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Clean up Pixie pipeline #856

Merged
merged 40 commits into from
Dec 19, 2022
Merged

Clean up Pixie pipeline #856

merged 40 commits into from
Dec 19, 2022

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alex-l-kong
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What is the purpose of this PR?

Closes #845. See issue for all the changes; we want to introduces some new file naming schemes, as well as some basic data reformatting.

How did you implement your changes

See issue page.

@alex-l-kong alex-l-kong self-assigned this Dec 8, 2022
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@alex-l-kong alex-l-kong marked this pull request as draft December 8, 2022 23:36
alex-l-kong and others added 14 commits December 8, 2022 15:37
@alex-l-kong
Merge branch 'main' into pixie_clean
cc48c19
@alex-l-kong
PYCODESTYLE
7583f7e
@alex-l-kong
Ensure 'size_norm_name' propagates into notebook
0c12025
@alex-l-kong
weights_name to cell_weights_name change in notebook
2d554c6
@alex-l-kong
Notebook variable adjustments
e4dba6c
@alex-l-kong
Make sure example dataset doesn't have any unnecessary prefixes in it
203eb4b
@alex-l-kong
Ensure cluster_counts_norm_name passed wherever necessary
417dd82
@alex-l-kong
Cell clustering documentation fixes
83cd2d6
@alex-l-kong
Write out cluster counts size norm instead of cell mat for cell clust…
02d01c6 
…er notebook test
@alex-l-kong
Don't write out extraneous cell_mat.feather
a72bb9d
@alex-l-kong
Ensure tests match up with updated sans-cell_mat process (we really n…
44d506b 
…eed to refactor to OOP...)
@alex-l-kong
Patch up test_utils dimensions for _make_neighborhood_matri
0e7333b
@alex-l-kong
Initial pass at reorganizing files
7338613
@alex-l-kong
Remove extraneous print statements
a58e8c2
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alex-l-kong commented Dec 13, 2022 •
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@cliu72 all the requests should be addressed. Gonna need to open separate mini PRs for these in the future lol.

And as usual, will make sure to change the example dataset revision back to main prior to merging this in.

@alex-l-kong
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@cliu72 final documentation request has been addressed.

@alex-l-kong alex-l-kong mentioned this pull request Dec 15, 2022
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ngreenwald
ngreenwald requested changes Dec 15, 2022
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Will you make sure that all references to notebook 2 are updated with the new name? The flowchart in the readme, any links elsewhere in the repo that point to the old URL, etc

@alex-l-kong alex-l-kong mentioned this pull request Dec 15, 2022
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alex-l-kong commented Dec 16, 2022 •
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@ngreenwald old notebook names are fixed, example dataset loading functionality has been moved to the beginning in the notebooks. @srivarra has the flowchart image on the README.md, so he opened #869 to address that.

ngreenwald
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Looks good to me, I'll let candace take a final look through

@srivarra srivarra mentioned this pull request Dec 16, 2022
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cliu72
cliu72 approved these changes Dec 17, 2022
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Looks good!

ngreenwald
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Just need to update huggingface

ark/utils/example_dataset_test.py Outdated Show resolved Hide resolved
ngreenwald
ngreenwald approved these changes Dec 18, 2022
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Sounds good

@alex-l-kong alex-l-kong merged commit 719e3a6 into main Dec 19, 2022
@alex-l-kong alex-l-kong deleted the pixie_clean branch December 19, 2022 10:35
@srivarra srivarra added the enhancement New feature or request label Jan 10, 2023
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@ngreenwald ngreenwald ngreenwald approved these changes

@cliu72 cliu72 cliu72 approved these changes

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Pixel clustering/cell clustering file cleanup
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@alex-l-kong @cliu72 @ngreenwald @srivarra