From 90596115b4a454c70232b2610fbca2aff913ceb6 Mon Sep 17 00:00:00 2001
From: Boud Roukema <boud@cosmo.torun.pl>
Date: Thu, 26 Nov 2020 05:39:50 +0100
Subject: All questions have now been responded to

This commit is intended to be submittable quality.

Point 56 was removed, and the later points renumbered,
because it was a point of Reviewer 5 described what we
have done - it was not a criticism to respond do. :)

The current word count (without abstract and references)
is 6091.
---
 paper.tex | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

(limited to 'paper.tex')

diff --git a/paper.tex b/paper.tex
index 9dca3c9..e19a7df 100644
--- a/paper.tex
+++ b/paper.tex
@@ -79,7 +79,7 @@ at the end (Appendices \ref{appendix:existingtools} and \ref{appendix:existingso
   \emph{Reproducible supplement} ---
   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 on \href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/makhlaghi/maneage-paper.git}{SoftwareHeritage}.
+  which is also archived at \href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/makhlaghi/maneage-paper.git}{SoftwareHeritage}.
 \end{abstract}
 
 % Note that keywords are not normally used for peer-review papers.
@@ -277,7 +277,7 @@ In such cases, it is best to immediately convert the data upon collection, and a
 \section{Proof of concept: Maneage}
 
 With the longevity problems of existing tools outlined above, a proof-of-concept tool is presented here via an implementation that has been tested in published papers \cite{akhlaghi19, infante20}.
-\new{Since the initial submission of this paper, it has also been used in \href{https://doi.org/10.5281/zenodo.3951151}{zenodo.3951151} (on the COVID-19 pandemic) and \href{https://doi.org/10.5281/zenodo.4062460}{zenodo.4062460}.}
+\new{Since the initial submission of this paper, it has also been used in \href{https://doi.org/10.5281/zenodo.3951151}{zenodo.3951151} (on the COVID-19 pandemic) and \href{https://doi.org/10.5281/zenodo.4062460}{zenodo.4062460} (which illustrates statistical reproducibility for parallelised code).}
 It was also awarded a Research Data Alliance (RDA) adoption grant for implementing the recommendations of the joint RDA and World Data System (WDS) working group on Publishing Data Workflows \cite{austin17}, from the researchers' perspective.
 
 The tool is called Maneage, for \emph{Man}aging data Lin\emph{eage} (the ending is pronounced as in ``lineage''), hosted at \url{https://maneage.org}.
@@ -1367,7 +1367,7 @@ Its design is based on a change-based provenance model using a custom VisTrails
 Since XML is a plane text format, as the user inspects the data and makes changes to the analysis, the changes are recorded as ``trails'' in the project's VisTrails repository that operates very much like common version control systems (see Appendix \ref{appendix:versioncontrol}).
 .
 However, even though XML is in plain text, it is very hard to edit manually.
-VisTrails therefore provides a graphic user interface with a visual representation of the project's inter-dependent steps (similar to Figure \ref{fig:analysisworkflow}).
+VisTrails therefore provides a graphic user interface with a visual representation of the project's inter-dependent steps (similar to Figure \ref{fig:datalineage}).
 Besides the fact that it is no longer maintained, VisTrails didn't control the software that is run, it only controls the sequence of steps that they are run in.
 
 
@@ -1613,8 +1613,8 @@ However, there is one directory which can be used to store files that must not b
 Popper\footnote{\inlinecode{\url{https://falsifiable.us}}} is a software implementation of the Popper Convention \citeappendix{jimenez17}.
 The Popper team's own solution is through a command-line program called \inlinecode{popper}.
 The \inlinecode{popper} program itself is written in Python.
-However, job management wash initially based on the HashiCorp configuration language (HCL) because HCL was used by ``GitHub Actions'' to manage workflows.
-However, from October 2019 Github changed to a custom YAML-based languguage, so Popper also depreciated HCL.
+However, job management was initially based on the HashiCorp configuration language (HCL) because HCL was used by ``GitHub Actions'' to manage workflows.
+Moreover, from October 2019 Github changed to a custom YAML-based languguage, so Popper also deprecated HCL.
 This is an important issue when low-level choices are based on service providers.
 
 To start a project, the \inlinecode{popper} command-line program builds a template, or ``scaffold'', which is a minimal set of files that can be run.
@@ -1622,9 +1622,10 @@ However, as of this writing, the scaffold isn't complete: it lacks a manuscript
 By default Popper runs in a Docker image (so root permissions are necessary and reproducible issues with Docker images have been discussed above), but Singularity is also supported.
 See Appendix \ref{appendix:independentenvironment} for more on containers, and Appendix \ref{appendix:highlevelinworkflow} for using high-level languages in the workflow.
 
-Igonoring the failure to comply with the completeness, minimal complexity and includig narrative, the scaffold that is provided by Popper is an output of the program that is not directly under version control.
-Hence tracking future changes in Popper and how they relate to the high level projects that depend on it will be very hard.
-In Maneage, the same \inlinecode{maneage} git branch is shared by the developers and users, any new feature or change in Maneage can thus be directly tracked with Git when the high-level project merges their branch with Maneage.
+Popper does not comply with the completeness, minimal complexity and including-narrative criteria.
+Moreover, the scaffold that is provided by Popper is an output of the program that is not directly under version control.
+Hence, tracking future changes in Popper and how they relate to the high-level projects that depend on it will be very hard.
+In Maneage, the same \inlinecode{maneage} git branch is shared by the developers and users; any new feature or change in Maneage can thus be directly tracked with Git when the high-level project merges their branch with Maneage.
 
 
 \subsection{Whole Tale (2017)}
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