ModuleNotFoundError: No module named 'anndata.io'

[Hastikabirsamadi]

Hello,
I've been trying to execute your Jupyter notebooks but i get error for importing "anndata.io".
I've already installed "anndata" package version 0.9.2, but it seems that this package doesn't contain anndata.io.
The error occurs like this:
import scarches as sca
from . import dataset, metrics, trainers, models, zenodo, plotting, utils, classifiers
from .trvae.trvae import trVAE
from .losses import mse, mmd, zinb, nb
from scvi.distributions import NegativeBinomial
from . import data, model, external, utils
from anndata.io import read_csv, read_loom, read_text
what can I do to resolve this problem?

[Koncopd]

Hello, where does this happen? Could you post the full traceback, the versions of anndata and scarches?

[Hastikabirsamadi]

sure, here it is:

ModuleNotFoundError Traceback (most recent call last)
Cell In[7], line 3
1 import scanpy as sc
2 import torch
----> 3 import scarches as sca
4 import numpy as np
5 import gdown

File ~/miniconda3/envs/hasti_env/lib/python3.8/site-packages/scArches-0.6.1-py3.8.egg/scarches/init.py:1
----> 1 from . import dataset, metrics, trainers, models, zenodo, plotting, utils, classifiers
3 author = ', '.join([
4 'Mohammad Lotfollahi',
5 'Sergei Rybakov',
6 'Marco Wagenstetter',
7 'Mohsen Naghipourfar',
8 ])
10 email = ', '.join([
11 '[email protected]',
12 '[email protected]'
13 ])

File ~/miniconda3/envs/hasti_env/lib/python3.8/site-packages/scArches-0.6.1-py3.8.egg/scarches/models/init.py:1
----> 1 from .trvae.trvae import trVAE
2 from .trvae.trvae_model import TRVAE
3 from .trvae.adaptors import Adaptor, attach_adaptors

File ~/miniconda3/envs/hasti_env/lib/python3.8/site-packages/scArches-0.6.1-py3.8.egg/scarches/models/trvae/trvae.py:9
6 import torch.nn.functional as F
8 from .modules import Encoder, Decoder
----> 9 from .losses import mse, mmd, zinb, nb
10 from ._utils import one_hot_encoder
11 from ..base._base import CVAELatentsModelMixin

File ~/miniconda3/envs/hasti_env/lib/python3.8/site-packages/scArches-0.6.1-py3.8.egg/scarches/models/trvae/losses.py:1
----> 1 from scvi.distributions import NegativeBinomial
2 import torch
3 from torch.autograd import Variable

File ~/miniconda3/envs/hasti_env/lib/python3.8/site-packages/scvi_tools-1.2.2.post2-py3.8.egg/scvi/init.py:11
8 from ._settings import settings
10 # this import needs to come after prior imports to prevent circular import
---> 11 from . import data, model, external, utils
13 from importlib.metadata import version
15 package_name = "scvi-tools"

File ~/miniconda3/envs/hasti_env/lib/python3.8/site-packages/scvi_tools-1.2.2.post2-py3.8.egg/scvi/data/init.py:2
1 from anndata import read_h5ad
----> 2 from anndata.io import read_csv, read_loom, read_text
4 from ._anntorchdataset import AnnTorchDataset
5 from ._datasets import (
6 annotation_simulation,
7 brainlarge_dataset,
(...)
23 synthetic_iid,
24 )

ModuleNotFoundError: No module named 'anndata.io'

[Koncopd]

This looks like a problem with scvi-tools version that is incompatible with your anndata version.

[Hastikabirsamadi]

which version should I use?

[Hastikabirsamadi]

my scvi-tools version is 1.2.2.post2
and anndata version is 0.9.2

[Koncopd]

Your anndata version is pretty old, i believe you need to update it.

[Hastikabirsamadi]

the problem is that pip and conda can only install this version for me. when I tried to install the latest version "0.11.3" using pip, i got an error. because pip couldn't find this version

[Koncopd]

you can do pip install --upgrade anndata