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scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data
http://scvi-tools.org/
BSD 3-Clause "New" or "Revised" License
1.25k stars 353 forks source link

Installation conflict between PyYaML versions #1996

Closed Angelos-Gk closed 1 year ago

Angelos-Gk commented 1 year ago

I am trying to install scvi-tools in python, I have PyYaML 6.0, It asks for 5.4.1 and automatically installs it but then asks for 6.0 I am using Jupyter Notebook if it matters.

!pip install scvi-tools
Requirement already satisfied: scvi-tools in c:\users\angel\anaconda3\lib\site-packages (0.14.6)
Requirement already satisfied: torchmetrics>=0.6.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (0.11.4)
Requirement already satisfied: numba>=0.41.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (0.56.4)
Requirement already satisfied: docrep>=0.3.2 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (0.3.2)
Requirement already satisfied: numpy>=1.17.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.21.5)
Requirement already satisfied: openpyxl>=3.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (3.0.10)
Requirement already satisfied: rich>=9.1.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (13.3.3)
Requirement already satisfied: pyro-ppl>=1.6.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.8.4)
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Requirement already satisfied: future>=0.17.1 in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.4,>=1.3->scvi-tools) (0.18.2)
Collecting PyYAML<=5.4.1,>=5.1
  Using cached PyYAML-5.4.1-cp39-cp39-win_amd64.whl (213 kB)
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Requirement already satisfied: pywinpty>=1.1.0 in c:\users\angel\anaconda3\lib\site-packages (from terminado>=0.8.3->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (2.0.2)
Requirement already satisfied: argon2-cffi-bindings in c:\users\angel\anaconda3\lib\site-packages (from argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (21.2.0)
Requirement already satisfied: websocket-client in c:\users\angel\anaconda3\lib\site-packages (from jupyter-server>=1.8->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.58.0)
Requirement already satisfied: anyio<4,>=3.1.0 in c:\users\angel\anaconda3\lib\site-packages (from jupyter-server>=1.8->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (3.5.0)
Requirement already satisfied: cffi>=1.0.1 in c:\users\angel\anaconda3\lib\site-packages (from argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (1.15.1)
Requirement already satisfied: soupsieve>1.2 in c:\users\angel\anaconda3\lib\site-packages (from beautifulsoup4->nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (2.3.2.post1)
Requirement already satisfied: webencodings in c:\users\angel\anaconda3\lib\site-packages (from bleach->nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.5.1)
Requirement already satisfied: sniffio>=1.1 in c:\users\angel\anaconda3\lib\site-packages (from anyio<4,>=3.1.0->jupyter-server>=1.8->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (1.2.0)
Requirement already satisfied: pycparser in c:\users\angel\anaconda3\lib\site-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (2.21)
Installing collected packages: PyYAML
  Attempting uninstall: PyYAML
    Found existing installation: PyYAML 6.0
    Uninstalling PyYAML-6.0:
      Successfully uninstalled PyYAML-6.0
Successfully installed PyYAML-5.4.1
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
conda-repo-cli 1.0.24 requires PyYAML==6.0, but you have pyyaml 5.4.1 which is incompatible.

Versions:

VERSION

Selected Jupyter core packages... IPython : 7.31.1 ipykernel : 6.15.2 ipywidgets : 7.6.5 jupyter_client : 7.4.7 jupyter_core : 4.11.2 jupyter_server : 1.18.1 jupyterlab : 3.5.0 nbclient : 0.5.13 nbconvert : 6.4.4 nbformat : 5.4.0 notebook : 6.5.2 qtconsole : 5.2.2 traitlets : 5.1.1

Python version: '3.9.15' Pip version: pip 22.2.2

adamgayoso commented 1 year ago

First line of the message shows

Requirement already satisfied: scvi-tools in c:\users\angel\anaconda3\lib\site-packages (0.14.6)

Can you upgrade to 0.20.3? Please follow the windows specific instructions on our installation page

