Issue installing cell2location

[szimmerman92]

Hello,

Thank you for the great tool. I am currently having difficulty installing cell2location. Below is the method I use to install the software.

export PYTHONNOUSERSITE="literallyanyletters"
export PYTHONPATH=""
conda create -y -n cell2loc_env python=3.9
conda activate cell2loc_env
pip install cell2location[tutorials]

The installation is successful but when I run the command below

import cell2location

I get the following error

  File "<stdin>", line 1, in <module>
  File "/Users/zimmerma/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/__init__.py", line 9, in <module>
    from . import models
  File "/Users/zimmerma/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/models/__init__.py", line 1, in <module>
    from ._cell2location_model import Cell2location
  File "/Users/zimmerma/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/models/_cell2location_model.py", line 29, in <module>
    from cell2location.models.base._pyro_base_loc_module import Cell2locationBaseModule
  File "/Users/zimmerma/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/models/base/_pyro_base_loc_module.py", line 6, in <module>
    from ._pyro_mixin import AutoGuideMixinModule, init_to_value
  File "/Users/zimmerma/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/models/base/_pyro_mixin.py", line 20, in <module>
    from scvi.model._utils import parse_use_gpu_arg
ImportError: cannot import name 'parse_use_gpu_arg' from 'scvi.model._utils' (/Users/zimmerma/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/scvi/model/_utils.py)

Help solving this would be greatly appreciated. Thank you very much.

Best Regards, Sam

[jerryzuo0214]

Same issue encountered. I have realized that this might be due to version conflict, so I downgraded some pkg versions like below.

export PYTHONNOUSERSITE="literallyanyletters" export PYTHONPATH="" conda create -y -n cell2loc_env python=3.9 conda activate cell2loc_env pip install cell2location[tutorials] pip install scvi-tools==1.0.4 pip install jaxlib==0.4.23 pip install jax==0.4.23

[jerryzuo0214]

Like issue #347 , this issue was occurred when I only downgrade the scvi-tools into 1.0.4, and then same error appeared as #347 , I therefore downgraded the version of both jax and jaxlib then, and all problem have solved successfully.

-- the version conflict might not due to single pkg, so the dependence limit should be update. --To the Developers.

[jerryzuo0214]

For a GPU-enabled setting, GPU-supported version of jax should be installed, here is the resolution. All the installation was performed in an Ubuntu physical machine. wish to help

conda deactivate

conda env remove -n cell2loc_env

export PYTHONNOUSERSITE="literallyanyletters" export PYTHONPATH="" conda create -y -n cell2loc_env python=3.9 conda activate cell2loc_env pip install scvi-tools==1.0.4 pip install -U "jax[cuda12_pip]==0.4.23" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html pip install cell2location[tutorials] pip install jupyter notebook

[SichenZhu]

Linux system with NVIDIA GPU: in my case, following commands successfully downgrade the installation and everything works as before.

conda create -y -n cell2loc_env python=3.9 conda activate cell2loc_env pip install cell2location[tutorials] conda install pytorch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 pytorch-cuda=12.1 -c pytorch -c nvidia pip install -U "jax[cuda12_pip]==0.4.23" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html pip install scvi-tools==1.0.4 conda install anaconda::ipykernel

[CHENyiru3]

export PYTHONNOUSERSITE="literallyanyletters" export PYTHONPATH="" conda create -y -n cell2loc_env python=3.9 conda activate cell2loc_env pip install cell2location[tutorials] pip install scvi-tools==1.0.4 pip install jaxlib==0.4.23 pip install jax==0.4.23

hello, why I can't install the cell2location[tutorials] correctly?It says no match. I can install cell2location, but without the tutorials. Is this OK for me ? I am trying now. Thank you!

[vitkl]

cell2location doesn't use JAX so it doesn't matter how JAX is installed as long as scvi-tools doesn't complain.

