jvail / vmapplet

VMAppleT

A refactored and enhanced implementation of MAppleT/StocaTree. Original sources copied and modified from openalea/incubator.

Major changes compared to MAppleT/StocaTree

• Build system and dependencies: All outdated and unmaintained dependencies have been removed or replaced
• Modularization: The L-Py file has been splitted up into several smaller modules
• Markov: A Python implementation of the semi-hidden Markov chain
• Configuration: An extended simulation and a Markov model configuration file in toml format
• Jupyter integration: Run and visualize simulations in Jupyter lab notebooks

Install

A local conda/miniconda installation is required. First clone/download the repository. The mamba install is optional but recommended.

Install mamba

conda install mamba -n base -c conda-forge

Create environment - with a development install of VMappleT

mamba env create -f binder/environment.yml
# or
# conda env create -f binder/environment.yml

Jupyter

conda activate vmapplet
jupyter lab --notebook-dir=notebooks

Script

activate vmapplet
python -m vmapplet vmapplet/data/simulation.toml out_folder