Error with normalize_total()

[sjbegg]

I'm running through the Buenrostro tutorial to test out using Episcanpy, but am hitting the following error when trying to normalize. I'd appreciate any pointers in what to do, please.

epi.pp.normalize_total(adata)

returns the following error:

FutureWarning:../lib/python3.9/site-packages/scanpy/preprocessing/_normalization.py:141: The `layer_norm` argument is deprecated. Specify the target size factor directly with `target_sum`.
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/tmp/ipykernel_378952/1227047011.py in <module>
----> 1 epi.pp.normalize_total(adata)

~/lib/python3.9/site-packages/episcanpy/preprocessing/_scanpy_fct.py in normalize_total(adata, target_sum, exclude_highly_expressed, max_fraction, key_added, layers, layer_norm, inplace)
    426     """
    427 
--> 428     sc.pp.normalize_total(adata, target_sum, exclude_highly_expressed, 
    429         max_fraction, key_added, layers, layer_norm, inplace)
    430 

~/lib/python3.9/site-packages/scanpy/preprocessing/_normalization.py in normalize_total(adata, target_sum, exclude_highly_expressed, max_fraction, key_added, layer, layers, layer_norm, inplace, copy)
    203         after = None
    204     else:
--> 205         raise ValueError('layer_norm should be "after", "X" or None')
    206 
    207     for layer_to_norm in layers if layers is not None else ():

ValueError: layer_norm should be "after", "X" or None

[DaneseAnna]

Hi, thank you for the feedback.

It looks like a new compatibility issue with scanpy. I will produce a fix on the main branch and will let you know when it's available.
In the mean time, you can try downgrading scanpy to 1.7.2

[sjbegg]

Thanks for replying so quickly - the scanpy downgrade has worked, and I'll update once you add the fix.

Thanks again!