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@@ -44,7 +44,7 @@ Mohammadreza Khellat,\\ David Valls-Gabaud, Roberto Baena-Gall\'e\\ - \footnotesize{Manuscript received June 5th, 2020; accepted April 7th, 2021; published on IEEE April 13th, 2021} + \footnotesize{Manuscript received June 5th, 2020; accepted April 7th, 2021; first published online April 13th, 2021} } %% The paper headers @@ -93,9 +93,9 @@ after main body of paper (Appendices \ref{appendix:existingtools} and \ref{appen \vspace{2.5mm} \emph{Reproducibility} --- - All products in \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}}, - Git history of this paper's source at \href{http://git.maneage.org/paper-concept.git}{\texttt{git.maneage.org/paper-concept.git}}, - which is also archived in Software Heritage\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:33d24ae2107e25c734067d704cdad9d33013588a;anchor=swh:1:rev:b858c601613d620f5cf4501816e161a2f8f2e100}{swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717}}}. + All products in \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}} and + Git history of this paper at \href{http://git.maneage.org/paper-concept.git}{\texttt{git.maneage.org/paper-concept.git}}, + also archived in Software Heritage\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:33d24ae2107e25c734067d704cdad9d33013588a;anchor=swh:1:rev:b858c601613d620f5cf4501816e161a2f8f2e100}{swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717}}\\To resolve the raw Software Heritage identifiers (SWHIDs), prefix them with \inlinecode{http://n2t.org/} (e.g., \inlinecode{http://n2t.org/swh:1:...}), but clicking on the SWHIDs in the digital format of this paper will provide more ``context''.}. \end{abstract} % Note that keywords are not normally used for peer-review papers. @@ -155,13 +155,13 @@ A basic review of the longevity of commonly used tools is provided here (for a m ). To isolate the environment, virtual machines (VMs) have sometimes been used, e.g., in SHARE\footnote{\inlinecode{\url{https://is.ieis.tue.nl/staff/pvgorp/share}}} (awarded second prize in the Elsevier Executable Paper Grand Challenge of 2011, discontinued in 2019). -However, containers (e.g., Docker or Singularity) are currently the most widely-used solution. +However, containers (e.g., Docker or Singularity) are currently more widely used. We will focus on Docker here because it is currently the most common. -It is hypothetically possible to precisely identify the used Docker ``images'' with their checksums (or ``digest'') to re-create an identical OS image later. +It is possible to precisely identify the used Docker ``images'' with their checksums (or ``digest'') to re-create an identical OS image later. However, that is rarely done. Usually images are imported with operating system (OS) names; e.g., Mesnard \& Barba\cite{mesnard20} use `\inlinecode{FROM ubuntu:16.04}'. -The extracted tarball (from \url{https://partner-images.canonical.com/core/xenial}) is updated almost monthly, and only the most recent five are archived there. +The extracted tarball URL\footnote{\inlinecode{\url{https://partner-images.canonical.com/core/xenial}}} is updated almost monthly, and only the most recent five are archived. Hence, if the image is built in different months, it will contain different OS components. In the year 2024, when this version's long-term support (LTS) expires (if not earlier, like CentOS 8 which will terminate 8 years early\footnote{\inlinecode{\url{https://blog.centos.org/2020/12/future-is-centos-stream}}}), the image will not be available at the expected URL. @@ -405,7 +405,7 @@ include $(foreach s,$(makesrc), \ Just before reaching the ultimate target (\inlinecode{paper.pdf}), the lineage reaches a bottleneck in \inlinecode{verify.mk} to satisfy the verification criteria. All project deliverables (macro files, plot or table data, and other datasets) are verified at this stage, with their checksums, to automatically ensure exact reproducibility. Where exact reproducibility is not possible (for example, due to parallelization), values can be verified by the project authors. -For