An Octave kernel for Jupyter

.. image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/Calysto/octave_kernel/main?urlpath=/lab/tree/octave_kernel.ipynb

Prerequisites

Jupyter Notebook <http://jupyter.readthedocs.org/en/latest/install.html>_ and GNU Octave_.

Installation

To install using pip::

pip install octave_kernel

Add --user to install in the user-level environment instead of the system environment.

To install using conda::

conda config --add channels conda-forge
conda install octave_kernel
conda install texinfo # For the inline documentation (shift-tab) to appear.

We require the octave executable to run the kernel. Add that executable's directory to the PATH environment variable or create the environment variable OCTAVE_EXECUTABLE to point to the executable itself. Note that on Octave 5 on Windows, the executable is in "Octave-5.x.x.x\mingw64\bin".

We automatically install a Jupyter kernelspec when installing the python package. This location can be found using jupyter kernelspec list. If the default location is not desired, remove the directory for the octave kernel, and install using python -m octave_kernel install. See python -m octave_kernel install --help for available options.

Usage

To use the kernel, run one of:

.. code:: shell

jupyter notebook  # or ``jupyter lab``, if available
# In the notebook interface, select Octave from the 'New' menu
jupyter qtconsole --kernel octave
jupyter console --kernel octave

This kernel is based on MetaKernel <http://pypi.python.org/pypi/metakernel>_, which means it features a standard set of magics (such as %%html). For a full list of magics, run %lsmagic in a cell.

A sample notebook is available online_.

Configuration

The kernel can be configured by adding an octave_kernel_config.py file to the jupyter config path. The OctaveKernel class offers plot_settings, inline_toolkit, kernel_json, and cli_options as configurable traits. The available plot settings are: 'format', 'backend', 'width', 'height', 'resolution', and 'plot_dir'.

.. code:: bash

cat ~/.jupyter/octave_kernel_config.py
# use Qt as the default backend for plots
c.OctaveKernel.plot_settings = dict(backend='qt')

The path to the Octave kernel JSON file can also be specified by creating an OCTAVE_KERNEL_JSON environment variable.

The command line options to Octave can also be specified with an OCTAVE_CLI_OPTIONS environment variable. The cli options be appended to the default opions of --interactive --quiet --no-init-file. Note that the init file is explicitly called after the kernel has set more off to prevent a lockup when the pager is invoked in ~/.octaverc.

The inline toolkit is the graphics_toolkit used to generate plots for the inline backend. It defaults to qt. The different backend can be used for inline plotting either by using this configuration or by using the plot magic and putting the backend name after inline:, e.g. plot -b inline:fltk.

Troubleshooting

Kernel Times Out While Starting

If the kernel does not start, run the following command from a terminal:

.. code:: shell

    python -m octave_kernel.check

This can help diagnose problems with setting up integration with Octave.  If in doubt,
create an issue with the output of that command.


Kernel is Not Listed
~~~~~~~~~~~~~~~~~~~~
If the kernel is not listed as an available kernel, first try the following command:

.. code:: shell

    python -m octave_kernel install --user

If the kernel is still not listed, verify that the following point to the same
version of python:

.. code:: shell

    which python  # use "where" if using cmd.exe
    which jupyter


Gnuplot Error
~~~~~~~~~~~~~
An error that starts with ``gnuplot> set terminal aqua enhanced title`` can be fixed by
adding ``setenv("GNUTERM","qt");`` to ``~/.octaverc`` on MacOS or by installing
``gunplot-x11`` and using ``setenv("GNUTERM", "X11")``.

Octave-Snap (Linux)
~~~~~~~~~~~~~~~~~~~
You can check if you are using a snap version on Linux by checking the path to your Octave
installation.

.. code:: shell

    which octave

If the returned path has ``snap`` in it, then Octave is running in a container and you will need to configure the kernel appropriately.

1) Set the environment variable ``OCTAVE_EXECUTABLE="octave"``

.. code:: shell

    echo export OCTAVE_EXECUTABLE=\"octave\" >> ~/.bashrc

2) Make a directory for the temporary plot directories that the kernel uses. This *cannot* be a hidden directory.

.. code:: shell

    mkdir ~/octavePlots

3) Set ``plot_dir`` to point to your plot directory in ``octave_kernel_config.py``.

.. code:: shell

	c.OctaveKernel.plot_settings = dict(plot_dir='<home>/octavePlots')

where ``<home>`` is the absolute path to your home directory. Do not use ``~`` as this resolves to a different location for Octave-Snap.


Blank Plot
~~~~~~~~~~
Specify a different format using the ``%plot -f <backend>`` magic or using a configuration setting.
On some systems, the default ``'png'`` produces a black plot.  On other systems ``'svg'`` produces a
black plot.

Local Installation
------------------

To install from a git checkout, run:

.. code:: shell

    make install


.. _Octave: https://www.gnu.org/software/octave/download.html
.. _online: http://nbviewer.ipython.org/github/Calysto/octave_kernel/blob/main/octave_kernel.ipynb