vivarium-ReaDDy

A Vivarium wrapper for ReaDDy

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Installation

Stable Release: pip install vivarium_readdy (coming soon)
Development Head: pip install git+https://github.com/vivarium-collective/vivarium-ReaDDy.git

Local editable installation with pyenv + conda

To see all pyenv versions:

pyenv install list

To install a particular version of python (or conda):

pyenv install anaconda3-5.3.1

Install dependencies using pyenv + conda:

pyenv local anaconda3-5.3.1 # or whatever version you have installed
pyenv virtualenv vivarium-models
pyenv local vivarium-models
conda env update -f env.yml

Local editable installation with conda alone

Install conda: https://docs.conda.io/en/latest/miniconda.html

Using conda, you can run

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

which will create and then activate a conda environment called vivarium-models with all the required dependencies (including ReaDDy) installed.

To update:

conda env update -f env.yml

Development

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

Commands You Need To Know

1. black vivarium_readdy

   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.