Metadata-Version: 2.1
Name: braian
Version: 1.0.3
Summary: A python library for easy navigation, visualisation, and analysis of whole-brain quantification data.
Home-page: https://silvalab.codeberg.page/BraiAn/
License: LGPL-3.0-or-later
Keywords: data-analysis,library,neuroscience,visualisation,visualization,whole-brain
Author: Carlo Castoldi
Author-email: carlo.castoldi@outlook.com
Requires-Python: >=3.11,<3.14
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: beautifulsoup4 (>=4.12.3,<5.0.0)
Requires-Dist: brainglobe-heatmap (>=v0.5.4,<0.6.0)
Requires-Dist: kaleido (==0.2.1)
Requires-Dist: numpy (>=2.0.2,<2.2)
Requires-Dist: pandas (>=2.2.3,<3.0.0)
Requires-Dist: plotly (>=5.24.1,<6.0.0)
Requires-Dist: python-igraph (>=0.11.8,<0.12.0)
Requires-Dist: pywin32 (>=306,<307) ; sys_platform == "win32"
Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
Requires-Dist: scipy (>=1.15.1,<2.0.0)
Requires-Dist: tables (>=3.9.2,<4.0.0)
Requires-Dist: urllib3 (>=1.26.16,<2.0.0)
Project-URL: Documentation, https://silvalab.codeberg.page/BraiAn/api-braian/
Project-URL: Repository, https://codeberg.org/SilvaLab/BraiAn
Description-Content-Type: text/markdown

<!--
SPDX-FileCopyrightText: 2024 Carlo Castoldi <carlo.castoldi@outlook.com>

SPDX-License-Identifier: CC-BY-4.0
-->

# ![braian logo](docs/assets/logo/network.svg) BraiAn
[![PyPI - Version](https://img.shields.io/pypi/v/braian)](https://pypi.org/project/braian)
[![status-badge](https://ci.codeberg.org/api/badges/13585/status.svg)](https://ci.codeberg.org/repos/13585)
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<!--install-start-->
## Installation
Once you are in an active `python>=3.11,<3.13` environment, you can run:
```bash
python3 -m pip install braian
```
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## Citing
If you use BraiAn in your work, please cite the paper below, currently in pre-print:

> Chiaruttini, N., Castoldi, C. et al. **ABBA, a novel tool for whole-brain mapping, reveals brain-wide differences in immediate early genes induction following learning**. _bioRxiv_ (2024).\
> [https://doi.org/10.1101/2024.09.06.611625](https://doi.org/10.1101/2024.09.06.611625)

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## Building
### Prerequisites
* [python>=3.11](https://www.python.org/downloads/):
  you can use [conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [pyenv](https://github.com/pyenv/pyenv)/[pyenv-win](https://pyenv-win.github.io/pyenv-win/#installation) to manage the correct version

* [Poetry](https://python-poetry.org/docs/#installation): for dependency management

### Step 1: Set-up an environment for BraiAn
Create and activate a new `python>=3.11,<3.13` environment.

<table border="0">
 <tr>
    <td>
      Using <a href="https://docs.continuum.io/anaconda/"><code>conda</code></a>:</p>
      <pre><code class="language-bash">conda create --name braian_env python=3.11
conda activate braian_env</code></pre>
    </td>
    <td>
      Using python venv:</p>
      <code class="language-bash">python3.11 -m venv /path/to/new/braian_env</code>
      </p>
      and <a href="https://docs.python.org/3/library/venv.html#how-venvs-work">activate it</a>
    </td>
 </tr>
</table>

### Step 2: clone the repository
```bash
git clone https://codeberg.org/SilvaLab/BraiAn.git /path/to/BraiAn
```

### Step 3: install BraiAn inside the environment with Poetry
With the environment set and Poetry installed:
```bash
(braian_env) cd /path/to/BraiAn
(braian_env) poetry install # --with docs, if building the documentation is of your interest
```
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