% LaTeX source of slides on reproducible paper.
%
% Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%
% This LaTeX source 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 LaTeX source 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 LaTeX source.  If not, see <https://www.gnu.org/licenses/>.

% Basic LaTeX settings.
\documentclass[9pt,usenames,dvipsnames,aspectratio=169]{beamer}

% Make it super short.
%\newcommand{\longformat}{}

% Read the current Git commit information
\include{git-commit}
\include{tex/preamble}

%% Beamer settings.
%\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{Introducing Maneage:\\
  Customizable framework for managing data lineage\\
  \vspace{2mm}{\small [RDA Europe Adoption grant recipient. Submitted to \href{https://www.computer.org/csdl/magazine/cs}{IEEE CiSE} (\textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}}), Comments welcome]}
}

%% Set the author
\author{\vspace{8mm}\\
  \href{https://akhlaghi.org}{Mohammad Akhlaghi}\\\vspace{0.5mm}
  \footnotesize
  Instituto de Astrof\'isica de Canarias ({\scriptsize IAC}), Tenerife, Spain
}

%% Set the date and insitutional logos.
\date{\footnotesize\vspace{0cm}\\
  \href{https://www.rd-alliance.org/rda-global-adoption-week-15-19-june-2020}{RDA Global Adoption week}\\June 18th, 2020\\
  \tiny\vspace{3mm}
  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-short.pdf}}\\
  \vspace{2mm}\hspace{-0.25cm}
  \raisebox{+0.4\height}{\includegraphics[width=2.5cm]{img/ministerio-ciencia.png}}
  \raisebox{+0.3\height}{\includegraphics[width=1.3cm]{img/sundial.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{+1.3\height}{\includegraphics[width=1.4cm]{img/ull.png}}
  { }\raisebox{+0.5\height}{\includegraphics[width=2cm]{img/gobierno-canarias.png}}\\
  \vspace{1cm}
}




















\begin{document}

  \begin{frame}
    \titlepage
  \end{frame}
  \usebackgroundtemplate{ }    %% undeclare it


  \begin{frame}{Challenges of the RDA-WDS Publishing Data Workflows WG {\small (DOI:\href{https://doi.org/10.1007/s00799-016-0178-2}{10.1007/s00799-016-0178-2})}}
    Challenges (also relevant to researchers, not just repositories)
    \begin{itemize}
    \item \emph{Bi-directional linking}: how to \alert{link data and publications}.
    \item \emph{\alert{Software management}:} how to manage, preserve, publish and cite software?
    \item \emph{Metrics:} \alert{how often} are data used.
    \item \emph{Incentives to researchers:} how to \alert{communicate benefits} of following good practices \alert{to researchers}.
    \end{itemize}

    \begin{center}
      \includegraphics[width=4cm]{img/rda.png}\hspace{1cm}
      \includegraphics[width=4cm]{img/wds.jpg}
    \end{center}

    \ifdefined\longformat\pause\fi

    ``\emph{We would like to see a workflow that results in all
      \textcolor{blue!30!green}{\bf scholarly objects being connected},
      linked, citable, and persistent to allow researchers to navigate
      smoothly and to \alert{\bf enable reproducible research}.  This
      includes \alert{{\bf linkages} between documentation, code, data, and
        journal articles in an integrated environment}. Furthermore,
      in the ideal workflow, all of these objects need to be
      \alert{\bf well documented} to enable other researchers (or
      citizen scientists etc) to reuse the data for new
      discoveries.}''
  \end{frame}

  \newcommand{\allopacity}{1}
  \ifdefined\longformat
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \fi
  \newcommand{\paperinit}{}
  \ifdefined\longformat
  \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
  \fi
  \newcommand{\sver}{}
  \newcommand{\srep}{}
  \newcommand{\dver}{}
  \newcommand{\ddver}{}
  \newcommand{\confopt}{}
  \newcommand{\confenv}{}
  \newcommand{\containers}{}
  \newcommand{\db}{}
  \newcommand{\calib}{}
  \newcommand{\corr}{}
  \newcommand{\runord}{}
  \newcommand{\runopt}{}
  \newcommand{\humanerr}{}
  \newcommand{\confirmbias}{}
  \newcommand{\depupdate}{}
  \newcommand{\coauth}{}
  \newcommand{\varsinpaper}{}
  \newcommand{\recordinfo}{}
  \newcommand{\softcite}{}
  \newcommand{\prevchange}{}
  \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{center}
      \includegraphics[width=0.9\linewidth]{img/nature-cartoon.jpg}
    \end{center}

