SimBio paper

To read the current HTML version, visit: https://maurosilber.github.io/simbio-paper

The following instructions assume you have cloned the repository

git clone https://github.com/maurosilber/simbio-paper

and are inside the simbio-paper directory.

Install dependencies

To run the benchmarking code and compile the article, you must install some dependencies.

If you have conda installed, create an environment from the included environment.yml file:

conda env create

and install the Python package included in the repository:

pip install -e .

To compile the article, you must also install Quarto: https://quarto.org

Run benchmarks and compile article

make

Note: as src/perfomance/figures/performance.png was commited to the repository, the benchmarking code is not actually triggered by the Makefile. Remove that file to re-run the benchmarks with make.