% LaTeX source of slides on reproducible paper.
%
% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
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% Basic LaTeX settings.
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\include{tex/preamble}

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%\setbeamertemplate{footline}[frame number]

%% Packages to import.
\usepackage{tcolorbox}          %For a color-box.
\usepackage{textcomp}           %For a copyright sign.

%% To simplify arXiv links
\newcommand{\arxivlink}[1]{{\footnotesize
    (\textcolor{blue}{\href{https://arxiv.org/abs/#1}{arXiv:#1}})}}

%% Set the title
\title{\huge\textbf{BIG} Data, \textbf{BIG} responsibility
  \\\vspace{2mm} \large Maneage: \emph{Man}aging data lin\emph{eage} for long-term and archivable reproducibility \\\vspace{1mm} \footnotesize (Published in CiSE 23 (3), pp 82-91: \textcolor{blue}{\href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}}, \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}})}

%% Set the author
\author{\\
  \href{https://akhlaghi.org}{Mohammad Akhlaghi}\\\vspace{0.5mm}
  \footnotesize
  Centro de Estudios de F\'isica del Cosmos de Arag\'on ({\scriptsize CEFCA}), Teruel, Spain\vspace{8mm}
}

%% Set the date and insitutional logos.
\date{\footnotesize\vspace{-5mm}\\
  \textcolor{black}{Royal Observatory Coffee talk; Edinburgh}\\
  \textcolor{black}{23rd of May 2023} \\
  \tiny\vspace{9mm}
  Most recent slides available in link below (this PDF is built from \href{http://git.maneage.org/slides-intro.git}{Git commit} \gitcommit):\\
  \footnotesize\textcolor{blue}{\url{https://maneage.org/pdf/slides-intro.pdf}}\\
  \vspace{2mm}
  \raisebox{+0.4\height}{\includegraphics[width=3cm]{img/jcava.jpg}}
  \includegraphics[width=1cm]{img/cefca.png}
  \includegraphics[width=1.2cm]{img/iac.png}
  \includegraphics[width=1cm]{img/eu-sundial.png}
  \raisebox{0.13\height}{\includegraphics[width=1cm]{img/eu-regional.png}}
  \raisebox{0.05\height}{\includegraphics[width=1cm]{img/eu-rdaeu4.png}}
  \raisebox{+0.1\height}{\includegraphics[width=1.4cm]{img/rda-europe.png}}
  \raisebox{+1\height}{\includegraphics[width=1.5cm]{img/aragon.png}}
  \raisebox{+0.8\height}{\includegraphics[width=1.6cm]{img/gobierno-canarias.png}}\\
  \vspace{1cm}
}




















\begin{document}

  \begin{frame}
    \titlepage
  \end{frame}

  \begin{frame}{Let's start with this nice image of the Wirlpool galaxy (M51): \small{\url{https://i.redd.it/jfqgpqg0hfk11.jpg}}}
    \begin{center}
      \includegraphics[width=0.8\linewidth]{img/m51-amateur.jpg}
    \end{center}
  \end{frame}





  \begin{frame}{Now, let's assume you want to study M51's outer structure, but you'll have to detect it first.}
    \footnotesize
    \begin{columns}
      \column{6cm} Example: Using a \alert{single exposure} SDSS image
      with NoiseChisel (a program that is part of `GNU Astronomy
      Utilities').

      \vspace{3mm}
      \begin{itemize}
        \setlength\itemsep{1.5mm}
      \item When optimized, outskirts detected down to
        $\rm{S/N}=$\alert{$1/4$}, or \alert{$28.3$} mag/arcsec$^2$. By
        default, it only reaches $\rm{S/N}>1/2$.
      \item
        Akhlaghi 2019
        (\textcolor{blue}{\href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230}})
        describes optimized result:
        \begin{itemize}
          \footnotesize
        \item \alert{Run-time} options/configuration.
        \item Steps \alert{before/after} NoiseChisel.
        \end{itemize}
      \item Deep/orange image from Watkins+2015
        (\textcolor{blue}{\href{https://arxiv.org/abs/1501.04599}{arXiv:1501.04599}}) shown for reference.
      \item Therefore:
        \begin{itemize}
          \footnotesize
        \item Default settings not enough.
        \item Final number not just from NoiseChisel (more software
          involved).
        \end{itemize}
      \end{itemize}

      \vspace{2mm}
      \begin{tcolorbox}[boxsep=0pt,left=1mm,right=1mm,top=1mm,bottom=1mm]
        Simply reporting in your paper that ``\emph{\alert{we used
            NoiseChisel}}'' is \alert{not enough} to reproduce,
        understand, or verify your result.
      \end{tcolorbox}

      \column{9cm}
        \begin{tikzpicture}

          \node[anchor=south west,inner sep=0] (image) at (0,0.362\linewidth)
               {\includegraphics[width=0.495\linewidth]
                 {img/m51-lf.pdf}};
               \node[anchor=south,white,font={\small}] at
               (0.25\linewidth,0.362\linewidth) {Input image};

          \node[anchor=south west,inner sep=0] (image) at
               (0.5\linewidth,0.362\linewidth)
               {\includegraphics[width=0.495\linewidth]
                 {img/m51-edge-default.pdf}};
               \node[anchor=south,white,font={\small}] at
               (0.75\linewidth,0.362\linewidth) {Default NoiseChisel};

          \node[anchor=south west,inner sep=0] (image) at (0,0)
               {\includegraphics[width=0.495\linewidth]
                 {img/m51-edge.pdf}};
               \node[anchor=south,white,font={\small}] at
               (0.25\linewidth,0) {Optimized NoiseChisel};

          \node[anchor=south west,inner sep=0] (image) at (0.5\linewidth,0)
               {\includegraphics[width=0.495\linewidth]
                 {img/m51-watkins-zoom.png}};
               \node[anchor=south,black,font={\small}] at
               (0.75\linewidth,0) {Much deeper image};
        \end{tikzpicture}
    \end{columns}
  \end{frame}





  \begin{frame}{Reproducibility crisis in the sciences/astronomy}
    \begin{tcolorbox}[title=Snakes on a Spaceship -- An Overview of Python in Heliophysics]
      \small ``...\alert{inadequate analysis descriptions} and loss of
      scientific data have made scientific studies \alert{difficult}
      or \alert{impossible} to replicate''. From Burrell+2018,
      \arxivlink{1901.00143}.
    \end{tcolorbox}
    \pause
    \begin{tcolorbox}[title=Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software]
      ``It is our interest that NASA adopt an open-code policy because
      without it, reproducibility in computational science is
      \alert{needlessly hampered}''. From Oishi+2018,
      \arxivlink{1801.08200}.
    \end{tcolorbox}
    \pause
    \begin{tcolorbox}[title=Schroedinger's code: source code availability and link persistence in astrophysics]
      ``We were \alert{unable to find source code} online ... for
      $40.4\%$ of the codes used in the research we looked at''. From
      Allen+2018, \arxivlink{1801.02094}.
    \end{tcolorbox}
  \end{frame}





  \begin{frame}
    \centering
    \includegraphics[width=0.45\linewidth]{img/schrodinger-code.jpg}

