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@@ -72,12 +72,12 @@ %% CONTEXT Analysis pipelines commonly use high-level technologies that are popular when created, but are unlikely to be readable, executable, or sustainable in the long term. %% AIM - A set of criteria is introduced to address this problem. + A set of criteria is introduced to address this problem: %% METHOD Completeness (no \new{execution requirement} beyond \new{a minimal Unix-like operating system}, no administrator privileges, no network connection, and storage primarily in plain text); modular design; minimal complexity; scalability; verifiable inputs and outputs; version control; linking analysis with narrative; and free software. They have been tested in several research publications in various fields. %% RESULTS - As a proof of concept, ``Maneage'' is introduced for storing projects in machine-actionable and human-readable plain text, enabling cheap archiving, provenance extraction, and peer verification. + As a proof of concept, ``Maneage'' is introduced, enabling cheap archiving, provenance extraction, and peer verification. %% CONCLUSION We show that longevity is a realistic requirement that does not sacrifice immediate or short-term reproducibility. The caveats (with proposed solutions) are then discussed and we conclude with the benefits for the various stakeholders. @@ -85,15 +85,15 @@ \vspace{2.5mm} \emph{Appendices} --- - Two comprehensive appendices that review existing solutions; available + Two comprehensive appendices that review the longevity of existing solutions; available \ifdefined\separatesupplement -at \href{https://arxiv.org/abs/\projectarxivid}{\texttt{arXiv:\projectarxivid}} or \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}}. +as supplementary ``Web extras'' on the journal webpage. \else -at the end (Appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}). +after main body of paper (Appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}). \fi \vspace{2.5mm} - \emph{Reproducible supplement} --- + \emph{Reproducibility} --- All products in \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}}, Git history of source at \href{https://gitlab.com/makhlaghi/maneage-paper}{\texttt{gitlab.com/makhlaghi/maneage-paper}}, which is also archived in \href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/makhlaghi/maneage-paper.git}{SoftwareHeritage}. @@ -147,19 +147,13 @@ Longevity is defined as the length of time that a project remains \emph{function Functionality is defined as \emph{human readability} of the source and its \emph{execution possibility} (when necessary). Many usage contexts of a project do not involve execution: for example, checking the configuration parameter of a single step of the analysis to re-\emph{use} in another project, or checking the version of used software, or the source of the input data. Extracting these from execution outputs is not always possible.} - -Longevity is as important in science as in some fields of industry, but not all; e.g., fast-evolving tools can be appropriate in short-term commercial projects. -To highlight the necessity, a short review of commonly-used tools is provided below: -(1) environment isolators (virtual machines, VMs, or containers); -(2) package managers (PMs, like Conda, Nix, or Spack); -(3) job management (like shell scripts or Make); -(4) notebooks (like Jupyter). -\new{A comprehensive review of existing tools and solutions is available in the +A basic review of the longevity of commonly-used tools is provided here \new{(for a more comprehensive review, please see \ifdefined\separatesupplement - \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{appendices}.% + the supplementary appendices% \else% - appendices (\ref{appendix:existingsolutions}).% + appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}% \fi% + ). } To isolate the environment, VMs have sometimes been used, e.g., in \href{https://is.ieis.tue.nl/staff/pvgorp/share}{SHARE} (awarded second prize in the Elsevier Executable Paper Grand Challenge of 2011, but discontinued in 2019). @@ -692,6 +686,7 @@ The Pozna\'n Supercomputing and Networking Center (PSNC) computational grant 314 \input{tex/src/appendix-existing-tools.tex} \input{tex/src/appendix-existing-solutions.tex} \input{tex/src/appendix-used-software.tex} +%\input{tex/src/appendix-necessity.tex} \bibliographystyleappendix{IEEEtran_openaccess} \bibliographyappendix{IEEEabrv,references} \fi |