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cannot import name 'LightningLoggerBase' from 'pytorch_lightning.loggers' #63

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zyll123 opened this issue Dec 8, 2024 · 3 comments
Open

cannot import name 'LightningLoggerBase' from 'pytorch_lightning.loggers' #63

zyll123 opened this issue Dec 8, 2024 · 3 comments
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bug Something isn't working

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@zyll123
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zyll123 commented Dec 8, 2024

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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

Click to view session session_info 1.0.0
Click 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 26.2.0

IPython 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
@zyll123 zyll123 added the bug Something isn't working label Dec 8, 2024
@marcovarrone
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Hi @zyll123, could you please tell me the scvi-tools and pytorch_lightning versions you have installed?

This would help me understand why this is happening!

@zyll123
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zyll123 commented Dec 9, 2024

Hi! @marcovarrone thanks for your reply! I am using scvi-tools 0.11.0 and pytorch_lightning 2.4.0. The full list of packages in the environment is shown below:

Name Version Build Channel
───────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge anaconda/cloud/conda-forge
_openmp_mutex 4.5 2_kmp_llvm anaconda/cloud/conda-forge
anndata 0.10.9 pyhd8ed1ab_0 anaconda/cloud/conda-forge
anyio 4.7.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
aom 3.6.1 h59595ed_0 anaconda/cloud/conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
argon2-cffi-bindings 21.2.0 py39h8cd3c5a_5 anaconda/cloud/conda-forge
array-api-compat 1.9.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
arrow 1.3.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
async-lru 2.0.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
attrs 24.2.0 pyh71513ae_1 anaconda/cloud/conda-forge
babel 2.16.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
backports 1.0 pyhd8ed1ab_5 anaconda/cloud/conda-forge
beautifulsoup4 4.12.3 pyha770c72_1 anaconda/cloud/conda-forge
blas 2.116 mkl anaconda/cloud/conda-forge
blas-devel 3.9.0 16_linux64_mkl anaconda/cloud/conda-forge
bleach 6.2.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
brotli-python 1.1.0 py39hf88036b_2 anaconda/cloud/conda-forge
bzip2 1.0.8 h4bc722e_7 anaconda/cloud/conda-forge
c-ares 1.34.3 hb9d3cd8_1 anaconda/cloud/conda-forge
ca-certificates 2024.8.30 hbcca054_0 anaconda/cloud/conda-forge
cachecontrol 0.14.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
cachecontrol-with-filecache 0.14.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
cached-property 1.5.2 hd8ed1ab_1 anaconda/cloud/conda-forge
cached_property 1.5.2 pyha770c72_1 anaconda/cloud/conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 anaconda/cloud/conda-forge
cffi 1.17.1 py39h15c3d72_0 anaconda/cloud/conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
cleo 2.2.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
colorama 0.4.6 pyhd8ed1ab_1 anaconda/cloud/conda-forge
comm 0.2.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
cpuonly 2.0 0 pytorch
cpython 3.9.21 py39hd8ed1ab_1 anaconda/cloud/conda-forge
crashtest 0.4.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
cryptography 44.0.0 py39h7170ec2_0 anaconda/cloud/conda-forge
dbus 1.13.6 h5008d03_3 anaconda/cloud/conda-forge
debugpy 1.8.9 py39hf88036b_0 anaconda/cloud/conda-forge
decorator 5.1.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
