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Minor typos and tune up to wording
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yarikoptic committed Dec 5, 2023
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6 changes: 3 additions & 3 deletions publishing/article/background.tex
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Expand Up @@ -23,12 +23,12 @@ \subsection{Reexecutable Research}
% Also cite for relevance of topic → doi:10.52294/001c.85104
Reexecutability is an emergent topic in research, with a few extant efforts attempting to provide solutions and tackle associated challenges.
Such efforts stem both from journals and independent researchers interested in the capabilities which reproducible outputs offer to the ongoing development of their projects.
A jounal-based effort \cite{eliferep} provides dynamic article figures based on the top-most data processing output and executable code conforming to journal standards.
eLife's journal-based effort \cite{eliferep} provides dynamic article figures based on the top-most data processing output and executable code conforming to journal standards.
Independent researcher efforts offer more comprehensive and flexible solutions, yet provide reference implementations which are either applied to comparatively simple analysis processes \cite{Dar2019} or tackle complex processes, but assume environment management capabilities which may not be widespread \cite{repsep}.

In order to optimally leverage extant efforts pertaining to full article reexecution and in order to test reexecutability in the face of high task complexity, we have selected a novel neuroimaging study, identified as OPFVTA based on author naming conventions \cite{opfvta}.
The 2022 article is accompanied by a programmatic workflow via which it can be fully regenerated — based solely on raw data, data analysis instructions, and the natural-language manuscript text — and which is initiated via a simple executable script in the ubiquitous GNU Bash \cite{bash} command language.
The reexecution process in this effort relies on an emerging infrastructure standard, RepSeP \cite{repsep}, also in use by other articles, thus providing a larger scope for conclusions that can be drawn from its study.
The reexecution process in this effort relies on an emerging infrastructure approach, RepSeP \cite{repsep}, also in use by other articles, thus providing a larger scope for conclusions that can be drawn from its study.


\subsection{Data Analysis}
Expand All @@ -41,7 +41,7 @@ \subsection{Data Analysis}
The OPFVTA article, which this study uses as an example, primarily studies effective connectivity, which is resolved via stimulus-evoked neuroimaging analysis.
The stimulus-evoked paradigm is widespread across neuroimaging research, and thus the data analysis workflow (both in terms of \emph{data processing} and \emph{data evaluation}) provides significant analogy to numerous other studies.
The data evaluation step for this sort of study is subdivided into “level one” (i.e. within-subject) analysis, and “level two” (i.e. across-subject) analysis, with the results of the latter being further reusable for higher-level analyses \cite{Friston1995}.
In the simplest terms, these steps represent iterative applications of General Linear Modelling (GLM), at increasingly higher orders of abstraction.
In the simplest terms, these steps represent iterative applications of General Linear Modeling (GLM), at increasingly higher orders of abstraction.

% Insert and reference example workflow figure

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2 changes: 1 addition & 1 deletion publishing/article/results.tex
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Expand Up @@ -69,7 +69,7 @@ \subsubsection{Errors should be fatal more often than not.}

By default, programs written in the majority of languages (including e.g. Python and C) will exit immediately when running into an unexpected operation.
POSIX shell and other similar or derived shells, such as bash and zsh, behave differently.
Their default is to continue with execution of the next scripted command, and only with a non-zero code when the list of commands is exhausted or the \texttt{exit} command is called explicitly.
Their default is to continue with execution of the next scripted command, and only exit with a non-zero code when the list of commands is exhausted or the \texttt{exit} command is called explicitly.
As a result, an execution of the script could continue for hours before it fails, and the original error message might be lost in the flood of output, making it hard or impossible to localize and address the original problem.
This behaviour can be mitigated by prepending \texttt{set -e} to the respective shell script, which changes the default behavior so that execution is stopped as soon as a command exits with an error code.
Additionally, shell scripts treat undefined variables as a variable having an empty value, with empty values causing no errors.
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