Angelos-Gk commented 1 year ago

Thank you for your response. pip show scvi-tools Name: scvi-tools Version: 0.14.6 Summary: Deep probabilistic analysis of single-cell omics data. Home-page: https://github.com/YosefLab/scvi-tools Author: Romain Lopez Author-email: romain_lopez@gmail.com License: BSD-3-Clause Location: c:\users\angel\anaconda3\lib\site-packages Requires: anndata, docrep, h5py, ipywidgets, numba, numpy, openpyxl, pandas, pyro-ppl, pytorch-lightning, rich, scikit-learn, setuptools, torch, torchmetrics, tqdm Required-by: Note: you may need to restart the kernel to use updated packages.

But when i try to import it i get: C:\Users\angel\anaconda3\lib\site-packages\torchvision\io\image.py:13: UserWarning: Failed to load image Python extension: 'Could not find module 'C:\Users\angel\anaconda3\Lib\site-packages\torchvision\image.pyd' (or one of its dependencies). Try using the full path with constructor syntax.'If you don't plan on using image functionality fromtorchvision.io, you can ignore this warning. Otherwise, there might be something wrong with your environment. Did you havelibjpegorlibpnginstalled before buildingtorchvision` from source? warn(

ImportError Traceback (most recent call last) ~\AppData\Local\Temp\ipykernel_22332\4292830130.py in ----> 1 import scvi # install with !pip install scvi-tools

~\anaconda3\lib\site-packages\scvi__init__.py in 5 6 from ._constants import _CONSTANTS ----> 7 from ._settings import settings 8 9 # this import needs to come after prior imports to prevent circular import

~\anaconda3\lib\site-packages\scvi_settings.py in 3 from typing import Union 4 ----> 5 import pytorch_lightning as pl 6 import torch 7 from rich.console import Console

~\anaconda3\lib\site-packages\pytorch_lightning__init__.py in 18 _PROJECT_ROOT = os.path.dirname(_PACKAGE_ROOT) 19 ---> 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

~\anaconda3\lib\site-packages\pytorch_lightning\metrics__init__.py in 13 # limitations under the License. 14 ---> 15 from pytorch_lightning.metrics.classification import ( # noqa: F401 16 Accuracy, 17 AUC,

~\anaconda3\lib\site-packages\pytorch_lightning\metrics\classification__init__.py in 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

~\anaconda3\lib\site-packages\pytorch_lightning\metrics\classification\accuracy.py in 16 from torchmetrics import Accuracy as _Accuracy 17 ---> 18 from pytorch_lightning.metrics.utils import deprecated_metrics 19 20

~\anaconda3\lib\site-packages\pytorch_lightning\metrics\utils.py in 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' (C:\Users\angel\anaconda3\lib\site-packages\torchmetrics\utilities\data.py`

