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The jupyternotbook analysis showing bug #6895

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honghh2018 opened this issue Jun 1, 2023 · 1 comment
Closed

The jupyternotbook analysis showing bug #6895

honghh2018 opened this issue Jun 1, 2023 · 1 comment
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bug status:Duplicate status:Needs Triage Applied to issues that need triage

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@honghh2018
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Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:
running below command in jypyter-notebook in Centos7.9 plotform:
$jupyter-notebook --version
6.5.4

IPython : 8.12.0
ipykernel : 6.19.2
ipywidgets : not installed
jupyter_client : 8.1.0
jupyter_core : 5.3.0
jupyter_server : 1.23.4
jupyterlab : not installed
nbclient : 0.5.13
nbconvert : 6.5.4
nbformat : 5.7.0
notebook : 6.5.4
qtconsole : not installed
traitlets : 5.7.1

scv.pl.velocity_embedding_stream(adata, basis="umap", color="cuqian4",figsize=(10,8),linewidth = 2.5,save="osteo_recluster.svg")

then conda environment:
Package Version


anndata 0.9.1
anyio 3.5.0
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.5
attrs 22.1.0
backcall 0.2.0
beautifulsoup4 4.12.2
bleach 4.1.0
cached-property 1.5.2
certifi 2023.5.7
cffi 1.15.1
charset-normalizer 3.1.0
click 8.1.3
colorama 0.4.6
comm 0.1.2
contourpy 1.0.7
cycler 0.11.0
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
executing 0.8.3
fastjsonschema 2.16.2
fonttools 4.39.4
h5py 3.8.0
hnswlib 0.7.0
idna 3.4
igraph 0.10.4
importlib-metadata 6.0.0
importlib-resources 5.2.0
ipykernel 6.19.2
ipython 8.12.0
ipython_genutils 0.2.0
jedi 0.18.1
Jinja2 3.1.2
joblib 1.2.0
jsonschema 4.17.3
jupyter_client 8.1.0
jupyter_core 5.3.0
jupyter-server 1.23.4
jupyterlab-pygments 0.1.2
kiwisolver 1.4.4
leidenalg 0.9.1
llvmlite 0.40.0
loompy 3.0.7
louvain 0.8.0
lxml 4.9.2
MarkupSafe 2.1.1
matplotlib 3.7.1
matplotlib-inline 0.1.6
mistune 0.8.4
munkres 1.1.4
natsort 8.3.1
nbclassic 0.5.5
nbclient 0.5.13
nbconvert 6.5.4
nbformat 5.7.0
nest-asyncio 1.5.6
networkx 3.1
notebook 6.5.4
notebook_shim 0.2.2
numba 0.57.0
numpy 1.24.3
numpy-groupies 0.9.22
packaging 23.0
pandas 2.0.2
pandocfilters 1.5.0
parso 0.8.3
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.5.0
pip 23.0.1
pkgutil_resolve_name 1.3.10
platformdirs 2.5.2
pooch 1.7.0
prometheus-client 0.14.1
prompt-toolkit 3.0.36
psutil 5.9.0
ptyprocess 0.7.0
pure-eval 0.2.2
pybind11 2.10.4
pycparser 2.21
Pygments 2.15.1
pynndescent 0.5.10
pyparsing 3.0.9
pyrsistent 0.18.0
PySocks 1.7.1
python-dateutil 2.8.2
python-igraph 0.10.4
pytz 2023.3
pyzmq 25.0.2
requests 2.31.0
scanpy 1.9.3
scikit-learn 1.2.2
scipy 1.10.1
scvelo 0.2.5
seaborn 0.12.2
Send2Trash 1.8.0
session-info 1.0.0
setuptools 67.8.0
six 1.16.0
sniffio 1.2.0
soupsieve 2.4
stack-data 0.2.0
statsmodels 0.14.0
stdlib-list 0.8.0
terminado 0.17.1
texttable 1.6.7
threadpoolctl 3.1.0
tinycss2 1.2.1
tornado 6.1
tqdm 4.65.0
traitlets 5.7.1
typing_extensions 4.5.0
tzdata 2023.3
umap-learn 0.5.3
unicodedata2 15.0.0
urllib3 2.0.2
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 0.58.0
wheel 0.38.4
zipp 3.11.0

Expected behavior
the jupyter bug showing for single cell scvelo analysis
like below :
[W 13:55:16.649 NotebookApp] Notebook Untitled2.ipynb is not trusted
[E 13:55:19.471 NotebookApp] Uncaught exception, closing connection.
Traceback (most recent call last):
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/iostream.py", line 700, in _handle_events
self._handle_write()
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/iostream.py", line 974, in _handle_write
self._write_buffer.advance(num_bytes)
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/iostream.py", line 183, in advance
assert 0 < size <= self._size
AssertionError
ERROR:asyncio:Exception in callback None()
handle:
Traceback (most recent call last):
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/asyncio/events.py", line 81, in _run
self._context.run(self._callback, *self._args)
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/platform/asyncio.py", line 189, in _handle_events
handler_func(fileobj, events)
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/iostream.py", line 700, in _handle_events
self._handle_write()
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/iostream.py", line 974, in _handle_write
self._write_buffer.advance(num_bytes)
File "/share/apps/virtualEnv/miniconda3-py38/envs/scVelocity/lib/python3.8/site-packages/tornado/iostream.py", line 183, in advance
assert 0 < size <= self._size
AssertionError

Screenshots
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Desktop (please complete the following information):

  • OS: Centos7.9
  • Browser: chrome
  • Version6.5.4

Additional context
Add any other context about the problem here.

@honghh2018 honghh2018 added the bug label Jun 1, 2023
@jupyterlab-probot jupyterlab-probot bot added the status:Needs Triage Applied to issues that need triage label Jun 1, 2023
@JasonWeill
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Closing as a duplicate of #6721.

@github-actions github-actions bot locked as resolved and limited conversation to collaborators Jun 6, 2024
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Labels
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