pycrop2ml

CropML Python library

https://github.com/agriculturalmodelexchangeinitiative/pycrop2ml

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
1 of 11 committers (9.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (5.8%) to scientific vocabulary

Keywords

crop-model program-transformation source-to-source transpiler

Scientific Fields

Sociology Social Sciences - 87% confidence

Last synced: 4 months ago · JSON representation ·

Repository

CropML Python library

Basic Info

Host: GitHub
Owner: AgriculturalModelExchangeInitiative
License: other
Language: Python
Default Branch: master
Homepage:
Size: 68.3 MB

Statistics

Stars: 19
Watchers: 4
Forks: 18
Open Issues: 23
Releases: 2

Topics

crop-model program-transformation source-to-source transpiler

Created almost 8 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Citation Authors

README.rst

=========
Pycrop2ml
=========
..  image:: https://readthedocs.org/projects/pycrop2ml/badge/?version=latest
    :target: http://pycrop2ml.readthedocs.io/en/latest/
    :alt: Documentation Status
 
..  image:: https://github.com/AgriculturalModelExchangeInitiative/PyCrop2ML/actions/workflows/codeql-analysis.yml/badge.svg
    :alt: CodeQL Status
    :target: https://github.com/AgriculturalModelExchangeInitiative/PyCrop2ML/actions/workflows/codeql-analysis.yml

.. image:: https://anaconda.org/amei/pycropml/badges/platforms.svg   
    :target: https://anaconda.org/amei/pycropml

.. image:: https://anaconda.org/amei/pycropml/badges/version.svg
    :target: https://anaconda.org/amei/pycropml

.. {# pkglts, doc

.. #}

A Python library to generate components from Crop2ML declarative language.

For more information, refer to `the documentation`__.

.. __: http://pycrop2ml.readthedocs.io/en/latest/



Installation
============

Using conda
~~~~~~~~~~~

    conda install -c amei -c openalea3 -c conda-forge pycropml
    
Usage
=====

From Platforms to Crop2ML
~~~~~~~~~~~~~~~~~~~~~~~~~

    cyml -c name_of_the_component_repository absolute_path_of_the_output source_language_or_platform

