How can I display the version of my Jupyter notebook and run cells in Jupyter notebooks? I get an error: bad interpreter

Question

I have installed Anaconda and I use the conda environments and the conda command to install software.

When I type: jupyter notebook --version

I get the following error:

zsh: /Users/cr517/.local/bin/jupyter: bad interpreter: /Users/cr517/anaconda/envs/snakes/bin/python: no such file or directory 5.2.1

I can open a jupyter notebook by typing: jupyter notebook xyz.ipynb but I cannot run any cells. The cell is marked with * after I run it. Soon, this message appears in a pop-up box:

The kernel has died, and the automatic restart has failed. It is possible the kernel cannot be restarted. If you are not able to restart the kernel, you will still be able to save the notebook, but running code will no longer work until the notebook is reopened.

I get this in the terminal after opening a jupyter notebok:

zsh: /Users/cr517/.local/bin/jupyter: bad interpreter: /Users/cr517/anaconda/envs/snakes/bin/python: no such file or directory
[I 21:01:55.558 NotebookApp] JupyterLab alpha preview extension loaded from /Users/cr517/anaconda/lib/python3.6/site-packages/jupyterlab
[I 21:01:55.558 NotebookApp] JupyterLab application directory is /Users/cr517/anaconda/share/jupyter/lab
[I 21:01:55.564 NotebookApp] Serving notebooks from local directory: /Users/cr517/Documents/teach/demonstrations/python/python-functions-and-modules-master
[I 21:01:55.564 NotebookApp] 0 active kernels
[I 21:01:55.564 NotebookApp] The Jupyter Notebook is running at:
[I 21:01:55.564 NotebookApp] http://localhost:8888/?token=0a0b3368be051aceea02ddfdb677ba5b48724f050e78fa59
[I 21:01:55.564 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 21:01:55.584 NotebookApp] 

    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://localhost:8888/?token=0a0b3368be051aceea02ddfdb677ba5b48724f050e78fa59
[I 21:01:55.852 NotebookApp] Accepting one-time-token-authenticated connection from ::1
[I 21:01:57.808 NotebookApp] Kernel started: 944ec290-db3a-4dc1-97fb-cf440cc384ce
/Users/cr517/anaconda/bin/python: No module named ipykernel_launcher
[I 21:02:00.804 NotebookApp] KernelRestarter: restarting kernel (1/5)
/Users/cr517/anaconda/bin/python: No module named ipykernel_launcher
[I 21:02:03.813 NotebookApp] KernelRestarter: restarting kernel (2/5)
/Users/cr517/anaconda/bin/python: No module named ipykernel_launcher
[I 21:02:06.824 NotebookApp] KernelRestarter: restarting kernel (3/5)
/Users/cr517/anaconda/bin/python: No module named ipykernel_launcher
[W 21:02:07.940 NotebookApp] Timeout waiting for kernel_info reply from 944ec290-db3a-4dc1-97fb-cf440cc384ce
[I 21:02:09.833 NotebookApp] KernelRestarter: restarting kernel (4/5)
kernel 944ec290-db3a-4dc1-97fb-cf440cc384ce restarted
/Users/cr517/anaconda/bin/python: No module named ipykernel_launcher
[W 21:02:12.841 NotebookApp] KernelRestarter: restart failed
[W 21:02:12.842 NotebookApp] Kernel 944ec290-db3a-4dc1-97fb-cf440cc384ce died, removing from map.
kernel 944ec290-db3a-4dc1-97fb-cf440cc384ce restarted failed!
[W 21:02:12.873 NotebookApp] 410 DELETE /api/sessions/eaa457a0-7628-42c4-927f-1428b4ec3b68 (::1): Kernel deleted before session
[W 21:02:12.873 NotebookApp] Kernel deleted before session
[W 21:02:12.873 NotebookApp] 410 DELETE /api/sessions/eaa457a0-7628-42c4-927f-1428b4ec3b68 (::1) 2.10ms referer=http://localhost:8888/notebooks/python_fm_1.ipynb

Indeed there is no /Users/cr517/anaconda/envs/snakes/bin/python but why is Jupyter Notebook trying to use this? I have a well-functioning Python here:

which python
/Users/cr517/anaconda/bin/python

?

which -a python
/Users/cr517/anaconda/bin/python
/usr/local/bin/python
/usr/bin/python

which -a jupyter
/Users/cr517/.local/bin/jupyter
/Users/cr517/.local/bin/jupyter
/Users/cr517/.local/bin/jupyter

