scvi-tools: scvi installing errors on get_num_classes and configure formatter 'console'

Hi,

I am one of the scvi users. When I installed the scvi tool in a conda env, I ended up with the below errors. I tested the installation in a conda env on Windows-based and Linux-based operating systems.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: D:\Programming\anaconda3\envs\scanal

  added / updated specs:
    - scvi-tools


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pyjwt-2.4.0                |     pyhd8ed1ab_0          19 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          19 KB

The following NEW packages will be INSTALLED:

  absl-py            conda-forge/noarch::absl-py-1.0.0-pyhd8ed1ab_0
  aiohttp            conda-forge/win-64::aiohttp-3.8.1-py38h294d835_1
  aiosignal          conda-forge/noarch::aiosignal-1.2.0-pyhd8ed1ab_0
  argon2-cffi        conda-forge/noarch::argon2-cffi-21.3.0-pyhd8ed1ab_0
  argon2-cffi-bindi~ conda-forge/win-64::argon2-cffi-bindings-21.2.0-py38h294d835_2
  asttokens          conda-forge/noarch::asttokens-2.0.5-pyhd8ed1ab_0
  async-timeout      conda-forge/noarch::async-timeout-4.0.2-pyhd8ed1ab_0
  attrs              conda-forge/noarch::attrs-21.4.0-pyhd8ed1ab_0
  backcall           conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
  beautifulsoup4     conda-forge/noarch::beautifulsoup4-4.11.1-pyha770c72_0
  blas               pkgs/main/win-64::blas-1.0-mkl
  bleach             conda-forge/noarch::bleach-5.0.0-pyhd8ed1ab_0
  blinker            conda-forge/noarch::blinker-1.4-py_1
  cachetools         conda-forge/noarch::cachetools-5.0.0-pyhd8ed1ab_0
  click              conda-forge/win-64::click-8.1.3-py38haa244fe_0
  commonmark         conda-forge/noarch::commonmark-0.9.1-py_0
  dataclasses        conda-forge/noarch::dataclasses-0.8-pyhc8e2a94_3
  debugpy            conda-forge/win-64::debugpy-1.6.0-py38h885f38d_0
  decorator          conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0
  defusedxml         conda-forge/noarch::defusedxml-0.7.1-pyhd8ed1ab_0
  docrep             conda-forge/noarch::docrep-0.3.2-pyh44b312d_0
  entrypoints        conda-forge/noarch::entrypoints-0.4-pyhd8ed1ab_0
  et_xmlfile         conda-forge/noarch::et_xmlfile-1.0.1-py_1001
  executing          conda-forge/noarch::executing-0.8.3-pyhd8ed1ab_0
  flit-core          conda-forge/noarch::flit-core-3.7.1-pyhd8ed1ab_0
  frozenlist         conda-forge/win-64::frozenlist-1.3.0-py38h294d835_1
  fsspec             conda-forge/noarch::fsspec-2022.3.0-pyhd8ed1ab_0
  future             conda-forge/win-64::future-0.18.2-py38haa244fe_5
  google-auth        conda-forge/noarch::google-auth-2.6.6-pyh6c4a22f_0
  google-auth-oauth~ conda-forge/noarch::google-auth-oauthlib-0.4.6-pyhd8ed1ab_0
  grpcio             conda-forge/win-64::grpcio-1.46.1-py38he5377a8_0
  importlib_resourc~ conda-forge/noarch::importlib_resources-5.7.1-pyhd8ed1ab_0
  ipykernel          conda-forge/win-64::ipykernel-6.13.0-py38h4317176_0
  ipython            conda-forge/win-64::ipython-8.3.0-py38haa244fe_0
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  ipywidgets         conda-forge/noarch::ipywidgets-7.7.0-pyhd8ed1ab_0
  jedi               conda-forge/win-64::jedi-0.18.1-py38haa244fe_1
  jsonschema         conda-forge/noarch::jsonschema-4.5.1-pyhd8ed1ab_0
  jupyter_client     conda-forge/noarch::jupyter_client-7.3.1-pyhd8ed1ab_0
  jupyter_core       conda-forge/win-64::jupyter_core-4.10.0-py38haa244fe_0
  jupyterlab_pygmen~ conda-forge/noarch::jupyterlab_pygments-0.2.2-pyhd8ed1ab_0
  jupyterlab_widgets conda-forge/noarch::jupyterlab_widgets-1.1.0-pyhd8ed1ab_0
  libprotobuf        conda-forge/win-64::libprotobuf-3.20.1-h7755175_0
  libsodium          conda-forge/win-64::libsodium-1.0.18-h8d14728_1
  libuv              conda-forge/win-64::libuv-1.43.0-h8ffe710_0
  markdown           conda-forge/noarch::markdown-3.3.7-pyhd8ed1ab_0
  matplotlib-inline  conda-forge/noarch::matplotlib-inline-0.1.3-pyhd8ed1ab_0
  mistune            conda-forge/win-64::mistune-0.8.4-py38h294d835_1005
  mkl-service        conda-forge/win-64::mkl-service-2.4.0-py38h4f8af0f_0
  multidict          conda-forge/win-64::multidict-6.0.2-py38h294d835_1