    \footnotesize Original image from \href{https://www.redbubble.com/people/seriesclothing/works/28520432-the-flash-ciscos-shirt-wanted-dead-and-alive-scr-dingers-cat}{\texttt{https://www.redbubble.com}}
  \end{frame}



  \begin{frame}{This problem isn't just limited to astronomy}
    \begin{tcolorbox}[title=Repeatability of published microarray gene expression analyses]
      \small Ioannidis+2009 evaluated the replication of data analyses in \alert{18 articles} ... in Nature Genetics and reproduced \alert{only 2} in principle.''. DOI:\href{https://doi.org/10.1038/ng.295}{10.1038/ng.295}.
    \end{tcolorbox}
    \pause

    \begin{tcolorbox}[title=Is Economics Research Replicable? 60 papers from Thirteen Journals Say ``Usually Not'']
      \small Chang\&Li2015 were are able to \alert{replicate less than half} of 67 papers in well-regarded journals. Even \emph{with help} from the authors.
      They ``assert that \alert{economics research is usually not replicable}''. DOI:\href{http://dx.doi.org/10.17016/FEDS.2015.083}{10.17016/FEDS.2015.083}
    \end{tcolorbox}

    \pause
    \begin{tcolorbox}[title=An empirical analysis of journal policy effectiveness
for computational reproducibility]
      \small Stodden+2018 studied a random sample of \alert{204} scientific papers in \emph{Science} and were able to obtain \alert{artifacts from 44\%} and \alert{reproduce the findings for 26\%}. DOI:\href{http://dx.doi.org/10.1073/pnas.1708290115}{10.1073/pnas.1708290115}
    \end{tcolorbox}
  \end{frame}





  \begin{frame}{``Reproducibility crisis'' in the sciences? (Baker 2016, Nature 533, 452, \textcolor{blue}{\href{https://doi.org/10.1038/533452a}{DOI:10.1038/533452a}})}
    \Large
    1576 researchers participated in a survey by Nature, \alert{$90\%$} believed in a crisis!

    \vspace{7mm}
    \begin{center}
      \begin{tabular}{ |l|r| }
        \hline
        Status                            & $\%$ agreed \\
        \hline
        \alert{Yes}, a significant crisis & \textcolor{red}{$52$} \\
        \alert{Yes}, a slight crisis      & \textcolor{red}{$38$} \\
        Don't know                        & $7$  \\
        No, there is no crisis            & $3$  \\
        \hline
      \end{tabular}
    \end{center}

    \vspace{7mm}
    Full PDF available at \textcolor{blue}{\url{https://www.nature.com/articles/533452a.pdf}}
  \end{frame}





  \begin{frame}{Our solution: CiSE 23 (3), pp 82-91: \textcolor{blue}{\href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}}, \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}}}
    \begin{columns}
      \column{0.4\linewidth}
      \includegraphics[width=\linewidth]{img/maneage-paper.png}
      \column{0.6\linewidth}
      \includegraphics[width=\linewidth]{img/maneage-webpage.png}
      \begin{center}
        \huge{https://maneage.org}
      \end{center}
    \end{columns}
  \end{frame}



  \begin{frame}{Recognition 1: RDA adoption grant (2019) to IAC for Maneage}
      \begin{center}
        \includegraphics[width=3cm]{img/rda.png}\hspace{1cm}
        \includegraphics[width=1.8cm]{img/iac.png}
        \includegraphics[width=\linewidth]{img/h2020.jpg}
      \end{center}

      \vspace{1cm} For Maneage, the \alert{IAC} is selected as
      a \alert{Top European organization} funded to adopt RDA
      Recommendations and Outputs.

      \vspace{1cm}
      \scriptsize
      \begin{itemize}
      \item Research Data Alliance was launched by the \alert{European
        Commission}, NSF, National Institute of Standards and
        Technology, and the Australian Government’s Department of
        Innovation.
      \item RDA Outputs are the technical and social infrastructure
        solutions developed by RDA Working Groups or Interest
        Groups that enable data sharing, exchange, and
        interoperability.
      \end{itemize}

      \vspace{0.2cm}
  \end{frame}





  \begin{frame}{Recognition 2: ``News and Views'' in Nature Astronomy (\textcolor{blue}{\href{https://ui.adsabs.harvard.edu/abs/2021NatAs...5..986K}{2021NatAs...5..986K}})}
    \begin{center}
      \includegraphics[width=\linewidth]{img/nature-astronomy.png}
    \end{center}

    \vspace{1cm}
    Free-to-read link: \textcolor{blue}{\url{https://rdcu.be/cmYVx}}\\
    DOI: \textcolor{blue}{\href{https://doi.org/10.1038/s41550-021-01402-3}{10.1038/s41550-021-01402-3}}
  \end{frame}





  \begin{frame}[t]{Definitions \& Clarification \hspace{1.6cm} {\normalsize(from the National Academies report in 2019, \href{http://doi.org/10.17226/25303}{DOI:10.17226/25303})}}
    \vspace{-5mm}
    \begin{columns}[t]
      \column{0.5\linewidth}
      \begin{center}
        \large\textbf{Replicability (hardware/statistical)}
        \rule{0.5\linewidth}{1pt}
      \end{center}
      \begin{itemize}
        \setlength\itemsep{0.5em}
      \item Involves data \alert{collection}.
      \item Inherently includes \alert{measurements errors}\\(can
        never be exactly reproduced).
      \item Example: Raw telescope image/spectra.
      \item \alert{\textbf{NOT DISCUSSED HERE.}}
      \end{itemize}

      \vspace{3.5mm}
      \begin{center}
        \vspace{-5mm}
        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus.jpg}\\
        \vspace{-0.6mm}
        \tiny \href{http://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/L07/index.html}{http://slittlefair.staff.shef.ac.uk}
      \end{center}

      \column{0.5\linewidth}
    \end{columns}
  \end{frame}
  \begin{frame}[t]{Definitions \& Clarification \hspace{1.6cm} {\normalsize(from the National Academies report in 2019, \href{http://doi.org/10.17226/25303}{DOI:10.17226/25303})}}
    \vspace{-5mm}
    \begin{columns}[t]
      \column{0.5\linewidth}
      \begin{center}
        \large\textbf{Replicability (hardware/statistical)}
        \rule{0.5\linewidth}{1pt}
      \end{center}
      \begin{itemize}
        \setlength\itemsep{0.5em}
      \item Involves data \alert{collection}.
      \item Inherently includes \alert{measurements errors}\\(can
        never be exactly reproduced).
      \item Example: Raw telescope image/spectra.
      \item \alert{\textbf{NOT DISCUSSED HERE.}}
      \end{itemize}

      \vspace{3.5mm}
      \begin{center}
        \vspace{-5mm}
        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus-marked.jpg}\\
        \vspace{-0.6mm}
        \tiny \href{https://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/l07}{http://slittlefair.staff.shef.ac.uk}
      \end{center}

      \column{0.5\linewidth}
    \end{columns}
  \end{frame}
  \begin{frame}[t]{Definitions \& Clarification \hspace{1.6cm} {\normalsize(from the National Academies report in 2019, \href{http://doi.org/10.17226/25303}{DOI:10.17226/25303})}}
    \vspace{-5mm}
    \begin{columns}[t]
      \column{0.5\linewidth}
      \begin{center}
        \large\textbf{Replicability (hardware/statistical)}
        \rule{0.5\linewidth}{1pt}
      \end{center}
      \begin{itemize}
        \setlength\itemsep{0.5em}
      \item Involves data \alert{collection}.
      \item Inherently includes \alert{measurements errors}\\(can
        never be exactly reproduced).
      \item Example: Raw telescope image/spectra.
      \item \alert{\textbf{NOT DISCUSSED HERE.}}
      \end{itemize}

