A refactored and enhanced implementation of MAppleT/StocaTree. Original sources copied and modified from openalea/incubator.
- Build system and dependencies: All outdated and unmaintained dependencies have been removed or replaced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
A local conda/miniconda installation is required.
First clone/download the repository. The mamba
install is optional but recommended.
conda install mamba -n base -c conda-forge
mamba env create -f binder/environment.yml
# or
# conda env create -f binder/environment.yml
conda activate vmapplet
jupyter lab --notebook-dir=notebooks
activate vmapplet
python -m vmapplet vmapplet/data/simulation.toml out_folder