[vitkl]

Re ImportError: cannot import name 'parse_use_gpu_arg' from 'scvi.model._utils' - at the moment you need to install the GitHub version to use the latest scvi-tools. I am working on a new release but these have been challenging few months.

[vitkl]

For example, you can do the following:

export PYTHONNOUSERSITE="aaaaa"
conda create -y -n cell2location_cuda118_torch22 python=3.10
conda activate cell2location_cuda118_torch22

pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118

pip3 install scvi-tools==1.1.2

pip install git+https://github.com/BayraktarLab/cell2location.git#egg=cell2location[tutorials]

[alexanderchang1]

I think this package could really use a conda installation release, the dependency solver for scvi-tools, jax, jax lib, pytorch are all preferred in conda, and when the cell2location is installed in pip, it causes a whole host of issues.

[alexanderchang1]

Also note, there is a depreciated trill removal in scipy 1.13.0, the above solutions also require a downgrade of scipy to 1.11.0

[minsu1794]

I did the following since I had initially error of :ImportError: cannot import name 'parse_use_gpu_arg' from 'scvi.model._utils' export PYTHONNOUSERSITE="aaaaa" conda create -y -n cell2location_cuda118_torch22 python=3.10 conda activate cell2location_cuda118_torch22

pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118

pip3 install scvi-tools==1.1.2

pip install git+https://github.com/BayraktarLab/cell2location.git#egg=cell2location[tutorials]

I tried running mod.train(max_epochs=250, use_gpu=True) but gives me error of : TypeError: Trainer.init() got an unexpected keyword argument 'use_gpu'

Is use_gpu not an available parameter?

[HSsnano]

I encountered the same issue a few days ago. Below are some code snippets that might help you resolve it. First, create a new conda environment and activate it:

conda create -n cell2loc python=3.11
conda activate cell2loc
pip3 install torch torchvision torchaudio
pip install cell2location==0.1.3
pip install scvi-tools==1.0.4

If you're running on a Linux system with an NVIDIA GPU, run:

pip install --upgrade jax==0.4.14 jaxlib==0.4.14+cuda12.cudnn89 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

If you're running on a Linux system with a CPU, run:

pip install --upgrade jax==0.4.14 jaxlib==0.4.14 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Finally, install orbax-checkpoint, flax, and scipy:

pip install orbax-checkpoint==0.4.1 flax==0.7.4
pip install scipy==1.11.3

[gu-shengchen]

I encountered the same issue a few days ago. Below are some code snippets that might help you resolve it. First, create a new conda environment and activate it:

conda create -n cell2loc python=3.11
conda activate cell2loc
pip3 install torch torchvision torchaudio
pip install cell2location==0.1.3
pip install scvi-tools==1.0.4

If you're running on a Linux system with an NVIDIA GPU, run:

pip install --upgrade jax==0.4.14 jaxlib==0.4.14+cuda12.cudnn89 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

If you're running on a Linux system with a CPU, run:

pip install --upgrade jax==0.4.14 jaxlib==0.4.14 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Finally, install orbax-checkpoint, flax, and scipy:

pip install orbax-checkpoint==0.4.1 flax==0.7.4
pip install scipy==1.11.3

I used the code you gave me and finally installed it successfully. Thank you very much.

[gu-shengchen]

Haha , the problem is finally solved, the steps are as follows: 1, from github search cell2location, and click on the upper right corner of the 'code', download the zip format source code file. (Figure 1 below) 2、Upload the source code file to the server/cluster

3. Extract the zip folder. 4、Use pip install . /folder name, successfully installed. (Figure 2)

Summary: this way to install cell2location is the latest version of 0.1.4, in addition to this way, the other ways to install all the 0.1.3 version, 0.1.3 version will be all kinds of errors, endless errors, to solve an error, there will be a new error. (By the way, don't forget to create a new python3.9 and above environment in advance, and enter the environment, and then do a local installation)

