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SchubertLab / mvTCR

MIT License
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Questions about dependency versions provided in requirements.txt #3

Closed gwentea closed 8 months ago

gwentea commented 1 year ago

Dear Authors,

Thanks for the great work.

I was able to install mvTCR and run your tutorials in a conda environment, but encountered several problems which I suppose were caused by differences in dependency versions.

With scirpy=0.6.1, I ran into errors when running the following scripts as ir.pp.merge_with_ir(adata, adata_tcr) did not create the IR_VDJ_1_junction_aa information in adata.obs when merging the TCR and RNA data notebook: /mvTCR/tutorials/01_preprocessing.ipynb

adata = adata[~adata.obs['IR_VDJ_1_junction_aa'].isna()]
adata = adata[~adata.obs['IR_VJ_1_junction_aa'].isna()].copy()

Switching to scirpy=0.7.0 resolved this issue.

Another problem was caused by optuna. optuna.structs is removed in optuna=3.0.3 (which was automatically installed since the version was not provided), and I haven't been able to locate the correct version of optuna... Could you please provide the specific optuna version that was used?

Thanks for you time!

drEast commented 1 year ago

Hi, Thanks for your interest in our tools. I updated the requirement file for a scirpy version >=0.7 and the optuna versions 2.10.1, which we used for our tests. This will hopefully resolve your issue. Thanks and best, Felix