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Diffstat (limited to 'paper.tex')
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@@ -37,27 +37,28 @@ %% Start writing. \begin{document} -%% Abstract, keywords and reproduction pipeline notice. +%% Project abstract and keywords. \includeabstract{ - You have completed the reproduction pipeline and are ready to configure - and implement it for your own research. This template reproduction - pipeline and document contains almost all the elements that you will need - in a research project containing the downloading of raw data, processing - it, including them in plots and report, including this abstract, figures - and bibliography. If you use this pipeline in your work, don't forget to - add a notice to clearly let the readers know that your work is - reproducible. If this pipeline proves useful in your research, please - cite \citet{gnuastro}. + 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 reproduction pipeline - \pipelineversion{} - (\url{https://gitlab.com/makhlaghi/reproducible-paper}).} + in this paper are exactly reproducible (version \pipelineversion{}, + \url{https://gitlab.com/makhlaghi/reproducible-paper}).} %% To add the first page's headers. \thispagestyle{firststyle} @@ -68,19 +69,18 @@ %% Start of the main body of text. \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. +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 outputs of the -programs as part of the reproduction pipeline and import them into \LaTeX{} -as macros through the \texttt{tex/pipeline/macros/pipeline.tex} file -(created after running the pipeline). 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 +source. Read them directly from your configuration files, or processing +outputs, and import them into \LaTeX{} as macros through the +\texttt{tex/pipeline/macros/pipeline.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 @@ -126,15 +126,15 @@ histogram and basic statstics were generated with Gnuastro's {\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. +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 @@ -142,7 +142,7 @@ 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 +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{\%}' @@ -173,13 +173,12 @@ 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{gnuastro}. +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 reproduction pipeline to a long-lasting host like -Zenodo (\url{https://zenodo.org}). +source code and the project's source to a long-lasting host like Zenodo +(\url{https://zenodo.org}). @@ -187,21 +186,22 @@ Zenodo (\url{https://zenodo.org}). \section{Acknowledgements} \new{Please include the following two paragraphs in the Acknowledgement - section of your paper. This reproduction pipeline was developed in + 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 any of these packages in the final/customized pipeline, please - remove them. } + 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 reproduction pipeline \pipelineversion. Work on -Gnuastro and the reproduction pipeline 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. +ascl.net/1801.009), and the reproducible paper template +\pipelineversion. 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. \input{tex/pipeline/macros/dependencies.tex} |