeX style file, you will probably not need to set them, and can also %% replace this "Title and author information" section with the journal's %% preferred format. \title{\large \uppercase{The paper's title goes here}} \author[1]{Your name} \author[2]{Coauthor one} \author[1,3]{Coauthor two} \affil[1]{The first affiliation in the list.; \url{your@email.address}} \affil[2]{Another affilation can be put here.} \affil[3]{And generally as many affiliations as you like. \par \emph{Received YYYY MM DD; accepted YYYY MM DD; published YYYY MM DD}} \date{} %% Start creating the paper. \begin{document} %% 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}. \vspace{0.25cm} \textsl{Keywords}: Add some keywords for your research here. \textsl{Reproducible paper}: All quantitave results (numbers and plots) in this paper are exactly reproducible with Maneage (version \projectversion{}, \url{https://maneage.org}).} %% To add the first page's headers. \thispagestyle{firststyle} %% 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}). %% End of main body. \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 \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 Scientific Research (21244012, 24253003), the European Research Council (ERC) advanced grant 339659-MUSICOS, European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No 721463 to the SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness (MINECO) under grant number AYA2016-76219-P. The reproducible paper template was also supported by European Union’s Horizon 2020 (H2020) research and innovation programme via the RDA EU 4.0 project (ref. GA no. 777388). %% Tell BibLaTeX to put the bibliography list here. \printbibliography %% Start appendix. \appendix %% Mention all used software in an appendix. \section{Software acknowledgement} \input{tex/build/macros/dependencies.tex} %% Finish LaTeX \end{document} %% This file is part of Maneage (https://maneage.org). % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the %% Free Software Foundation, either version 3 of the License, or (at your %% option) any later version. % %% This file is distributed in the hope that it will be useful, but WITHOUT %% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or %% FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License %% for more details. % %% You should have received a copy of the GNU General Public License along %% with this file. If not, see .