Update pycytominer pipelines #23
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Great PR, and I LOVE the formatting of how to run through all of the plates in one notebook!
I left a few comments with questions. They are mainly inquiring if some lines of code can be removed to make it more concise, specifically in Cameron's method (based on my understanding of the process). Once these are addressed, this PR is good to merge!
3.processing_features/scripts/2.pycytominer_singlecell_pipelines.py
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| @@ -7,6 +7,7 @@ dependencies: | |||
| # this is restricted to Python 3.8 at this time due to other conflicts | |||
| - conda-forge::python=3.8 | |||
| - conda-forge::ipykernel | |||
| - conda-forge::jupyterlab | |||
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Can you remind me what jupyterlab is for here?
Also, are you still having issues with getting this environment downloaded?
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Can you remind me what jupyterlab is for here?
I use jupyter lab for development :)
Also, are you still having issues with getting this environment downloaded?
Yes, I think the issue is the same one Dayna was having with centrosome. Do you remember the fix?
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I think the issues were resolved in a recent release of CellProfiler 4.2.6 in which centrosome was causing issues for all 4.0 versions (IIRC). This should be solved if you try now. Let me know if not.
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Merging now! The html are produced by this line: https://github.com/WayScience/nf1_cellpainting_data/pull/23/files#diff-cb84f5f726165335245592b5bc3e7b535affde3de98a8a8adff909f423ba140fR13 |
Big PR to update pycytominer pipelines, please feel free to only review the nbconverted
.ipynbfiles.