Metadata-Version: 2.1
Name: SimBio
Version: 0.2.2
Summary: Simulation of Biological Systems
Author-email: "Hernán E. Grecco" <hernan.grecco@gmail.com>, Mauro Silberberg <maurosilber@gmail.com>
Project-URL: Homepage, https://github.com/hgrecco/simbio
Project-URL: Bug Tracker, https://github.com/hgrecco/simbio/issues
Keywords: mass action,michaelis menten,ode,compartment,reaction,SBML,poincare
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Requires-Dist: poincare>=0.3.1
Provides-Extra: io
Requires-Dist: python-libsbml; extra == "io"
Requires-Dist: biomodels; extra == "io"
Provides-Extra: test
Requires-Dist: simbio[io]; extra == "test"
Requires-Dist: pytest; extra == "test"
Provides-Extra: docs
Requires-Dist: simbio[test]; extra == "docs"
Requires-Dist: jupyter-book; extra == "docs"
Requires-Dist: jupytext; extra == "docs"
Requires-Dist: numba; extra == "docs"
Requires-Dist: simbio-corbat2018; extra == "docs"

# SimBio

`simbio` is a Python-based library of biological systems simulation.
As a comparison with other libraries we can enumerate:

- Models are composables,
  so you can create bigger models using smaller ones
- Models are python classes,
  so it is easier to understand the inners
  and easy to compose into bigger models
- Posibility to do `numba` JIT compilation
- Small footprint library,
  can be imported on a bigger application without fuzz

## Installation

If you are using pip,
it can be installed directly from PyPI:

```
pip install simbio
```

or the latest version from GitHub:

```
pip install git+https://github.com/hgrecco/simbio
```

## Examples

On the folder `src/simbio/tests/examples`,
we included some examples for the library usage.

## Development

We are using pytest for testing,
and pre-commit hooks to format and lint the codebase.

To easily set-up a development environment,
run the following commands:

```
git clone https://github.com/hgrecco/simbio
cd simbio
conda env create --file environment-dev.yml
pre-commit install
```

which assume you have git and conda preinstalled.