      \vspace{3.5mm}
      \begin{center}
        \vspace{-5mm}
        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus.jpg}\\
        \vspace{-0.6mm}
        \tiny \href{https://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/l07}{http://slittlefair.staff.shef.ac.uk}
      \end{center}

      \column{0.5\linewidth}
      \begin{center}
        \large\textbf{Reproducibility (Software/Deterministic)}
        \rule{0.5\linewidth}{1pt}
      \end{center}
      \begin{itemize}
        \setlength\itemsep{1em}
      \item Involves data \alert{analysis}, or simulations.
      \item Starts \alert{after} data is collected/digitized.
      \item Example: $2+2=4$ (i.e., sum of datasets).
      \item \textbf{\textcolor{green!50!black}{DISCUSSED HERE.}}
      \end{itemize}

      \centering
      \vspace{3mm}
      \includegraphics[width=0.88\linewidth]{img/binary-blue.jpg}\\
      \vspace{-0.6mm}
      \tiny \href{https://commons.wikimedia.org/wiki/File:Binary_blue.jpg}{Wikimedia Commons}
    \end{columns}
  \end{frame}






  %% Step-by-step slides.
  \newcommand{\allopacity}{1}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\paperinit}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\sver}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \begin{frame}[t]{Different package managers have different versions of software (repology.org, 2021/12/02)}
    \begin{columns}
      \column{7cm} \center
      Astropy\\
      \includegraphics[width=2.8cm]{img/distros-astropy.pdf}
      \column{7cm} \center
      GNU Astronomy Utilities (Gnuastro)\\
      \includegraphics[trim={0 8cm 0 0}, clip, width=2.9cm]{img/distros-gnuastro.pdf}
      \includegraphics[trim={0 0 0 16cm}, clip, width=2.9cm]{img/distros-gnuastro.pdf}
    \end{columns}
  \end{frame}
  \newcommand{\srep}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\dver}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\ddver}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\confopt}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\confenv}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \begin{frame}{Example: Matplotlib (a Python visualization library) build dependencies}
    \Wider[5em]{
      %\vspace{5mm}
      \begin{center}
        \includegraphics[width=0.9\linewidth]{img/matplotlib.png}
      \end{center}

      \vspace{3mm}\tiny From ``Attributing and Referencing (Research)
      Software: Best Practices and Outlook from Inria'' (Alliez et
      al. 2020, CiSE, DOI:\textcolor{blue}{\href{https://doi.org/10.1109/MCSE.2019.2949413}{10.1109/MCSE.2019.2949413}}).
    }
  \end{frame}
  \begin{frame}{Impact of ``Dependency hell'' on native building in various hardware (CPU architectures), retrieved from Debian on 2021/12/02}
    \begin{columns}
      \column{7cm}
      \includegraphics[width=\linewidth]{img/cpu-arch-astropy.png}
      Astropy depends on Matplotlib
      \column{6cm}
      \includegraphics[width=1.05\linewidth]{img/cpu-arch-gnuastro.png}
      GNU Astronomy Utilities doesn't.
    \end{columns}
  \end{frame}
  \newcommand{\containers}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\db}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\calib}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\corr}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\runord}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\runopt}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\humanerr}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\confirmbias}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\depupdate}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\coauth}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\varsinpaper}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\recordinfo}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\softcite}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \begin{frame}
    \begin{tcolorbox}[title={Di Cosmo \& Pellegrini (2019) \small Encouraging a wider usage of software derived from research}]
      \centering ``\textbf{Software is a hybrid} object in the world research as it is equally a driving force (as a \alert{tool}), a \alert{result} (as proof of the existence of a solution) and an \alert{object of study} (as an artefact)''.
    \end{tcolorbox}
  \end{frame}
  \newcommand{\prevchange}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \newcommand{\paperfinal}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}


  %% Don't show the happy scientist or the existing containers box.
  \let\paperinit\undefined
  \let\allopacity\undefined
  \let\paperfinal\undefined
  \let\containers\undefined





  \begin{frame}{Science is a tricky business}

    \begin{tcolorbox}[boxsep=0pt,left=1mm,right=1mm,top=1mm,bottom=1mm]
      \large Data analysis [...] is a \alert{human
        behavior}. Researchers who hunt hard enough will turn up a
      result that fits statistical criteria, but their
      \alert{discovery} will probably be a \alert{false positive}.

      \vspace{3mm}
      \small
      \hfill Five ways to fix statistics (Nature, 551, Nov 2017; DOI:\textcolor{blue}{\href{https://doi.org/10.1038/d41586-017-07522-z}{10.1038/d41586-017-07522-z}}).
    \end{tcolorbox}
  \end{frame}





  \begin{frame}
    \begin{tcolorbox}[title={Buckheit \& Donoho (1996) \small Lecture Notes in Statistics (vol 103, DOI:\textcolor{blue!10!white}{\href{https://doi.org/10.1007/978-1-4612-2544-7\_5}{10.1007/978-1-4612-2544-7\_5}})}]
      \centering ``An \alert{article} about computational science [\emph{today: almost all sciences}] ... is not the scholarship itself, it is merely \textbf{ADVERTISING} of the \textbf{SCHOLARSHIP}.

      \vspace{5mm}
      \pause
      The \textbf{ACTUAL SCHOLARSHIP} is the \alert{complete software development environment} and the \alert{complete set of instructions} which generated the figures.''
    \end{tcolorbox}
  \end{frame}





  \begin{frame}{Principles behind proposed solution}
    \begin{tcolorbox}[title=Basic/simple principle:]
      \centering Science is defined by its METHOD, \alert{not} its
      result.
    \end{tcolorbox}

    \pause
    \begin{itemize}
    \item \textbf{Complete/self-contained:}
      \begin{itemize}
      \item \alert{Only dependency} should be \alert{POSIX} tools \textcolor{gray}{(discards Conda or Jupyter which need Python)}.
        \pause
      \item Must \alert{not require root} permissions \textcolor{gray}{(discards tools like Docker or Nix/Guix)}.
        \pause
      \item Should be \alert{non-interactive} or runnable in batch (user interaction is an incompleteness).
        \pause
      \item Should be usable \alert{without internet} connection.
      \end{itemize}

      \pause
    \item \textbf{Modularity:} Parts of the project should be \alert{re-usable} in other projects.
      \pause
    \item \textbf{Plain text:} Project's source should be in \alert{plain-text} \textcolor{gray}{(binary formats need special software)}
      \begin{itemize}
      \item This includes high-level analysis.
      \item It is easily publishable (very low volume of $\times100$KB), archivable, and parse-able.
      \item \alert{Version control} (e.g., with Git) can track project's history.
      \end{itemize}
      \pause
    \item \textbf{Minimal complexity:} Occum’s rasor: “Never posit pluralities without necessity”.
      \begin{itemize}
      \item Avoiding the \alert{fashionable} tool of the day: tomorrow another tool will take its place!
      \item Easier \alert{learning curve}, also doesn't create a \alert{generational gap}.
      \item Is \alert{compatible} and \alert{extensible}.
      \end{itemize}
      \pause
    \item \textbf{Verifable inputs and outputs:} Inputs and Outputs must be \alert{automatically verified}.
      \pause
    \item \textbf{Free and open source software:} \alert{Free software} is essential: non-free software is not configurable, not distributable, and dependent on non-free provider (which may discontinue it in N years).
    \end{itemize}
  \end{frame}





  \newcommand{\focusonpackages}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \let\focusonpackages\undefined





  \begin{frame}{Predefined/exact software tools}
    \small
    \begin{columns}
      \column{10cm}
      \begin{tcolorbox}[width=\linewidth, boxsep=1pt, left=1pt, right=1pt,
                        top=1pt, bottom=1pt, title=Reproducibility \&
                        software]
        \footnotesize Reproducing the environment (specific
        \alert{software versions}, \alert{build instructions} and
        \alert{dependencies}) is also critically important for
        reproducibility.
      \end{tcolorbox}

      \vspace{2cm}

      \begin{itemize}
        \setlength\itemsep{0.6cm}
      \item \emph{Containers} or \emph{Virtual Machines} are a
        \alert{binary black box}.

