cannot import name 'LightningLoggerBase' from 'pytorch_lightning.loggers' #63
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when I try to import the packages
import anndata as ad
import squidpy as sq
import cellcharter as cc
import pandas as pd
import scanpy as sc
import scvi
import numpy as np
import matplotlib.pyplot as plt
from lightning.pytorch import seed_everything
seed_everything(12345)
scvi.settings.seed = 12345
the error occurred:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[5], line 6
4 import pandas as pd
5 import scanpy as sc
----> 6 import scvi
7 import numpy as np
8 import matplotlib.pyplot as plt
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/__init__.py:10
7 from ._settings import settings
9 # this import needs to come after prior imports to prevent circular import
---> 10 from . import data, model, external
12 # https://github.com/python-poetry/poetry/pull/2366#issuecomment-652418094
13 # https://github.com/python-poetry/poetry/issues/144#issuecomment-623927302
14 try:
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/model/__init__.py:1
----> 1 from ._autozi import AUTOZI
2 from ._condscvi import CondSCVI
3 from ._destvi import DestVI
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/model/_autozi.py:12
10 from scvi import _CONSTANTS
11 from scvi._compat import Literal
---> 12 from scvi.model.base import UnsupervisedTrainingMixin
13 from scvi.module import AutoZIVAE
15 from .base import BaseModelClass, VAEMixin
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/model/base/__init__.py:4
2 from ._base_model import BaseModelClass
3 from ._rnamixin import RNASeqMixin
----> 4 from ._training_mixin import UnsupervisedTrainingMixin
5 from ._vaemixin import VAEMixin
7 __all__ = [
8 "ArchesMixin",
9 "BaseModelClass",
(...)
12 "UnsupervisedTrainingMixin",
13 ]
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/model/base/_training_mixin.py:6
3 import numpy as np
5 from scvi.dataloaders import DataSplitter
----> 6 from scvi.train import TrainingPlan, TrainRunner
9 class UnsupervisedTrainingMixin:
10 """General purpose unsupervised train method."""
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/train/__init__.py:1
----> 1 from ._trainer import Trainer
2 from ._trainingplans import (
3 AdversarialTrainingPlan,
4 ClassifierTrainingPlan,
(...)
7 TrainingPlan,
8 )
9 from ._trainrunner import TrainRunner
File /public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/scvi/train/_trainer.py:8
6 import pytorch_lightning as pl
7 from pytorch_lightning.callbacks.early_stopping import EarlyStopping
----> 8 from pytorch_lightning.loggers import LightningLoggerBase
10 from scvi import settings
11 from scvi._compat import Literal
ImportError: cannot import name 'LightningLoggerBase' from 'pytorch_lightning.loggers' (/public/home/yzhang/micromamba/envs/Cellcharter/lib/python3.9/site-packages/pytorch_lightning/loggers/__init__.py)
It might be caused by changes in pytorch_lightning, could the authors made adaptive changes or provide the versions of packages for their codes?
Version information
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session_info 1.0.0Click to view modules imported as dependencies
anyio NA arrow 1.3.0 asttokens NA attr 24.2.0 attrs 24.2.0 babel 2.16.0 brotli 1.1.0 certifi 2024.08.30 charset_normalizer 3.4.0 colorama 0.4.6 comm 0.2.2 cython_runtime NA dateutil 2.9.0.post0 debugpy 1.8.9 decorator 5.1.1 exceptiongroup 1.2.2 executing 2.1.0 fastjsonschema NA fqdn NA idna 3.10 importlib_metadata NA ipykernel 6.29.5 isoduration NA jedi 0.19.2 jinja2 3.1.4 json5 0.10.0 jsonpointer 3.0.0 jsonschema 4.23.0 jsonschema_specifications NA jupyter_events 0.10.0 jupyter_server 2.14.2 jupyterlab_server 2.27.3 markupsafe 3.0.2 nbformat 5.10.4 overrides NA packaging 24.2 parso 0.8.4 pexpect 4.9.0 pickleshare 0.7.5 platformdirs 4.3.6 prometheus_client NA prompt_toolkit 3.0.48 psutil 6.1.0 ptyprocess 0.7.0 pure_eval 0.2.3 pydev_ipython NA pydevconsole NA pydevd 3.2.3 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.18.0 pythonjsonlogger NA referencing NA requests 2.32.3 rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rpds NA send2trash NA six 1.17.0 sniffio 1.3.1 socks 1.7.1 stack_data 0.6.3 tornado 6.4.2 traitlets 5.14.3 typing_extensions NA uri_template NA urllib3 1.26.20 wcwidth 0.2.13 webcolors NA websocket 1.8.0 yaml 6.0.2 zipp NA zmq 26.2.0IPython 8.18.1
jupyter_client 8.6.3
jupyter_core 5.7.2
jupyterlab 4.3.2
Python 3.9.21 | packaged by conda-forge | (main, Dec 5 2024, 13:51:40) [GCC 13.3.0]
Linux-3.10.0-1160.95.1.el7.x86_64-x86_64-with-glibc2.17
Session information updated at 2024-12-08 22:19