ImportError: cannot import name 'AlignedViewMixin'

[1QiGuo]

Hello,

Thanks for developing this package. I have been following the Liana+ tutorial, and came across an import error after installing liana package. The python version is 3.9.

#import liana
import liana as li

ImportError Traceback (most recent call last)
Cell In[8], line 2
1 # import liana
----> 2 import liana as li
3 # needed for visualization and toy data
4 import scanpy as sc

File ~/.conda/envs/qi/envs/lianaplus/lib/python3.9/site-packages/liana/init.py:3
1 version = '1.4.0'
----> 3 from liana import method as mt, plotting as pl, resource as rs, multi as mu, utils as ut, testing
5 # done after everything has been imported (adapted from scanpy)
6 import sys

File ~/.conda/envs/qi/envs/lianaplus/lib/python3.9/site-packages/liana/method/init.py:3
1 import numpy as np
----> 3 from liana.method.sc._Method import Method, MethodMeta, _show_methods
4 from liana.method.sc._rank_aggregate import AggregateClass, _rank_aggregate_meta as aggregate_meta
5 from liana.method.sc import cellphonedb, connectome, logfc, natmi, singlecellsignalr, geometric_mean, cellchat, scseqcomm

File ~/.conda/envs/qi/envs/lianaplus/lib/python3.9/site-packages/liana/method/sc/init.py:1
----> 1 from ._rank_aggregate import _rank_aggregate_meta
2 from ._cellphonedb import cellphonedb
3 from ._logfc import logfc
...
27 )
28 from anndata._core.views import DataFrameView
30 from .file_backing import MuDataFileManager

ImportError: cannot import name 'AlignedViewMixin' from 'anndata._core.aligned_mapping' (/home/qiguo/.conda/envs/qi/envs/lianaplus/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py)

Thanks,
Qi

[dbdimitrov]

Hi @1QiGuo,

This is likely an issue related to MuData. Can you try up- downgrading your current version. If this doesn't work, I can only help if you provide your environment.

Daniel

[DanScarc]

Hi @dbdimitrov,

I have the same issue:

Traceback

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[1], line 34
     31 import matplotlib.lines as mlines
     33 # C2C communication
---> 34 import liana as li
     35 import decoupler as dc
     36 import omnipath as op

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/__init__.py:3](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/__init__.py#line=2)
      1 __version__ = '1.4.0'
----> 3 from liana import method as mt, plotting as pl, resource as rs, multi as mu, utils as ut, testing
      5 # done after everything has been imported (adapted from scanpy)
      6 import sys

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/__init__.py:3](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/__init__.py#line=2)
      1 import numpy as np
----> 3 from liana.method.sc._Method import Method, MethodMeta, _show_methods
      4 from liana.method.sc._rank_aggregate import AggregateClass, _rank_aggregate_meta as aggregate_meta
      5 from liana.method.sc import cellphonedb, connectome, logfc, natmi, singlecellsignalr, geometric_mean, cellchat, scseqcomm

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/__init__.py:1](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/__init__.py#line=0)
----> 1 from ._rank_aggregate import _rank_aggregate_meta
      2 from ._cellphonedb import cellphonedb
      3 from ._logfc import logfc

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/_rank_aggregate.py:3](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/_rank_aggregate.py#line=2)
      1 from __future__ import annotations
----> 3 from liana.method.sc._Method import MethodMeta
      4 from liana.method.sc._liana_pipe import liana_pipe
      5 from liana._docs import d

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/_Method.py:3](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/_Method.py#line=2)
      1 from __future__ import annotations
----> 3 from liana.method.sc._liana_pipe import liana_pipe
      4 from liana._logging import _logg
      5 from liana._docs import d

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/_liana_pipe.py:20](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/liana/method/sc/_liana_pipe.py#line=19)
     17 from liana.method._pipe_utils._aggregate import _aggregate
     18 from liana._constants import MethodColumns as M, CommonColumns as C, \
     19                             PrimaryColumns as P, InternalValues as I
---> 20 from mudata import MuData
     21 from liana.utils import mdata_to_anndata
     23 def liana_pipe(adata: anndata.AnnData,
     24                groupby: str,
     25                resource_name: str,
   (...)
     45                mdata_kwargs: dict = dict(),
     46                ):

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/mudata/__init__.py:3](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/mudata/__init__.py#line=2)
      1 """Multimodal omics analysis framework"""
----> 3 from ._core.mudata import MuData
      4 from ._core import utils
      5 from ._core.io import *

File [~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/mudata/_core/mudata.py:21](http://localhost:8888/lab/workspaces/auto-f/tree/notebooks/c2c_communication/~/miniforge3/envs/preprocess-c2c/lib/python3.9/site-packages/mudata/_core/mudata.py#line=20)
     19 from anndata import AnnData
     20 from anndata.utils import convert_to_dict
---> 21 from anndata._core.aligned_mapping import (
     22     AxisArrays,
     23     AlignedViewMixin,
     24     AxisArraysBase,
     25     PairwiseArrays,
     26     PairwiseArraysView,
     27 )
     28 from anndata._core.views import DataFrameView
     30 from .file_backing import MuDataFileManager

ImportError: cannot import name 'AlignedViewMixin' from 'anndata._core.aligned_mapping'

Environment (env.yml)

name: preprocess-c2c
channels:
  - bioconda
  - conda-forge
dependencies:
  - conda-forge::jupyterlab
  - conda-forge::leidenalg
  - conda-forge::louvain
  - conda-forge::igraph
  - conda-forge::numba
  - conda-forge::python=3.9
  - conda-forge::python-igraph
  - conda-forge::pip
  - conda-forge::session-info
  - pip:
      - pydeseq2
      - decoupler
      - omnipath

After installing the packages in env.yml, I run pip install git+https://github.com/saezlab/liana-py.

Could you also please provide a minimal .yml for liana to run issue-free?

Thanks in advance!
Daniele

[dbdimitrov]

Hi @DanScarc,

Thanks. I would need versions from your environment to be able to debug.

You could install liana with poetry, if you clone the repo, and you would have an identical environment to my dev environment.

Though, it might be easier to just try upgrading your Python version to 3.10, as there were recently some changes to Anndata's dependencies which seem to be causing the issue. If you share your versions, I can debug.

Daniel

[DanScarc]

Upgrading to Python 3.10 worked. Thanks @dbdimitrov!

Here is my yml with versions:

name: liana
channels:
  - bioconda
  - conda-forge
dependencies:
  - conda-forge::jupyterlab=4.2.5
  - conda-forge::leidenalg=0.10.2
  - conda-forge::louvain=0.8.2
  - conda-forge::igraph=0.10.13
  - conda-forge::numba=0.60.0
  - conda-forge::python=3.10
  - conda-forge::python-igraph=0.11.6
  - conda-forge::pip=24.2
  - pip:
      - pydeseq2==0.4.12
      - decoupler==1.8.0
      - omnipath==1.0.8
      - liana