adamgayoso commented 1 year ago

you will need to upgrade scvi-tools to version 0.20.3

Angelos-Gk commented 1 year ago

i tried this command %pip install scvi-tools --upgrade

and got this output

Requirement already satisfied: scvi-tools in c:\users\angel\anaconda3\lib\site-packages (0.14.6) Collecting scvi-tools Using cached scvi_tools-0.20.3-py3-none-any.whl (330 kB) Requirement already satisfied: torch>=1.8.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (2.0.0) Collecting pytorch-lightning<1.10.0,>=1.9.0 Using cached pytorch_lightning-1.9.4-py3-none-any.whl (827 kB) Requirement already satisfied: anndata>=0.7.5 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (0.8.0) Collecting ml-collections>=0.1.1 Using cached ml_collections-0.1.1.tar.gz (77 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: pyro-ppl>=1.6.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.8.4) Requirement already satisfied: docrep>=0.3.2 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (0.3.2) Requirement already satisfied: torchmetrics>=0.11.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (0.11.4) Requirement already satisfied: h5py>=2.9.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (3.7.0) Collecting numpyro Using cached numpyro-0.11.0-py3-none-any.whl (300 kB) Collecting chex Using cached chex-0.1.7-py3-none-any.whl (89 kB) Collecting optax Using cached optax-0.1.4-py3-none-any.whl (154 kB) Collecting mudata>=0.1.2 Using cached mudata-0.2.2-py3-none-any.whl (23 kB) Requirement already satisfied: openpyxl>=3.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (3.0.10) Requirement already satisfied: scipy in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.9.3) Requirement already satisfied: tqdm>=4.56.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (4.64.1) Requirement already satisfied: scikit-learn>=0.21.2 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.0.2) Collecting scvi-tools Using cached scvi_tools-0.20.2-py3-none-any.whl (330 kB) Using cached scvi_tools-0.20.1-py3-none-any.whl (330 kB) Using cached scvi_tools-0.20.0-py3-none-any.whl (330 kB) Using cached scvi_tools-0.19.0-py3-none-any.whl (296 kB) Using cached scvi_tools-0.18.0-py3-none-any.whl (290 kB) Collecting pytorch-lightning<1.8,>=1.6.0 Using cached pytorch_lightning-1.7.7-py3-none-any.whl (708 kB) Collecting scvi-tools Using cached scvi_tools-0.17.4-py3-none-any.whl (272 kB) Using cached scvi_tools-0.17.3-py3-none-any.whl (271 kB) Using cached scvi_tools-0.17.2-py3-none-any.whl (271 kB) Using cached scvi_tools-0.17.1-py3-none-any.whl (271 kB) Using cached scvi_tools-0.17.0-py3-none-any.whl (271 kB) Using cached scvi_tools-0.16.4-py3-none-any.whl (262 kB) Collecting pytorch-lightning<1.6,>=1.5 Using cached pytorch_lightning-1.5.10-py3-none-any.whl (527 kB) Collecting protobuf<=3.20.1 Using cached protobuf-3.20.1-cp39-cp39-win_amd64.whl (904 kB) Requirement already satisfied: rich>=9.1.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (13.3.3) Requirement already satisfied: ipywidgets in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (7.6.5) Collecting jax>=0.3 Using cached jax-0.4.8.tar.gz (1.2 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting flax Using cached flax-0.6.8-py3-none-any.whl (216 kB) Requirement already satisfied: pandas>=1.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.4.4) Requirement already satisfied: numpy>=1.17.0 in c:\users\angel\anaconda3\lib\site-packages (from scvi-tools) (1.21.5) Requirement already satisfied: packaging>=20 in c:\users\angel\anaconda3\lib\site-packages (from anndata>=0.7.5->scvi-tools) (21.3) Requirement already satisfied: natsort in c:\users\angel\anaconda3\lib\site-packages (from anndata>=0.7.5->scvi-tools) (8.3.1) Requirement already satisfied: six in c:\users\angel\anaconda3\lib\site-packages (from docrep>=0.3.2->scvi-tools) (1.16.0) Requirement already satisfied: