extract prepare from main install #887
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bkmartinjr
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Aug 20, 2019
bkmartinjr
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* Document how to install cellxgene prepare after pr #887 merged * formatting * remove reference to cellxgene[louvain]
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I've extracted the prepare requirements from the main requirements for installing cellxgene. This give us the ability to remove scanpy as a requirement which causes occasional trouble with conflicting versions of upstream dependencies with the trade-off that now users will need to install cellxgene[prepare] to get the requirements to use cellxgene prepare.
I'm in the process of chatting with Andrew Nacin to see if we can collapse the install for prepare and for louvain so that it's just one special install.
I was able to remove the scikit-learn and matplotlib dependancies in the process because of improvements to scanpy's requirements file and we no longer need it for launch since we are not using scanpy there (and that was what was causing the bug in anaconda -- I've tested locally).
I'm also going to add a github issue to socialize this proposal.