Iāve just installed MNE-Python 1.5.0 (on Centos 7). Starting a Jupyter Notebook only opens a blank page. It works with version 1.4.0, so Iām guessing the problem is the new Notebook version 7.0.2. The old version shows a warning that with version 7 there may be problems with some extensions.
Any ideas how to address this?
Hello Olaf, how did you install MNE? How do you start the notebook?
Best wishes,
Richard
Hi Richard.
I installed it on Linux with installer and sh ./MNE-Python-1.5.0_0-Linux.sh.
Then I activate the conda enviroment, load a module to use the correct graphics libraries (could these have changed?), and then start the notebook via jupyter notebook --ip=127.0.0.1.
Do you get any helpful output in the console?
Itās not helpful to me (or our IT guy), but please have a look at below. I note in particular āConfig option kernel_spec_manager_class not recognized by JupyterNotebookApp.ā
2023-08-23 17:14:10.083 ServerApp] Package notebook took 0.0000s to import
[I 2023-08-23 17:14:10.124 ServerApp] Package jupyter_lsp took 0.0397s to import
[W 2023-08-23 17:14:10.124 ServerApp] A _jupyter_server_extension_points function was not found in jupyter_lsp. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[I 2023-08-23 17:14:10.231 ServerApp] Package jupyter_server_proxy took 0.1066s to import
[I 2023-08-23 17:14:10.243 ServerApp] Package jupyter_server_terminals took 0.0114s to import
[I 2023-08-23 17:14:10.244 ServerApp] Package jupyterlab took 0.0000s to import
[I 2023-08-23 17:14:10.369 ServerApp] Package notebook_shim took 0.0000s to import
[W 2023-08-23 17:14:10.369 ServerApp] A _jupyter_server_extension_points function was not found in notebook_shim. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[I 2023-08-23 17:14:10.370 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2023-08-23 17:14:10.370 ServerApp] jupyter_server_proxy | extension was successfully linked.
[W 2023-08-23 17:14:10.373 TerminalsExtensionApp] Config option kernel_spec_manager_class not recognized by TerminalsExtensionApp. Did you mean terminal_manager_class?
[W 2023-08-23 17:14:10.374 TerminalsExtensionApp] Config option kernel_spec_manager_class not recognized by TerminalsExtensionApp. Did you mean terminal_manager_class?
[W 2023-08-23 17:14:10.377 TerminalsExtensionApp] Config option kernel_spec_manager_class not recognized by TerminalsExtensionApp. Did you mean terminal_manager_class?
[I 2023-08-23 17:14:10.378 ServerApp] jupyter_server_terminals | extension was successfully linked.
[W 2023-08-23 17:14:10.380 LabApp] Config option kernel_spec_manager_class not recognized by LabApp.
[W 2023-08-23 17:14:10.381 LabApp] Config option kernel_spec_manager_class not recognized by LabApp.
[W 2023-08-23 17:14:10.385 LabApp] Config option kernel_spec_manager_class not recognized by LabApp.
[I 2023-08-23 17:14:10.385 ServerApp] jupyterlab | extension was successfully linked.
[W 2023-08-23 17:14:10.387 JupyterNotebookApp] Config option kernel_spec_manager_class not recognized by JupyterNotebookApp.
[W 2023-08-23 17:14:10.388 JupyterNotebookApp] Config option kernel_spec_manager_class not recognized by JupyterNotebookApp.
[W 2023-08-23 17:14:10.391 JupyterNotebookApp] Config option kernel_spec_manager_class not recognized by JupyterNotebookApp.
[I 2023-08-23 17:14:10.392 ServerApp] notebook | extension was successfully linked.
[I 2023-08-23 17:14:10.804 ServerApp] notebook_shim | extension was successfully linked.
[I 2023-08-23 17:14:11.339 ServerApp] [nb_conda_kernels] enabled, 32 kernels found
[I 2023-08-23 17:14:11.368 ServerApp] notebook_shim | extension was successfully loaded.
[I 2023-08-23 17:14:11.371 ServerApp] jupyter_lsp | extension was successfully loaded.
[I 2023-08-23 17:14:11.415 ServerApp] jupyter_server_proxy | extension was successfully loaded.