opt-einsum in c:\users\angel\anaconda3\lib\site-packages (from jax>=0.3->scvi-tools) (3.3.0) Collecting ml-dtypes>=0.0.3 Using cached ml_dtypes-0.0.4-cp39-cp39-win_amd64.whl (97 kB) Requirement already satisfied: et_xmlfile in c:\users\angel\anaconda3\lib\site-packages (from openpyxl>=3.0->scvi-tools) (1.1.0) Requirement already satisfied: pytz>=2020.1 in c:\users\angel\anaconda3\lib\site-packages (from pandas>=1.0->scvi-tools) (2022.1) Requirement already satisfied: python-dateutil>=2.8.1 in c:\users\angel\anaconda3\lib\site-packages (from pandas>=1.0->scvi-tools) (2.8.2) Requirement already satisfied: pyro-api>=0.1.1 in c:\users\angel\anaconda3\lib\site-packages (from pyro-ppl>=1.6.0->scvi-tools) (0.1.2) Collecting pyDeprecate==0.3.1 Using cached pyDeprecate-0.3.1-py3-none-any.whl (10 kB) Requirement already satisfied: PyYAML>=5.1 in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.6,>=1.5->scvi-tools) (5.4.1) Requirement already satisfied: tensorboard>=2.2.0 in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.6,>=1.5->scvi-tools) (2.12.1) Requirement already satisfied: typing-extensions in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.6,>=1.5->scvi-tools) (4.4.0) Requirement already satisfied: future>=0.17.1 in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.6,>=1.5->scvi-tools) (0.18.2) Requirement already satisfied: fsspec[http]!=2021.06.0,>=2021.05.0 in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.6,>=1.5->scvi-tools) (2022.11.0) Requirement already satisfied: setuptools==59.5.0 in c:\users\angel\anaconda3\lib\site-packages (from pytorch-lightning<1.6,>=1.5->scvi-tools) (59.5.0) Requirement already satisfied: markdown-it-py<3.0.0,>=2.2.0 in c:\users\angel\anaconda3\lib\site-packages (from rich>=9.1.0->scvi-tools) (2.2.0) Requirement already satisfied: pygments<3.0.0,>=2.13.0 in c:\users\angel\anaconda3\lib\site-packages (from rich>=9.1.0->scvi-tools) (2.14.0) Requirement already satisfied: threadpoolctl>=2.0.0 in c:\users\angel\anaconda3\lib\site-packages (from scikit-learn>=0.21.2->scvi-tools) (2.2.0) Requirement already satisfied: joblib>=0.11 in c:\users\angel\anaconda3\lib\site-packages (from scikit-learn>=0.21.2->scvi-tools) (1.1.1) Requirement already satisfied: jinja2 in c:\users\angel\anaconda3\lib\site-packages (from torch>=1.8.0->scvi-tools) (2.11.3) Requirement already satisfied: filelock in c:\users\angel\anaconda3\lib\site-packages (from torch>=1.8.0->scvi-tools) (3.6.0) Requirement already satisfied: sympy in c:\users\angel\anaconda3\lib\site-packages (from torch>=1.8.0->scvi-tools) (1.11.1) Requirement already satisfied: networkx in c:\users\angel\anaconda3\lib\site-packages (from torch>=1.8.0->scvi-tools) (2.8.4) Requirement already satisfied: colorama in c:\users\angel\anaconda3\lib\site-packages (from tqdm>=4.56.0->scvi-tools) (0.4.5) Collecting orbax Using cached orbax-0.1.7-py3-none-any.whl (77 kB) Requirement already satisfied: msgpack in c:\users\angel\anaconda3\lib\site-packages (from flax->scvi-tools) (1.0.3) Collecting tensorstore Using cached tensorstore-0.1.35-cp39-cp39-win_amd64.whl (8.3 MB) Requirement already satisfied: widgetsnbextension~=3.5.0 in c:\users\angel\anaconda3\lib\site-packages (from ipywidgets->scvi-tools) (3.5.2) Requirement already satisfied: ipykernel>=4.5.1 in c:\users\angel\anaconda3\lib\site-packages (from ipywidgets->scvi-tools) (6.15.2) Requirement already satisfied: ipython>=4.0.0 in c:\users\angel\anaconda3\lib\site-packages (from ipywidgets->scvi-tools) (7.31.1) Requirement already satisfied: traitlets>=4.3.1 in c:\users\angel\anaconda3\lib\site-packages (from ipywidgets->scvi-tools) (5.1.1) Requirement already satisfied: ipython-genutils~=0.2.0 in c:\users\angel\anaconda3\lib\site-packages (from ipywidgets->scvi-tools) (0.2.0) Requirement already satisfied: nbformat>=4.2.0 in c:\users\angel\appdata\roaming\python\python39\site-packages (from ipywidgets->scvi-tools) (5.4.0) Requirement already satisfied: jupyterlab-widgets>=1.0.0 in c:\users\angel\anaconda3\lib\site-packages (from ipywidgets->scvi-tools) (1.0.0) Requirement already satisfied: multipledispatch in c:\users\angel\anaconda3\lib\site-packages (from numpyro->scvi-tools) (0.6.0) Collecting numpyro Using cached numpyro-0.10.1-py3-none-any.whl (292 kB) Using cached numpyro-0.10.0-py3-none-any.whl (291 kB) Using cached numpyro-0.9.2-py3-none-any.whl (283 kB) Using cached numpyro-0.9.1-py3-none-any.whl (283 kB) Using cached numpyro-0.9.0-py3-none-any.whl (282 kB) Using cached numpyro-0.8.0-py3-none-any.whl (264 kB) Using cached numpyro-0.7.2-py3-none-any.whl (250 kB) Using cached numpyro-0.7.1-py3-none-any.whl (250 kB) Using cached numpyro-0.7.0-py3-none-any.whl (247 kB) Using cached numpyro-0.6.0-py3-none-any.whl (218 kB) Using cached numpyro-0.5.0-py3-none-any.whl (194 kB) Using cached numpyro-0.4.1-py3-none-any.whl (176 kB) Using cached numpyro-0.4.0-py3-none-any.whl (175 kB) Using cached numpyro-0.3.0-py3-none-any.whl (157 kB) Using cached numpyro-0.2.4-py3-none-any.whl (159 kB) Using cached numpyro-0.2.3-py3-none-any.whl (145 kB) Using cached numpyro-0.2.2-py3-none-any.whl (145 kB) Using cached numpyro-0.2.1-py3-none-any.whl (141 kB) Using cached numpyro-0.2.0-py3-none-any.whl (95 kB) Using cached numpyro-0.1.0.tar.gz (73 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' INFO: pip is looking at multiple versions of ipywidgets to determine which version is compatible with other requirements. This could take a while. Collecting ipywidgets Using cached ipywidgets-8.0.6-py3-none-any.whl (138 kB) INFO: pip is looking at multiple versions of flax to determine which version is compatible with other requirements. This could take a while. Collecting flax Using cached flax-0.6.7-py3-none-any.whl (214 kB) Using cached flax-0.6.6-py3-none-any.whl (210 kB) Requirement already satisfied: matplotlib in c:\users\angel\anaconda3\lib\site-packages (from flax->scvi-tools) (3.6.2) Using cached flax-0.6.4-py3-none-any.whl (204 kB) Using cached flax-0.6.3-py3-none-any.whl (197 kB) Using cached flax-0.6.2-py3-none-any.whl (189 kB) Using cached flax-0.6.1-py3-none-any.whl (185 kB) Using cached flax-0.6.0-py3-none-any.whl (180 kB) Collecting rich>=9.1.0 Using cached rich-11.2.0-py3-none-any.whl (217 kB) INFO: pip is looking at multiple versions of flax to determine which version is compatible with other requirements. This could take a while. Collecting flax Using cached flax-0.5.3-py3-none-any.whl (202 kB) Using cached flax-0.5.2-py3-none-any.whl (197 kB) Using cached flax-0.5.1-py3-none-any.whl (197 kB) Using cached flax-0.5.0-py3-none-any.whl (190 kB) Using cached flax-0.4.2-py3-none-any.whl (186 kB) INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C. Using cached flax-0.4.1-py3-none-any.whl (184 kB) Using cached flax-0.4.0-py3-none-any.whl (176 kB) Using cached flax-0.3.6-py3-none-any.whl (207 kB) Using cached flax-0.3.5-py3-none-any.whl (193 kB) Using cached flax-0.3.4-py3-none-any.whl (183 kB) Using cached flax-0.3.3-py3-none-any.whl (179 kB) Using cached flax-0.3.2-py3-none-any.whl (170 kB) Using cached flax-0.3.1-py3-none-any.whl (166 kB) Using cached flax-0.3.0-py3-none-any.whl (154 kB) Using cached flax-0.2.2-py3-none-any.whl (148 kB) Using cached flax-0.2.1-py3-none-any.whl (142 kB) Using cached flax-0.2.0-py3-none-any.whl (84 kB) Using cached flax-0.1.0-py3-none-any.whl (77 kB) Collecting dataclasses Using cached dataclasses-0.6-py3-none-any.whl (14 kB) INFO: pip is looking at multiple versions of tqdm to determine which version is compatible with other requirements. This could take a while. Collecting tqdm>=4.56.0 Using cached tqdm-4.65.0-py3-none-any.whl (77 kB) INFO: pip is looking at multiple versions of torchmetrics to determine which version is compatible with other requirements. This