# bmtool
A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
[](https://github.com/cyneuro/bmtool/blob/master/LICENSE)
## In depth documentation and examples can be found [here](https://cyneuro.github.io/bmtool/)
## Getting Started
**Installation**
```bash
pip install bmtool
```
For developers who will be pulling down additional updates to this repository regularly use the following instead.
```bash
git clone https://github.com/cyneuro/bmtool.git
cd bmtool
python setup.py develop
```
Then download updates (from this directory) with
```bash
git pull
```
BMTool provides several modules to simplify the development of computational neuroscience models with NEURON and the Brain Modeling Toolkit (BMTK). It offers functionality for:
- **Single Cell Modeling**: Analyze passive properties, current injection, FI curves, and impedance profiles
- **Synapse Development**: Tools for tuning synaptic properties and gap junctions
- **Network Construction**: Connectors for building complex network structures
- **Visualization**: Plot connection matrices, network positions, and more
- **Simulation Management**: Run simulations on SLURM clusters with parameter sweeps
- **Analysis**: Process simulation results efficiently
## Development
### Code Quality Tools
BMTool now uses modern Python code quality tools to maintain high standards:
- **Ruff**: A fast Python linter for code style and error checking
- **Pyright**: Static type checker to catch type-related bugs early
To install development dependencies in your conda environment:
```bash
# Activate your conda environment
conda activate bmtk
# Install development dependencies
pip install -e ".[dev]"
```
To run the tools:
```bash
# Run Ruff linter
ruff check bmtool/
# Run Ruff with auto-fix
ruff check --fix bmtool/
# Run Pyright type checker
pyright
```
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