simbio

A Python-based package for simulation of Chemical Reaction Networks (CRNs). It extends poincare, a package for modelling dynamical systems, to add functionality for CRNs.

Usage

See simbio's documentation on the dyscolab page, or go directly to the intro tutorial.

Install

Using pixi, install from PyPI with:

pixi add --pypi simbio

or install the latest development version from GitHub with:

pixi add --pypi simbio@https://github.com/dyscolab/simbio.git

Otherwise, use pip or your pip-compatible package manager:

pip install simbio  # from PyPI
pip install git+https://github.com/dyscolab/simbio.git  # from GitHub

Development

This project is managed by pixi. You can install it for development using:

git clone https://github.com/dyscolab/simbio
cd simbio
pixi run pre-commit-install

Pre-commit hooks are used to lint and format the project.

Testing

Run tests using:

pixi run test

Publishing to PyPI

When a tagged commit is pushed to GitHub, the GitHub Action defined in .github/workflows/ci.yml builds and publishes the package to PyPI.

Tag a commit and push the tags with:

git tag <my-tag>
git push --tags

Trusted publishing must be enabled once in PyPI Publishing. Fill the following values in the form:

PyPI Project Name: simbio
            Owner: maurosilber
  Repository name: simbio
    Workflow name: ci.yml
 Environment name: pypi