distlib 0.3.9 pyhd8ed1ab_1 anaconda/cloud/conda-forge
dnspython 2.7.0 pyhff2d567_1 anaconda/cloud/conda-forge
dulwich 0.21.7 py39h8cd3c5a_1 anaconda/cloud/conda-forge
entrypoints 0.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
et_xmlfile 2.0.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
executing 2.1.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
expat 2.6.4 h5888daf_0 anaconda/cloud/conda-forge
ffmpeg 4.4.2 gpl_hdf48244_113 anaconda/cloud/conda-forge
filelock 3.16.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 anaconda/cloud/conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 anaconda/cloud/conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 anaconda/cloud/conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 anaconda/cloud/conda-forge
fontconfig 2.15.0 h7e30c49_1 anaconda/cloud/conda-forge
fonts-conda-ecosystem 1 0 anaconda/cloud/conda-forge
fonts-conda-forge 1 0 anaconda/cloud/conda-forge
fqdn 1.5.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
freetype 2.12.1 h267a509_2 anaconda/cloud/conda-forge
fsspec 2024.10.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
future 1.0.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
gettext 0.22.5 he02047a_3 anaconda/cloud/conda-forge
gettext-tools 0.22.5 he02047a_3 anaconda/cloud/conda-forge
giflib 5.2.2 hd590300_0 anaconda/cloud/conda-forge
gmp 6.3.0 hac33072_2 anaconda/cloud/conda-forge
gmpy2 2.1.5 py39h7196dd7_3 anaconda/cloud/conda-forge
gnutls 3.7.9 hb077bed_0 anaconda/cloud/conda-forge
h11 0.14.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
h2 4.1.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
h5py 3.12.1 nompi_py39h30a5a8d_102 anaconda/cloud/conda-forge
hdf5 1.14.3 nompi_h2d575fe_107 anaconda/cloud/conda-forge
hpack 4.0.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
httpcore 1.0.7 pyh29332c3_1 anaconda/cloud/conda-forge
httpx 0.28.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
hyperframe 6.0.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
hyperopt 0.1.2 py_0 anaconda/cloud/conda-forge
idna 3.10 pyhd8ed1ab_1 anaconda/cloud/conda-forge
importlib-metadata 8.5.0 pyha770c72_1 anaconda/cloud/conda-forge
importlib_resources 6.4.5 pyhd8ed1ab_1 anaconda/cloud/conda-forge
ipykernel 6.29.5 pyh3099207_0 anaconda/cloud/conda-forge
ipython 8.18.1 pyh707e725_3 anaconda/cloud/conda-forge
ipywidgets 8.1.5 pyhd8ed1ab_1 anaconda/cloud/conda-forge
isoduration 20.11.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jaraco.classes 3.4.0 pyhd8ed1ab_2 anaconda/cloud/conda-forge
jedi 0.19.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jeepney 0.8.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
jinja2 3.1.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
joblib 1.4.2 pyhd8ed1ab_0 anaconda/cloud/conda-forge
json5 0.10.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jsonpointer 3.0.0 py39hf3d152e_1 anaconda/cloud/conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_1 anaconda/cloud/conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jupyter_core 5.7.2 pyh31011fe_1 anaconda/cloud/conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jupyter_server 2.14.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jupyterlab 4.3.2 pyhd8ed1ab_0 anaconda/cloud/conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 anaconda/cloud/conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
jupyterlab_widgets 3.0.13 pyhd8ed1ab_1 anaconda/cloud/conda-forge
keyring 24.3.1 pyha804496_1 anaconda/cloud/conda-forge
keyutils 1.6.1 h166bdaf_0 anaconda/cloud/conda-forge
krb5 1.21.3 h659f571_0 anaconda/cloud/conda-forge
lame 3.100 h166bdaf_1003 anaconda/cloud/conda-forge
lcms2 2.16 hb7c19ff_0 anaconda/cloud/conda-forge
ld_impl_linux-64 2.43 h712a8e2_2 anaconda/cloud/conda-forge
