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Improved wording
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Co-authored-by: Yaroslav Halchenko <[email protected]>
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TheChymera and yarikoptic authored Oct 20, 2023
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Expand Up @@ -69,7 +69,7 @@ \subsubsection{Errors should be fatal more often than not}

\subsubsection{Avoid assuming or hard-coding absolute paths to resources}
Ensuring layout compatibility in different article execution environments is contingent on executable resources being able to find code or data required for execution.
Explicitly hardcoded in the scripts absolute paths are likely to not exist anywhere but the original execution environment, and hence scripts guaranteed to fail.
Explicitly hardcoded in the scripts absolute paths are likely to not exist anywhere but the original execution environment, and hence scripts can very easily fail.
This problem is best avoided by adhering to YODA principles~\cite{yoda} of being able to reference all needed resources (data, scripts, container images, etc.) \emph{under} the study folder.
Use of relative paths within the study scripts then improve their portability.
Paths to external resources (scratch folders, reusable resources such as atlases etc. if not present within study folder) should be allowed to be specified dynamically via command line options or via an environment variable during execution.
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