python stuck while running sc.tl.velocity_graph with 0% progress but without showing error

[didiren]

...I am writing to ask for help with using scvelo. I installed the latest version of scvelo. All codes were run fine without error following the tutorial except running sc.tl.velocity_graph step in python 3.8.7.

The issue is python indicate it start to run this step, sc.tl.velocity_graph without error. But the progress showing 0% even after 2days. May I ask whether you could offer some comments of why this step are stuck or what I should do to solve this issue ?

sc.tl.velocity_graph (adata)```

<!-- Error Output -->
<details>

<summary> Error output </summary>

```pytb
# paste the error output here, if applicable

Package Version

---

absl-py 2.1.0 anndata 0.9.2 anyio 4.2.0 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 arrow 1.3.0 asttokens 2.4.1 async-lru 2.0.4 attrs 23.2.0 Babel 2.14.0 backcall 0.2.0 beautifulsoup4 4.12.3 bleach 6.1.0 certifi 2024.2.2 cffi 1.16.0 charset-normalizer 3.3.2 click 8.1.7 colorama 0.4.6 comm 0.2.1 contourpy 1.1.1 cycler 0.12.1 debugpy 1.8.1 decorator 5.1.1 defusedxml 0.7.1 exceptiongroup 1.2.0 executing 2.0.1 fastjsonschema 2.19.1 flatbuffers 2.0.7 fonttools 4.48.1 fqdn 1.5.1 get-annotations 0.1.2 gitdb 4.0.11 GitPython 3.1.41 h5py 3.10.0 idna 3.6 igraph 0.10.8 importlib-metadata 7.0.1 importlib-resources 6.1.1 ipykernel 6.29.2 ipython 8.12.3 ipython-genutils 0.2.0 ipywidgets 7.7.1 isoduration 20.11.0 jax 0.3.13 jaxlib 0.3.7 jedi 0.19.1 Jinja2 3.1.3 joblib 1.3.2 json5 0.9.14 jsonpointer 2.4 jsonschema 4.21.1 jsonschema-specifications 2023.12.1 jupyter_client 8.6.0 jupyter_core 5.7.1 jupyter-events 0.9.0 jupyter-lsp 2.2.2 jupyter_server 2.12.5 jupyter_server_terminals 0.5.2 jupyterlab 4.0.12 jupyterlab_pygments 0.3.0 jupyterlab_server 2.25.2 jupyterlab_widgets 3.0.10 kiwisolver 1.4.5 llvmlite 0.41.1 loompy 3.0.7 louvain 0.8.1 MarkupSafe 2.1.5 matplotlib 3.7.4 matplotlib-inline 0.1.6 mistune 3.0.2 multivelo 0.1.3 natsort 8.4.0 nbclient 0.9.0 nbconvert 7.16.0 nbformat 5.9.2 nest-asyncio 1.6.0 networkx 3.1 notebook 7.0.8 notebook_shim 0.2.3 numba 0.58.1 numpy 1.24.4 numpy_groupies 0.9.22 opt-einsum 3.3.0 overrides 7.7.0 packaging 23.2 pandas 2.0.3 pandocfilters 1.5.1 parso 0.8.3 patsy 0.5.6 pickleshare 0.7.5 pillow 10.2.0 pip 24.0 pkgutil_resolve_name 1.3.10 platformdirs 4.2.0 prometheus-client 0.19.0 prompt-toolkit 3.0.43 psutil 5.9.8 pure-eval 0.2.2 pycparser 2.21 Pygments 2.17.2 pynndescent 0.5.11 pyparsing 3.1.1 python-dateutil 2.8.2 python-json-logger 2.0.7 pytz 2024.1 pywin32 306 pywinpty 2.0.12 PyYAML 6.0.1 pyzmq 25.1.2 referencing 0.33.0 requests 2.31.0 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rpds-py 0.17.1 scanpy 1.9.8 scikit-learn 1.1.3 scipy 1.10.1 scvelo 0.3.1 seaborn 0.13.2 Send2Trash 1.8.2 session-info 1.0.0 setuptools 49.2.1 six 1.16.0 smmap 5.0.1 sniffio 1.3.0 soupsieve 2.5 stack-data 0.6.3 statsmodels 0.14.1 stdlib-list 0.10.0 terminado 0.18.0 texttable 1.7.0 threadpoolctl 3.2.0 tinycss2 1.2.1 tomli 2.0.1 tornado 6.4 tqdm 4.66.2 traitlets 5.14.1 types-python-dateutil 2.8.19.20240106 typing_extensions 4.9.0 tzdata 2024.1 umap-learn 0.5.5 uri-template 1.3.0 urllib3 2.2.0 wcwidth 0.2.13 webcolors 1.13 webencodings 0.5.1 websocket-client 1.7.0 widgetsnbextension 3.6.6 zipp 3.17.0

# paste the ouput of scv.logging.print_versions() here

[WeilerP]

Seems like a duplicate of #1196.

[didiren]

paste the ouput of scv.logging.print_versions() here

scvelo==0.3.1 scanpy==1.9.8 anndata==0.9.2 loompy==3.0.7 numpy==1.24.4 scipy==1.10.1 matplotlib==3.7.4 sklearn==1.1.3 pandas==2.0.3

[didiren]

Seems like a duplicate of #1196.

Hi, I have emailed and raised this question before, sorry for the delay but I have pasted the scv.logging.print_versions() here if it will help to identify the issue. scvelo==0.3.1 scanpy==1.9.8 anndata==0.9.2 loompy==3.0.7 numpy==1.24.4 scipy==1.10.1 matplotlib==3.7.4 sklearn==1.1.3 pandas==2.0.3