  nbclient           conda-forge/noarch::nbclient-0.6.3-pyhd8ed1ab_0
  nbconvert          conda-forge/noarch::nbconvert-6.5.0-pyhd8ed1ab_0
  nbconvert-core     conda-forge/noarch::nbconvert-core-6.5.0-pyhd8ed1ab_0
  nbconvert-pandoc   conda-forge/noarch::nbconvert-pandoc-6.5.0-pyhd8ed1ab_0
  nbformat           conda-forge/noarch::nbformat-5.4.0-pyhd8ed1ab_0
  nest-asyncio       conda-forge/noarch::nest-asyncio-1.5.5-pyhd8ed1ab_0
  ninja              conda-forge/win-64::ninja-1.10.2-h2d74725_1
  notebook           conda-forge/noarch::notebook-6.4.11-pyha770c72_0
  oauthlib           conda-forge/noarch::oauthlib-3.2.0-pyhd8ed1ab_0
  openpyxl           conda-forge/noarch::openpyxl-3.0.9-pyhd8ed1ab_0
  opt_einsum         conda-forge/noarch::opt_einsum-3.3.0-pyhd8ed1ab_1
  pandoc             conda-forge/win-64::pandoc-2.18-h57928b3_0
  pandocfilters      conda-forge/noarch::pandocfilters-1.5.0-pyhd8ed1ab_0
  parso              conda-forge/noarch::parso-0.8.3-pyhd8ed1ab_0
  pickleshare        conda-forge/noarch::pickleshare-0.7.5-py_1003
  prometheus_client  conda-forge/noarch::prometheus_client-0.14.1-pyhd8ed1ab_0
  prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.29-pyha770c72_0
  protobuf           conda-forge/win-64::protobuf-3.20.1-py38haa244fe_0
  psutil             conda-forge/win-64::psutil-5.9.0-py38h294d835_1
  pure_eval          conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0
  pyasn1             conda-forge/noarch::pyasn1-0.4.8-py_0
  pyasn1-modules     conda-forge/noarch::pyasn1-modules-0.2.7-py_0
  pydeprecate        conda-forge/noarch::pydeprecate-0.3.0-pyhd8ed1ab_0
  pyjwt              conda-forge/noarch::pyjwt-2.4.0-pyhd8ed1ab_0
  pyro-api           conda-forge/noarch::pyro-api-0.1.2-pyhd8ed1ab_0
  pyro-ppl           conda-forge/noarch::pyro-ppl-1.8.0-pyhd8ed1ab_0
  pyrsistent         conda-forge/win-64::pyrsistent-0.18.1-py38h294d835_1
  python-fastjsonsc~ conda-forge/noarch::python-fastjsonschema-2.15.3-pyhd8ed1ab_0
  pytorch            pkgs/main/win-64::pytorch-1.10.2-cpu_py38h907fbb5_0
  pytorch-lightning  conda-forge/noarch::pytorch-lightning-1.3.8-pyhd8ed1ab_0
  pyu2f              conda-forge/noarch::pyu2f-0.1.5-pyhd8ed1ab_0
  pywin32            conda-forge/win-64::pywin32-303-py38h294d835_0
  pywinpty           conda-forge/win-64::pywinpty-0.5.7-py38haa244fe_1
  pyyaml             conda-forge/win-64::pyyaml-5.4.1-py38h294d835_1
  pyzmq              conda-forge/win-64::pyzmq-22.3.0-py38h09162b1_2
  requests-oauthlib  conda-forge/noarch::requests-oauthlib-1.3.1-pyhd8ed1ab_0
  rich               conda-forge/noarch::rich-12.4.1-pyhd8ed1ab_0
  rsa                conda-forge/noarch::rsa-4.8-pyhd8ed1ab_0
  scvi-tools         bioconda/noarch::scvi-tools-0.14.5-pyhdfd78af_0
  send2trash         conda-forge/noarch::send2trash-1.8.0-pyhd8ed1ab_0
  soupsieve          conda-forge/noarch::soupsieve-2.3.1-pyhd8ed1ab_0
  stack_data         conda-forge/noarch::stack_data-0.2.0-pyhd8ed1ab_0
  tensorboard        conda-forge/noarch::tensorboard-2.9.0-pyhd8ed1ab_0
  tensorboard-data-~ conda-forge/win-64::tensorboard-data-server-0.6.0-py38haa244fe_2
  tensorboard-plugi~ conda-forge/noarch::tensorboard-plugin-wit-1.8.1-pyhd8ed1ab_0
  terminado          conda-forge/win-64::terminado-0.9.5-py38haa244fe_0
  tinycss2           conda-forge/noarch::tinycss2-1.1.1-pyhd8ed1ab_0
  torchmetrics       conda-forge/noarch::torchmetrics-0.8.2-pyhd8ed1ab_0
  tornado            conda-forge/win-64::tornado-6.1-py38h294d835_3
  traitlets          conda-forge/noarch::traitlets-5.2.0-pyhd8ed1ab_0
  typing-extensions  conda-forge/noarch::typing-extensions-4.2.0-hd8ed1ab_1
  typing_extensions  conda-forge/noarch::typing_extensions-4.2.0-pyha770c72_1
  wcwidth            conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_2
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  werkzeug           conda-forge/noarch::werkzeug-2.1.2-pyhd8ed1ab_1
  widgetsnbextension conda-forge/win-64::widgetsnbextension-3.6.0-py38haa244fe_0
  winpty             conda-forge/win-64::winpty-0.4.3-4
  yaml               conda-forge/win-64::yaml-0.2.5-h8ffe710_2
  yarl               conda-forge/win-64::yarl-1.7.2-py38h294d835_2
  zeromq             conda-forge/win-64::zeromq-4.3.4-h0e60522_1


