coder
HoloViews/ hvplot not working in code-server Jupyter Notebook on Binder
CROSSPOST OF: https://github.com/holoviz/holoviews/issues/5182
I'm trying to create a nice repository for me and Sophia M Yang for a blog post and tutorial. I would also like to show case that the HoloViz ecosystem works with VS Code. So I added the code-server to the Binder environment.
Unfortunately it seems not to work
Reproducible Steps
https://user-images.githubusercontent.com/42288570/149618402-0d65e26d-c85d-435c-8c28-8a6b34981754.mp4 (The video is speeded up with a factor 1.7)
Repo: https://github.com/MarcSkovMadsen/hvplot_interactive commit 3cd8bf19dc326a76efe20e2dd3fedb7f1ff6e6af
- Open https://mybinder.org/v2/gh/marcskovmadsen/hvplot_interactive/3cd8bf19dc326a76efe20e2dd3fedb7f1ff6e6af
- Open VS Code
- View Output - Jupyter to see log message
- Create a new notebook
- Make sure the kernel is
notebook
print('hello')
import hvplot.pandas
Notice how it took a long time to execute this cell
print('hello')
Notice the console how you get an error message as you print hello.
import holoviews as hv
hv.extension("bokeh")
In the video this load pretty quickly (8secs) but I've also experienced it running for minutes before I've given up.
import panel as pn
It stopped working.
Versions
jupyter_bokeh bokeh Version: 0.12.6 Name: holoviews Version: 1.14.7 Name: hvplot Version: 0.7.3 Name: ipykernel Version: 6.7.0 Name: jupyter-bokeh Version: 3.0.4 Name: bokeh Version: 2.4.2 python Python 3.7.12 Python VS Code extension Version: ms-python v2021.12.1559732655 Jupyter VS Code extension Version: ms-toolsai v2021.11.1001552333 code-server Version: 4.0.1 735c6da829535969ff7193c79379299e4a1cb9bc
Log for Output - Jupyter window
Additional Context
- I don't experience the same problems in "real" VS Code on my laptop.
- I experience similar problems on my Jupyter Hub for work where code-server is also running.
Thanks for the report and URL to reproduce. Unfortunately I'm not a user of Jupyter Notebook, Binder and don't write Python regularly so I'm not sure what to expect here?
I did try following your steps and I'm seeing some errors but I'm not sure what HoloViews is or how hvplot is supposed to work.
Can you elaborate on what you expect? I don't see anything specific that could cause this but it's also very hard to isolate the problem because they are so many variables at play. I noticed you said to use notebook for the kernel and it is provided by conda. Have you tried removing conda from the equation?
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I did a quick check at https://demo.jupyter.b-data.ch (Image R (verse:latest) + code-server).
When a cell does not finish executing, i see the following in the container log over and over again:
[I 2022-07-22 13:18:43.962 SingleUserLabApp log:189] 101 GET /user/benz0li/code-server/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false (benz0li@[redacted]) 2.91ms
[I 2022-07-22 13:18:43.962 SingleUserLabApp handlers:432] Trying to establish websocket connection to ws://localhost:33777/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false
[I 2022-07-22 13:18:43.968 SingleUserLabApp handlers:439] Websocket connection established to ws://localhost:33777/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false
[13:18:44] [127.0.0.1][c68db751][ExtensionHostConnection] The client has reconnected.
When executing cell by cell
import holoviews as hv
hv.extension("bokeh")
leads to
[I 2022-07-22 13:31:42.510 SingleUserLabApp log:189] 101 GET /user/benz0li/code-server/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false (benz0li@[redacted]) 4.80ms
[I 2022-07-22 13:31:42.511 SingleUserLabApp handlers:432] Trying to establish websocket connection to ws://localhost:33777/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false
[I 2022-07-22 13:31:42.517 SingleUserLabApp handlers:439] Websocket connection established to ws://localhost:33777/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false
[13:31:42] [127.0.0.1][aa56c074][ExtensionHostConnection] The client has reconnected.
[E 2022-07-22 13:31:44.101 SingleUserLabApp websocket:1578] Uncaught exception
Traceback (most recent call last):
File "/usr/local/lib/python3.9/dist-packages/tornado/websocket.py", line 635, in _run_callback
result = callback(*args, **kwargs)
File "/usr/local/lib/python3.9/dist-packages/tornado/websocket.py", line 1523, in on_message
return self._on_message(message)
File "/usr/local/lib/python3.9/dist-packages/tornado/websocket.py", line 1529, in _on_message
self._on_message_callback(message)
File "/usr/local/lib/python3.9/dist-packages/jupyter_server_proxy/handlers.py", line 420, in message_cb
self.write_message(message, binary=isinstance(message, bytes))
File "/usr/local/lib/python3.9/dist-packages/tornado/websocket.py", line 336, in write_message
raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
[I 2022-07-22 13:31:44.411 SingleUserLabApp log:189] 101 GET /user/benz0li/code-server/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false (benz0li@[redacted]) 2.64ms
[I 2022-07-22 13:31:44.411 SingleUserLabApp handlers:432] Trying to establish websocket connection to ws://localhost:33777/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false
[I 2022-07-22 13:31:44.416 SingleUserLabApp handlers:439] Websocket connection established to ws://localhost:33777/stable-30d9c6cd9483b2cc586687151bcbcd635f373630?type=ExtensionHost&reconnectionToken=[redacted]&reconnection=true&skipWebSocketFrames=false
[13:31:44] [127.0.0.1][aa56c074][ExtensionHostConnection] The client has reconnected.
with the last four lines repeating over and over again.
One can reproduce this locally with docker, too.
Initial startup:
docker run -it --rm -p 8888:8888 -v $PWD:/home/jovyan -e GEN_CERT=yes registry.gitlab.b-data.ch/jupyterlab/r/verse
Subsequent startups:
docker run -it --rm -p 8888:8888 -v $PWD:/home/jovyan registry.gitlab.b-data.ch/jupyterlab/r/verse start-notebook.sh --NotebookApp.certfile=~/.local/share/jupyter/notebook.pem
Run the initial command in an empty directory so that the container populates it.
Visit https://127.0.0.1:8888/lab?token=<token> in a browser to load JupyterLab.