jung233
commented
3 weeks ago When I used the provided omicverse_gpu.yml, I encountered the same problem as you. Finally, I used the pip method to solve it. But it still has problems with SCSA, hope it helps you #176
pip install rapids-singlecell
#rapids
pip install \
--extra-index-url=https://pypi.nvidia.com \
cudf-cu12==24.4.* dask-cudf-cu12==24.4.* cuml-cu12==24.4.* \
cugraph-cu12==24.4.* cuspatial-cu12==24.4.* cuproj-cu12==24.4.* \
cuxfilter-cu12==24.4.* cucim-cu12==24.4.* pylibraft-cu12==24.4.* \
raft-dask-cu12==24.4.* cuvs-cu12==24.4.*
#cupy
pip install cupy-cuda12x
pip install omicversePackage Version Editable project location
------------------------- -------------- --------------------------------------------------------------------------------------------------
absl-py 2.1.0
adjustText 1.2.0
aiohappyeyeballs 2.4.2
aiohttp 3.10.6
aiosignal 1.3.1
anndata 0.10.9
annoy 1.17.3
anyio 4.6.0
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
array_api_compat 1.8
arrow 1.3.0
asttokens 2.4.1
async-timeout 4.0.3
attrs 24.2.0
autocommand 2.2.2
autograd 1.7.0
autograd-gamma 0.5.0
backports.tarfile 1.2.0
beautifulsoup4 4.12.3
biopython 1.84
bleach 6.1.0
bokeh 3.5.2
boltons 24.0.0
cachetools 5.5.0
certifi 2024.8.30
cffi 1.17.1
cfgv 3.4.0
charset-normalizer 3.3.2
click 8.1.7
cloudpickle 3.0.0
colorcet 3.1.0
comm 0.2.2
contourpy 1.3.0
ctxcore 0.2.0
cucim-cu12 24.4.0
cuda-python 12.6.0
cudf-cu12 24.4.1
cugraph-cu12 24.4.0
cuml-cu12 24.4.0
cuproj-cu12 24.4.0
cupy-cuda12x 13.3.0
cuspatial-cu12 24.4.0
cuvs-cu12 24.4.0
cuxfilter-cu12 24.4.1
cycler 0.12.1
Cython 3.0.11
cytoolz 0.12.3
dask 2024.1.1
dask-cuda 24.4.0
dask-cudf-cu12 24.4.1
dask-expr 0.4.0
datashader 0.16.3
DateTime 5.5
debugpy 1.8.6
decorator 5.1.1
defusedxml 0.7.1
Deprecated 1.2.14
dill 0.3.8
distlib 0.3.8
distributed 2024.1.1
einops 0.8.0
exceptiongroup 1.2.2
executing 2.1.0
fastjsonschema 2.20.0
fastrlock 0.8.2
fcsparser 0.2.8
filelock 3.16.1
fonttools 4.54.1
formulaic 1.0.2
fqdn 1.5.1
frozendict 2.4.4
frozenlist 1.4.1
fsspec 2024.9.0
future 1.0.0
gdown 5.2.0
geopandas 1.0.1
graphtools 1.5.3
grpcio 1.66.1
h5py 3.12.1
harmonypy 0.0.10
holoviews 1.19.1
huggingface-hub 0.25.1
identify 2.6.1
idna 3.10
igraph 0.11.6
imageio 2.35.1
importlib_metadata 8.5.0
importlib_resources 6.4.0
inflect 7.3.1
interface-meta 1.3.0
ipykernel 6.29.5
ipython 8.27.0
ipywidgets 8.1.5
isoduration 20.11.0
jaraco.collections 5.1.0
jaraco.context 5.3.0
jaraco.functools 4.0.1
jaraco.text 3.12.1
jax 0.4.33
jaxlib 0.4.33
jaxopt 0.8.3
jedi 0.19.1
Jinja2 3.1.4
joblib 1.4.2
jsonpointer 3.0.0
jsonschema 4.23.0
jsonschema-specifications 2023.12.1
jupyter_client 8.6.3
jupyter_core 5.7.2
jupyter-events 0.10.0
jupyter_server 2.14.2
jupyter_server_proxy 4.4.0
jupyter_server_terminals 0.5.3
jupyterlab_pygments 0.3.0
jupyterlab_widgets 3.0.13
kiwisolver 1.4.7
ktplotspy 0.2.4
lazy_loader 0.4
legacy-api-wrap 1.4
leidenalg 0.10.2
lifelines 0.29.0
linkify-it-py 2.0.3
llvmlite 0.43.0
locket 1.0.0
loompy 3.0.7
Markdown 3.7
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.6.3
matplotlib-inline 0.1.7
mdit-py-plugins 0.4.2
mdurl 0.1.2
mellon 1.4.3
metatime 1.3.0
mistune 3.0.2
mizani 0.9.3
ml_dtypes 0.5.0
mofax 0.3.6
more-itertools 10.3.0
mpmath 1.3.0
msgpack 1.1.0
multidict 6.1.0
multipledispatch 1.0.0
multiprocess 0.70.16
natsort 8.4.0
nbclient 0.10.0
nbconvert 7.16.4
nbformat 5.10.4
ncls 0.0.68
nest_asyncio 1.6.0
networkx 3.3
nodeenv 1.9.1
numba 0.60.0
