Core codebase for the Kymata Atlas
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Kymata Core is the central codebase underlying the Kymata Atlas.[^1] It is maintained by the Kymata Research Group.
The central pipeline includes:
The codebase is released under an MIT license to ensure the transparency of the results in the Kymata Atlas. While comments and issues are welcomed, we are unable to prioritise installation or usage support (please see our code of conduct).
This provides an overview of how to set Kymata Core locally.
Python
Confirm you have the correct version of Python installed. Type
$ pyenv versions
This should confirm that python 3.11 or above is installed. If it isn't already there,
install it using pyenv install
. You should be able to confirm
you are using the correct version using
$ python -V
Poetry
This package uses Poetry to manage packages. See python-poetry.org for installation instructions.
Clone this repository:
$ git clone https://github.com/kymata-atlas/kymata-core.git
To install the python packages you will need to use Poetry. Assuming you have installed Poetry, type:
$ poetry install
to load the pakages needed.
At this point, you should be able to either run the xx from the terminal
$ poetry run invokers/run_gridsearch.py
or activate in this environment in an IDE such as PyCharm.
This will be done automatically via Github actions.
To run the tests manually, run:
$ poetry run pytest
To run linting manually, run:
$ poetry run ruff check
To serve the documentation locally, run:
$ poetry run mkdocs serve check
Please refer to the documentation, or see the demos/
folder for example code, including test
data.
Please use the following reference when citing the codebase or the kymata
package:
TBC
Distributed under the MIT License. See LICENSE
for more information.
[^1]: Thwaites, Wieser, Soltan, Wingfield, Parish, Yang, Lakra, Woolgar, Zhang (2024) The Kymata Atlas (In Prep.) [^2]: Thwaites, Zhang and Woolgar (2024) Information Processing Pathway Maps: A New Frontier in Cortical Processing (In Prep.)