Issues with ingest

Hi all,

I am trying to use ingest to integrate different datasets.
I found a couple of issues.

• ingest requires that the var_names are the same in the reference and the new object. I can select the intersection between the datasets; however, it requires that the genes are in the same order if not ref_var_names.equals(new_var_names). I think this if could be modified using set (e.g., len(set(ref_var_names).difference(set(new_var_names))) == 0). I tried to order the .var dataframe, but the .X remains the same. In such a way, the expression of the genes does not correspond to the correct one. I can generate a dataframe and recreate the .X, but it could be very nice that the .X will be modified according to .var or .obs modifications (i.e., ordering).

• although it is possible to set embedding_method=umap, ingest requires the PCA components. I used autoencoders instead of PCA, and I cannot run ingest only considering the UMAP. Can you fix it?

Thank you in advance.
Best,
Andrea

Start by tracing the ingest entry point and its handling of var_names, .var, .obs, and .X. Reproduce the ordering case and the embedding_method=umap case, then verify that gene expression remains aligned and that ingest can use UMAP without PCA components.