[Bioc-devel] Merging or renaming a fork, and appropriate journal for package updates

Pariksheet Nanda p@r|k@heet@n@nd@ @end|ng |rom uconn@edu
Wed Dec 1 13:17:57 CET 2021

Hi folks,

I'm wrapping up my dissertation and one of the chapters touches on a 
summer of patching a Bioconductor package that currently lives as a 
separate GitHub fork (the list of changes is here [1]).  2 of the 
questions I've been asked by a member of my committee are whether to:

(1) associate a publication with the work, and
(2) republish the code with the original or as a separate package.

For (1) while I appreciate the traditional unit of research output is 
the publication, I'm struggling to think of a suitable journal for what 
essentially is discussion about enhancements and some bugfixes.  I've 
seen R package updates published in the Journal of Statistical Software 
(JSS) which might be appropriate?  I suppose any place that gets indexed 
on pubmed would work (yes, JSS is part of the NLM catalog [2]).  What 
would you suggest?  Perhaps the Bioconductor project collect metrics for 
publication activity about its packages to get more funding and has some 

For (2) I would prefer to merge back with the original Bioconductor 
package.  I tried upstreaming an early changeset [3], but besides my 
issue being open, there are currently 2 other open GitHub issues with no 
response which makes me wonder if upstream is dead.  If that's the case, 
would someone from the Bioconductor core team be willing to work with me 
to proxy commit to git.bioconductor.org?  I've made some API breaking 
changes, so I expect I would need to create at least 2 branches: one 
that can be commit with a deprecation warning for upcoming API breaking 
changes, and a second branch with API breaking changes to be commit at 
the subsequent Bioconductor release.  Or maybe I would need to create a 
branch for each feature change; honestly I don't know if that would be 
or less work but certainly it would be easier to read the git history.


[1] https://github.com/coregenomics/groHMM/blob/1.99.x/NEWS
[2] https://www.ncbi.nlm.nih.gov/nlmcatalog/101307056
[3] https://github.com/Kraus-Lab/groHMM/issues/2

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