instruct Jupyter to run Octave code on the Octave flatpack app

[YousefSaber]

Ubuntu 19.10 repository provides an outdated old 4.4 version of Octave, how do I instruct Jupyter to use Octave flatpack app to run Octave Code

[blink1073]

Does the flatpack app have a /bin dir or otherwise have an octave-cli executable in it? If so, you can point your OCTAVE_EXECUTABLE environment variable to that executable.

[YousefSaber]

@blink1073 flatpack Octave can enter the CLI mode as follows

joseph@joseph-X541UJ:~/Downloads$ flatpak run org.octave.Octave 
Gtk-Message: 00:49:45.102: Failed to load module "canberra-gtk-module"
Gtk-Message: 00:49:45.102: Failed to load module "canberra-gtk-module"
GNU Octave, version 5.1.0
Copyright (C) 2019 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type 'warranty'.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
For information about changes from previous versions, type 'news'.

octave:1> x = 5
x =  5
octave:2> 

and please show me step by step how to edit the OCTAVE_EXECUTABLE environment variable I'm very beginner , just learned Jupyter notebook today

as for bin files for flatpack app I can't exactly locate it

[YousefSaber]

Does the flatpack app have a /bin dir or otherwise have an octave-cli executable in it? If so, you can point your OCTAVE_EXECUTABLE environment variable to that executable.

edit I have located the bin files

joseph@joseph-X541UJ:/var/lib/flatpak/exports/bin$ pwd
/var/lib/flatpak/exports/bin
joseph@joseph-X541UJ:/var/lib/flatpak/exports/bin$ ./org.octave.Octave 
Gtk-Message: 01:21:52.023: Failed to load module "canberra-gtk-module"
Gtk-Message: 01:21:52.023: Failed to load module "canberra-gtk-module"
GNU Octave, version 5.1.0
Copyright (C) 2019 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type 'warranty'.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at https://www.octave.org.

Please contribute if you find this software useful.
For more information, visit https://www.octave.org/get-involved.html

Read https://www.octave.org/bugs.html to learn how to submit bug reports.
For information about changes from previous versions, type 'news'.

octave:1> 

[blink1073]

What is the output of:

echo $SHELL
ls /var/lib/flatpak/exports/bin

[YousefSaber]

What is the output of:

echo $SHELL
ls /var/lib/flatpak/exports/bin

here is the output @blink1073

joseph@joseph-X541UJ:/var/lib/flatpak/exports/bin$ echo $SHELL
/bin/bash
joseph@joseph-X541UJ:/var/lib/flatpak/exports/bin$ ls /var/lib/flatpak/exports/bin
org.octave.Octave

[blink1073]

You should be able to add:

export OCTAVE_EXECUTABLE=/var/lib/flatpak/exports/bin/org.octave.Octave

To the end of your ~/.bashrc file, and then run the following to see if it worked:

source ~/.bashrc
jupyter console --kernel octave

[YousefSaber]

You should be able to add:

export OCTAVE_EXECUTABLE=/var/lib/flatpak/exports/bin/org.octave.Octave

To the end of your ~/.bashrc file, and then run the following to see if it worked:

source ~/.bashrc
jupyter console --kernel octave

@blink1073 it gives me this error message

joseph@joseph-X541UJ:~$ jupyter console --kernel octave
[MetaKernelApp] ERROR | Exception in message handler:
Traceback (most recent call last):
  File "/home/joseph/.local/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 268, in dispatch_shell
    yield gen.maybe_future(handler(stream, idents, msg))
  File "/home/joseph/.local/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 654, in kernel_info_request
    content.update(self.kernel_info)
  File "/home/joseph/.local/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 647, in kernel_info
    'language_info': self.language_info,
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 78, in language_info
    'version': self.language_version,
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 69, in language_version
    ver = self.octave_engine.eval('version', silent=True)
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 96, in octave_engine
    logger=self.log)
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 170, in __init__
    self.executable = self._get_executable()
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 453, in _get_executable
    raise OSError('OCTAVE_EXECUTABLE does not point to an octave-cli file, please see README')
OSError: OCTAVE_EXECUTABLE does not point to an octave-cli file, please see README
[MetaKernelApp] ERROR | Exception in message handler:
Traceback (most recent call last):
  File "/home/joseph/.local/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 268, in dispatch_shell
    yield gen.maybe_future(handler(stream, idents, msg))
  File "/home/joseph/.local/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 654, in kernel_info_request
    content.update(self.kernel_info)
  File "/home/joseph/.local/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 647, in kernel_info
    'language_info': self.language_info,
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 78, in language_info
    'version': self.language_version,
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 69, in language_version
    ver = self.octave_engine.eval('version', silent=True)
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 96, in octave_engine
    logger=self.log)
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 170, in __init__
    self.executable = self._get_executable()
  File "/home/joseph/.local/lib/python3.7/site-packages/octave_kernel/kernel.py", line 453, in _get_executable
    raise OSError('OCTAVE_EXECUTABLE does not point to an octave-cli file, please see README')
OSError: OCTAVE_EXECUTABLE does not point to an octave-cli file, please see README
Traceback (most recent call last):
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_console/ptshell.py", line 336, in init_kernel_info
    reply = self.client.get_shell_msg(timeout=1)
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_client/client.py", line 77, in get_shell_msg
    return self.shell_channel.get_msg(*args, **kwargs)
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_client/blocking/channels.py", line 57, in get_msg
    raise Empty
_queue.Empty

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/joseph/.local/bin/jupyter-console", line 10, in <module>
    sys.exit(main())
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_core/application.py", line 268, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/home/joseph/.local/lib/python3.7/site-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "</home/joseph/.local/lib/python3.7/site-packages/decorator.py:decorator-gen-117>", line 2, in initialize
  File "/home/joseph/.local/lib/python3.7/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_console/app.py", line 142, in initialize
    self.init_shell()
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_console/app.py", line 115, in init_shell
    confirm_exit=self.confirm_exit,
  File "/home/joseph/.local/lib/python3.7/site-packages/traitlets/config/configurable.py", line 412, in instance
    inst = cls(*args, **kwargs)
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_console/ptshell.py", line 282, in __init__
    self.init_kernel_info()
  File "/home/joseph/.local/lib/python3.7/site-packages/jupyter_console/ptshell.py", line 339, in init_kernel_info
    raise RuntimeError("Kernel didn't respond to kernel_info_request")
RuntimeError: Kernel didn't respond to kernel_info_request