lerc 4.0.0 h27087fc_0 anaconda/cloud/conda-forge
libaec 1.1.3 h59595ed_0 anaconda/cloud/conda-forge
libasprintf 0.22.5 he8f35ee_3 anaconda/cloud/conda-forge
libasprintf-devel 0.22.5 he8f35ee_3 anaconda/cloud/conda-forge
libblas 3.9.0 16_linux64_mkl anaconda/cloud/conda-forge
libcblas 3.9.0 16_linux64_mkl anaconda/cloud/conda-forge
libcurl 8.10.1 hbbe4b11_0 anaconda/cloud/conda-forge
libdeflate 1.22 hb9d3cd8_0 anaconda/cloud/conda-forge
libdrm 2.4.124 hb9d3cd8_0 anaconda/cloud/conda-forge
libedit 3.1.20191231 he28a2e2_2 anaconda/cloud/conda-forge
libegl 1.7.0 ha4b6fd6_2 anaconda/cloud/conda-forge
libev 4.33 hd590300_2 anaconda/cloud/conda-forge
libexpat 2.6.4 h5888daf_0 anaconda/cloud/conda-forge
libffi 3.4.2 h7f98852_5 anaconda/cloud/conda-forge
libgcc 14.2.0 h77fa898_1 anaconda/cloud/conda-forge
libgcc-ng 14.2.0 h69a702a_1 anaconda/cloud/conda-forge
libgettextpo 0.22.5 he02047a_3 anaconda/cloud/conda-forge
libgettextpo-devel 0.22.5 he02047a_3 anaconda/cloud/conda-forge
libgfortran 14.2.0 h69a702a_1 anaconda/cloud/conda-forge
libgfortran-ng 14.2.0 h69a702a_1 anaconda/cloud/conda-forge
libgfortran5 14.2.0 hd5240d6_1 anaconda/cloud/conda-forge
libgl 1.7.0 ha4b6fd6_2 anaconda/cloud/conda-forge
libglib 2.82.2 h2ff4ddf_0 anaconda/cloud/conda-forge
libglvnd 1.7.0 ha4b6fd6_2 anaconda/cloud/conda-forge
libglx 1.7.0 ha4b6fd6_2 anaconda/cloud/conda-forge
libgomp 14.2.0 h77fa898_1 anaconda/cloud/conda-forge
libhwloc 2.11.2 default_h0d58e46_1001 anaconda/cloud/conda-forge
libiconv 1.17 hd590300_2 anaconda/cloud/conda-forge
libidn2 2.3.7 hd590300_0 anaconda/cloud/conda-forge
libjpeg-turbo 3.0.0 hd590300_1 anaconda/cloud/conda-forge
liblapack 3.9.0 16_linux64_mkl anaconda/cloud/conda-forge
liblapacke 3.9.0 16_linux64_mkl anaconda/cloud/conda-forge
libllvm14 14.0.6 hcd5def8_4 anaconda/cloud/conda-forge
liblzma 5.6.3 hb9d3cd8_1 anaconda/cloud/conda-forge
libnghttp2 1.64.0 h161d5f1_0 anaconda/cloud/conda-forge
libnsl 2.0.1 hd590300_0 anaconda/cloud/conda-forge
libpciaccess 0.18 hd590300_0 anaconda/cloud/conda-forge
libpng 1.6.44 hadc24fc_0 anaconda/cloud/conda-forge
libsodium 1.0.20 h4ab18f5_0 anaconda/cloud/conda-forge
libsqlite 3.47.0 hadc24fc_1 anaconda/cloud/conda-forge
libssh2 1.11.1 hf672d98_0 anaconda/cloud/conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 anaconda/cloud/conda-forge
libstdcxx-ng 14.2.0 h4852527_1 anaconda/cloud/conda-forge
libtasn1 4.19.0 h166bdaf_0 anaconda/cloud/conda-forge
libtiff 4.7.0 hc4654cb_2 anaconda/cloud/conda-forge
libunistring 0.9.10 h7f98852_0 anaconda/cloud/conda-forge
libuuid 2.38.1 h0b41bf4_0 anaconda/cloud/conda-forge
libva 2.22.0 h8a09558_1 anaconda/cloud/conda-forge
libvpx 1.13.1 h59595ed_0 anaconda/cloud/conda-forge
libwebp 1.4.0 h2c329e2_0 anaconda/cloud/conda-forge
libwebp-base 1.4.0 hd590300_0 anaconda/cloud/conda-forge
libxcb 1.17.0 h8a09558_0 anaconda/cloud/conda-forge
libxcrypt 4.4.36 hd590300_1 anaconda/cloud/conda-forge
libxml2 2.13.5 h0d44e9d_1 anaconda/cloud/conda-forge
libzlib 1.3.1 hb9d3cd8_2 anaconda/cloud/conda-forge
lightning-utilities 0.11.9 pyhff2d567_0 anaconda/cloud/conda-forge
llvm-openmp 15.0.7 h0cdce71_0 anaconda/cloud/conda-forge
llvmlite 0.43.0 py39hf8b6b1a_1 anaconda/cloud/conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
markupsafe 3.0.2 py39h9399b63_1 anaconda/cloud/conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_1 anaconda/cloud/conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
mistune 3.0.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
mkl 2022.1.0 h84fe81f_915 anaconda/cloud/conda-forge
mkl-devel 2022.1.0 ha770c72_916 anaconda/cloud/conda-forge
mkl-include 2022.1.0 h84fe81f_915 anaconda/cloud/conda-forge
more-itertools 10.5.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
mpc 1.3.1 h24ddda3_1 anaconda/cloud/conda-forge
