Error occurred when importing scvelo. TypeError: 'ABCMeta' object is not subscriptable

[18520964064]

To conduct RNA velocity analysis, I need to download the scvelo package for Python. However, due to insufficient local computer memory, I rented a shared server and attempted to download the scvelo package using Python 3 in Jupyterlab on the shared server. After the download was completed, I encountered frequent errors when importing it. I have no idea how to solve this problem. If I create a new virtual environment on my local computer, I can successfully download and import the scvelo package. But on the shared server, I don't have the permission to create the required virtual environment, so I'm at a loss. Can anyone help me?

The error-reporting code is as follows:

TypeError Traceback (most recent call last)
Cell In[2], line 1
----> 1 import scvelo
2 print(scvelo.version)

File ~/.local/lib/python3.8/site-packages/scvelo/init.py:4
1 """scvelo - RNA velocity generalized through dynamical modeling."""
2 from anndata import AnnData
----> 4 from scvelo import datasets, logging
5 from scvelo import plotting as pl
6 from scvelo import preprocessing as pp

File ~/.local/lib/python3.8/site-packages/scvelo/datasets/init.py:1
----> 1 from ._datasets import (
2 bonemarrow,
3 dentategyrus,
4 dentategyrus_lamanno,
5 forebrain,
6 gastrulation,
7 gastrulation_e75,
8 gastrulation_erythroid,
9 pancreas,
10 pbmc68k,
11 toy_data,
12 )
13 from ._simulate import simulation
15 all = [
16 "bonemarrow",
17 "dentategyrus",
(...)
26 "toy_data",
27 ]

File ~/.local/lib/python3.8/site-packages/scvelo/datasets/_datasets.py:9
5 import pandas as pd
7 from scanpy import read
----> 9 from scvelo.core import cleanup
10 from scvelo.read_load import load
12 url_datadir = "https://github.com/theislab/scvelo_notebooks/raw/master/"

File ~/.local/lib/python3.8/site-packages/scvelo/core/init.py:1
----> 1 from ._anndata import (
2 clean_obs_names,
3 cleanup,
4 get_df,
5 get_initial_size,
6 get_modality,
7 get_size,
8 make_dense,
9 make_sparse,
10 merge,
11 set_initial_size,
12 set_modality,
13 show_proportions,
14 )
15 from ._arithmetic import clipped_log, invert, multiply, prod_sum, sum
16 from ._linear_models import LinearRegression

File ~/.local/lib/python3.8/site-packages/scvelo/core/_anndata.py:14
10 from scipy.sparse import csr_matrix, issparse, spmatrix
12 from anndata import AnnData
---> 14 from scvelo import logging as logg
15 from ._arithmetic import sum
16 from ._utils import deprecated_arg_names

File ~/.local/lib/python3.8/site-packages/scvelo/logging/init.py:1
----> 1 from ._logging import (
2 error,
3 hint,
4 info,
5 msg,
6 print_version,
7 ProgressReporter,
8 switch_verbosity,
9 warn,
10 )
12 all = [
13 "error",
14 "hint",
(...)
20 "warn",
21 ]

File ~/.local/lib/python3.8/site-packages/scvelo/logging/_logging.py:211
207 _DEPENDENCIES_PLOTTING = ["matplotlib"]
210 # Adapted from https://github.com/theislab/cellrank/blob/main/src/cellrank/logging/_logging.py#L98-L128
--> 211 def _versions_dependencies(dependencies: Iterable[str]):
212 # this is not the same as the requirements!
213 for mod in dependencies:
214 mod_name, dist_name = mod if isinstance(mod, tuple) else (mod, mod)

TypeError: 'ABCMeta' object is not subscriptable

[hanshanmengqi]

Hello @18520964064,

I think this problem is related to the Python version.

For me, I solved it by switching from Python 3.8 to Python 3.6.

Hope this helps.

Han

[Caizhengwen123]

if your python version <3.9, then you can try replace "from collections.abc import Iterable" in /scvelo/logging/_logging.py with "from typing import Iterable".