Here is the Chinese version: 中文版的说明： 哈哈 ，问题终于解决啦，步骤如下： 1、从github中搜索cell2location，并点击右上角中的'code'，下载zip格式的源码文件。（下方图1） 2、将源码文件上传到服务器/集群 3、将zip格式的文件夹解压 4、利用pip install ./文件夹名，成功安装。（下方图2）

总结：这种方式安装的cell2location是最新版本的，即0.1.4，除了这种方式，其他方式安装的全是0.1.3的版本，0.1.3的版本就会各种报错，无穷无尽的报错，解决一个报错，还会有新的报错。（对了，别忘了提前新建一个python3.9及以上的环境欧，并进入环境，然后进行本地安装）

[JiahaoWongg]

https://github.com/BayraktarLab/cell2location/issues/348#issuecomment-2206893785

@HSsnano solved my issue! god bless you!

[LiuXintongPKU]

Hi~I follow your instruction, but I cannot successfully import cell2loction... Could you please help me out? Here is my enviroment.

Name Version Build Channel

_libgcc_mutex 0.1 main https://mirrors.bfsu.edu.cn/anaconda/pkgs/main _openmp_mutex 5.1 1_gnu https://mirrors.bfsu.edu.cn/anaconda/pkgs/main absl-py 2.1.0 pypi_0 pypi aiohttp 3.9.5 pypi_0 pypi aiosignal 1.3.1 pypi_0 pypi anndata 0.10.8 pypi_0 pypi annotated-types 0.7.0 pypi_0 pypi anyio 4.4.0 pypi_0 pypi array-api-compat 1.8 pypi_0 pypi arrow 1.3.0 pypi_0 pypi attrs 23.2.0 pypi_0 pypi backoff 2.2.1 pypi_0 pypi beautifulsoup4 4.12.3 pypi_0 pypi blessed 1.20.0 pypi_0 pypi boto3 1.34.149 pypi_0 pypi botocore 1.34.149 pypi_0 pypi bzip2 1.0.8 h5eee18b_6 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main ca-certificates 2024.7.2 h06a4308_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main cell2location 0.1.3 pypi_0 pypi certifi 2024.7.4 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi chex 0.1.7 pypi_0 pypi click 8.1.7 pypi_0 pypi contextlib2 21.6.0 pypi_0 pypi contourpy 1.2.1 pypi_0 pypi croniter 1.4.1 pypi_0 pypi cycler 0.12.1 pypi_0 pypi dateutils 0.6.12 pypi_0 pypi deepdiff 7.0.1 pypi_0 pypi dm-tree 0.1.8 pypi_0 pypi dnspython 2.6.1 pypi_0 pypi docrep 0.3.2 pypi_0 pypi editor 1.6.6 pypi_0 pypi email-validator 2.2.0 pypi_0 pypi etils 1.9.2 pypi_0 pypi fastapi 0.111.1 pypi_0 pypi fastapi-cli 0.0.4 pypi_0 pypi filelock 3.15.4 pypi_0 pypi flax 0.7.4 pypi_0 pypi fonttools 4.53.1 pypi_0 pypi frozenlist 1.4.1 pypi_0 pypi fsspec 2024.6.1 pypi_0 pypi h11 0.14.0 pypi_0 pypi h5py 3.11.0 pypi_0 pypi httpcore 1.0.5 pypi_0 pypi httptools 0.6.1 pypi_0 pypi httpx 0.27.0 pypi_0 pypi idna 3.7 pypi_0 pypi importlib-resources 6.4.0 pypi_0 pypi inquirer 3.3.0 pypi_0 pypi itsdangerous 2.2.0 pypi_0 pypi jax 0.4.14 pypi_0 pypi jaxlib 0.4.14+cuda12.cudnn89 pypi_0 pypi jinja2 3.1.4 pypi_0 pypi jmespath 1.0.1 pypi_0 pypi joblib 1.4.2 pypi_0 pypi kiwisolver 1.4.5 pypi_0 pypi ld_impl_linux-64 2.38 h1181459_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main legacy-api-wrap 1.4 pypi_0 pypi libffi 3.4.4 h6a678d5_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main libgcc-ng 11.2.0 h1234567_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main libgomp 11.2.0 h1234567_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main libstdcxx-ng 11.2.0 h1234567_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main libuuid 1.41.5 h5eee18b_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main lightning 2.0.9.post0 pypi_0 pypi lightning-cloud 0.5.70 pypi_0 pypi lightning-utilities 0.11.6 pypi_0 pypi llvmlite 0.43.0 pypi_0 pypi markdown-it-py 3.0.0 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib 3.9.1 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi ml-collections 0.1.1 pypi_0 pypi ml-dtypes 0.4.0 pypi_0 pypi mpmath 1.3.0 pypi_0 pypi msgpack 1.0.8 pypi_0 pypi mudata 0.2.4 pypi_0 pypi multidict 6.0.5 pypi_0 pypi multipledispatch 1.0.0 pypi_0 pypi natsort 8.4.0 pypi_0 