example see \inlinecode{verify-parameter-statistically.sh}\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:cnt:dae4e6de5399a061ab4df01ea51f4757fd7e293a;origin=https://codeberg.org/boud/elaphrocentre.git;visit=swh:1:snp:54f00113661ea30c800b406eee55ea7a7ea35279;anchor=swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e;path=/reproduce/analysis/bash/verify-parameter-statistically.sh}{swh:1:cnt:dae4e6de5399a061ab4df01ea51f4757fd7e293a}}} of \href{https://doi.org/10.5281/zenodo.4062460}{zenodo.4062460}. +For example see \inlinecode{\small verify-parameter-statistically.sh}\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:cnt:dae4e6de5399a061ab4df01ea51f4757fd7e293a;origin=https://codeberg.org/boud/elaphrocentre.git;visit=swh:1:snp:54f00113661ea30c800b406eee55ea7a7ea35279;anchor=swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e;path=/reproduce/analysis/bash/verify-parameter-statistically.sh}{swh:1:cnt:dae4e6de5399a061ab4df01ea51f4757fd7e293a}}} of \href{https://doi.org/10.5281/zenodo.4062460}{zenodo.4062460}. \begin{figure*}[t] \begin{center} \includetikz{figure-branching}{scale=1}\end{center} @@ -465,7 +465,7 @@ It can thus easily be published or archived in many servers, for example, it can label=code:branching, caption={Starting a new project with Maneage, and building it}, ] -# Cloning main Maneage branch and branching off it. +# Cloning Maneage and branching off of it. $ git clone https://git.maneage.org/project.git $ cd project $ git remote rename origin origin-maneage @@ -571,6 +571,10 @@ For example, see \href{https://doi.org/10.5281/zenodo.1163746}{zenodo.1163746}, % use section* for acknowledgment \section*{Acknowledgment} +This project (commit \inlinecode{\projectversion}) is maintained in Maneage (\emph{Man}aging data lin\emph{eage}). +The latest merged Maneage branch commit was \inlinecode{\maneageversion} (\maneagedate). +This project was built on an \inlinecode{\machinearchitecture} machine with {\machinebyteorder} byte-order and address sizes {\machineaddresssizes}. + The authors wish to thank (sorted alphabetically) Julia Aguilar-Cabello, Dylan A\"issi, @@ -605,17 +609,12 @@ and Peter Wittenburg for their useful help, suggestions, and feedback on Maneage and this paper. The five referees and editors of CiSE (Lorena Barba and George Thiruvathukal) provided many points that greatly helped to clarify this paper. -This project (commit \inlinecode{\projectversion}) is maintained in Maneage (\emph{Man}aging data lin\emph{eage}). -The latest merged Maneage branch commit was \inlinecode{\maneageversion} (\maneagedate). -This project was built on an \inlinecode{\machinearchitecture} machine with {\machinebyteorder} byte-order and address sizes {\machineaddresssizes}. - Work on Maneage, and this paper, has been partially funded/supported by the following institutions: The Japanese MEXT PhD scholarship to M.A and its Grant-in-Aid for Scientific Research (21244012, 24253003). The European Research Council (ERC) advanced grant 339659-MUSICOS. The European Union (EU) Horizon 2020 (H2020) research and innovation programmes No 777388 under RDA EU 4.0 project, and Marie Sk\l{}odowska-Curie grant agreement No 721463 to the SUNDIAL ITN. -The State Research Agency (AEI) of the Spanish Ministry of Science, Innovation and Universities (MCIU) and the European -Regional Development Fund (ERDF) under the grant AYA2016-76219-P. -The IAC project P/300724, financed by the MCIU, through the Canary Islands Department of Economy, Knowledge and Employment. +The State Research Agency (AEI-MCINN) of the Spanish Ministry of Science and Innovation (SMSI) under the grant "The structure and evolution of galaxies and their central regions" with reference PID2019-105602GB-I00/10.13039/501100011033. +The IAC project P/300724, financed by the SMSI, through the Canary Islands Department of Economy, Knowledge and Employment. The ``A next-generation worldwide quantum sensor network with optical atomic clocks'' project of the TEAM IV programme of the Foundation for Polish Science co-financed by the EU under ERDF. The Polish MNiSW grant DIR/WK/2018/12. |