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| -rw-r--r-- | Makefile | 2 | ||||
| -rw-r--r-- | img/cnrs.png | bin | 16388 -> 0 bytes | |||
| -rw-r--r-- | img/cral.png | bin | 45217 -> 0 bytes | |||
| -rw-r--r-- | img/erc.png | bin | 48016 -> 0 bytes | |||
| -rw-r--r-- | img/iac.png | bin | 0 -> 56166 bytes | |||
| -rw-r--r-- | img/muse.png | bin | 63621 -> 0 bytes | |||
| -rw-r--r-- | img/univ-lyon.png | bin | 16867 -> 0 bytes | |||
| -rw-r--r-- | reproducible-paper.tex | 84 |
8 files changed, 44 insertions, 42 deletions
@@ -1,5 +1,5 @@ # PDF slides: -reproducible-paper.pdf: +reproducible-paper.pdf: reproducible-paper.tex # We'll run pdflatex two times so the page numbers and # internal links also work. pdflatex reproducible-paper diff --git a/img/cnrs.png b/img/cnrs.png Binary files differdeleted file mode 100644 index c93f342..0000000 --- a/img/cnrs.png +++ /dev/null diff --git a/img/cral.png b/img/cral.png Binary files differdeleted file mode 100644 index 2780f8a..0000000 --- a/img/cral.png +++ /dev/null diff --git a/img/erc.png b/img/erc.png Binary files differdeleted file mode 100644 index 8221779..0000000 --- a/img/erc.png +++ /dev/null diff --git a/img/iac.png b/img/iac.png Binary files differnew file mode 100644 index 0000000..21aa8d4 --- /dev/null +++ b/img/iac.png diff --git a/img/muse.png b/img/muse.png Binary files differdeleted file mode 100644 index 80f83b4..0000000 --- a/img/muse.png +++ /dev/null diff --git a/img/univ-lyon.png b/img/univ-lyon.png Binary files differdeleted file mode 100644 index cbbee20..0000000 --- a/img/univ-lyon.png +++ /dev/null diff --git a/reproducible-paper.tex b/reproducible-paper.tex index c4cf260..b188711 100644 --- a/reproducible-paper.tex +++ b/reproducible-paper.tex @@ -21,20 +21,13 @@ %% Set the author -\author{Mohammad Akhlaghi\\\vspace{2mm}\footnotesize Centre de - Recherche Astrophysique de Lyon({\scriptsize CRAL}),\\Universit\'e de - Lyon, France.\\ - \vspace{1.5cm} - \includegraphics[width=3.5cm]{img/muse.png}\\ - \includegraphics[width=1.4cm]{img/cral.png} - \includegraphics[width=1.9cm]{img/univ-lyon.png} - \includegraphics[width=1cm]{img/cnrs.png} - \includegraphics[width=1cm]{img/erc.png}\\ +\author{Mohammad Akhlaghi\\\vspace{2mm}\footnotesize Instituto de + Astrof\'isica de Canarias ({\scriptsize IAC}),\\Tenerife, Spain } %% Set the date and insitutional logos. -\date{} +\date{\includegraphics[width=2cm]{img/iac.png}} @@ -62,7 +55,7 @@ result}. \item But these factors have also greatly increased the \alert{complexity} of an analysis. Making it impossible to - exactly descibe all steps in a published paper. + exactly describe all steps in a published paper. \item Most scientific papers thus ignore the ``details'' (as they interpret it). \item But due to the complexity, even a small deviation from the @@ -83,7 +76,7 @@ \begin{frame}{Values in final report/paper} All necessary analysis/processing \alert{input} and \alert{output} - values are writen into the final report as \LaTeX{} macros. Shown + values are written into the final report as \LaTeX{} macros. Shown here is a portion of the \textsf{NoiseChisel} paper and its source (\textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}). @@ -93,7 +86,7 @@ \begin{frame}{Values in final report/paper} All necessary analysis/processing \alert{input} and \alert{output} - values are writen into the final report as \LaTeX{} macros. Shown + values are written into the final report as \LaTeX{} macros. Shown here is a portion of the \textsf{NoiseChisel} paper and its source (\textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}). @@ -181,29 +174,33 @@ \begin{frame}{Reproducing the result and report/paper} - Once software dependencies are installed, the two \alert{simple} - and \alert{familiar} commands below are enough to exactly - reproduce the results at any time (as in - \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}): + The two \alert{simple} and \alert{familiar} commands below are + enough to exactly reproduce the results at any time. \begin{itemize} - \item[] \texttt{\$ ./configure{ }{ }{ }{ }{ }{ }\# To - define top-level local directories.