Just ran "conda upgrade notebook" to get .5.3.1 now notebook won't start

[Tom Brander]

Got no error on the upgrade but get this now when trying to run notebook so I'm stuck!

Some sort of config issue?

Help appreciated!

tom@tomServal:~$ jupyter notebook

Traceback (most recent call last):

  File "/home/tom/anaconda3/bin/jupyter-notebook", line 4, in <module>

    import notebook.notebookapp

  File "/home/tom/anaconda3/lib/python3.6/site-packages/notebook/__init__.py", line 25, in <module>

    from .nbextensions import install_nbextension

  File "/home/tom/anaconda3/lib/python3.6/site-packages/notebook/nbextensions.py", line 27, in <module>

    from jupyter_core.utils import ensure_dir_exists

ImportError: cannot import name 'ensure_dir_exists'

[Brian Granger]

can you try updating the jupyter_core package using conda or pip. We
may have forgotten to update a dependency version.

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[Tom Brander]

Thanks so much running conda update juypyter_core seems to have it kicking some it complained about terminado being out of date so I did a conda update on that also but I'm still left with these error which I don't yet see if they impact me but:

The GPU one has been around for a long time..

but the [E 16:17:54.358 NotebookApp] 500 GET /api/kernelspecs (127.0.0.1) 4.72ms referer=http://localhost:8888/tree

is worrisome and repeats?,, I did just also update tornado just in case..

[E 16:26:18.014 NotebookApp] Uncaught exception GET /api/kernelspecs (127.0.0.1)

    HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/api/kernelspecs', version='HTTP/1.1', remote_ip='127.0.0.1', headers={'Host': 'localhost:8888', 'Connection': 'keep-alive', 'Accept': '*/*', 'X-Requested-With': 'XMLHttpRequest', 'X-Xsrftoken': '2|c604aaf7|d2ca94a4861a397f298c5ca77bb7887a|1515006983', 'Save-Data': 'on', 'User-Agent': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.132 Safari/537.36', 'Referer': 'http://localhost:8888/tree', 'Accept-Encoding': 'gzip, deflate, br', 'Accept-Language': 'en-US,en;q=0.9', 'Cookie': '_xsrf=2|c604aaf7|d2ca94a4861a397f298c5ca77bb7887a|1515006983; username-localhost-8888="2|1:0|10:1516659977|23:username-localhost-8888|44:NGUyZGViNjk3ODIzNDM3MzgzZTdhYWVjNmJjZDhlMDg=|ac458ec291a81facd8bdf89545bfd55959a89f4254c4f32d68baed01a9e0cb93"'})

    Traceback (most recent call last):

      File "/home/tom/anaconda3/lib/python3.6/site-packages/tornado/web.py", line 1510, in _execute

        result = method(*self.path_args, **self.path_kwargs)

      File "/home/tom/anaconda3/lib/python3.6/site-packages/tornado/web.py", line 2898, in wrapper

        return method(self, *args, **kwargs)

      File "/home/tom/anaconda3/lib/python3.6/site-packages/notebook/services/kernelspecs/handlers.py", line 57, in get

        for kernel_name, kernel_info in ksm.get_all_specs().items():

      File "/home/tom/anaconda3/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 224, in get_all_specs

        } for kname in d}

      File "/home/tom/anaconda3/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 224, in <dictcomp>

        } for kname in d}

      File "/home/tom/anaconda3/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 192, in _get_kernel_spec_by_name

        return self.kernel_spec_class.from_resource_dir(resource_dir)

      File "/home/tom/anaconda3/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 39, in from_resource_dir

        with io.open(kernel_file, 'r', encoding='utf-8') as f:

    FileNotFoundError: [Errno 2] No such file or directory: '/home/tom/anaconda3/lib/python3.6/site-packages/nb_conda_kernels/logos/python/kernel.json'

[W 16:26:18.015 NotebookApp] Unhandled error

[E 16:26:18.015 NotebookApp] {

      "Host": "localhost:8888",

      "Connection": "keep-alive",

      "Accept": "*/*",

      "X-Requested-With": "XMLHttpRequest",

      "X-Xsrftoken": "2|c604aaf7|d2ca94a4861a397f298c5ca77bb7887a|1515006983",

      "Save-Data": "on",

      "User-Agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.132 Safari/537.36",

      "Referer": "http://localhost:8888/tree",

      "Accept-Encoding": "gzip, deflate, br",

      "Accept-Language": "en-US,en;q=0.9",

      "Cookie": "_xsrf=2|c604aaf7|d2ca94a4861a397f298c5ca77bb7887a|1515006983; username-localhost-8888=\"2|1:0|10:1516659977|23:username-localhost-8888|44:NGUyZGViNjk3ODIzNDM3MzgzZTdhYWVjNmJjZDhlMDg=|ac458ec291a81facd8bdf89545bfd55959a89f4254c4f32d68baed01a9e0cb93\""

    }

[E 16:26:18.015 NotebookApp] 500 GET /api/kernelspecs (127.0.0.1) 4.58ms referer=http://localhost:8888/tree

[Tom Brander]

Confirming that this error seems to prevent the sessions from starting with a kernel?