      \item Maneage \alert{installs fixed versions} of all
        necessary research software and their dependencies.

      \item Installs similar environment on \alert{GNU/Linux}, or
        \alert{macOS} systems.

      \item Works very much like a package manager (e.g.,
        \alert{\texttt{apt}} or \alert{\texttt{brew}}).
      \end{itemize}

      \column{5cm}
      \includegraphics[width=\linewidth]{img/version.png}
    \end{columns}
  \end{frame}





  \begin{frame}{Predefined/exact software tools}
    \small
    \begin{columns}
      \column{10cm}
      \begin{tcolorbox}[width=\linewidth, boxsep=1pt, left=1pt, right=1pt,
                        top=1pt, bottom=1pt, title=Reproducibility \&
                        software]
        \footnotesize Reproducing the environment (specific
        \alert{software versions}, \alert{build instructions} and
        \alert{dependencies}) is also critically important for
        reproducibility.
      \end{tcolorbox}

      \vspace{2cm}

      \begin{itemize}
        \setlength\itemsep{0.6cm}
      \item \emph{Containers} or \emph{Virtual Machines} are a
        \alert{binary black box}.

      \item Maneage \alert{installs fixed versions} of all
        necessary research software and their dependencies.

      \item Installs similar environment on \alert{GNU/Linux}, or
        \alert{macOS} systems.

      \item Works very much like a package manager (e.g.,
        \alert{\texttt{apt}} or \alert{\texttt{brew}}).
      \end{itemize}

      \column{5cm}
      \includegraphics[width=\linewidth]{img/version-highlighted.png}
    \end{columns}
  \end{frame}





  \begin{frame}{Controlled environment and build instructions}
    \small
    \begin{columns}
      \column{5.5cm}
      \includegraphics[width=0.9\linewidth]{img/env.png}
      \column{5.5cm}
      \includegraphics[width=0.9\linewidth]{img/build.png}
    \end{columns}
  \end{frame}

  \begin{frame}{Controlled environment and build instructions}
    \small
    \begin{columns}
      \column{5.5cm}
      \includegraphics[width=0.9\linewidth]{img/env-highlighted.png}
      \column{5.5cm}
      \includegraphics[width=0.9\linewidth]{img/build-highlighted.png}
    \end{columns}
  \end{frame}





  \begin{frame}{Example: Matplotlib (a Python visualization library) build dependencies}
    \Wider[5em]{
      %\vspace{5mm}
      \begin{center}
        \includegraphics[width=0.9\linewidth]{img/matplotlib.png}
      \end{center}

      \vspace{3mm}\tiny From ``Attributing and Referencing (Research)
      Software: Best Practices and Outlook from Inria'' (Alliez et
      al. 2019,
      \textcolor{blue}{\href{https://hal.archives-ouvertes.fr/hal-02135891}{hal-02135891}})
    }
  \end{frame}





  \newcommand{\prjdir}{\textcolor{gray}{/PROJECT}}
  \newcommand{\lcolor}[1]{\textcolor{green!80!black}{#1}}
  \begin{frame}{All high-level dependencies are under control (e.g., NoiseChisel's dependencies)}
    \scriptsize
    \begin{columns}
      \column{8cm}
      \begin{center} {\large \textbf{GNU/Linux distribution}} \end{center}

        \texttt{\$ ldd .local/bin/astnoisechisel}\\
        \hspace{0.5cm}\texttt{\lcolor{libgnuastro.so.7} => \textcolor{gray}{\prjdir}/libgnuastro.so.7 (0x00007f6745f39000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libgit2.so.26} => \prjdir/libgit2.so.26 (0x00007f6745df1000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libtiff.so.5} => \prjdir/libtiff.so.5 (0x00007f6745d77000)}\\
        \hspace{0.5cm}\texttt{\lcolor{liblzma.so.5} => \prjdir/liblzma.so.5 (0x00007f6745d4f000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libjpeg.so.9} => \prjdir/libjpeg.so.9 (0x00007f6745d12000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libwcs.so.6} => \prjdir/libwcs.so.6 (0x00007f6745ba8000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libcfitsio.so.8} => \prjdir/libcfitsio.so.8 (0x00007f674588b000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libcurl.so.4} => \prjdir/libcurl.so.4 (0x00007f6745811000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libssl.so.1.1} => \prjdir/libssl.so.1.1 (0x00007f6745777000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libcrypto.so.1.1} => \prjdir/libcrypto.so.1.1 (0x00007f6745491000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libz.so.1} => \prjdir/libz.so.1 (0x00007f6745474000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libgsl.so.23} => \prjdir/libgsl.so.23 (0x00007f67451e3000)}\\
        \hspace{0.5cm}\texttt{\lcolor{libgslcblas.so.0} => \prjdir/libgslcblas.so.0 (0x00007f67451a1000)}\\
        \hspace{0.5cm}\texttt{\lcolor{linux-vdso.so.1} (0x00007fffdcbf7000)}\\
        \hspace{0.5cm}\texttt{\textcolor{blue}{libpthread.so.0} => /usr/lib/libpthread.so.0 (0x00007f6745006000)}\\
        \hspace{0.5cm}\texttt{\textcolor{blue}{libm.so.6} => /usr/lib/libm.so.6 (0x00007f6745027000)}\\
        \hspace{0.5cm}\texttt{\textcolor{blue}{libc.so.6} => /usr/lib/libc.so.6 (0x00007f6744e43000)}\\
        \hspace{0.5cm}\texttt{\textcolor{blue}{libdl.so.2} => /usr/lib/libdl.so.2 (0x00007f6744e1e000)}\\
        \hspace{0.5cm}\texttt{\textcolor{blue}{/lib64/ld-linux-x86-64.so.2} => /usr/lib64/ld-linux-x86-64.so.2}

      \column{7.5cm}
        \begin{center} {\large \textbf{macOS}} \end{center}

        \texttt{\$ otool -L .local/bin/astnoisechisel}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libgnuastro.7.dylib} (comp ver 8.0.0, cur ver 8.0.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libgit2.26.dylib} (comp ver 26.0.0, cur ver 0.26.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libtiff.5.dylib} (comp ver 10.0.0, cur ver 10.0.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{liblzma.5.dylib} (comp ver 8.0.0, cur ver 8.4.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libjpeg.9.dylib} (comp ver 12.0.0, cur ver 12.0.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libwcs.6.2.dylib} (comp ver 6.0.0, cur ver 6.2.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libcfitsio.8.dylib} (comp ver 8.0.0, cur ver 8.3.47)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libcurl.4.dylib} (comp ver 10.0.0, cur ver 10.0.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libssl.1.1.dylib} (comp ver 1.1.0, cur ver 1.1.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libcrypto.1.1.dylib} (comp ver 1.1.0, cur ver 1.1.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libz.1.dylib} (comp ver 1.0.0, cur ver 1.2.11)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libgsl.23.dylib} (comp ver 25.0.0, cur ver 25.0.0)}\\
        \hspace{0.5cm}\texttt{\prjdir/\lcolor{libgslcblas.0.dylib} (comp ver 1.0.0, cur ver 1.0.0)}\\
        \hspace{0.5cm}\alert{/usr/lib/libSystem.B.dylib} (comp ver 1.0.0, cur ver 1252.50.4)

        \vspace{1.1cm}
    \end{columns}

    \vspace{2mm}
    \begin{tcolorbox}[boxsep=0pt,left=1mm,right=1mm,top=1mm,bottom=1mm]
      \small

      \lcolor{Project libraries:} High-level libraries built from
      source for each project (note the same version in both OSs).