From Crop2ML to Platforms
~~~~~~~~~~~~~~~~~~~~~~~~~

    cyml -p name_of_the_Crop2ML_package target_language_or_platform

Owner

Name: AgriculturalModelExchangeInitiative
Login: AgriculturalModelExchangeInitiative
Kind: organization

Repositories: 7
Profile: https://github.com/AgriculturalModelExchangeInitiative

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  PyCrop2ML : Python library to exchange and reuse crop
  model compponents between languages and platforms 
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Cyrille Ahmed
    family-names: Midingoyi
    affiliation: CIRAD
    email: cyrille_ahmed.midingoyi@cirad.fr
  - given-names: Christophe
    family-names: Pradal
    email: christophe.pradal@cirad.fr
    affiliation: CIRAD
    orcid: 'https://orcid.org/0000-0002-2555-761X'
  - given-names: 'Andreas '
    family-names: Enders
    affiliation: >-
      Institute of Crop Science and Resource Conservation
      (INRES), University of Bonn, Bonn, Germany,
  - given-names: Davide
    family-names: Fumagalli
    affiliation: Institute for Environment and Sustainability
  - given-names: Patrice
    family-names: Lecharpentier
    affiliation: INRAE
  - given-names: 'Hélène '
    family-names: Raynal
    affiliation: INRAE
  - given-names: 'Marcello '
    family-names: Donatelli
    affiliation: CREAA
  - given-names: Ioannis N.
    family-names: Athanasiadis
    affiliation: 'Wageningen University, Wageningen, The Netherlands'
  - given-names: 'Cheryl '
    family-names: Porter
    affiliation: >-
      Agricultural & Biological Engineering, University of
      Florida, Gainesville, USA
  - given-names: 'Gerrit '
    family-names: Hoogenboom
    affiliation: >-
      Agricultural & Biological Engineering, University of
      Florida, Gainesville, USA
  - given-names: 'Fabio '
    family-names: Oliveira
    affiliation: >-
      Agricultural & Biological Engineering, University of
      Florida, Gainesville, USA
  - given-names: 'Dean '
    family-names: Holzworth
    affiliation: 'CSIRO Agriculture and Food, Toowoomba, Australia'
  - given-names: Pierre
    family-names: Martre
    affiliation: INRAE
    email: pierre.martre@inrae.fr
repository-code: >-
  https://github.com/AgriculturalModelExchangeInitiative/PyCrop2ML
url: 'https://crop2ml.org'
abstract: >-
  The increasing impact of climate change and variability on
  food security and agriculture, and the need for
  agroecological transition require improving the
  performance of crop simulation models and to model new
  biophysical processes to tackle new challenges. Recently,
  the Agricultural Models Exchange Initiative (AMEI)
  proposed Crop2ML, an open-source modeling framework for
  exchanging and reusing crop model components between
  modeling platforms. This framework provides a unified
  description of model components at a high level of
  abstraction based on shared concepts, lifting constraints
  of modeling platforms through an automatic system that
  transforms high-level models into platform-compliant
  components. This paper presents an approach based on
  reverse engineering to automatically extract and transform
  meta-information and algorithms of existing crop model
  processes into a platform-independent model component. A
  search algorithm using Crop2ML concepts, and a many-to-one
  transformation system was adopted as the main reverse
  engineering techniques to produce high-level models. The
  system consists in parsing the codebase of model
  components from different high-level languages (Python, R,
  Java, C++, C#, and Fortran) using the ANother Tool for
  Language Recognition (ANTLR) parser generator and
  processing the generated syntax trees to produce the
  various model implementations. It is implemented and
  evaluated on three crop model components: an energy
  balance model provided by BioMA platform and two soil
  temperature models provided by SIMPLACE and DSSAT
  platforms. We demonstrated the extensibility of our
  approach with the STICS, OpenAlea, and SiriusQuality
  modeling platforms. CyMLTx is a significant contribution
  towards the interoperability of crop modeling platforms
  and the reuse of crop model components beyond programming
  languages. It will thus contribute to foster model
  intercomparison and improvement activities. 
keywords:
  - Crop2ML
  - AMEI
  - Crop Model
  - DSSAT
  - SimPlace
  - STICS
  - APSIM
  - OpenAlea
  - BioMA
  - RECORD
license: CECILL-C

GitHub Events

Total

Issues event: 11
Watch event: 1
Delete event: 5
Member event: 1
Issue comment event: 7
Push event: 28
Pull request review event: 3
Pull request event: 36
Fork event: 1
Create event: 4

Last Year

Issues event: 11
Watch event: 1
Delete event: 5
Member event: 1
Issue comment event: 7
Push event: 28
Pull request review event: 3
Pull request event: 36
Fork event: 1
Create event: 4

Committers

Last synced: 4 months ago

All Time

Total Commits: 605
Total Committers: 11
Avg Commits per committer: 55.0
Development Distribution Score (DDS): 0.296

Past Year

Commits: 55
Committers: 4
Avg Commits per committer: 13.75
Development Distribution Score (DDS): 0.364

Top Committers

Name	Email	Commits
cyrillemidingoyi	a**i@y**r	426
pradal	c**l@i**r	145
Michael Berg-Mohnicke	m**g@z**e	14
Cyrille Ahmed MIDINGOYI	m**y@S**N	8
lorenefifame	l**e@g**m	3
Nicolas Brichet	n**t@i**r	3
Cyril	c**l@l**n	2
Teiki RAIHAUTI	r**i@s**n	1
Nicolas Brichet	n**t@i**r	1
MIDINGOYI	M**I@l**n	1
Cyrille Ahmed MIDINGOYI	m**y@s**n	1

Committer Domains (Top 20 + Academic)

supagro.inra.lan: 3 lps-cotonou.supagro.inra.lan: 1 inrae.fr: 1 lps-moustache.supagro.inra.lan: 1 inra.fr: 1 zalf.de: 1 inria.fr: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 35
Total pull requests: 124
Average time to close issues: almost 2 years
Average time to close pull requests: 19 days
Total issue authors: 6
Total pull request authors: 5
Average comments per issue: 0.86
Average comments per pull request: 0.11
Merged pull requests: 116
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 8
Pull requests: 41
Average time to close issues: about 3 hours
Average time to close pull requests: 3 days
Issue authors: 4
Pull request authors: 4
Average comments per issue: 0.38
Average comments per pull request: 0.05
Merged pull requests: 37
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

pradal (19)
orianebro (9)
cyrillemidingoyi (5)
plecharpent (2)
hol353 (1)
PierrickRoyer (1)

Pull Request Authors

cyrillemidingoyi (107)
pradal (23)
bergm (7)
TeikiRaihauti (2)
dependabot[bot] (1)

Top Labels

Issue Labels

enhancement (3)

Pull Request Labels

dependencies (1)

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 4

proxy.golang.org: github.com/AgriculturalModelExchangeInitiative/PyCrop2ML

Documentation: https://pkg.go.dev/github.com/AgriculturalModelExchangeInitiative/PyCrop2ML#section-documentation
License: other
Latest release: v1.2.0
published over 2 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

proxy.golang.org: github.com/agriculturalmodelexchangeinitiative/pycrop2ml

Documentation: https://pkg.go.dev/github.com/agriculturalmodelexchangeinitiative/pycrop2ml#section-documentation
License: other
Latest release: v1.2.0
published over 2 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

Dependencies

requirements.txt pypi

Cython *
IPython *
antlr4-python3-runtime *
graphviz *
nbformat *
nbsphinx *
networkx *
numpy *
path.py *
pydot *
pytest *
pytest-mock *
pyyaml *
six *
sphinx *
unyt *

.github/workflows/codeql-analysis.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/conda-package-build.yml actions

actions/checkout v3 composite
haya14busa/action-cond v1 composite
openalea/action-build-publish-anaconda v0.1.4 composite

Dockerfile docker

continuumio/conda-ci-linux-64-python3.7 latest build

setup.py pypi