[E 16:31:52.282 NotebookApp] 500 GET /api/kernelspecs (127.0.0.1) 396.99ms referer=http://localhost:8888/notebooks/Documents/InfluenceH/Working_copies/CCS_propensity_wking/propensity_dnn.ipynb

The notebook opens but stays in a busy state and does not say the correct kernel name on the upper right,, the kernels are listed on the Conda kernel page though?

dunno why I can' bottom post here (a groups setting I think?)

[Brian Granger]

Looks like you are/were using nb_conda_kernels to manage kernels and
that one of the kernels isn't there as expected?

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[Tom Brander]

solution? reinstall kernel? re register?

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[Brian Granger]

I haven't used nb_conda_kernels so not sure the best path.

> https://groups.google.com/d/msgid/jupyter/CANg1obZDYHxWYJVaxv0f6LCLb6hQWG9B_xcrt61Ja5YK-hZCrg%40mail.gmail.com.

[Tom Brander]

I never explicitly used Conda kernels but I do remember having to do some hocus-pocus to register Jupyter kernels?

[Tom Brander]

So as of now having doe the update of terminado as suggested (as well as Jupyter, jupyter_core, ipython and tornado)

As well as conda update ipykernel

and:

tom@tomServal:~$ python -m ipykernel install --user

Installed kernelspec python3 in /home/tom/.local/share/jupyter/kernels/python3

I still am getting: [E 22:05:30.138 NotebookApp] Uncaught exception GET /api/kernelspecs (127.0.0.1)

and no kernels in the menu and hangs when opening a notebook (due to no kernels I guess..

So when I attempt to create a new notebook that option is grayed out..

oddly when I run:

tom@tomServal:~$ jupyter kernelspec list

Available kernels:

  clojure    /home/tom/anaconda3/share/jupyter/kernels/clojure

  groovy     /home/tom/anaconda3/share/jupyter/kernels/groovy

  java       /home/tom/anaconda3/share/jupyter/kernels/java

  kotlin     /home/tom/anaconda3/share/jupyter/kernels/kotlin

  python3    /home/tom/anaconda3/share/jupyter/kernels/python3

  scala      /home/tom/anaconda3/share/jupyter/kernels/scala

  sql        /home/tom/anaconda3/share/jupyter/kernels/sql

And my envs are as follows (these were all available in Jupyter before I updated to 5.3.1

tom@tomServal:~$ conda info --envs

# conda environments:

#

py27                     /home/tom/anaconda3/envs/py27

py36                     /home/tom/anaconda3/envs/py36

py362                    /home/tom/anaconda3/envs/py362

py36j                    /home/tom/anaconda3/envs/py36j

py36n                    /home/tom/anaconda3/envs/py36n

pyfolioenv               /home/tom/anaconda3/envs/pyfolioenv

tf13rccpu                /home/tom/anaconda3/envs/tf13rccpu

tf3rc                    /home/tom/anaconda3/envs/tf3rc

tf4                      /home/tom/anaconda3/envs/tf4

tf4n                     /home/tom/anaconda3/envs/tf4n

root                  *  /home/tom/anaconda3

As mentioned they are are still visible on the conda tab in the notebook

Given that many if not the majority of jupyter users now use conda this seems like an issue..!

I am happy to provide more diagnostic info or accept suggestions as to how to fix it? Seems like a missing or misplaced config file of some sort (something got moved or is now being pointed to in a new place?)

But At the moment I'm stuck...

[Tom Brander]

also just noticed that the notebook start up messages have:

[I 22:05:29.402 NotebookApp] [nb_conda_kernels] enabled, 11 kernels found

[Thomas Kluyver]

See https://github.com/Anaconda-Platform/nb_conda_kernels/issues/74

I'm not sure if it's the same issue, but there's also a suggestion that nb_conda_kernels is incompatible with the most recent conda:
https://github.com/Anaconda-Platform/nb_conda_kernels/issues/73

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[Tom Brander]

Thomas, Thanks for the note, problem identified and fix should be posted tomorrow they hope https://github.com/jupyter/jupyter_client/issues/338 Kind of a complex issue between Conda and Jupyter

MinRk was spectacular in finding it.

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