multiVAE and organize_multiome_anndatas: module 'scarches.models' has no attribute

[Yansr3]

Hi I have been trying to follow to tutorial of Integration and reference mapping with multigrate https://docs.scarches.org/en/latest/multigrate.html. However, I was having trouble loading the multiVAE and organize_multiome_anndatas from models. I am wondering if these two models are still available. Or is it cuased by the installing process?

import scarches.models.organize_multiome_anndatas

ModuleNotFoundError Traceback (most recent call last)
Cell In[3], line 1
----> 1 import scarches.models.organize_multiome_anndatas

ModuleNotFoundError: No module named 'scarches.models.organize_multiome_anndatas'

import scarches.models.MultiVAE

ModuleNotFoundError Traceback (most recent call last)
Cell In[3], line 1
----> 1 import scarches.models.MultiVAE

ModuleNotFoundError: No module named 'scarches.models.MultiVAE'

adata = sca.models.organize_multiome_anndatas(
adatas = [[rna_cite, rna_multiome], [None, atac], [adt, None]], # a list of anndata objects per modality, RNA-seq always goes first
layers = [['counts', 'counts'], [None, 'log-norm'], ['clr', None]], # if need to use data from .layers, if None use .X
)
adata

AttributeError Traceback (most recent call last)
Cell In[14], line 1
----> 1 adata = sca.models.organize_multiome_anndatas(
2 adatas = [[rna_cite, rna_multiome], [None, atac], [adt, None]], # a list of anndata objects per modality, RNA-seq always goes first
3 layers = [['counts', 'counts'], [None, 'log-norm'], ['clr', None]], # if need to use data from .layers, if None use .X
4 )
5 adata

AttributeError: module 'scarches.models' has no attribute 'organize_multiome_anndatas'

Version is as follows:
scarches 0.5.9 pypi_0 pypi
multigrate 0.0.2 pypi_0 pypi
python 3.10.9 he7542f4_0_cpython conda-forge

[alitinet]

Hi @Yansr3,

Thanks for reporting this! Could you try installing both scarches and multigrate from github?

[Yansr3]

Hi @alitinet,

Thank you for replying. The error is fixed by installing from github. Thank you!

[4ivage32]

Hi I encountered the same problem while trying multiVAE as you written. And I installed both scarches and multigrate from github but the error occurred again. Could you please teach me how you fix this problem? Thank you!

[M0hammadL]

@alitinet @Koncopd