{"id":39919469,"url":"https://github.com/openalea-incubator/lgrass","last_synced_at":"2026-01-18T17:08:19.829Z","repository":{"id":49035344,"uuid":"249497745","full_name":"openalea-incubator/lgrass","owner":"openalea-incubator","description":"A 3D Functionnal Structural Plant Model of perennial grasses morphogenesis and phenology","archived":false,"fork":false,"pushed_at":"2024-03-20T08:51:04.000Z","size":26756,"stargazers_count":8,"open_issues_count":9,"forks_count":9,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-04-18T11:14:14.304Z","etag":null,"topics":["flowering","fspm","grass","heading","lsystem","morphogenesis","openalea","phenology","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/openalea-incubator.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null}},"created_at":"2020-03-23T17:24:09.000Z","updated_at":"2023-12-15T06:32:22.000Z","dependencies_parsed_at":"2024-03-20T10:00:12.564Z","dependency_job_id":null,"html_url":"https://github.com/openalea-incubator/lgrass","commit_stats":{"total_commits":133,"total_committers":8,"mean_commits":16.625,"dds":0.4586466165413534,"last_synced_commit":"deba64791ccacda9e5582808dd86ad5c8b4d9983"},"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/openalea-incubator/lgrass","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openalea-incubator%2Flgrass","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openalea-incubator%2Flgrass/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openalea-incubator%2Flgrass/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openalea-incubator%2Flgrass/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/openalea-incubator","download_url":"https://codeload.github.com/openalea-incubator/lgrass/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openalea-incubator%2Flgrass/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28543862,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T14:59:57.589Z","status":"ssl_error","status_checked_at":"2026-01-18T14:59:46.540Z","response_time":98,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["flowering","fspm","grass","heading","lsystem","morphogenesis","openalea","phenology","python"],"created_at":"2026-01-18T17:08:19.230Z","updated_at":"2026-01-18T17:08:19.822Z","avatar_url":"https://github.com/openalea-incubator.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![License](https://img.shields.io/badge/license-CeCILL--C-blue )](https://img.shields.io/badge/license-CeCILL--C-blue )\n\n[![Documentation Status](https://readthedocs.org/projects/lgrass/badge/?version=latest)](https://lgrass.readthedocs.io/en/latest/?badge=latest)\n\n# L-Grass\nL-Grass is a Functional Structural Plant Model (FSPM) of perennial rye grass morphogenesis and phenology.\n\nL-Grass simulates:\n* Above-ground 3D architecture and morphogenesis (leaf extension, growth and tillering) as a self-regulated system. See [Verdenal *et al.* (2008)](https://doi.org/10.1071/FP08050).\n* Morphogenesis of the root system in 3D. The model is inspired from ArchiSimple model and accounts for C partioning between shoot and roots. See [Migault thesis (2015)] (https://hal.inrae.fr/tel-02799991)\n* Floral transition of individual apex and heading of the spike according to temperature, photoperiod and vegetative morphogenesis. See [Rouet *et al.* (2022)](https://doi.org/10.1093/insilicoplants/diac012).\n\n# Table of Contents\n- [Installation](#installation)\n  * [Prerequisites](#prerequisites)\n  * [Installing](#installing)\n    + [Users](#users)\n    + [Developers](#developers)\n- [Usage](#usage)\n- [Credits](#credits)\n  * [Authors](#authors)\n  * [Contributors](#contributors)\n  * [Funding](#funding)\n- [License](#license)\n\n\n# Installation\n\n*Lgrass* has been tested on Windows 10 64 bit. *Lgrass* was iniatially implemented in Python 2.7 and is now under Python 3.