vivarium-MEDYAN

A Vivarium wrapper for MEDYAN

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Installation

First, we recommend you create an environment (with pyenv, conda, or similar).

Then, to install: Stable Release: pip install vivarium_medyan (coming soon)
Development Head: pip install git+https://github.com/vivarium-collective/vivarium-MEDYAN.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

The MedyanProcess will download the latest MEDYAN image from Simularium Docker Hub the first time it runs, and use that to simulate in MEDYAN.

Development

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

Commands You Need To Know

1. black vivarium_medyan

   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.