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pyprep
======
For documentation, see the:
- `stable documentation <http://pyprep.readthedocs.io/en/stable/>`_
- `latest (development) documentation <http://pyprep.readthedocs.io/en/latest/>`_
.. docs_readme_include_label
``pyprep`` is a Python implementation of the
`Preprocessing Pipeline (PREP) <https://doi.org/10.3389/fninf.2015.00016>`_
for EEG data, working with `MNE-Python <https://mne.tools>`_.
**ALPHA SOFTWARE.**
**This package is currently in its early stages of iteration.**
**It may change both its internals or its user-facing API in the near future.**
**Any feedback and ideas on how to improve either of these is welcome!**
**Use this software at your own risk.**
Installation
============
``pyprep`` requires Python version ``3.8`` or higher to run properly.
We recommend to run ``pyprep`` in a dedicated virtual environment
(for example using `conda <https://docs.conda.io/en/latest/miniconda.html>`_).
For installing the **stable** version of ``pyprep``, call:
.. code-block:: Text
pip install pyprep
or, as an alternative to ``pip``, call:
.. code-block:: Text
conda install -c conda-forge pyprep
For installing the **latest (development)** version of ``pyprep``, call:
.. code-block:: Text
pip install git+https://github.com/sappelhoff/pyprep.git@main
Both the *stable* and the *latest* installation will additionally install
all required dependencies automatically.
The dependencies are defined in the ``setup.cfg`` file under the
``options.install_requires`` section.
Contributions
=============
**We are actively looking for contributors!**
Please chime in with your ideas on how to improve this software by opening
a GitHub issue, or submitting a pull request.
See also our `CONTRIBUTING.md <https://github.com/sappelhoff/pyprep/blob/main/.github/CONTRIBUTING.md>`_
file for help with submitting a pull request.
Potential contributors should install ``pyprep`` in the following way:
#. First they should fork ``pyprep`` to their own GitHub account.
#. Then they should run the following commands,
adequately replacing ``<gh-username>`` with their GitHub username.
.. code-block:: Text
git clone https://github.com/<gh-username>/pyprep
cd pyprep
pip install -r requirements-dev.txt
pre-commit install
pip install -e .
Citing
======
If you use this software in academic work, please cite it using the `Zenodo entry <https://zenodo.org/badge/latestdoi/129240824>`_.
Please also consider citing the original publication on PREP (see "References" below).
Metadata is encoded in the `CITATION.cff` file.
References
==========
1. Bigdely-Shamlo, N., Mullen, T., Kothe, C., Su, K.-M., & Robbins, K. A.
(2015). The PREP pipeline: standardized preprocessing for large-scale EEG
analysis. Frontiers in Neuroinformatics, 9, 16. doi:
`10.3389/fninf.2015.00016 <https://doi.org/10.3389/fninf.2015.00016>`_
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