mpfr 4.2.1 h90cbb55_3 anaconda/cloud/conda-forge
mpmath 1.3.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
msgpack-python 1.1.0 py39h74842e3_0 anaconda/cloud/conda-forge
natsort 8.4.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
nbclient 0.10.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
nbconvert-core 7.16.4 pyhff2d567_2 anaconda/cloud/conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
ncurses 6.5 he02047a_1 anaconda/cloud/conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
nettle 3.9.1 h7ab15ed_0 anaconda/cloud/conda-forge
networkx 3.2.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
numba 0.60.0 py39h0320e7d_0 anaconda/cloud/conda-forge
numpy 2.0.2 py39h9cb892a_1 anaconda/cloud/conda-forge
openh264 2.3.1 hcb278e6_2 anaconda/cloud/conda-forge
openjpeg 2.5.2 h488ebb8_0 anaconda/cloud/conda-forge
openpyxl 3.1.5 py39h79730dd_1 anaconda/cloud/conda-forge
openssl 3.4.0 hb9d3cd8_0 anaconda/cloud/conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
overrides 7.7.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
p11-kit 0.24.1 hc5aa10d_0 anaconda/cloud/conda-forge
packaging 24.2 pyhd8ed1ab_2 anaconda/cloud/conda-forge
pandas 2.2.3 py39h3b40f6f_1 anaconda/cloud/conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
parso 0.8.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
pcre2 10.44 hba22ea6_2 anaconda/cloud/conda-forge
pexpect 4.9.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
pickleshare 0.7.5 pyhd8ed1ab_1004 anaconda/cloud/conda-forge
pillow 11.0.0 py39h538c539_0 anaconda/cloud/conda-forge
pip 24.3.1 pyh8b19718_0 anaconda/cloud/conda-forge
pkginfo 1.12.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 anaconda/cloud/conda-forge
platformdirs 4.3.6 pyhd8ed1ab_1 anaconda/cloud/conda-forge
poetry 1.8.4 linux_pyha804496_1 anaconda/cloud/conda-forge
poetry-core 1.9.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
poetry-plugin-export 1.8.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
prometheus_client 0.21.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
prompt-toolkit 3.0.48 pyha770c72_1 anaconda/cloud/conda-forge
psutil 6.1.0 py39h8cd3c5a_0 anaconda/cloud/conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 anaconda/cloud/conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
pycparser 2.22 pyh29332c3_1 anaconda/cloud/conda-forge
pygments 2.18.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
pymongo 4.10.1 py39hf88036b_0 anaconda/cloud/conda-forge
pyproject_hooks 1.2.0 pyh7850678_0 anaconda/cloud/conda-forge
pyro-api 0.1.2 pyhd8ed1ab_0 anaconda/cloud/conda-forge
pyro-ppl 1.9.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
pysocks 1.7.1 pyha55dd90_7 anaconda/cloud/conda-forge
python 3.9.21 h9c0c6dc_1_cpython anaconda/cloud/conda-forge
python-build 1.2.2.post1 pyhff2d567_1 anaconda/cloud/conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 anaconda/cloud/conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
python-installer 0.7.0 pyhff2d567_1 anaconda/cloud/conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 anaconda/cloud/conda-forge
python-tzdata 2024.2 pyhd8ed1ab_1 anaconda/cloud/conda-forge
python_abi 3.9 5_cp39 anaconda/cloud/conda-forge
pytorch 2.5.1 py3.9_cpu_0 pytorch
pytorch-lightning 2.4.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
pytorch-mutex 1.0 cpu pytorch
pytz 2024.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
pyyaml 6.0.2 py39h8cd3c5a_1 anaconda/cloud/conda-forge
pyzmq 26.2.0 py39h4e4fb57_3 anaconda/cloud/conda-forge
readline 8.2 h8228510_1 anaconda/cloud/conda-forge
referencing 0.35.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
requests 2.32.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