    \vspace{-0.3cm}\hfill
    {\tiny Image from nature.com
      (``\href{https://www.nature.com/articles/d41586-017-07522-z}{Five
        ways to fix statistics}'', Nov 2017)}\hspace{7mm}

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

      \hfill Five ways to fix statistics, Nature, 551, Nov 2017.
    \end{tcolorbox}
  \end{frame}





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

    \ifdefined\longformat\pause\fi
    \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)}.
      \item Must \alert{not require root} permissions \textcolor{gray}{(discards tools like Docker or Nix/Guix)}.
      \item Should be \alert{non-interactive} or runnable in batch (user interaction is an incompleteness).
      \item Should be usable \alert{without internet} connection.
      \end{itemize}

    \ifdefined\longformat\pause\fi
    \item \textbf{Modularity:} Parts of the project should be \alert{re-usable} in other projects.
    \ifdefined\longformat\pause\fi
    \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}
    \ifdefined\longformat\pause\fi
    \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}
    \ifdefined\longformat\pause\fi
    \item \textbf{Verifable inputs and outputs:} Inputs and Outputs must be \alert{automatically verified}.
    \ifdefined\longformat\pause\fi
    \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




  \ifdefined\longformat
  \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}
  \fi




  \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}{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}{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}




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

  \ifdefined\longformat
  \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}
  \fi

  \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




  \ifdefined\longformat
  \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}
  \fi
  \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

  \ifdefined\longformat
  \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}
  \fi

  \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}




  \ifdefined\longformat
  \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}
  \fi
  \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}






  \ifdefined\longformat
  \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}
  \fi
  \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}), as done in \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}} for a demo.}
    \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}


  \ifdefined\longformat
  \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.}
  \fi

  \ifdefined\longformat
  \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.}
  \else
  \makedemoslide{img/data-lineage-14.pdf}
                {All analysis steps cascade down to paper.pdf (URL and checksum of input in \texttt{INPUTS.conf}).}
  \fi

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

























  \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}




  \ifdefined\longformat
  \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}{}
  \else
  \newcommand{\projinit}{}
  \newcommand{\projwork}{}
  \newcommand{\tempevolve}{}
  \newcommand{\mergewithtemp}{}
  \newcommand{\tofuture}{}
  \newcommand{\githappy}{}
  \newcommand{\gitverified}{}
  \fi
  \begin{frame}{New projects branch from Maneage} \include{tex/git-branch} \end{frame}

  \ifdefined\longformat
  \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}
  \fi

  \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}{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).

    \vspace{1cm} 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.3872248}{zenodo.3872248}}) and given a unique DOI.
    \end{itemize}
  \end{frame}





  \begin{frame}[t]{General outline of using Maneage (for example \href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018})}
    \vspace{1cm}
    \texttt{\$ git clone https://gitlab.com/makhlaghi/maneage-paper{ }{ }{ }{ }\textcolor{gray}{\# Import the project.}}\\

    \ifdefined\longformat\pause\fi
    \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).}}

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



  \ifdefined\longformat
    \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}
  \fi



    \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 and its principles are described in \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}}.
    It is 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 Modification of part of the analysis will only
        result in re-doing that part, not the whole project.
      \item Using LaTeX macros, paper's figures, tables and numbers
        will be \alert{Automatically updated} after a change in
        analysis. Allowing the scientist to focus on the scientific
        interpretation.
      \item The whole project is under \alert{version control} (Git)
        to allow easy reversion to a previous state. This
        \alert{encourages tests/experimentation} in the analysis.
      \item The \alert{Git commit hash} of the project source, is
        \alert{printed} in the published paper and \alert{saved on
          output} data products.  Ensuring the
        integrity/reproducibility of the result.
      \item \colorbox{green!30!white}{These slides are available at
        \textcolor{blue}{\url{https://maneage.org/pdf/slides-intro-short.pdf}}.}
      \item \colorbox{green!15!white}{Longer 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}{\footnotesize\url{https://gitlab.com/maneage/project/-/blob/maneage/README-hacking.md}}
    \end{tcolorbox}
  \end{frame}


\ifdefined\longformat
\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}
\fi
\end{document}