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BuildACell / bioCRNpyler

A modular compiler for biological chemical reaction networks
BSD 3-Clause "New" or "Revised" License
39 stars 24 forks source link

Roadrunner as an "extra" dependency requirement #196

Closed ayush9pandey closed 3 years ago

ayush9pandey commented 4 years ago

How do we feel about having libroadrunner as an extra dependency that gets installed with pip install biocrnpyler[all] . Since, this is a plotting library it would make sense to include this with the other plotting libraries networkx, and fa2 as the extra dependencies.

zoltuz commented 4 years ago

Hi Ayush, I was thinking about this on the other day and came to the same conclusion. My rationale was pip install biocrnpyler[all] means all dependencies. An alternative would be pip install biocrnpyler[simulators], which installs libroadrunner (and bioscrape in the future), but not the plotting libraries. (For example, when you do parameter inference on a server, you might not need the plotting functions.)

ayush9pandey commented 4 years ago

Yeah, if we wanna go that route, we could have "all" get literally all dependencies and then "plotting" gets the only the plotting ones and "simulators" gets the simulators to provide all options? Doesn't hurt I guess..

WilliamIX commented 3 years ago

Go for it if you want!