\n\n## Prerequisites\n*Lgrass* has the following dependencies (see documentation in the links provided, instructions for their installation are given in [Installing](#installing)):\n* To run the model: \n    * [Python](http://www.python.org) \u003e= 3.7 (old releases in Python 2.7)\n    * [NumPy](http://www.numpy.org/)\n    * [SciPy](http://www.scipy.org/)\n    * [Pandas](http://pandas.pydata.org/)\n    * [Openalea.MTG](https://github.com/openalea/mtg)\n    * [Openalea.Plantgl](https://github.com/openalea/plantgl)\n    * [Openalea.Lpy](https://github.com/openalea/lpy)\n    * [Alinea.Caribu](https://github.com/openalea-incubator/caribu) \n    * [ephem](https://pypi.org/project/ephem/)\n    * [geopy](https://pypi.org/project/geopy/)\n    * [xlrd](https://pypi.org/project/xlrd/)\n    \n## Installing\n*Lgrass* has to be installed in a conda environment containing all dependencies.\n\n* Install Miniconda 2 or 3 for Python 3.7: https://docs.conda.io/en/latest/miniconda.html\n* Create a new environment in an Anaconda prompt:\n   `conda create -n Lgrass python=3.7 openalea.mtg openalea.plantgl openalea.lpy alinea.caribu ephem geopy xlrd -c conda-forge -c fredboudon`\n   \n### Users\n* Download Lgrass package from https://github.com/openalea-incubator/lgrass/archive/master.zip\n* Extract archive\n* Open an Anaconda promt in your local copy of *Lgrass*,\n* Activate the conda environment: `conda activate Lgrass`\n* Run command: `python setup.py install --user` \n\n### Developers\n* Fork Lgrass repository in your own account\n* Clone your fork with git : `git clone https://github.com/my_account/lgrass.git`\n* Open an Anaconda promt in your cloned copy of *Lgrass*,\n* Activate the conda environment: `conda activate Lgrass`\n* Run command: `python setup.py develop --user` \n\n#### Updating submodules\n\nIf you want to update *Lgrass*:\n\n    git pull origin/master\n\n# Usage\n\n* For a basic usage of *Lgrass*, go to `lgrass/lgrass` and open `lgrass.lpy` with the Lpy software which was installed in your conda environment. Then click on `Run`\n* For external call of *lgrass*, examples are provided in `lgrass/example`\n\nThe version of lgrass integrating the flowering stages (Lgrass-F) is available in: \n\n* `lgrass/example/calibration_GEVES_2021`\n\n## calibration_GEVES_2021\nThis example deals with the implementation of the reproductive development in the model and its calibration by Rouet et coll. \nThis work led to the research article [Rouet *et al.* (2022)](https://doi.org/10.1093/insilicoplants/diac012).\nResults were obtained from the tag paper_ISPLANTS_2022. To run the model used for the paper, please download the code archives at [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6873725.svg)](https://doi.org/10.5281/zenodo.6873725)\n\n# Credits\n## Authors\n* Alban VERDENAL - model designing, development and validation\n* Vincent MIGAULT - model designing, development and validation\n* Simon ROUET - model designing, development and validation - [SimonRouet](https://github.com/SimonRouet)\n* Abraham ESCOBAR-GUTIERREZ - model designing and validation, scientific project management\n* Didier COMBES - model designing, development and validation, scientific project management - [dicombes](https://github.com/dicombes)\n\n## Contributors\n* Romain BARILLOT - [rbarillot](https://github.com/rbarillot)\n* Thibault RAQUET - [traquet](https://github.com/traquet)\n* Jean-Louis DURAND\n\n## Funding\n* [INRAE](https://www.inrae.fr/): salaries of permanent staff \n* [itk](https://www.itk.fr/en/) company and [ANRT](http://www.anrt.asso.fr/fr): funded the [Cifre](http://www.anrt.asso.fr/fr/cifre-7843) PhD thesis of V. Migault\n* Région Nouvelle-Aquitaine: funding of PhD thesis of S. Rouet\nto be continued...\n\n# License\nThis project is licensed under the CeCILL-C License - see file [LICENSE](LICENSE) for details\n \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenalea-incubator%2Flgrass","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenalea-incubator%2Flgrass","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenalea-incubator%2Flgrass/lists"}