Install poetry and run poetry install from the repository root.
We use pytest and place tests in the tests directory parallel to the source package in the repository root.
For a fast test suite, run pytest tests -m 'not slow' and make sure to mark any new tests that run slowly with @pytest.mark.slow.
To run the tutorial notebooks as integration tests, you will probably want to use the parallel feature provided by pytest-xdist. Add -n 5 to the pytest command to run on 5 threads, for example.
You may want to avoid some of the tutorials: the adaptive control tutorial requires ldsctrlest which can be hard to install and the video visualization tutorial takes about 3 minutes to run.
We use NumPy/SciPy-style docstrings, which are supported by Sphinx and will allow us to host the documentation with readthedocs.io.
Use Sphinx references (e.g., :func:, :class:, :meth:, :attr:, :ref:) whenever possible, which creates links.
Try to keep docstring line width to 75 characters.
Example:
my_function(a, b='B'):
"""A one-line summary that does not use variable names or the function name.
An extended summary of functionality.
Parameters
----------
a : int or tuple of int
Description of parameter a
b : {'B', 'be', 'bee'}, optional
Description of parameter b
Returns
-------
x : int
The answer
Examples
--------
>>>my_function(1)
42
"""
# start coding hereWe will use Black-style formatting, as implemented (faster) by Ruff. The easiest way is to enable Ruff as the formatter in your IDE with auto-formatting on save.
I was going to lint using flake8 but then I realized, this is a small research code package! We don't need super pretty, consistent code. Just try to follow Python conventions and use Black.
Originally, the intention was for opto and electrodes to live under stimulators and recorders, respectively. This made opto_stim = cleo.opto.OptogeneticIntervention(...) possible but not for importing from that second-level shortcut (from cleo.opto import ...). Thus, they were moved up a level.
We still have some import shortcuts for users, making everything in the ephys subpackage (the contents of lfp, spiking, and probes modules) available under cleo.ephys. We do this by importing the submodules' contents in __init__.py files. We can then test the shortcut imports by making sure to use them in the unit tests. However, we must use the full import path in the source code itself to avoid circular import errors.
Please use nbdev for Git-friendly Jupyter.