Annotate - update BE dependencies

chanzuckerberg / cellxgene

An interactive explorer for single-cell transcriptomics data

https://chanzuckerberg.github.io/cellxgene/

MIT License

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Annotate - update BE dependencies #2618

Closed dsadgat closed 10 months ago

dsadgat commented 1 year ago

https://github.com/chanzuckerberg/cellxgene/pulls

[ ] Update and pin BE dependencies
[ ] Deploy and sanity check that nothing is broken
[ ] Update how-to-upgrade-dependencies.md

atarashansky commented 1 year ago

It appears that a FE plugin called obsolete-webpack-plugin is interfering with the GHA testrunner (see failing tests on https://github.com/chanzuckerberg/cellxgene/pull/2634).

Assuming that the issue is due to out-of-date FE dependencies, then this ticket is blocked by the one to upgrade FE annotate deps (#2617).

joyceyan commented 11 months ago

@dsadgat Just as an FYI, cellxgene as it currently is does not appear to work on my M2 machine. A fresh install of main's requirements-dev.txt on my machine on a clean virtual environment does not work. This will probably end up taking me a bit longer than someone without an M1/M2 machine, since I'll have to first figure out how to get my local environment set up to run cellxgene as it is (if possible) before I can start updating the backend dependencies.

dsadgat commented 11 months ago

@atarashansky I believe you have annotate working? Could you take this one over and pin the Werkzeug dependency via https://czi-sci.slack.com/archives/C0247APK621/p1699544094837979