      \textcolor{blue}{GNU C Library:} Project specific build is in progress (\url{http://savannah.nongnu.org/task/?15390}).

      \alert{Closed operating system files}: We have no control on low-level non-free operating systems components.
    \end{tcolorbox}
  \end{frame}





  \begin{frame}{Advantages of this build system}
    \begin{columns}
      \column{11cm}
      \begin{itemize}
        \setlength\itemsep{0.7cm}
      \item Project runs in fixed/controlled environment: custom build
        of \alert{Bash}, \alert{Make}, GNU Coreutils
        (\alert{\texttt{ls}}, \alert{\texttt{cp}},
        \alert{\texttt{mkdir}} and etc), \alert{AWK}, or \alert{SED},
        \alert{\LaTeX}, etc.
      \item No need for \alert{root}/administrator \alert{permissions}
        (on servers or super computers).
      \item Whole system is built \alert{automatically} on any
        Unix-like operating system \\(less 2 hours).
      \item Dependencies of different projects will \alert{not conflict}.
      \item Everything in \alert{plain text} (human \& computer
        readable/archivable).
      \end{itemize}
      \column{4cm}
      \includegraphics[width=\linewidth]{img/unchained.jpg}\\
      \tiny \url{https://natemowry2.wordpress.com}
    \end{columns}
  \end{frame}



  \begin{frame}{Software citation automatically generated in paper (including Astropy)}
    \centering
    \includegraphics[width=0.8\linewidth]{img/software-cite.jpg}
  \end{frame}
  \begin{frame}{Software citation automatically generated in paper (including Astropy)}
    \centering
    \includegraphics[width=0.8\linewidth]{img/software-cite-highlighted.jpg}
  \end{frame}




  \begin{frame}{Software citation automatically generated in paper (only GNU Astronomy Utilities)}
    \centering
    \includegraphics[width=0.4\linewidth]{img/software-cite-no-py.jpg}
  \end{frame}
  \begin{frame}{Software citation automatically generated in paper (only GNU Astronomy Utilities)}
    \centering
    \includegraphics[width=0.4\linewidth]{img/software-cite-no-py-highlighted.jpg}
  \end{frame}










  %% Hardware/data
  \newcommand{\focusonhardware}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \let\focusonhardware\undefined

  \begin{frame}{Input data source and integrity is documented and checked}
    \small
    \begin{columns}
      \column{10cm}
      Stored information about each input file:
      \begin{itemize}
      \item \alert{PID} (where available).
      \item Download \alert{URL}.
      \item \alert{MD5}-sum to check integrity.
      \end{itemize}

      \vspace{0.75cm} All inputs are \alert{downloaded} from the given
      PID/URL when necessary\\(during the analysis).

      \vspace{0.75cm} MD5-sums are \alert{checked} to make sure the
      download was done properly or the file is the same (hasn't
      changed on the server/source).

      \vspace{0.75cm}Example from the reproducible paper \textcolor{blue}{\href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230}}.\\
      This paper needs three input files (two images, one catalog).

      \column{5cm}
      \includegraphics[width=\linewidth]{img/inputs.png}
    \end{columns}
  \end{frame}

  \begin{frame}{Input data source and integrity is documented and checked}
    \small
    \begin{columns}
      \column{10cm}
      Stored information about each input file:
      \begin{itemize}
      \item \alert{PID} (where available).
      \item Download \alert{URL}.
      \item \alert{MD5}-sum to check integrity.
      \end{itemize}

      \vspace{0.75cm} All inputs are \alert{downloaded} from the given
      PID/URL when necessary\\(during the analysis).

      \vspace{0.75cm} MD5-sums are \alert{checked} to make sure the
      download was done properly or the file is the same (hasn't
      changed on the server/source).

      \vspace{0.75cm}Example from the reproducible paper \textcolor{blue}{\href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230}}.\\
      This paper needs three input files (two images, one catalog).

      \column{5cm}
      \includegraphics[width=\linewidth]{img/inputs-highlighted.png}
    \end{columns}
  \end{frame}











  %% Analysis
  \newcommand{\focusonrun}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \let\focusonrun\undefined





  \begin{frame}{Reproducible science: Maneage is managed through a Makefile}
    \small
    \begin{columns}
      \column{10cm}

      All steps (downloading and analysis) are managed by Makefiles\\
      (example from
      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}):

      \vspace{5mm}
      \begin{itemize}
        \setlength\itemsep{0.7cm}
      \item Unlike a script which always starts from the top, a
        Makefile \alert{starts from the end} and steps that don't
        change will be left untouched (not remade).
      \item A single \emph{rule} can \alert{manage any number of
        files}.
      \item Make can identify independent steps internally and do them
        in \alert{parallel}.
      \item Make was \alert{designed for complex projects} with
        thousands of files (all major Unix-like components), so it is
        highly evolved and efficient.
      \item Make is a very \alert{simple} and \alert{small} language,
        thus easy to learn with great and free documentation (for
        example
        \textcolor{blue}{\href{https://www.gnu.org/software/make/manual/}{GNU
            Make's manual}}).
      \end{itemize}

      \column{5cm}
      \includegraphics[width=\linewidth]{img/reproducible-makefile.png}
    \end{columns}
  \end{frame}
  \begin{frame}{Reproducible science: Maneage is managed through a Makefile}
    \small
    \begin{columns}
      \column{10cm}

      All steps (downloading and analysis) are managed by Makefiles\\
      (example from
      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}):

      \vspace{5mm}
      \begin{itemize}
        \setlength\itemsep{0.7cm}
      \item Unlike a script which always starts from the top, a
        Makefile \alert{starts from the end} and steps that don't
        change will be left untouched (not remade).
      \item A single \emph{rule} can \alert{manage any number of
        files}.
      \item Make can identify independent steps internally and do them
        in \alert{parallel}.
      \item Make was \alert{designed for complex projects} with
        thousands of files (all major Unix-like components), so it is
        highly evolved and efficient.
      \item Make is a very \alert{simple} and \alert{small} language,
        thus easy to learn with great and free documentation (for
        example
        \textcolor{blue}{\href{https://www.gnu.org/software/make/manual/}{GNU
            Make's manual}}).
      \end{itemize}

      \column{5cm}
      \includegraphics[width=\linewidth]{img/reproducible-makefile-highlighted-1.png}
    \end{columns}
  \end{frame}
  \begin{frame}{Reproducible science: Maneage is managed through a Makefile}
    \small
    \begin{columns}
      \column{10cm}

