How to install BioCRNPyler

Installing BioCRNPyler with pip (recommended)

BioCRNPyler is available through the Python Package Index (PyPI).

pip install biocrnpyler

BioCRNPyler only requires python-libsbml to be functional. For plotting simulation results, further packages are required such as numpy, matplotlib, bokeh, fa2, and networkx and these will automatically be installed. But be prepared to install them if they are not automatically handled.

Attention! zsh users need to pay attention to brackets: see here

Virtual environment (optional)

As a best practice, we recommend working inside a virtual environment, such as a conda, virtualenv, or pipenv virtual environment. A good explanation for virtual environments in python can be found here.

Installing BioCRNPyler from source (optional)

mkdir biocrnpyler
git clone https://github.com/BuildACell/BioCRNPyler.git biocrnpyler
cd biocrnpyler
pip install --user .

To install all dependencies:

pip install --user .

getting an update

When you install from the source, we recommend removing BioCRNPyler before installing a new version. (pip update, might not work as the version number might not change between commits to a GitHub repo)

pip uninstall biocrnpyler
git pull 
pip install --user .

If you are planning to edit the core code of the package, please install with a -e option

pip install --user -e .

Installing the dev branch on GitHub

The dev branch on GitHub contains the latest developments, and you may install it at your own risk!

pip install git+git://github.com/BuildACell/BioCRNPyler.git@dev

It is strongly recommended to install experimental code, such as the dev branch, inside a virtual environment!