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broadinstitute / lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project
BSD 3-Clause "New" or "Revised" License
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Update pycytominer version #53

Closed gwaybio closed 3 years ago

gwaybio commented 3 years ago

we have made substantial progress in pycytominer since version 0.1 release. We need to update the environment.yml file and update the profiling pipeline to account for this change.

gwaybio commented 3 years ago

Let's go with git+https://github.com/cytomining/pycytominer@0205e2519dd08bde2624f50bcd05518d19cc7f32 in the new environment.yml. All necessary functionality is present in this commit.

gwaybio commented 3 years ago

We will eventually want to upgrade pycytominer to a more stable version.

Perhaps this happens after @michaelbornholdt 1) makes the final connections between DeepProfiler and pycytominer, and 2) processes and uploads LINCS Cell Painting feature embeddings for batch 1 and batch 2 LINCS data

(☝️ related to #2 )

This will happen after the version 1.0 data release