| Name | neuromorphopy JSON |
| Version |
0.2.0
JSON |
| download |
| home_page | None |
| Summary | Lightweight python package for downloading neuron morphologies from the NeuroMorpho archives. |
| upload_time | 2024-11-01 23:25:26 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.11 |
| 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. |
| keywords |
morphology
neuromorpho
neurons
neuroscience
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# neuromorphopy
[](https://img.shields.io/github/license/kpeez/neuromorphopy)
[](https://neuromorphopy.readthedocs.io/)
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
You can install neuromorphopy directly from PyPI:
```bash
pip install neuromorphopy
```
### 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 more detailed usage, see our [documentation](getting_started.md).
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"description": "# neuromorphopy\n\n[](https://img.shields.io/github/license/kpeez/neuromorphopy)\n[](https://neuromorphopy.readthedocs.io/)\n\nLightweight python package for downloading neuron morphologies from the [NeuroMorpho archives](https://neuromorpho.org/).\n\n- **Github repository**: <https://github.com/kpeez/neuromorphopy/>\n\n## Features\n\n- Simple and intuitive API for searching NeuroMorpho.org\n- Efficient concurrent downloads of neuron morphologies\n- Flexible query system with validation\n- Automatic metadata handling\n- Support for both synchronous and asynchronous operations\n\n## Requirements\n\n- Python >= 3.11\n\n## Installation\n\nYou can install neuromorphopy directly from PyPI:\n\n```bash\npip install neuromorphopy\n```\n\n### Development\n\nFor development work, we recommend using [uv](https://github.com/astral-sh/uv) for faster dependency resolution and better reproducibility:\n\n```bash\n# Install uv if you haven't already\ncurl -LsSf https://astral.sh/uv/install.sh | sh\n\n# Clone and install\ngit clone https://github.com/kpeez/neuromorphopy.git\ncd neuromorphopy\nuv venv\nuv sync\n```\n\n## Usage\n\nCreate a query file (YAML or JSON) to specify what neurons you want:\n\n```yaml\n# query.yml\nfilters:\n species: [\"mouse\"]\n brain_region: [\"neocortex\"]\n cell_type: [\"pyramidal\"]\nsort: # sorting is optional\n field: \"brain_region\"\n ascending: true\n```\n\nUse the command line interface to search and download neurons:\n\n```bash\nneuromorpho search -q query.yml -o ./data\n```\n\nFor more detailed usage, see our [documentation](getting_started.md).\n",
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