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mims-harvard / TDC

Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science
https://tdcommons.ai
MIT License
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scperturb issue #289

Closed amva13 closed 4 months ago

amva13 commented 5 months ago

For the perturb-seq dataset, there might be some problem:

from tdc.multi_pred.perturboutcome import PerturbOutcome

data = PerturbOutcome(name = 'scperturb_drug_SrivatsanTrapnell2020_sciplex2')

split = data.get_split() # this line has a problem

print_sys("processing cell line", cell_line)

TypeError: print_sys() takes 1 positional argument but 2 were given

abearab commented 5 months ago

also https://github.com/mims-harvard/TDC/issues/256

amva13 commented 4 months ago

will be fixed by https://github.com/mims-harvard/TDC/pull/290 issue from commit during geneperturb. note: reduce mem foot print of scperturb test so it can actually run in cicd and catch this type of issue.