could take a while. Collecting torchmetrics>=0.6.0 Using cached torchmetrics-0.11.4-py3-none-any.whl (519 kB) INFO: pip is looking at multiple versions of torch to determine which version is compatible with other requirements. This could take a while. Collecting torch>=1.8.0 Using cached torch-2.0.0-cp39-cp39-win_amd64.whl (172.3 MB) INFO: pip is looking at multiple versions of scikit-learn to determine which version is compatible with other requirements. This could take a while. Collecting scikit-learn>=0.21.2 Using cached scikit_learn-1.2.2-cp39-cp39-win_amd64.whl (8.4 MB) INFO: pip is looking at multiple versions of rich to determine which version is compatible with other requirements. This could take a while. Collecting rich>=9.1.0 Using cached rich-13.3.3-py3-none-any.whl (238 kB) INFO: pip is looking at multiple versions of pydeprecate to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of pytorch-lightning to determine which version is compatible with other requirements. This could take a while. Collecting pytorch-lightning<1.6,>=1.5 Using cached pytorch_lightning-1.5.9-py3-none-any.whl (527 kB) INFO: pip is looking at multiple versions of pyro-ppl to determine which version is compatible with other requirements. This could take a while. Collecting pyro-ppl>=1.6.0 Using cached pyro_ppl-1.8.4-py3-none-any.whl (730 kB) INFO: pip is looking at multiple versions of protobuf to determine which version is compatible with other requirements. This could take a while. 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c:\users\angel\anaconda3\lib\site-packages (from nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.2.2) Requirement already satisfied: testpath in c:\users\angel\anaconda3\lib\site-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.6.0) Requirement already satisfied: beautifulsoup4 in c:\users\angel\anaconda3\lib\site-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (4.11.1) Requirement already satisfied: defusedxml in c:\users\angel\anaconda3\lib\site-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.7.1) Requirement already satisfied: mistune<2,>=0.8.1 in c:\users\angel\anaconda3\lib\site-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.8.4) Requirement already satisfied: nbclient<0.6.0,>=0.5.0 in c:\users\angel\anaconda3\lib\site-packages (from 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c:\users\angel\anaconda3\lib\site-packages (from argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (1.15.1) Requirement already satisfied: soupsieve>1.2 in c:\users\angel\anaconda3\lib\site-packages (from beautifulsoup4->nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (2.3.2.post1) Requirement already satisfied: webencodings in c:\users\angel\anaconda3\lib\site-packages (from bleach->nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (0.5.1) Requirement already satisfied: sniffio>=1.1 in c:\users\angel\anaconda3\lib\site-packages (from anyio<4,>=3.1.0->jupyter-server>=1.8->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (1.2.0) Requirement already satisfied: pycparser in c:\users\angel\anaconda3\lib\site-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->scvi-tools) (2.21) Note: you may need to restart the kernel to use updated packages.

but when i try this command (after restarting the kernel):

pip show scvi-tools

i still get the same output:

Name: scvi-tools Version: 0.14.6 Summary: Deep probabilistic analysis of single-cell omics data. Home-page: https://github.com/YosefLab/scvi-tools Author: Romain Lopez Author-email: romain_lopez@gmail.com License: BSD-3-Clause Location: c:\users\angel\anaconda3\lib\site-packages Requires: anndata, docrep, h5py, ipywidgets, numba, numpy, openpyxl, pandas, pyro-ppl, pytorch-lightning, rich, scikit-learn, setuptools, torch, torchmetrics, tqdm Required-by: Note: you may need to restart the kernel to use updated packages.