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Merged
merged 25 commits into from
Mar 20, 2024
Merged

Scgpt dev #755

merged 25 commits into from
Mar 20, 2024

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dorien-er
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@dorien-er dorien-er commented Mar 20, 2024 •
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Changelog

merge scgpt-dev branch into scgpt

Checklist before requesting a review

  • I have performed a self-review of my code

  • Conforms to the Contributor's guide

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

  • Proposed changes are described in the CHANGELOG.md

  • CI tests succeed!

dorien-er and others added 25 commits March 6, 2024 11:16
@dorien-er
preproc script
78954c0
@dorien-er
preproc script
9068e7a
@dorien-er
tokenize and pad script
dbe5204
@dorien-er
tokenize and pad script
89a9c6a
@dorien-er
embedding script
9e446f8
@dorien-er
test resourcers and evaluation script
94dd10c
@dorien-er
cross check gene set
3edf3c0
@dorien-er
pad_tokenize module
085cdc4
@dorien-er
updat image
724427e
@dorien-er
remove test resources, update inputs
f9aadfa
@dorien-er
use pytorch image
33c9ffe
@dorien-er
remove integration component
0c6316d
@dorien-er
remove nvidia reqs
47f5dda
@jakubmajercik
Merge branch 'main' of github.com:openpipelines-bio/openpipeline into…
9d2ffd0 
… scgpt
@dorien-er
remove load_model option
0f74ebd
@DriesSchaumont @dorien-er
Fix retag for viash-hub not using correct namespace separator (#745)
52fb38c
@DriesSchaumont @dorien-er
CI - Build: Fix second occurance of namespace separator (#746)
accf980
@dorien-er
script to download scgpt test data
b1dd6ce
@dorien-er
remove test resources script
18db6d6
@dorien-er
adjust preprocessing script
6c3fec0
@dorien-er
add scgpt full preproc module
acd3600
@dorien-er
integration submodule
3e31204
@dorien-er
integration submodule and add normalize_total flag
b5d1970
@dorien-er
add params
ec326f8
@dorien-er
Merge pull request #751 from openpipelines-bio/scgpt-preprocessor
2dddc1c 
scGPT integration preproc module
@dorien-er dorien-er merged commit bd7a32f into scgpt Mar 20, 2024
@dorien-er dorien-er deleted the scgpt-dev branch March 20, 2024 09:32
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3 participants

@dorien-er @jakubmajercik @DriesSchaumont