Metadata-Version: 2.1
Name: bsb
Version: 4.0.0a18
Summary: A package for modelling morphologically detailed neuronal microcircuits.
Home-page: https://github.com/dbbs-lab/bsb
Author: Robin De Schepper, Alice Geminiani, Alberto Antonietti, Stefano Casali, Egidio D'Angelo, Claudia Casellato
Author-email: robingilbert.deschepper@unipv.it
License: GPLv3
Project-URL: Bug Tracker, https://github.com/dbbs-lab/bsb/issues/
Project-URL: Documentation, https://bsb.readthedocs.io/
Project-URL: Source Code, https://github.com/dbbs-lab/bsb/
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Requires-Python: ~=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: h5py (~=3.0)
Requires-Dist: numpy (~=1.19)
Requires-Dist: scipy (~=1.5)
Requires-Dist: scikit-learn (~=1.0)
Requires-Dist: plotly (~=5.5)
Requires-Dist: colour (~=0.1)
Requires-Dist: errr (~=1.1.1)
Requires-Dist: rtree (~=0.9)
Requires-Dist: psutil (~=5.8)
Requires-Dist: pynrrd (~=0.4)
Requires-Dist: mpilock (~=1.1)
Requires-Dist: morphio (~=3.3)
Requires-Dist: mpi4py
Requires-Dist: zwembad
Requires-Dist: toml
Requires-Dist: requests
Requires-Dist: appdirs (~=1.4)
Provides-Extra: arbor
Requires-Dist: arbor (~=0.6) ; extra == 'arbor'
Provides-Extra: dev
Requires-Dist: sphinx ; extra == 'dev'
Requires-Dist: furo ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: black (==22.3.0) ; extra == 'dev'
Requires-Dist: nrn-subprocess (==1.3.4) ; extra == 'dev'
Requires-Dist: sphinxemoji ; extra == 'dev'
Requires-Dist: sphinx-design ; extra == 'dev'
Provides-Extra: mpi
Requires-Dist: mpi4py ; extra == 'mpi'
Requires-Dist: zwembad ; extra == 'mpi'
Requires-Dist: mpilock ; extra == 'mpi'
Provides-Extra: neuron
Requires-Dist: dbbs-models (~=2.0.0) ; extra == 'neuron'
Requires-Dist: nrn-patch (~=3.0.1) ; extra == 'neuron'

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Documentation Status](https://readthedocs.org/projects/bsb/badge/?version=latest)](https://bsb.readthedocs.io/en/latest/?badge=latest)
[![Build Status](https://travis-ci.com/dbbs-lab/bsb.svg?branch=master)](https://travis-ci.com/dbbs-lab/bsb)
[![codecov](https://codecov.io/gh/dbbs-lab/bsb/branch/master/graph/badge.svg)](https://codecov.io/gh/dbbs-lab/bsb)

<h3>:closed_book: Read the documentation on https://bsb.readthedocs.io/en/latest</h3>

# BSB: A scaffold modelling framework
This package is intended to facilitate spatially, topologically and morphologically
detailed simulations of brain regions developed by the Department of Brain and
Behavioral Sciences at the University of Pavia.

## Installation

The BSB requires Python 3.8+.

### pip

This software can be installed as a Python package from PyPI through pip:

```
pip install "bsb>=4.0.0a0"
```

### Developers

Developers best use pip's *editable* install. This creates a live link between the
installed package and the local git repository:

```
 git clone git@github.com:dbbs-lab/bsb
 cd bsb
 pip install -e .[dev]
 pre-commit install
```

## Usage

The scaffold framework is best used in a project context. Create a working directory for
each of your modelling projects and use the command line to configure, reconstruct or
simulate your models.

### Creating a project

You can create a quickstart project using:

```
bsb new my_model --quickstart
cd my_model
```

### Reconstructing a network

You can use your project to create reconstructions of your model, generating cell positions
and connections:

```
bsb compile -p
```

This creates a network file and plots the network.

### Simulating a network

The default project currently contains no simulation config.

# Contributing

All contributions are very much welcome.
Take a look at the [contribution guide](CONTRIBUTING.md)

# Known issues

## Simulation interfaces are not reinstated yet in v4

Shouldn't be much work, famous last words.


