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A nice counter example of research software code that adheres to general software engineering best practices and is easy to pick up and use is the OSMNX project: https://github.com/gboeing/osmnx
Props to Geoff for setting a nice standard.
Keep in mind that there're different kinds of research software. Take Seurat[1] as an example. There's CI, issue tracking, etc. It might not be the prettiest code you ever seen, but it absolutely has to be maintainable as it's being actively developed. Such projects are rare, but the low quality is often an indication of a software that isn't used by anyone.
1. https://github.com/satijalab/seurat
– Their solution product https://cknowledge.io/ and source code https://github.com/ctuning/ck\
I guess it should be helpful to the researchers community.
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