some progress matlab-kernel, a python path problem?

some progress matlab-kernel, a python path problem?

[Uwe Brauer]

Hi

So I switched from finks python 3.7 to MacOS 3.8
I think I set all paths (mac does not locate them in 
HOME/.local but in 
HOME/Library

However when I fire up the org-babel command the iphthon console reads
as

,----
| Traceback (most recent call last):
|   File "/Users/oub/Library/Python/3.8/bin/jupyter-console", line 10, in <module>
|     sys.exit(main())
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_core/application.py", line 254, in launch_instance
|     return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py", line 844, in launch_instance
|     app.initialize(argv)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py", line 87, in inner
|     return method(app, *args, **kwargs)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py", line 136, in initialize
|     self.init_shell()
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py", line 103, in init_shell
|     JupyterConsoleApp.initialize(self)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py", line 343, in initialize
|     self.init_kernel_manager()
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py", line 295, in init_kernel_manager
|     self.kernel_manager.start_kernel(**kwargs)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 337, in start_kernel
|     kernel_cmd, kw = self.pre_start_kernel(**kw)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 292, in pre_start_kernel
|     kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 210, in format_kernel_cmd
|     cmd = self.kernel_spec.argv + extra_arguments
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 114, in kernel_spec
|     self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
|   File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/kernelspec.py", line 230, in get_kernel_spec
|     raise NoSuchKernel(kernel_name)
| jupyter_client.kernelspec.NoSuchKernel: No such kernel named matlab
| 
| Process kernel-matlab exited abnormally with code 1
`----

But the matlab_kernel is installed

I am puzzled, any python guru could enlighten me please?

Regards

Uwe Brauer 

Re: some progress matlab-kernel, a python path problem?

[John Kitchin]

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I would see if you can open a jupyter notebook and start a notebook with
the mat lab kernel. If not, it either isn’t installed, or maybe is
installed in a different jupyter.

If you get errors here, the issue is outside of org mode. For example, the
hylang kernel quit working for me a while ago.

See
https://github.com/Calysto/matlab_kernel#kernel-times-out-while-starting
for some troubleshooting tips.

On Wed, Jun 16, 2021 at 11:48 AM Uwe Brauer <oub@mat.ucm.es> wrote:

>
>
> Hi
>
> So I switched from finks python 3.7 to MacOS 3.8
> I think I set all paths (mac does not locate them in
> HOME/.local but in
> HOME/Library
>
> However when I fire up the org-babel command the iphthon console reads
> as
>
> ,----
> | Traceback (most recent call last):
> |   File "/Users/oub/Library/Python/3.8/bin/jupyter-console", line 10, in
> <module>
> |     sys.exit(main())
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_core/application.py",
> line 254, in launch_instance
> |     return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py",
> line 844, in launch_instance
> |     app.initialize(argv)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py",
> line 87, in inner
> |     return method(app, *args, **kwargs)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py",
> line 136, in initialize
> |     self.init_shell()
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py",
> line 103, in init_shell
> |     JupyterConsoleApp.initialize(self)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py",
> line 343, in initialize
> |     self.init_kernel_manager()
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py",
> line 295, in init_kernel_manager
> |     self.kernel_manager.start_kernel(**kwargs)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py",
> line 337, in start_kernel
> |     kernel_cmd, kw = self.pre_start_kernel(**kw)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py",
> line 292, in pre_start_kernel
> |     kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py",
> line 210, in format_kernel_cmd
> |     cmd = self.kernel_spec.argv + extra_arguments
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py",
> line 114, in kernel_spec
> |     self._kernel_spec =
> self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
> |   File
> "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/kernelspec.py",
> line 230, in get_kernel_spec
> |     raise NoSuchKernel(kernel_name)
> | jupyter_client.kernelspec.NoSuchKernel: No such kernel named matlab
> |
> | Process kernel-matlab exited abnormally with code 1
> `----
>
> But the matlab_kernel is installed
>
> I am puzzled, any python guru could enlighten me please?
>
> Regards
>
> Uwe Brauer
>
>
> --
John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

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Re: some progress matlab-kernel, a python path problem?

[Uwe Brauer]

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>>> "JK" == John Kitchin <jkitchin@andrew.cmu.edu> writes:

> I would see if you can open a jupyter notebook and start a notebook with
> the mat lab kernel. If not, it either isn’t installed, or maybe is
> installed in a different jupyter.

> If you get errors here, the issue is outside of org mode. For example, the
> hylang kernel quit working for me a while ago.

> See
> https://github.com/Calysto/matlab_kernel#kernel-times-out-while-starting
> for some troubleshooting tips.

> On Wed, Jun 16, 2021 at 11:48 AM Uwe Brauer <oub@mat.ucm.es> wrote:

Thanks that looks very interesting. 

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[SOLVED] (was: some progress matlab-kernel, a python path problem?)

[Uwe Brauer]

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>>> "JK" == John Kitchin <jkitchin@andrew.cmu.edu> writes:

> I would see if you can open a jupyter notebook and start a notebook with
> the mat lab kernel. If not, it either isn’t installed, or maybe is
> installed in a different jupyter.

> If you get errors here, the issue is outside of org mode. For example, the
> hylang kernel quit working for me a while ago.

> See
> https://github.com/Calysto/matlab_kernel#kernel-times-out-while-starting
> for some troubleshooting tips.

It turned out that I need to install
pip3 install --user numpy
pip3 install --user pymatbridge

Where pip3 is the MaCOS 10.15 version

Now everything is fine.

Thanks 

Uwe 

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