echo $PATH
/usr/local/opt/[email protected]/bin:/Users/cr517/Documents/phd/project/output/software/DEXTRACTOR:/Users/cr517/Documents/phd/project/output/software/DAZZ_DB:/Users/cr517/Documents/phd/project/output/software/DASCRUBBER:/Users/cr517/Documents/phd/project/output/software/subread-1.5.2-MaxOSX-x86_64/bin:/Users/cr517/Documents/phd/project/output/software/SHRiMP_2_2_2/utils:/Users/cr517/Documents/phd/project/output/software:/Users/cr517/Documents/phd/project/output/software/fastx/bin:/Users/cr517/.local/bin:/Users/cr517/Documents/phd/project/output/software/DAZZ_DB:/Users/cr517/Documents/phd/project/output/software/DASCRUBBER:/Users/cr517/Documents/phd/project/output/software/subread-1.5.2-MaxOSX-x86_64/bin:/Users/cr517/Documents/phd/project/output/software/SHRiMP_2_2_2/utils:/Users/cr517/Documents/phd/project/output/software:/Users/cr517/Documents/phd/project/output/software/fastx/bin:/Users/cr517/.local/bin:/Users/cr517/Documents/phd/project/output/software/DASCRUBBER:/Users/cr517/Documents/phd/project/output/software/subread-1.5.2-MaxOSX-x86_64/bin:/Users/cr517/Documents/phd/project/output/software/SHRiMP_2_2_2/utils:/Users/cr517/Documents/phd/project/output/software:/Users/cr517/Documents/phd/project/output/software/fastx/bin:/Users/cr517/.local/bin:/Users/cr517/Documents/phd/project/output/software/subread-1.5.2-MaxOSX-x86_64/bin:/Users/cr517/Documents/phd/project/output/software/SHRiMP_2_2_2/utils:/Users/cr517/Documents/phd/project/output/software:/Users/cr517/Documents/phd/project/output/software/fastx/bin:/Users/cr517/.local/bin:/Users/cr517/Documents/phd/project/output/software:/Users/cr517/Documents/phd/project/output/software/STAR:/Users/cr517/Documents/phd/project/output/software/fastx/bin:/Users/cr517/.local/bin:/Users/cr517/.local/bin:/Users/cr517/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin:/Users/cr517/Documents/phd/project/multibreak-sv/lib:/Users/cr517/Documents/phd/project/output/software/PBSuite_15.8.24/pbsuite:/Users/cr517/Documents/phd/project/output/software/PBSuite_15.8.24/bin/:/Users/cr517/Documents/phd/project/output/software/blobology
    /Users/cr517/.local/bin/jupyter
    /Users/cr517/.local/bin/jupyter
    /Users/cr517/.local/bin/jupyter
    /Users/cr517/anaconda/bin/jupyter
    /usr/local/bin/jupyter

jupyter kernelspec list
zsh: /Users/cr517/.local/bin/jupyter: bad interpreter: /Users/cr517/anaconda/envs/snakes/bin/python: no such file or directory
Available kernels:
  python3    /Users/cr517/anaconda/lib/python3.6/site-packages/ipykernel/resources
  ir         /Users/cr517/anaconda/share/jupyter/kernels/ir
  python2    /usr/local/share/jupyter/kernels/python2

jupyter notebook opens my directory in a web browser but does not create a new notebook.

I typed python --version in the terminal and got:

Python 3.6.3 :: Anaconda custom (x86_64)

Solution 1

*How to check iPython version

You can check it with conda list ipython

Solution 2

From your terminal, you can simply do:

jupyter --version

Or, if you are using a notebook then do:

!jupyter --version

Here is the output in my case:

jupyter core     : 4.5.0
jupyter-notebook : 5.2.2
qtconsole        : 4.5.2
ipython          : 5.5.0
ipykernel        : 4.10.1
jupyter client   : 5.3.1
jupyter lab      : not installed
nbconvert        : 5.5.0
ipywidgets       : 7.5.0
nbformat         : 4.4.0
traitlets        : 4.3.2

Solution 3

• This is definitely a path issue : You have your anacondda python interpreter path in /Users/cr517/anaconda/bin/python
• But your jupyter is pointing to /Users/cr517/.local/bin/jupyter but it should have pointed to /Users/cr517/anaconda/bin/jupyter
• Run the following command gedit /Users/cr517/anaconda/bin/jupyter
• Check the first line of the opened file which will have the hardcoded path of jupyter and check whether the path in the file is correct or not
• If the path is not /Users/cr517/anaconda/bin/jupyter than make it /Users/cr517/anaconda/bin/jupyter
• But the problem may not solve here because there are other jupyter files if you do ls *jupyter* many of these files have the hardcoded path which might be wrong which might be reason why you are able to open he ipynb but cannot create the cell
• This is too much work to do ... to manually change path for every file
• Just reinstall anaconda and your problem will be solved
• In case you are reinstalling run this bash Anaconda....sh -b -p "Users/cr517/anaconda"

Comments

[Usernamenotfound]

do you have another jupyter notebook version outside of the one you got from anaconda?

[Usernamenotfound]

what do you get when you type "python --version" in the kernel?

[shevy]

But what does version 5.4.1 mean here? I currently have a related problem in that there is a rounding difference. I am using python 3.8.2 normally, but jupyter seems to return (or have been used) by someone else that returns another rounding number. I can find out which version the rounding error originates from, but I guess I'd love to know what python version was used upstream (it is a student assignment from a university, so I assume they may have used another python version)

[Vainmonde De Courtenay]

How does this answer the question? :/

[Romeu Fronzaroli]

When I tried, I have to put "!" first. Like: !jupyter --version