https://github.com/jvail/vmapplet
https://github.com/jvail/vmapplet
Last synced: about 1 year ago
JSON representation
- Host: GitHub
- URL: https://github.com/jvail/vmapplet
- Owner: jvail
- License: other
- Created: 2022-04-08T09:27:29.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-06-19T12:28:39.000Z (about 2 years ago)
- Last Synced: 2025-04-05T21:25:36.545Z (over 1 year ago)
- Language: Python
- Size: 1.91 MB
- Stars: 1
- Watchers: 3
- Forks: 3
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
- License: LICENSE.txt
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README
# VMAppleT
A refactored and enhanced implementation of MAppleT/StocaTree. Original sources copied and modified from [openalea/incubator](https://github.com/openalea-incubator/MAppleT).
[](https://mybinder.org/v2/gh/jvail/vmapplet/master?urlpath=lab/tree/notebooks/simple_simulation.ipynb)
## 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* Build system and dependencies: All outdated and unmaintained dependencies have been removed or replaced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
```sh
conda install mamba -n base -c conda-forge
```
#### Create environment - with a development install of VMappleT
```sh
mamba env create -f binder/environment.yml
# or
# conda env create -f binder/environment.yml
```
## Jupyter
```sh
conda activate vmapplet
jupyter lab --notebook-dir=notebooks
```
## Script
```sh
activate vmapplet
python -m vmapplet vmapplet/data/simulation.toml out_folder
```