Colab error when running setup_anndata()

theislab / cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

BSD 3-Clause "New" or "Revised" License

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Colab error when running setup_anndata() #15

Closed znavidi closed 9 months ago

znavidi commented 1 year ago

Hi,

When I run the CPA colab tutorial, in the following line:

cpa.CPA.setup_anndata(adata, perturbation_keys={ 'perturbation': 'condition', 'dosage': 'dose_val', }, categorical_covariate_keys=['cell_type'], control_key='control', )

the below error occures in both tutorial:

TypeError: CategoricalDataFrameField.init() got an unexpected keyword argument 'obs_key'

I would appreciate any help to be able to run it.

M0hammadL commented 1 year ago

Hi Zeinab, thanks for your interest; we are updating the code and adding new tutorials. Hopefully, we will have the next update by the end of the week or early next week.

znavidi commented 1 year ago

Thanks a lot for your prompt reply! Looking forward to it!

sumeer1 commented 1 year ago

@M0hammadL Hi,

Is there any update on this? I am getting the same error.