vivarium-cytosim

A Vivarium wrapper for Cytosim

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Installation

Stable Release: pip install vivarium_cytosim (coming soon)
Development Head: pip install git+https://github.com/vivarium-collective/vivarium-cytosim.git Local Editable Install pip install -e .[dev] (or pip install -e .\[dev\] on mac) from repo root directory

Or use Conda with the env.yml file to create the environment:

conda env create -f env.yml
conda activate vivarium-models

Cytosim Installation

First, clone the repo:

git clone https://gitlab.com/f-nedelec/cytosim.git

Change the header to allow for 3D in file src/math/dim.h:

#define DIM 3 # instead of 2

Then, make the executable (avoid the GLEW functionality):

make sim
make report

Development

See CONTRIBUTING.md for information related to developing the code.

Commands You Need To Know

1. black vivarium_cytosim

   This will fix lint issues.

2. make build

   This will run tox which will run all your tests as well as lint your code.

3. make clean

   This will clean up various Python and build generated files so that you can ensure that you are working in a clean environment.