numpy 1.26.4
numpy-groupies 0.11.2
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 9.1.0.70
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.6.68
nvidia-nvtx-cu12 12.1.105
nvtx 0.2.10
omicverse 1.6.7
opt_einsum 3.4.0
overrides 7.7.0
packaging 24.1
palantir 1.3.3
pandas 2.2.1
pandocfilters 1.5.1
panel 1.5.0
param 2.1.1
parso 0.8.4
partd 1.4.2
patsy 0.5.6
pexpect 4.9.0
phate 1.0.11
pickleshare 0.7.5
pillow 10.4.0
pip 24.2
platformdirs 4.3.6
plotly 5.24.1
plotnine 0.12.4
pre-commit 3.8.0
progressbar2 4.5.0
prometheus_client 0.21.0
prompt_toolkit 3.0.48
protobuf 4.25.5
psutil 6.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
pyarrow 14.0.2
pycparser 2.22
pyct 0.5.0
pydeseq2 0.4.11
pygam 0.8.0
Pygments 2.18.0
PyGSP 0.5.1
pylibcugraph-cu12 24.4.0
pylibraft-cu12 24.4.0
pynndescent 0.5.13
pynvjitlink-cu12 0.3.0
pynvml 11.4.1
pyogrio 0.9.0
pyparsing 3.1.4
pyproj 3.6.1
pyranges 0.1.2
PySocks 1.7.1
python-circos 0.3.0
python-dateutil 2.9.0
python-dotplot 0.0.1
python-json-logger 2.0.7
python-utils 3.9.0
pytz 2024.2
pyviz_comms 3.0.3
PyYAML 6.0.2
pyzmq 26.2.0
raft-dask-cu12 24.4.0
rapids-dask-dependency 24.4.1
rapids_singlecell 0.10.8
referencing 0.35.1
regex 2024.9.11
requests 2.32.3
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rich 13.8.1
rmm-cu12 24.4.0
rpds-py 0.20.0
ruff 0.6.8
s-gd2 1.8.1
safetensors 0.4.5
scanpy 1.10.3
scikit-image 0.22.0
scikit-learn 1.5.2
scikit-misc 0.5.1
scipy 1.11.4
scprep 1.1.0
scrublet 0.2.3
scvelo 0.3.2
seaborn 0.13.2
SEACells 0.3.3
Send2Trash 1.8.3
session_info 1.0.0
setuptools 75.1.0
shapely 2.0.6
simpervisor 1.0.0
six 1.16.0
sniffio 1.3.1
sorted-nearest 0.0.39
sortedcontainers 2.4.0
soupsieve 2.6
stack-data 0.6.2
statsmodels 0.14.3
stdlib-list 0.10.0
sympy 1.13.3
tabulate 0.9.0
tasklogger 1.2.0
tblib 3.0.0
tenacity 9.0.0
tensorboard 2.18.0
tensorboard-data-server 0.7.2
termcolor 2.4.0
terminado 0.18.1
texttable 1.7.0
threadpoolctl 3.5.0
tifffile 2024.9.20
tinycss2 1.3.0
tokenizers 0.20.0
tomli 2.0.1
toolz 0.12.1
torch 2.4.1
torch-geometric 2.6.1
tornado 6.4.1
tqdm 4.66.5
traitlets 5.14.3
transformers 4.45.1
treelite 4.1.2
triton 3.0.0
typeguard 4.3.0
types-python-dateutil 2.9.0.20240906
typing_extensions 4.12.2
tzdata 2024.2
uc-micro-py 1.0.3
ucx-py-cu12 0.37.0
umap-learn 0.5.6
uri-template 1.3.0
urllib3 2.2.3
virtualenv 20.26.5
wcwidth 0.2.13
webcolors 24.8.0
webencodings 0.5.1
websocket-client 1.8.0
Werkzeug 3.0.4
wheel 0.44.0
widgetsnbextension 4.0.13
wrapt 1.16.0
xarray 2024.9.0
xyzservices 2024.9.0
yarl 1.13.0
zict 3.0.0
zipp 3.20.2
zope.interface 7.0.3
Starlitnightly
Describe the bug
I am encountering issues while trying to use the omicverse library after setting up the virtual environment using
omicverse_gpu.yml. Below are the steps I followed and the errors that occurred.To Reproduce
Created a virtual environment using
omicverse_gpu.yml. Installed the required packages. Ran the following commands:Errors encountered
If applicable, add screenshots to help explain your problem. Dependency Error:
AttributeError:
Additional Information
Omicverse Version: 1.6.6 pandas Version: 2.2.3
Tutorial Reference: Omicverse Documentation
Environment Details
Python version: [python 3.10.14 ] Operating System: [Linux]
Request
Could you please provide guidance on resolving the dependency issue related to
scrublet? Additionally, any information regarding theAttributeErrorwith pandas would be greatly appreciated.Thank you for your help!