      All steps (downloading and analysis) are managed by Makefiles\\
      (example from
      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}):

      \vspace{5mm}
      \begin{itemize}
        \setlength\itemsep{0.7cm}
      \item Unlike a script which always starts from the top, a
        Makefile \alert{starts from the end} and steps that don't
        change will be left untouched (not remade).
      \item A single \emph{rule} can \alert{manage any number of
        files}.
      \item Make can identify independent steps internally and do them
        in \alert{parallel}.
      \item Make was \alert{designed for complex projects} with
        thousands of files (all major Unix-like components), so it is
        highly evolved and efficient.
      \item Make is a very \alert{simple} and \alert{small} language,
        thus easy to learn with great and free documentation (for
        example
        \textcolor{blue}{\href{https://www.gnu.org/software/make/manual/}{GNU
            Make's manual}}).
      \end{itemize}

      \column{5cm}
      \includegraphics[width=\linewidth]{img/reproducible-makefile-highlighted-2.png}
    \end{columns}
  \end{frame}

























  \newcommand{\focusonpaper}{}
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \let\focusonpaper\undefined


  \begin{frame}{Values in final report/paper}
    All analysis \alert{results} (numbers, plots, tables) written in
    paper's PDF as \alert{\LaTeX{} macros}. They are thus
    \alert{updated automatically} on any change.\\ Shown here is a
    portion of the \textsf{NoiseChisel} paper and its \LaTeX{} source
    (\textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}).

    \vspace{0.4cm}
    \includegraphics[width=\linewidth]{img/reproducible-latex.png}
  \end{frame}

  \begin{frame}{Values in final report/paper}
    All analysis \alert{results} (numbers, plots, tables) written in
    paper's PDF as \alert{\LaTeX{} macros}. They are thus
    \alert{updated automatically} on any change.\\ Shown here is a
    portion of the \textsf{NoiseChisel} paper and its \LaTeX{} source
    (\textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}).

    \vspace{0.4cm}
    \includegraphics[width=\linewidth]{img/reproducible-latex-highlighted.png}
  \end{frame}





  \begin{frame}{Analysis step results/values concatenated into a single file.}
    All \LaTeX{} macros come from a \alert{single file}.
    \begin{center}
      \includegraphics[width=0.6\linewidth]{img/reproducible-macros.png}
    \end{center}
  \end{frame}
  \begin{frame}{Analysis step results/values concatenated into a single file.}
    All \LaTeX{} macros come from a \alert{single file}.
    \begin{center}
      \includegraphics[width=0.6\linewidth]{img/reproducible-macros-highlighted.png}
    \end{center}
  \end{frame}







  \begin{frame}{Analysis results stored as \LaTeX{} macros}
    The analysis scripts write/update the \LaTeX{} macro values
    automatically.
    \begin{center}
      \includegraphics[width=0.6\linewidth]{img/reproducible-write-macro.png}
    \end{center}
  \end{frame}
  \begin{frame}{Analysis results stored as \LaTeX{} macros}
    The analysis scripts write/update the \LaTeX{} macro values
    automatically.
    \begin{center}
      \includegraphics[width=0.6\linewidth]{img/reproducible-write-macro-highlight.png}
    \end{center}
  \end{frame}


  %% Make demo.
  \begin{frame}{Let's look at the data lineage to replicate Figure 1C (green/tool) of Menke+2020 \\(DOI:\href{https://doi.org/10.1101/2020.01.15.908111}{10.1101/2020.01.15.908111})}
    \begin{columns}
      \column{0.55\linewidth}
      \textcolor{blue}{ORIGINAL PLOT}

      The Green plot shows the fraction of papers mentioning software tools from 1997 to 2019.
      \column{0.45\linewidth}
      \includegraphics[width=\linewidth]{img/tools-per-year-orig.jpg}
    \end{columns}

    \rule{\textwidth}{1pt}

    \begin{columns}
      \column{0.4\linewidth}
      \textcolor{green!70!black}{OUR enhanced REPLICATION}

      The green line is same as above but over their full historical range.

      Red histogram is the number of papers studied in each year
      \column{0.6\linewidth}
      \vspace{1cm}
      \includegraphics[width=\linewidth]{img/tools-per-year.pdf}
    \end{columns}
  \end{frame}
  \makedemoslide{img/data-lineage-1.pdf}
                {Makefiles (\texttt{\*.mk}) keep contextually separate parts of the project, all imported into \texttt{top-make.mk}}
  \makedemoslide{img/data-lineage-2.pdf}
                {The ultimate purpose of the project is to produce a paper/report (in PDF).}
  \makedemoslide{img/data-lineage-3.pdf}
                {The narrative description, typography and references are in \texttt{paper.tex} \& \texttt{references.tex}.}
  \makedemoslide{img/data-lineage-4.pdf}
                {Analysis outputs (blended into the PDF as \LaTeX{} macros) come from \texttt{project.tex}.}
  \makedemoslide{img/data-lineage-5.pdf}
                {But analysis outputs must first be \emph{verified} (with checksums) before entering the report/paper.}
  \makedemoslide{img/data-lineage-6.pdf}
                {Basic project info comes from \texttt{initialize.tex}.}
  \makedemoslide{img/data-lineage-7.pdf}
                {The paper includes some information about the plot.}
  \makedemoslide{img/data-lineage-8.pdf}
                {The final plotted data are calculated and stored in \texttt{tools-per-year.txt}.}
  \makedemoslide{img/data-lineage-9.pdf}
                {The plot's calculation is done on a formatted sub-set of the raw input data.}
  \makedemoslide{img/data-lineage-10.pdf}
                {The raw data that were downloaded are stored in XLSX format.}
  \makedemoslide{img/data-lineage-11.pdf}
                {The download URL \emph{and} a \alert{checksum to validate} the raw inputs, are stored in \texttt{INPUTS.conf}.}
  \makedemoslide{img/data-lineage-12.pdf}
                {We also need to report the URL in the paper...}
  \makedemoslide{img/data-lineage-13.pdf}
                {Some general info about the full dataset may also be reported.}
  \makedemoslide{img/data-lineage-14.pdf}
                {We report the number of papers studied in a special year, desired year is stored in \texttt{.conf} file.}

  \makedemoslide{img/data-lineage-15.pdf}
                {It is very easy to expand the project and add new analysis steps (this solution is scalable)}





  \begin{frame}{\LARGE The whole project is a directed graph (codifying the data's lineage).}
    \LARGE
    \begin{itemize}
      \setlength\itemsep{1cm}
    \item Every \alert{file} (source or built) is a \alert{node} in the graph (connected to others).\\
      {\large (The links/connections/dependencies between the nodes, defined by the Makefiles: \texttt{*.mk})}
    \item There are two types of nodes/files:
      \begin{itemize}
        \LARGE
        \setlength\itemsep{4mm}
      \item \alert{Source} nodes (\texttt{*.conf} and \texttt{paper.tex}) only have an \alert{outward} link.
      \item \alert{Built} files always have \alert{inward} \emph{and} {\normalsize (except \texttt{paper.pdf})} \alert{outward} link(s).
      \end{itemize}
    \item All built files ultimately originate from a \texttt{*.conf} file,\\
      ... and ultimately conclude in \texttt{paper.pdf}.
    \end{itemize}
  \end{frame}