pypi ncurses 6.4 h6a678d5_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main nest-asyncio 1.6.0 pypi_0 pypi networkx 3.3 pypi_0 pypi numba 0.60.0 pypi_0 pypi numpy 1.26.4 pypi_0 pypi numpyro 0.15.1 pypi_0 pypi nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi nvidia-cudnn-cu12 9.1.0.70 pypi_0 pypi nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi nvidia-curand-cu12 10.3.2.106 pypi_0 pypi nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi nvidia-nccl-cu12 2.20.5 pypi_0 pypi nvidia-nvjitlink-cu12 12.5.82 pypi_0 pypi nvidia-nvtx-cu12 12.1.105 pypi_0 pypi opencv-python 4.10.0.84 pypi_0 pypi openssl 3.0.14 h5eee18b_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main opt-einsum 3.3.0 pypi_0 pypi optax 0.2.1 pypi_0 pypi orbax-checkpoint 0.4.1 pypi_0 pypi ordered-set 4.1.0 pypi_0 pypi packaging 24.1 pypi_0 pypi pandas 2.2.2 pypi_0 pypi patsy 0.5.6 pypi_0 pypi pillow 10.4.0 pypi_0 pypi pip 24.0 py311h06a4308_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main protobuf 5.27.2 pypi_0 pypi psutil 6.0.0 pypi_0 pypi pydantic 2.1.1 pypi_0 pypi pydantic-core 2.4.0 pypi_0 pypi pygments 2.18.0 pypi_0 pypi pyjwt 2.8.0 pypi_0 pypi pynndescent 0.5.13 pypi_0 pypi pyparsing 3.1.2 pypi_0 pypi pyro-api 0.1.2 pypi_0 pypi pyro-ppl 1.9.1 pypi_0 pypi python 3.11.9 h955ad1f_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main python-dateutil 2.9.0.post0 pypi_0 pypi python-dotenv 1.0.1 pypi_0 pypi python-multipart 0.0.9 pypi_0 pypi pytorch-lightning 2.3.3 pypi_0 pypi pytz 2024.1 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi readchar 4.1.0 pypi_0 pypi readline 8.2 h5eee18b_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main requests 2.32.3 pypi_0 pypi rich 13.7.1 pypi_0 pypi runs 1.2.2 pypi_0 pypi s3transfer 0.10.2 pypi_0 pypi scanpy 1.10.2 pypi_0 pypi scikit-learn 1.5.1 pypi_0 pypi scipy 1.11.3 pypi_0 pypi scvi-tools 1.0.4 pypi_0 pypi seaborn 0.13.2 pypi_0 pypi session-info 1.0.0 pypi_0 pypi setuptools 69.5.1 py311h06a4308_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main shellingham 1.5.4 pypi_0 pypi six 1.16.0 pypi_0 pypi sniffio 1.3.1 pypi_0 pypi soupsieve 2.5 pypi_0 pypi sparse 0.15.4 pypi_0 pypi sqlite 3.45.3 h5eee18b_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main starlette 0.37.2 pypi_0 pypi starsessions 1.3.0 pypi_0 pypi statsmodels 0.14.2 pypi_0 pypi stdlib-list 0.10.0 pypi_0 pypi sympy 1.13.1 pypi_0 pypi tensorstore 0.1.63 pypi_0 pypi threadpoolctl 3.5.0 pypi_0 pypi tk 8.6.14 h39e8969_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main toolz 0.12.1 pypi_0 pypi torch 2.4.0 pypi_0 pypi torchaudio 2.4.0 pypi_0 pypi torchmetrics 1.4.0.post0 pypi_0 pypi torchvision 0.19.0 pypi_0 pypi tqdm 4.66.4 pypi_0 pypi traitlets 5.14.3 pypi_0 pypi triton 3.0.0 pypi_0 pypi typer 0.12.3 pypi_0 pypi types-python-dateutil 2.9.0.20240316 pypi_0 pypi typing-extensions 4.12.2 pypi_0 pypi tzdata 2024.1 pypi_0 pypi umap-learn 0.5.6 pypi_0 pypi urllib3 2.2.2 pypi_0 pypi uvicorn 0.30.3 pypi_0 pypi uvloop 0.19.0 pypi_0 pypi watchfiles 0.22.0 pypi_0 pypi wcwidth 0.2.13 pypi_0 pypi websocket-client 1.8.0 pypi_0 pypi websockets 12.0 pypi_0 pypi wheel 0.43.0 py311h06a4308_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main xarray 2024.6.0 pypi_0 pypi xmod 1.8.1 pypi_0 pypi xz 5.4.6 h5eee18b_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main yarl 1.9.4 pypi_0 pypi zipp 3.19.2 pypi_0 pypi zlib 1.2.13 h5eee18b_1 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main