} - \item[] \texttt{\$ make{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\# To reproduce the analysis and paper.} + \item[] \texttt{\$ ./configure} + \item[] \texttt{\$ make} \end{itemize} - \vspace{0.5cm} Enabling version control (e.g. \alert{Git}) will - make it very easy to test different ideas while not harming the - initial/base result (thus encouraging \alert{creativity} and - brainstorming during the project). + With \texttt{./configure}, you specify the local directories to + use. All necessary \alert{software} are then \alert{downloaded} + and installed there (independent of your OS or other projects). - \vspace{0.5cm} The pipeline can also \alert{download input} data - from online archives (databases) if not locally available (as in + \vspace{0.3cm} With \texttt{make}, input \alert{data} from online + archives (databases) are \alert{downloaded}, if not locally + available, the processing is done, and the \LaTeX{} paper is built + as a PDF (e.g., see \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}} - and - \textcolor{blue}{\href{https://gitlab.com/makhlaghi/reproducible-paper}{template}}). + or + \textcolor{blue}{\small\href{https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf}{template's + output}}). - \vspace{0.5cm} After publication, \alert{readers} can + \vspace{0.3cm} Enabling version control (e.g., with \alert{Git}) + encourages testing different ideas while not harming the + initial/base result (thus encouraging \alert{creativity} and + brainstorming during the project). + + \vspace{0.3cm} After publication, \alert{readers} can \alert{change} the input configurations and the numbers and figures of the reproduced paper will respectively change. This encourages creativity and brainstorming after the project as well @@ -215,19 +212,19 @@ \begin{frame}{Publication of the pipeline} - A reproduction pipeline like this will have the following + A reproducible project using this template will have the following (\alert{plain text}) components: \begin{itemize} \item Makefiles. \item \LaTeX{} source files. - \item Configuration files. + \item Configuration files for software used in analysis. \item Scripts/programming files (e.g., Python, Shell, AWK, C). \end{itemize} - The \alert{volume} of the reproduction pipeline will thus be + The \alert{volume} of the project's source will thus be \alert{negligible} compared to a single figure in a paper - (especially after compression). + (usually $\sim100$ kilo-bytes). - \vspace{1.5cm} The reproduction pipeline can be \alert{published} in + \vspace{1cm} The reproduction pipeline can be \alert{published} in \begin{itemize} \item \alert{arXiv}: uploaded with the \TeX{} source to always stay with the paper \\(for example @@ -244,16 +241,21 @@ \begin{frame} - A template/blank pipeline has been written and is ready to use, - with implementation guidelines and practical tips and - recommendations (see the template's + A template/blank pipeline has been written and is ready to use + (see the template's \textcolor{blue}{\href{https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf}{output}}): - \textcolor{blue}{\url{https://gitlab.com/makhlaghi/reproducible-paper}} + \textcolor{blue}{\footnotesize\url{https://gitlab.com/makhlaghi/reproducible-paper}} + + \vspace{1.5cm} For a technical description of the template's + implementation, as well as a checklist to customize it, and tips + on good practices, please see this page: + + \textcolor{blue}{\footnotesize\url{https://gitlab.com/makhlaghi/reproducible-paper/blob/pipeline/README-hacking.md}} - \vspace{2.5cm} - Please see this page for more: + \vspace{1.5cm} For more on the necessity of reproducible research, + please see: - \textcolor{blue}{\url{http://akhlaghi.org/reproducible-science.html}} + \textcolor{blue}{\footnotesize\url{http://akhlaghi.org/reproducible-science.html}} \end{frame} \end{document} |
