Metadata-Version: 2.4
Name: physbeh
Version: 0.6.4
Summary: Miscellaneous functions for tracking analysis in Python using DeepLabCut at Physics for Medicine
Project-URL: repository, https://github.com/FelipeCybis/physbeh
Author-email: Felipe Cybis Pereira <felipe.cybispereira@gmail.com>
License: Copyright 2026 Felipe Cybis Pereira
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
        
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
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Description-Content-Type: text/x-rst

|zenodo| |version| |python| |build| |ruff|

.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.15494995.svg
  :target: https://doi.org/10.5281/zenodo.15494995

.. |version| image:: https://img.shields.io/badge/version-0.6.4-orange.svg
    :target: https://github.com/FelipeCybis/physbeh/
    :alt: physbeh version

.. |python| image:: https://img.shields.io/badge/python-3.10_%7C_3.11_%7C_3.12_%7C_3.13-blue.svg
    :target: https://www.python.org/
    :alt: Python

.. |build| image:: https://github.com/FelipeCybis/physbeh/actions/workflows/run_workflows.yml/badge.svg
    :target: https://github.com/FelipeCybis/physbeh/actions/workflows/run_workflows.yml
    :alt: Build

.. |ruff| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
    :target: https://github.com/astral-sh/ruff
    :alt: Ruff

PhysBeh
=======

.. start-quickstart
.. start-about

This repository contains the main function and classes written in Python for
analysis of tracking data in the Physics for Medicine lab.

The code is written in the format of a Python package (`physbeh`).

This is the core package used for the behavioral analysis in the following paper:

1. Cybis Pereira, F., Castedo, S.H., Meur-Diebolt, S.L., Ialy-Radio, N., Bhattacharya, S., Ferrier, J., Osmanski, B.F., Cocco, S., Monasson, R., Pezet, S., et al. (2026). A vascular code for speed in the spatial navigation system. Cell Reports 45. https://doi.org/10.1016/j.celrep.2025.116791.


.. stop-about

Installation
------------

.. start-installation

1. Setup a virtual environment
******************************

Create and activate a new python environment (if familiarisation with virtual
environments is needed, you can start `here
<https://docs.python.org/3/library/venv.html>`__ or `here
<https://ioflood.com/blog/python-venv-virtual-environment/>`__):

- Using `venv` (recommended):

  On Linux

  .. code-block:: bash

    python3 -m venv /path_to_env
    source /path_to_env/bin/activate

  On Windows

  .. code-block:: powershell

    python3 -m venv /path_to_env
    /path_to_env/Script/activate

- Using `conda <https://docs.conda.io/projects/conda/en/stable/>`_:

  .. code-block:: bash

    conda create -n physbeh python=3.11
    conda activate physbeh

2. Install PhysBeh from source
******************************

PhysBeh is a private package developed by Iconeus and Physics for Medicine and is not
available from PyPI.

.. code-block:: bash

  python -m pip install git+https://github.com/FelipeCybis/physbeh.git

3. Check installation
*********************

Check that all tests pass:

.. code-block:: python

  import physbeh

If no error is raised, you have installed PhysBeh correctly.

.. stop-installation

.. stop-quickstart

Authors
-------

- Felipe Cybis Pereira (felipe.cybispereira@gmail.com)