I encountered the same issue a few days ago. Below are some code snippets that might help you resolve it. First, create a new conda environment and activate it:

conda create -n cell2loc python=3.11
conda activate cell2loc
pip3 install torch torchvision torchaudio
pip install cell2location==0.1.3
pip install scvi-tools==1.0.4

If you're running on a Linux system with an NVIDIA GPU, run:

pip install --upgrade jax==0.4.14 jaxlib==0.4.14+cuda12.cudnn89 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

If you're running on a Linux system with a CPU, run:

pip install --upgrade jax==0.4.14 jaxlib==0.4.14 \
-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Finally, install orbax-checkpoint, flax, and scipy:

pip install orbax-checkpoint==0.4.1 flax==0.7.4
pip install scipy==1.11.3

[yunbokai]

Hi every one, I got one account that can run cell2location successfully. Here is my version:

_libgcc_mutex             0.1                 conda_forge    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
absl-py                   2.0.0                    pypi_0    pypi
aiohttp                   3.8.6                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
annotated-types           0.6.0                    pypi_0    pypi
anyio                     3.7.1                    pypi_0    pypi
arrow                     1.3.0                    pypi_0    pypi
asttokens                 2.4.1                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     23.1.0                   pypi_0    pypi
backoff                   2.2.1                    pypi_0    pypi
beautifulsoup4            4.12.2                   pypi_0    pypi
blessed                   1.20.0                   pypi_0    pypi
boto3                     1.29.2                   pypi_0    pypi
botocore                  1.32.2                   pypi_0    pypi
bzip2                     1.0.8                hd590300_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates           2023.7.22            hbcca054_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cell2location             0.1.3                    pypi_0    pypi
certifi                   2023.7.22                pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
chex                      0.1.7                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
comm                      0.2.0                    pypi_0    pypi
contextlib2               21.6.0                   pypi_0    pypi
contourpy                 1.2.0                    pypi_0    pypi
croniter                  1.4.1                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dateutils                 0.6.12                   pypi_0    pypi
debugpy                   1.8.0                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
deepdiff                  6.7.1                    pypi_0    pypi
dm-tree                   0.1.8                    pypi_0    pypi
docrep                    0.3.2                    pypi_0    pypi
etils                     1.5.2                    pypi_0    pypi
exceptiongroup            1.1.3                    pypi_0    pypi
executing                 2.0.1                    pypi_0    pypi
fastapi                   0.104.1                  pypi_0    pypi
filelock                  3.13.1                   pypi_0    pypi
flax                      0.7.5                    pypi_0    pypi
fonttools                 4.44.3                   pypi_0    pypi
frozenlist                1.4.0                    pypi_0    pypi
fsspec                    2023.10.0                pypi_0    pypi
get-annotations           0.1.2                    pypi_0    pypi
h11                       0.14.0                   pypi_0    pypi
h5py                      3.10.0                   pypi_0    pypi
idna                      3.4                      pypi_0    pypi
igraph                    0.10.8                   pypi_0    pypi
importlib-metadata        6.8.0                    pypi_0    pypi
importlib-resources       6.1.1                    pypi_0    pypi
inquirer                  3.1.3                    pypi_0    pypi
ipykernel                 6.26.0                   pypi_0    pypi
ipython                   8.17.2                   pypi_0    pypi
itsdangerous              2.1.2                    pypi_0    pypi
jax                       0.4.20                   pypi_0    pypi
jaxlib                    0.4.20                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
jupyter-client            8.6.0                    pypi_0    pypi
jupyter-core              5.5.0                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
leidenalg                 0.10.1                   pypi_0    pypi
libffi                    3.4.2                h7f98852_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng                 13.2.0               h807b86a_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   13.2.0               h807b86a_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnsl                    2.0.1                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsqlite                 3.44.0               h2797004_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid                   2.38.1               h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libzlib                   1.2.13               hd590300_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lightning                 2.0.9.post0              pypi_0    pypi
lightning-cloud           0.5.54                   pypi_0    pypi
lightning-utilities       0.9.0                    pypi_0    pypi
llvmlite                  0.41.1                   pypi_0    pypi
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multidict                 6.0.4                    pypi_0    pypi
