Metadata-Version: 2.3
Name: neuromorphopy
Version: 0.1.0
Summary: Lightweight python package for downloading neuron morphologies from the NeuroMorpho archives.
Project-URL: repository, https://github.com/kpeez/neuromorphopy
Project-URL: documentation, https://neuromorphopy.readthedocs.io/en/latest/
Author-email: Kyle Puhger <krpuhger@gmail.com>
License: MIT License
        
        Copyright (c) 2022, Kyle Puhger
        
        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
Keywords: morphology,neuromorpho,neurons,neuroscience
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Requires-Python: >=3.11
Requires-Dist: aiohttp>=3.10.10
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pydantic>=2.9.2
Requires-Dist: tqdm
Requires-Dist: typer>=0.12.5
Description-Content-Type: text/markdown

# neuromorphopy

[![License](https://img.shields.io/github/license/kpeez/neuromorphopy)](https://img.shields.io/github/license/kpeez/neuromorphopy)
[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://kpeez.github.io/neuromorphopy/)

Lightweight python package for downloading neuron morphologies from the [NeuroMorpho archives](https://neuromorpho.org/).

- **Github repository**: <https://github.com/kpeez/neuromorphopy/>

## Features

- Simple and intuitive API for searching NeuroMorpho.org
- Efficient concurrent downloads of neuron morphologies
- Flexible query system with validation
- Automatic metadata handling
- Support for both synchronous and asynchronous operations

## Requirements

- Python >= 3.11

## Installation

The easiest way to install is using pip:

```bash
git clone https://github.com/kpeez/neuromorphopy.git
cd neuromorphopy
pip install -r requirements.txt
pip install -e .
```

### Development

For development work, we recommend using [uv](https://github.com/astral-sh/uv) for faster dependency resolution and better reproducibility:

```bash
# Install uv if you haven't already
curl -LsSf https://astral.sh/uv/install.sh | sh

# Clone and install
git clone https://github.com/kpeez/neuromorphopy.git
cd neuromorphopy
uv venv
uv sync
```

## Usage

Create a query file (YAML or JSON) to specify what neurons you want:

```yaml
# query.yml
filters:
  species: ["mouse"]
  brain_region: ["neocortex"]
  cell_type: ["pyramidal"]
sort: # sorting is optional
  field: "brain_region"
  ascending: true
```

Use the command line interface to search and download neurons:

```bash
neuromorpho search -q query.yml -o ./data
```

For advanced usage and programmatic API, see our [documentation](https://neuromorphopy.readthedocs.io/).