Proceed ([y]/n)? y


Downloading and Extracting Packages
pyjwt-2.4.0          | 19 KB     | ##################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: \ Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: ok
Exception ignored in: <function Application.__del__ at 0x0000018992B59310>
Traceback (most recent call last):
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 955, in __del__
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 945, in close_handlers
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\traitlets.py", line 683, in __get__
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\traitlets.py", line 657, in get
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\traitlets.py", line 1428, in _notify_observers
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 273, in _observe_logging_default
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 278, in _configure_logging
  File "D:\Programming\anaconda3\envs\scanal\lib\logging\config.py", line 808, in dictConfig
  File "D:\Programming\anaconda3\envs\scanal\lib\logging\config.py", line 545, in configure
ValueError: Unable to configure formatter 'console'

done

And furthurmore I got this below when I imported scvi in the jupyter notebook.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import scvi

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\scvi\__init__.py:7, in <module>
      4 import logging
      6 from ._constants import _CONSTANTS
----> 7 from ._settings import settings
      9 # this import needs to come after prior imports to prevent circular import
     10 from . import data, model, external, utils

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\scvi\_settings.py:5, in <module>
      2 from pathlib import Path
      3 from typing import Union
----> 5 import pytorch_lightning as pl
      6 import torch
      7 from rich.console import Console

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\__init__.py:20, in <module>
     17 _PACKAGE_ROOT = os.path.dirname(__file__)
     18 _PROJECT_ROOT = os.path.dirname(_PACKAGE_ROOT)
---> 20 from pytorch_lightning import metrics  # noqa: E402
     21 from pytorch_lightning.callbacks import Callback  # noqa: E402
     22 from pytorch_lightning.core import LightningDataModule, LightningModule  # noqa: E402

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\__init__.py:15, in <module>
      1 # Copyright The PyTorch Lightning team.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     12 # See the License for the specific language governing permissions and
     13 # limitations under the License.
---> 15 from pytorch_lightning.metrics.classification import (  # noqa: F401
     16     Accuracy,
     17     AUC,
     18     AUROC,
     19     AveragePrecision,
     20     ConfusionMatrix,
     21     F1,
     22     FBeta,
     23     HammingDistance,
     24     IoU,
     25     Precision,
     26     PrecisionRecallCurve,
     27     Recall,
     28     ROC,
     29     StatScores,
     30 )
     31 from pytorch_lightning.metrics.metric import Metric, MetricCollection  # noqa: F401
     32 from pytorch_lightning.metrics.regression import (  # noqa: F401
     33     ExplainedVariance,
     34     MeanAbsoluteError,
   (...)
     39     SSIM,
     40 )

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\classification\__init__.py:14, in <module>
      1 # Copyright The PyTorch Lightning team.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     12 # See the License for the specific language governing permissions and
     13 # limitations under the License.
---> 14 from pytorch_lightning.metrics.classification.accuracy import Accuracy  # noqa: F401
     15 from pytorch_lightning.metrics.classification.auc import AUC  # noqa: F401
     16 from pytorch_lightning.metrics.classification.auroc import AUROC  # noqa: F401

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\classification\accuracy.py:18, in <module>
     14 from typing import Any, Callable, Optional
     16 from torchmetrics import Accuracy as _Accuracy
---> 18 from pytorch_lightning.metrics.utils import deprecated_metrics
     21 class Accuracy(_Accuracy):
     23     @deprecated_metrics(target=_Accuracy)
     24     def __init__(
     25         self,
   (...)
     32         dist_sync_fn: Callable = None,
     33     ):

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\utils.py:22, in <module>
     20 from torchmetrics.utilities.data import dim_zero_mean as _dim_zero_mean
     21 from torchmetrics.utilities.data import dim_zero_sum as _dim_zero_sum
---> 22 from torchmetrics.utilities.data import get_num_classes as _get_num_classes
     23 from torchmetrics.utilities.data import select_topk as _select_topk
     24 from torchmetrics.utilities.data import to_categorical as _to_categorical

ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (D:\Programming\anaconda3\envs\scanal\lib\site-packages\torchmetrics\utilities\data.py)

Please if there is any help with this issue. Thanks!

Best