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Diffstat (limited to 'paper.tex')
| -rw-r--r-- | paper.tex | 86 |
1 files changed, 57 insertions, 29 deletions
@@ -53,7 +53,9 @@ \textsl{Keywords}: Add some keywords for your research here. - \textsl{Reproducible paper}: Reproduction pipeline \pipelineversion{} + \textsl{Reproducible paper}: All quantitave results (numbers and plots) + in this paper are exactly reproducible with reproduction pipeline + \pipelineversion{} (\url{https://gitlab.com/makhlaghi/reproducible-paper}).} %% To add the first page's headers. @@ -69,8 +71,8 @@ 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{} +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 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 @@ -83,14 +85,12 @@ or 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 -{\small PGFP}lots package), in Figure \ref{deleteme} we show a simple -plot, where the Y axis is the square of the X axis. 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). +Figure \ref{deleteme} 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{deleteme} is available under the \texttt{tex/build/tikz/} directory of your build directory. You @@ -100,15 +100,6 @@ progress or after publishing the work). If you want to directly use the 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. -{\small PGFP}lots 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}[t] \includetikz{delete-me} @@ -116,10 +107,39 @@ your paper. demonstration.} \end{figure} +Figure \ref{deleteme-wfpc2} 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{deleteme-wfpc2}(b) explains this +difference between the mean and median. Also, the value of quantile +$\deletemewfpcquantile$ (set in the pipeline configuration file +\texttt{delete-me-wfpc2-quant.mk}) is $\deletemewfpctwoquantile$. 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 reproduction +pipeline. 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), so -the final plot blends in your paper much more nicely. It also has a -wonderful +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 pipeline also defines two \LaTeX{} macros that allow you to mark text @@ -135,7 +155,15 @@ 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-wfpc2} + \captionof{figure}{\label{deleteme-wfpc2} (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} @@ -177,12 +205,12 @@ SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness The following free software tools were also critical component of this research (in alphabetical order): Bzip2 \bziptwoversion, CFITSIO -\cfitsioversion, CMake \cmakeversion, cURL \curlversion, Git \gitversion, -GNU Bash \bashversion, GNU Coreutils \coreutilsversion, GNU AWK -\gawkversion, GNU Grep \grepversion, GNU Libtool \libtoolversion, GNU Make -\makeversion, GNU Sed \sedversion, GNU Scientific Library (GSL) -\gslversion, GNU Tar \tarversion, GNU Which \whichversion, Lzip -\lzipversion, GPL Ghostscript \ghostscriptversion, Libgit2 +\cfitsioversion, CMake \cmakeversion, cURL \curlversion, Discoteq flock +\flockversion, Git \gitversion, GNU Bash \bashversion, GNU Coreutils +\coreutilsversion, GNU AWK \gawkversion, GNU Grep \grepversion, GNU Libtool +\libtoolversion, GNU Make \makeversion, GNU Sed \sedversion, GNU Scientific +Library (GSL) \gslversion, GNU Tar \tarversion, GNU Which \whichversion, +Lzip \lzipversion, GPL Ghostscript \ghostscriptversion, Libgit2 \libgitwoversion, Libtiff \libtiffversion, WCSLIB \wcslibversion, XZ Utils \xzversion, and ZLib \zlibversion. The final paper was produced with \TeX{} Live \texliveversion, using the following packages: \TeX{} \textexversion, |