multipledispatch          1.0.0                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
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nest-asyncio              1.5.8                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
numba                     0.58.1                   pypi_0    pypi
numpy                     1.26.2                   pypi_0    pypi
numpyro                   0.13.2                   pypi_0    pypi
nvidia-cublas-cu12        12.1.3.1                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.1.105                 pypi_0    pypi
nvidia-cudnn-cu12         8.9.2.26                 pypi_0    pypi
nvidia-cufft-cu12         11.0.2.54                pypi_0    pypi
nvidia-curand-cu12        10.3.2.106               pypi_0    pypi
nvidia-cusolver-cu12      11.4.5.107               pypi_0    pypi
nvidia-cusparse-cu12      12.1.0.106               pypi_0    pypi
nvidia-nccl-cu12          2.18.1                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.3.101                 pypi_0    pypi
nvidia-nvtx-cu12          12.1.105                 pypi_0    pypi
opencv-python             4.8.1.78                 pypi_0    pypi
openssl                   3.1.4                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
optax                     0.1.7                    pypi_0    pypi
orbax-checkpoint          0.4.2                    pypi_0    pypi
ordered-set               4.1.0                    pypi_0    pypi
packaging                 23.2                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
patsy                     0.5.3                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
pip                       23.3.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
platformdirs              4.0.0                    pypi_0    pypi
prompt-toolkit            3.0.41                   pypi_0    pypi
protobuf                  4.25.1                   pypi_0    pypi
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ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pydantic                  2.1.1                    pypi_0    pypi
pydantic-core             2.4.0                    pypi_0    pypi
pygments                  2.16.1                   pypi_0    pypi
pyjwt                     2.8.0                    pypi_0    pypi
pynndescent               0.5.10                   pypi_0    pypi
pyparsing                 3.1.1                    pypi_0    pypi
pyro-api                  0.1.2                    pypi_0    pypi
pyro-ppl                  1.8.6                    pypi_0    pypi
python                    3.9.18          h0755675_0_cpython    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python-editor             1.0.4                    pypi_0    pypi
python-igraph             0.10.8                   pypi_0    pypi
python-multipart          0.0.6                    pypi_0    pypi
pytorch-lightning         2.1.2                    pypi_0    pypi
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pyyaml                    6.0.1                    pypi_0    pypi
pyzmq                     25.1.1                   pypi_0    pypi
readchar                  4.0.5                    pypi_0    pypi
readline                  8.2                  h8228510_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
requests                  2.31.0                   pypi_0    pypi
rich                      13.7.0                   pypi_0    pypi
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seaborn                   0.12.2                   pypi_0    pypi
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six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.0                    pypi_0    pypi
soupsieve                 2.5                      pypi_0    pypi
sparse                    0.14.0                   pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
starlette                 0.27.0                   pypi_0    pypi
starsessions              1.3.0                    pypi_0    pypi
statsmodels               0.14.0                   pypi_0    pypi
stdlib-list               0.9.0                    pypi_0    pypi
sympy                     1.12                     pypi_0    pypi
tensorstore               0.1.50                   pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.2.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
toolz                     0.12.0                   pypi_0    pypi
torch                     2.1.1                    pypi_0    pypi
torchmetrics              1.2.0                    pypi_0    pypi
tornado                   6.3.3                    pypi_0    pypi
tqdm                      4.66.1                   pypi_0    pypi
traitlets                 5.13.0                   pypi_0    pypi
triton                    2.1.0                    pypi_0    pypi
types-python-dateutil     2.8.19.14                pypi_0    pypi
typing-extensions         4.8.0                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
urllib3                   1.26.18                  pypi_0    pypi
uvicorn                   0.24.0.post1             pypi_0    pypi
wcwidth                   0.2.10                   pypi_0    pypi
websocket-client          1.6.4                    pypi_0    pypi
websockets                12.0                     pypi_0    pypi
wheel                     0.41.3             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xarray                    2023.10.1                pypi_0    pypi
xz                        5.2.6                h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
yarl                      1.9.2                    pypi_0    pypi
zipp                      3.17.0                   pypi_0    pypi