requests-toolbelt 1.0.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 anaconda/cloud/conda-forge
rich 13.9.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
rpds-py 0.22.3 py39he612d8f_0 anaconda/cloud/conda-forge
scikit-learn 1.5.2 py39h4b7350c_1 anaconda/cloud/conda-forge
scipy 1.13.1 py39haf93ffa_0 anaconda/cloud/conda-forge
scprep 1.2.3 pyhdfd78af_0 anaconda/cloud/bioconda
scvi-tools 0.11.0 pyhdfd78af_0 anaconda/cloud/bioconda
secretstorage 3.3.3 py39hf3d152e_3 anaconda/cloud/conda-forge
send2trash 1.8.3 pyh0d859eb_1 anaconda/cloud/conda-forge
setuptools 75.6.0 pyhff2d567_1 anaconda/cloud/conda-forge
shellingham 1.5.4 pyhd8ed1ab_1 anaconda/cloud/conda-forge
six 1.17.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
soupsieve 2.5 pyhd8ed1ab_1 anaconda/cloud/conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
svt-av1 1.4.1 hcb278e6_0 anaconda/cloud/conda-forge
sympy 1.13.3 pyh2585a3b_104 anaconda/cloud/conda-forge
tbb 2021.13.0 hceb3a55_1 anaconda/cloud/conda-forge
terminado 0.18.1 pyh0d859eb_0 anaconda/cloud/conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 anaconda/cloud/conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
tk 8.6.13 noxft_h4845f30_101 anaconda/cloud/conda-forge
toml 0.10.2 pyhd8ed1ab_0 anaconda/cloud/conda-forge
tomli 2.2.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
tomlkit 0.13.2 pyha770c72_1 anaconda/cloud/conda-forge
torchaudio 2.5.1 py39_cpu pytorch
torchmetrics 1.5.2 pyhe5570ce_0 anaconda/cloud/conda-forge
torchvision 0.20.1 py39_cpu pytorch
tornado 6.4.2 py39h8cd3c5a_0 anaconda/cloud/conda-forge
tqdm 4.67.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
trove-classifiers 2024.10.21.16 pyhd8ed1ab_1 anaconda/cloud/conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 anaconda/cloud/conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 anaconda/cloud/conda-forge
typing_extensions 4.12.2 pyha770c72_1 anaconda/cloud/conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
tzdata 2024b hc8b5060_0 anaconda/cloud/conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
urllib3 2.2.3 pyhd8ed1ab_1 anaconda/cloud/conda-forge
virtualenv 20.28.0 pyhd8ed1ab_0 anaconda/cloud/conda-forge
wayland 1.23.1 h3e06ad9_0 anaconda/cloud/conda-forge
wayland-protocols 1.37 hd8ed1ab_0 anaconda/cloud/conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 anaconda/cloud/conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 anaconda/cloud/conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 anaconda/cloud/conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
wheel 0.45.1 pyhd8ed1ab_1 anaconda/cloud/conda-forge
widgetsnbextension 4.0.13 pyhd8ed1ab_1 anaconda/cloud/conda-forge
x264 1!164.3095 h166bdaf_2 anaconda/cloud/conda-forge
x265 3.5 h924138e_3 anaconda/cloud/conda-forge
xorg-libx11 1.8.10 h4f16b4b_1 anaconda/cloud/conda-forge
xorg-libxau 1.0.11 hb9d3cd8_1 anaconda/cloud/conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 anaconda/cloud/conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 anaconda/cloud/conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 anaconda/cloud/conda-forge
yaml 0.2.5 h7f98852_2 anaconda/cloud/conda-forge
zeromq 4.3.5 h3b0a872_7 anaconda/cloud/conda-forge
zipp 3.21.0 pyhd8ed1ab_1 anaconda/cloud/conda-forge
zstandard 0.23.0 py39h08a7858_1 anaconda/cloud/conda-forge
zstd 1.5.6 ha6fb4c9_0 anaconda/cloud/conda-forge

@marcovarrone
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Then the reason is an incompatibility between a very old version of scvi-tools and a quite recent version of pytorch_lightning.
Is there a specific reason why you are restricted to a version of scvi-tools which is almost 3-4 years old?

If not, I would suggest you to install a more recent version of scvi-tools.

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