  \begin{frame}{Benefits of using Make}
    \Large
    \begin{itemize}
      \setlength\itemsep{4mm}
    \item Make can \alert{parallelize} the analysis: \\Make knows
      which steps are indepenent and will run them at the same time.\\
    \item Make can \alert{automatically detect a change} and will
      re-do \emph{only} the affected steps.\\ {\normalsize (for
        example to change the multiple of sigma in a configuration
        file to see its effect)}
    \item Easily \alert{backtrace} any step (without needing to remember!).\\
      {\normalsize (very useful to find problems/improvements)}
    \item The above will speed up your work, and \alert{encourage experimentation} on methods.
    \item Make is \alert{available} on any system: many people are \alert{already familiar} with it.
    \item And again: its \alert{all in plain text}!\\{\normalsize (doesn't take much space, easy to read, distribute, parse automatically, or archive)}
    \item Recall that the project's \alert{software installation} was also managed in Make.
    \end{itemize}
  \end{frame}

  \begin{frame}{Files organized in directories by context (here are some of the files discussed before)}
    \centering
    \includegraphics[width=0.85\linewidth]{img/figure-file-architecture-1.pdf}
  \end{frame}

  \begin{frame}{Files organized in directories by context (now with other project files and symbolic links)}
    \centering
    \includegraphics[width=0.85\linewidth]{img/figure-file-architecture-2.pdf}
  \end{frame}



















  \newcommand{\allopacity}{1}
  \begin{frame}{All questions have an answer now (in
        \alert{plain text}: human \& computer readable/archivable).}
    \include{tex/project-graph} \end{frame}
  \newcommand{\gitlogo}{}
  \begin{frame}{All questions have an answer now (in
        \alert{plain text}: so we can use Git to keep its history).}
    \include{tex/project-graph}
  \end{frame}




  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\tomorrow}{1}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\abstractify}{1}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\projinit}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\projwork}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\tempevolve}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\mergewithtemp}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\tofuture}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\githappy}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}
  \newcommand{\gitverified}{}
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}

  \begin{frame}{Two recent examples (publishing Git checksum in abstract)}
    \begin{columns}
      \column{0.5\linewidth}
      \centering
      \includegraphics[width=0.8\linewidth]{img/firstpage-190911230.png}
      \column{0.5\linewidth}
      \centering
      \includegraphics[width=0.8\linewidth]{img/firstpage-mnras491.png}
    \end{columns}
  \end{frame}

  \begin{frame}{Two recent examples (publishing Git checksum in abstract)}
    \begin{columns}
      \column{0.5\linewidth}
      \centering
      \includegraphics[width=0.8\linewidth]{img/firstpage-190911230-highlighted.png}
      \column{0.5\linewidth}
      \centering
      \includegraphics[width=0.8\linewidth]{img/firstpage-mnras491-highlighted.png}
    \end{columns}
  \end{frame}



  \begin{frame}{Any Git-based workflow is possible.}
    \centering
    \includegraphics[width=1.2\linewidth]{img/figure-branching.pdf}
  \end{frame}




  \begin{frame}{Publication of the project}

    A reproducible project using Maneage will have the following
    (\alert{plain text}) components:
    \begin{itemize}
    \item Makefiles.
    \item \LaTeX{} source 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 project's source will thus be
    \alert{negligible} compared to a single figure in a paper
    (usually $\sim100$ kilo-bytes).

    \pause

    \vspace{7mm} The project's pipeline (customized Maneage) can be
    \alert{published} in
    \begin{itemize}
    \item \alert{arXiv}: uploaded with the \LaTeX{} source to always
      stay with the paper \\(for example
      \textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}} or \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}}).
    \item \alert{Zenodo}: Along with all the input datasets (many
      Gigabytes) and software \\(for example
      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.3872247}{zenodo.3872247}}) and given a unique DOI.
      \begin{itemize}
      \item ... and put links to data in paper! See ending of caption of Figure 1 in the \textcolor{blue}{\href{https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9403875}{Maneage paper}}.
      \end{itemize}
    \item \alert{Software Heritage}: to archive the full version-controlled history of the project.\\(for example
      {\small \textcolor{blue}{\href{https://archive.softwareheritage.org/swh:1:dir:33fea87068c1612daf011f161b97787b9a0df39f;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:89af43c4b076a17d9298299f224247038af355ea;anchor=swh:1:rev:313db0b04bd3499f83d9e79fd7e92578cd367c2b}{swh:1:dir:33fea87068c1612daf011f161b97787b9a0df39fk}}})
      \begin{itemize}
      \item ... and put links to exact parts of the code! See caption of Listing 1 in the \textcolor{blue}{\href{https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9403875}{Maneage paper}}.
      \end{itemize}
    \end{itemize}
  \end{frame}





  \begin{frame}{Software Heritage IDs (SWHID); persistent identifier for source code (or any text!)}

    \vspace{5mm}
    \includegraphics[width=\linewidth]{img/SWHIDs.png}
    \vspace{5mm}

    {\hfill\small For more details, see SoftwareHeritage FAQ (at \textcolor{blue}{\url{https://www.softwareheritage.org/faq}}})
  \end{frame}





  \begin{frame}{Project source and its execution}
    \begin{tcolorbox}
      Programs \textcolor{gray}{[here: Scientific projects]} must be
      written for \alert{people to read}...

      \hfill ...and only \emph{incidentally} for machines to
      \emph{execute}.

      \vspace{2mm}
      \hfill \footnotesize Harold Abelson, Structure and Interpretation of Computer Programs
    \end{tcolorbox}
  \end{frame}





  \begin{frame}[t]{General outline of using this system (for example \href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230})}
    \vspace{1cm}
    \texttt{\$ git clone http://gitlab.com/makhlaghi/iau-symposium-355{ }{ }{ }{ }\textcolor{gray}{\# Import the project.}}\\

    \pause
    \vspace{1.5cm}
    \texttt{\$ ./project configure { }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# You will specify the build directory on your system,}}\\
    \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# and it will build all software (about 1.5 hours).}}

    \pause
    \vspace{1.5cm}
    \texttt{\$ ./project make { }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# Does all the analysis and makes final PDF.}}\\
  \end{frame}






    \begin{frame}{Future prospects...}
    \large Adoption of reproducibility by many researchers will enable
    the following:

    \vspace{1em}
    \begin{itemize}
      \setlength\itemsep{3mm}
    \item A repository for education/training \textcolor{gray}{(PhD
      students, or researchers in other fields)}.
    \item Easy \alert{verification}/\alert{understanding} of other
      research projects \textcolor{gray}{(when necessary)}.
    \item Trivially \alert{test} different steps of others' work
      \textcolor{gray}{(different configurations, software and etc)}.
    \item Science can progress \alert{incrementally}
      \textcolor{gray}{(shorter papers actually building on each
        other!)}.
    \item \alert{Extract meta-data} after the publication of a dataset
      \textcolor{gray}{(for future ontologies or vocabularies)}.
    \item Applying \alert{machine learning} on reproducible research
      projects will allow us to solve some Big Data Challenges:

