Bug running harmony batch correction with multiple covariates

Thanks for making this awesome package! I'm having some problems when running sc.pp.harmony. I previously had v2.7.0 installed and ran into an issue when defining multiple covariates in the batch argument. I updated the package installation to v2.7.1 and the function works as expected with a single covariate. However, if I provide a list of covariates, I get the following error:

My coworker and I tracked down the problem to trying to create a pandas df with pd.DataFrame(adata.obs[batch]). If you simply run pd.DataFrame(adata.obs) without using the slicing operator to retrieve specific columns, the df is created properly. We also tried pd.DataFrame(adata.obs[:][batch]) and the df with the batch covariates is properly created. Not sure if we're right, but we think this is related to snapatac2 trying to use a reference to the actual data for making the covariate df.

Would love to hear your thoughts. Thanks so much for your help!

Start by reproducing the failure in sc.pp.harmony with multiple covariates in the batch argument, comparing pd.DataFrame(adata.obs[batch]) with the working alternatives described in the report. Trace the covariate DataFrame construction and verify that multiple covariates complete without the reported error while preserving the single-covariate behavior.