Comments (5)
Appreciate your help, thank you @qinqian.. I have run the docs/source/notebook/pancreas.ipynb on Windows platform with GPU GTX1050Ti. My environment.yml
below may help others.
name: pyrovelocity
channels:
- pytorch
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
- https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
- conda-forge
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
- defaults
dependencies:
- asttokens=2.0.8=pyhd8ed1ab_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- blas=1.0=mkl
- bzip2=1.0.8=h8ffe710_4
- ca-certificates=2022.9.24=h5b45459_0
- cudatoolkit=10.2.89=hb195166_10
- debugpy=1.6.3=py38h885f38d_0
- decorator=5.1.1=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_0
- executing=1.1.1=pyhd8ed1ab_0
- freetype=2.4.10=0
- intel-openmp=2022.1.0=h57928b3_3787
- ipykernel=6.16.1=pyh025b116_0
- ipython=8.5.0=pyh08f2357_1
- jedi=0.18.1=pyhd8ed1ab_2
- jpeg=8d=0
- jupyter_client=7.4.3=pyhd8ed1ab_0
- jupyter_core=4.11.1=py38haa244fe_0
- libblas=3.9.0=16_win64_mkl
- libcblas=3.9.0=16_win64_mkl
- libffi=3.4.2=h8ffe710_5
- liblapack=3.9.0=16_win64_mkl
- libpng=1.6.17=0
- libsodium=1.0.18=h8d14728_1
- libsqlite=3.39.4=hcfcfb64_0
- libtiff=4.0.2=1
- libuv=1.44.2=h8ffe710_0
- libwebp=1.2.4=h8ffe710_0
- libwebp-base=1.2.4=h8ffe710_0
- libzlib=1.2.13=hcfcfb64_4
- matplotlib-inline=0.1.6=pyhd8ed1ab_0
- mkl=2022.1.0=h6a75c08_874
- msys2-conda-epoch=20160418=1
- nest-asyncio=1.5.6=pyhd8ed1ab_0
- ninja=1.7.2=0
- numpy=1.23.4=py38h90ce339_1
- openssl=3.0.5=hcfcfb64_2
- packaging=21.3=pyhd8ed1ab_0
- parso=0.8.3=pyhd8ed1ab_0
- pickleshare=0.7.5=py_1003
- pip=22.3=pyhd8ed1ab_0
- prompt-toolkit=3.0.31=pyha770c72_0
- psutil=5.9.3=py38h91455d4_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- pygments=2.13.0=pyhd8ed1ab_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- python=3.8.13=hcf16a7b_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python_abi=3.8=2_cp38
- pytorch=1.8.1=py3.8_cuda10.2_cudnn7_0
- pywin32=303=py38h294d835_0
- pyzmq=24.0.1=py38ha85f68a_0
- six=1.16.0=pyh6c4a22f_0
- sqlite=3.39.4=hcfcfb64_0
- stack_data=0.5.1=pyhd8ed1ab_0
- tbb=2021.6.0=h91493d7_0
- tk=8.6.12=h8ffe710_0
- torchaudio=0.8.1=py38
- torchvision=0.9.1=py38_cu102
- tornado=6.2=py38h294d835_0
- traitlets=5.5.0=pyhd8ed1ab_0
- typing_extensions=4.4.0=pyha770c72_0
- ucrt=10.0.20348.0=h57928b3_0
- vc=14.2=hac3ee0b_8
- vs2015_runtime=14.29.30139=h890b9b1_8
- wcwidth=0.2.5=pyh9f0ad1d_2
- wheel=0.37.1=pyhd8ed1ab_0
- xz=5.2.6=h8d14728_0
- zeromq=4.3.4=h0e60522_1
- zlib=1.2.13=hcfcfb64_4
- pip:
- absl-py==1.3.0
- adjusttext==0.7.3
- aiohttp==3.8.3
- aiosignal==1.2.0
- anndata==0.8.0
- astropy==5.1.1
- async-timeout==4.0.2
- attrs==22.1.0
- cachetools==5.2.0
- certifi==2022.9.24
- charset-normalizer==2.1.1
- click==8.1.3
- colorama==0.4.6
- commonmark==0.9.1
- contourpy==1.0.5
- cycler==0.11.0
- docrep==0.3.2
- et-xmlfile==1.1.0
- fonttools==4.38.0
- frozenlist==1.3.1
- fsspec==2022.10.0
- future==0.18.2
- google-auth==2.13.0
- google-auth-oauthlib==0.4.6
- grpcio==1.50.0
- h5py==3.7.0
- idna==3.4
- importlib-metadata==5.0.0
- ipywidgets==8.0.2
- joblib==1.2.0
- jupyterlab-widgets==3.0.3
- kiwisolver==1.4.4
- llvmlite==0.39.1
- loompy==3.0.7
- markdown==3.4.1
- markupsafe==2.1.1
- matplotlib==3.6.0
- multidict==6.0.2
- natsort==8.2.0
- networkx==2.8.7
- numba==0.56.3
- numpy-groupies==0.9.20
- oauthlib==3.2.2
- openpyxl==3.0.10
- opt-einsum==3.3.0
- pandas==1.5.1
- patsy==0.5.3
- pillow==9.2.0
- protobuf==3.19.6
- pyasn1==0.4.8
- pyasn1-modules==0.2.8
- pydeprecate==0.3.0
- pyerfa==2.0.0.1
- pynndescent==0.5.7
- pyro-api==0.1.2
- pyro-ppl==1.6.0
- pyrovelocity==0.1.0
- pytorch-lightning==1.3.8
- pytz==2022.5
- pyyaml==5.4.1
- requests==2.28.1
- requests-oauthlib==1.3.1
- rich==12.6.0
- rsa==4.9
- scanpy==1.9.1
- scikit-learn==1.1.3
- scipy==1.9.3
- scvelo==0.2.4
- scvi-tools==0.13.0
- seaborn==0.12.1
- session-info==1.0.0
- setuptools==59.5.0
- statsmodels==0.13.2
- stdlib-list==0.8.0
- tensorboard==2.10.1
- tensorboard-data-server==0.6.1
- tensorboard-plugin-wit==1.8.1
- threadpoolctl==3.1.0
- torchmetrics==0.5.0
- tqdm==4.64.1
- umap-learn==0.5.3
- urllib3==1.26.12
- werkzeug==2.2.2
- widgetsnbextension==4.0.3
- yarl==1.8.1
- zipp==3.10.0
prefix: F:\ProgrammingEnvironment\Anaconda\Anaconda\envs\pyrovelocity
from pyrovelocity.
I think that scvi-tools is installed by uncorrected version or other packages. Can you share your conda evironment by .yaml file, which help me install all dependencies correctly.
from pyrovelocity.
from pyrovelocity.
Sure, please see environment.yml
below. My guess might be that the latest scvi-tools are not compatible with our package, please consider downgrading to 0.13.0
. I cannot find a windows GPU machine to test the package yet, thank you for your help!
name: pyrovelocity
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python==3.8.8
- pyro-ppl==1.6.0
- seaborn==0.11.2
- scvelo
- scvi-tools==0.13.0
- pytorch-lightning==1.3.0
- pytorch-gpu=1.8.*=*cuda*
- torchmetrics==0.5.1
- h5py==3.2.1
- anndata==0.7.5
- adjusttext
- astropy
- jupyterlab
from pyrovelocity.
Thank you for sharing the solution @HuangDDU. I'll pin this issue.
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