      \vspace{1em}
      \begin{itemize}
        \setlength\itemsep{2mm}
      \item \emph{Extract the relevant parameters automatically}.
      \item \emph{Translate the science to enormous samples}.
      \item \emph{Believe the results when no one will have time to
        reproduce}.
      \item \emph{Have confidence in results derived using machine
        learning or AI}.
      \end{itemize}
    \end{itemize}
  \end{frame}





  \begin{frame}{Summary:}

    Maneage is introduced as a customizable template that will do the
    following steps/instructions (all in simple plain text files).
    \begin{itemize}
      \item \alert{Automatically downloads} the necessary
        \emph{software} and \emph{data}.
      \item \alert{Builds} the software in a \alert{closed
        environment}.
      \item Runs the software on data to \alert{generate} the final
        \alert{research results}.
      \item Only parts affected by a modifcation are re-done.
      \item Using LaTeX macros, paper's figures, tables and numbers
        will be \alert{Automatically updated}.
      \item The whole project is under \alert{version control} (Git)
        \alert{encouraging tests/experimentation}.
      \item The \alert{Git commit hash} of the project source, is
        \alert{printed} in the paper and \alert{on output} data
        products.
      \item \colorbox{green!30!white}{These slides are available at
        \textcolor{blue}{\url{https://maneage.org/pdf/slides-intro.pdf}}.}
    \end{itemize}

    \begin{tcolorbox}[width=\linewidth, boxsep=1pt, left=1pt, right=1pt,
                      top=1pt, bottom=1pt]
      For a technical description of Maneage's implementation, as well
      as a checklist to customize it, and tips on good practices,
      please see this page:

      \textcolor{blue}{\url{https://gitlab.com/maneage/project/-/blob/maneage/README-hacking.md}}

      \vspace{3mm}
      \hfill \colorbox{green!30!white}{Feel free to contact me: \textcolor{blue}{\large{\url{mohammad@akhlaghi.org}}}}
    \end{tcolorbox}
  \end{frame}
\end{document}






\begin{frame}{Existing technologies (Independent environment)}
  \begin{itemize}
    \setlength\itemsep{7mm}
  \item \textbf{Virtual machines:}
    \begin{itemize}
      \setlength\itemsep{3mm}
    \item Contain the \alert{full operating system}, are thus very large ($\times$Gigabytes).
    \item In \emph{binary} format (decoding a built VM's environment is extremely hard and inaccurate).
    \end{itemize}
  \item \textbf{Containers:} (For example Docker or Singularity)
    \begin{itemize}
      \setlength\itemsep{3mm}
    \item Similar to virtual machines, but \alert{without low-level kernel} (use host's kernel).
    \item \alert{Will fail} as soon as kernel is no longer supported\\(for example Docker currently only supports Linux kernel 3.10 and above \alert{from 2013}).
    \item Good solutions for software engineers (that need to \emph{reproduce a bug's environment today}).
    \item Docker is modular, needs root previlages (not available in HPCs), Dockerfiles allow incompleteness\\(especially in the common scenario of using the operating system's package manager, see next slide)
    \item Singularity is monolithic and thus can be very large.
    \item In \alert{binary} format (similar to VMs, especially when OS package managers are used).
    \end{itemize}
  \end{itemize}

  \vspace{3mm}
In summary, they only \alert{store a built} environment (they are outputs, not good for archiving).

\end{frame}





%\begin{frame}{Existing technologies (Package managers)}
%
%  \begin{itemize}
%  \item \textbf{Operating system package managers:}
%    \begin{itemize}
%      \setlength\itemsep{2mm}
%    \item For example \texttt{apt} or \texttt{yum} for Debian-based and RedHat-based GNU/Linux operating systems\\(the most common way to install software).
%    \item Tightly intertwined with the operating system's components\\(arbitrary control of software versions is not easily possible).
%    \item Older software (for example +5 years) is usually removed.
%    \end{itemize}
%  \item \textbf{Conda/Anaconda:}
%    \begin{itemize}
%      \setlength\itemsep{2mm}
%    \item Conda has build instructions for software and their dependencies.
%    \item But it doesn't go down to the C library or the lower-level components of operating system.
%    \item It is written in Python (can't be used later when current Python is depreciated).
%    \item Authors of Uhse+2019\footnote{\url{http://dx.doi.org/10.1002/cppb.20097}} report\footnote{\url{https://github.com/conda-forge/conda-forge.github.io/issues/787}} that their Conda environment breaks roughly every 3 months\\(Conda environments need to be updated to be used later! Breaking reproducibility).
%    \end{itemize}
%  \item \textbf{Nix, or GNU Guix:}
%    \begin{itemize}
%      \setlength\itemsep{2mm}
%    \item Deliver perfectly reproducible builds (bit-wise reproducibility of software), needs root access.
%    \item Doesn't \emph{require} documentation of dependencies.
%    \end{itemize}
%  \item \textbf{Spack:} Similar to Nix/Guix but written in Python.
%  \end{itemize}
%\end{frame}
%
%\begin{frame}{Existing technologies (workflow tools)}
%  \begin{itemize}
%    \setlength\itemsep{4mm}
%  \item \textbf{Binder:} (\url{https://mybinder.org}) Docker+Conda.
%  \item \textbf{Galaxy:} (\url{https://galaxyproject.org}) A web-based user interface, primarily designed for genomics. The GUI make it hard to automate, and has too many dependencies. Very similar to GenePattern (2008 to 2017): with +40,000 users and $\sim4000$ jobs running per week, but cut due to funding.
%  \item \textbf{Sciunit:} (\url{https://sciunit.run}) Parses program binaries to try to infer their dependencies and copy them.
%  \item \textbf{Popper:} (\url{https://falsifiable.us}), HCL (previously used by GitHub Actions) + Conda + Docker.
%  \item \textbf{WholeTale:} (\url{https://wholetale.org}) Jupyter + Conda + Docker.
%  \item \textbf{Image Processing On Line (IPOL) journal:} The best example of publishing algorithms/methods I have seen, only useful for very basic/low-level software.
%  \end{itemize}
%  \alert{Summary}: except for IPOL, most solutions surveyed have far too many dependencies to be usable \alert{beyond the immediate future}.
\end{frame}



%  \begin{frame}{Funding to help adoption of template}
%    \begin{itemize}
%      \setlength\itemsep{5mm}
%    \item With the RDA grant, \alert{we have funding} to support the
%      travel and stay of several researchers from outside of
%      astronomy/astrophysics to the IAC \alert{for one week} to help
%      in adopting the template in their research.
%    \item Conditions:
%      \begin{itemize}
%        \setlength\itemsep{3mm}
%      \item The exact date will be set in coordination with the
%        selected researchers.
%      \item \alert{Early Career Researchers} (PhD students or Postdocs) will
%        be preferred.
%      \item Your project can be done with \alert{Free
%        Sofware} [1].\\ {\footnotesize (Note that non-free software are
%        by definition non-reproducible:\\ A random researcher can't
%        run and redistribute them as they wish, or study and modify
%        their source.)}
%      \item Your project can be run in \alert{Unix-like operating
%        systems}, ideally GNU/Linux distributions [2].\\(but other Unix-like OSs are also fine, for example BSD-based distributions, or macOS).
%      \end{itemize}
%    \item Please contact me by the end of November 2019 if you are
%      interested
%      (\textcolor{blue}{\href{mailto:mohammad@akhlaghi.org}{mohammad@akhlaghi.org}}).\\ {\footnotesize (If positions aren't filled by then, we will still accept letters of interest, and generally, we would be happy to help in adoption remotely. So if you are interested, please get in touch any way!)}
%    \end{itemize}
%
%    \vspace{3mm}
%    \footnotesize
%    1. \url{https://www.gnu.org/philosophy/free-sw.en.html}\\
%    2. For example: Mint, Debian, Ubuntu, OpenSUSE, Manjaro, Fedora, CentOS, Redhat, and many others.
%  \end{frame}