[I 2023-08-23 17:14:11.416 ServerApp] jupyter_server_terminals | extension was successfully loaded.
[I 2023-08-23 17:14:11.424 LabApp] JupyterLab extension loaded from /imaging/local/software/mne_python/mne1.5.0_0/lib/python3.11/site-packages/jupyterlab
[I 2023-08-23 17:14:11.424 LabApp] JupyterLab application directory is /imaging/local/software/mne_python/mne1.5.0_0/share/jupyter/lab
[I 2023-08-23 17:14:11.424 LabApp] Extension Manager is āpypiā.
[I 2023-08-23 17:14:11.427 ServerApp] jupyterlab | extension was successfully loaded.
[I 2023-08-23 17:14:11.433 ServerApp] notebook | extension was successfully loaded.
[I 2023-08-23 17:14:11.434 ServerApp] Serving notebooks from local directory: /home/olaf
[I 2023-08-23 17:14:11.434 ServerApp] Jupyter Server 2.7.1 is running at:
[I 2023-08-23 17:14:11.434 ServerApp] http://127.0.0.1:8888/tree?token=ce205bb8b7de7958b696330a82780c500eb686a862e51d27
[I 2023-08-23 17:14:11.434 ServerApp] http://127.0.0.1:8888/tree?token=ce205bb8b7de7958b696330a82780c500eb686a862e51d27
[I 2023-08-23 17:14:11.434 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
Some possible things to try:
-
start the notebook server with
--debugflag, it should tell you where the config files are that itās using -
look at those config files (probably
$HOME/.jupyter/jupyter_config.jsonor possibly$HOME/.jupyter/jupyter_notebook_config.json). If the offending config key is in there, remove it. (probably itās not in there ā itās most likely being set dynamically bynb_conda_kernels) -
update
nb_conda_kernels(longshot, probably already latest version)
My suspicion is that none of this will fix it.
Next, take a look at the output of jupyter server extension list. This will tell you which extensions you have installed. Disable them all and see if it works (jupyter server extension disable NAME_OF_EXTENSION). If it does, re-enable one by one until it fails (same as above but swap enable for disable), then you know which extension(s) to update, replace, or abandon.
1 Like
Silly question: how do I update np_conda_kernels?
Below is the output I get from jupyter server extension list. I disabled them all but it didnāt change anything.
(/imaging/local/software/mne_python/mne1.5.0_0) [olaf@login-gpu03 ~]$ jupyter server extension list
Config option kernel_spec_manager_class not recognized by ListServerExtensionsApp.
Config dir: /home/olaf/.jupyter
Config dir: /imaging/local/software/mne_python/mne1.5.0_0/etc/jupyter
jupyter_lsp enabled
- Validating jupyter_lspā¦
Package jupyter_lsp took 0.0172s to import
A _jupyter_server_extension_points function was not found in jupyter_lsp. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
jupyter_lsp 2.2.0 OK
jupyter_server_proxy enabled
- Validating jupyter_server_proxyā¦
Package jupyter_server_proxy took 0.0764s to import
jupyter_server_proxy OK
jupyter_server_terminals enabled
- Validating jupyter_server_terminalsā¦
Package jupyter_server_terminals took 0.0094s to import
jupyter_server_terminals 0.4.4 OK
jupyterlab enabled
- Validating jupyterlabā¦
Package jupyterlab took 0.0956s to import
jupyterlab 4.0.5 OK
notebook enabled
- Validating notebookā¦
Package notebook took 0.0000s to import
notebook 7.0.2 OK
notebook_shim enabled
- Validating notebook_shimā¦
Package notebook_shim took 0.0000s to import
A _jupyter_server_extension_points function was not found in notebook_shim. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
notebook_shim OK
Config dir: /usr/local/etc/jupyter
@olafhauk, what do you actually see in the browser? Just a blank page without any content, i.e., all is white? Or are there any buttons, anythingā¦?
can be conda upgrade nb_conda_kernels or pip install --upgrade nb_conda_kernels
dang 
at this point I would probably raise an issue here Issues Ā· jupyter/notebook Ā· GitHub, they will have better debugging advice than me
You might find a resolution by consulting with experts knowledgeable in Jupyter Notebook https://tech-stack.com/services/big-data-and-analytics