[rocketeer1998]

@HSsnano solved my problems!

[heshidian]

Haha , the problem is finally solved, the steps are as follows: 1, from github search cell2location, and click on the upper right corner of the 'code', download the zip format source code file. (Figure 1 below) 2、Upload the source code file to the server/cluster 3. Extract the zip folder. 4、Use pip install . /folder name, successfully installed. (Figure 2)

Summary: this way to install cell2location is the latest version of 0.1.4, in addition to this way, the other ways to install all the 0.1.3 version, 0.1.3 version will be all kinds of errors, endless errors, to solve an error, there will be a new error. (By the way, don't forget to create a new python3.9 and above environment in advance, and enter the environment, and then do a local installation)

Here is the Chinese version: 中文版的说明： 哈哈 ，问题终于解决啦，步骤如下： 1、从github中搜索cell2location，并点击右上角中的'code'，下载zip格式的源码文件。（下方图1） 2、将源码文件上传到服务器/集群 3、将zip格式的文件夹解压 4、利用pip install ./文件夹名，成功安装。（下方图2）

总结：这种方式安装的cell2location是最新版本的，即0.1.4，除了这种方式，其他方式安装的全是0.1.3的版本，0.1.3的版本就会各种报错，无穷无尽的报错，解决一个报错，还会有新的报错。（对了，别忘了提前新建一个python3.9及以上的环境欧，并进入环境，然后进行本地安装）

Awesome！