Complete Refactoring

.github/workflows/openalea_ci.yml

@@ -0,0 +1,33 @@
+name: OpenAlea CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - 'v*'
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+  release:
+    types:
+      - published
+  workflow_dispatch:
+    inputs:
+      check_before_tag:
+        description: "Run OpenAlea CI pre-tag build"
+        required: false
+        default: "true"
+        type: boolean
+
+run-name: >
+  ${{ github.event_name == 'workflow_dispatch' && 'OpenAlea CI pre-tag build' || 'OpenAlea CI' }}
+
+jobs:
+  build:
+    uses: openalea/action-build-publish-anaconda/.github/workflows/openalea_ci.yml@main
+    secrets:
+      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}

README.md

@@ -2,9 +2,15 @@
 
 A refactored and enhanced implementation of MAppleT/StocaTree. Original sources copied and modified from [openalea/incubator](https://github.com/openalea-incubator/MAppleT).
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jvail/vmapplet/master?urlpath=lab/tree/notebooks/simple_simulation.ipynb)
 
 
+[![Docs](https://readthedocs.org/projects/vmapplet/badge/?version=latest)](https://vmapplet.readthedocs.io/en/latest/?badge=latest)
+[![Build Status](https://github.com/openalea/vmapplet/actions/workflows/openalea_ci.yml/badge.svg)](https://github.com/openalea/vmapplet/actions/workflows/openalea_ci.yml)
+[![Python Version](https://img.shields.io/badge/3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)](https://www.python.org/downloads/)
+[![Anaconda-Server Badge](https://anaconda.org/openalea3/openalea.vmapplet/badges/version.svg)](https://anaconda.org/openalea3/openalea.vmapplet)
+[![License](https://img.shields.io/badge/License--CeCILL-C-blue)](https://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html)
+[![Binder](https://mybinder.org/badge_logo.svg)](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 * Build system and dependencies: All outdated and unmaintained dependencies have been removed or replaced
@@ -13,35 +19,61 @@ A refactored and enhanced implementation of MAppleT/StocaTree. Original sources
 * Configuration: An extended simulation and a Markov model configuration file in toml format
 * Jupyter integration: Run and visualize simulations in Jupyter lab notebooks
 
+### Authors
+
+> - Thomas Cokelaer
+> - Colin Smith
+> - Jan Vaillant
+> - Frederic Boudon
+
+### Institutes
+
+CIRAD / inria / INRAE
+
+### Status
+
+Python package
+
+### License
+
+CecILL-C
+
 ## Install
 
 A local conda/miniconda installation is required.
 First clone/download the repository. The `mamba` install is optional but recommended.
 
-#### Install mamba
+### Installation
 
-```sh
-conda install mamba -n base -c conda-forge
+#### for user
+Creating a new conda environment with vmapplet and its dependencies installed
+```bash
+mamba create -n vmapplet -c openalea3 -c conda-forge openalea.vmapplet
+```
+In an existing conda environment:
+```bash
+mamba install -c openalea3 -c conda-forge openalea.vmapplet
 ```
 
-#### Create environment - with a development install of VMappleT
-
-```sh
-mamba env create -f binder/environment.yml
-# or
-# conda env create -f binder/environment.yml
+#### for developer
+```bash
+mamba env create -f ./conda/environment.yml
 ```
 
 ## Jupyter
 
 ```sh
 conda activate vmapplet
-jupyter lab --notebook-dir=notebooks
+jupyter-lab --notebook-dir=notebooks
 ```
 
-## Script
+[//]: # (## Script)
 
-```sh
-activate vmapplet
-python -m vmapplet vmapplet/data/simulation.toml out_folder
-```
+[//]: # ()
+[//]: # (```sh)
+
+[//]: # (activate vmapplet)
+
+[//]: # (python -m vmapplet vmapplet/data/simulation.toml out_folder)
+
+[//]: # (```)

conda/environment.yml

@@ -0,0 +1,23 @@
+name: vmapplet_dev
+channels:
+  - openalea3
+  - conda-forge
+dependencies:
+  - python
+  - jupyterlab
+  - jupyterlab_widgets
+  - ipywidgets
+  - toml
+  - matplotlib-base
+  - scipy
+  - openalea.lpy
+  - openalea.plantgl
+  - openalea.mtg
+  - xlrd
+  - pip
+  - numpy
+  - flake8
+  - mypy
+  - black
+  - pip:
+      - -e .."[doc, test]"

conda/meta.yaml

@@ -0,0 +1,55 @@
+{% set pyproject = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
+{% set name = pyproject.get('project').get('name') %}
+{% set description = pyproject.get('project').get('description') %}
+{% set version = environ.get('SETUPTOOLS_SCM_PRETEND_VERSION', "0.1.0.dev0") %}
+{% set license = pyproject.get('project').get('license') %}
+{% set home = pyproject.get('project', {}).get('urls', {}).get('Homepage', '') %}
+{% set build_deps = pyproject.get("build-system", {}).get("requires", []) %}
+{% set deps = pyproject.get('project', {}).get('dependencies', []) %}
+{% set conda_deps = pyproject.get('tool', {}).get('conda', {}).get('environment', {}).get('dependencies',[]) %}
+{% set test_deps = pyproject.get('project', {}).get('optional-dependencies', {}).get('test',[]) %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  path: ..
+
+build:
+  noarch: python
+  number: 0
+  preserve_egg_dir: True
+  script:
+    - {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
+
+requirements:
+  host:
+    - python
+    {% for dep in build_deps %}
+    - {{ dep }}
+    {% endfor  %}
+
+  run:
+    - python
+    {% for dep in deps + conda_deps %}
+    - {{ dep }}
+    {% endfor %}
+
+test:
+  requires:
+    {% for dep in test_deps %}
+    - {{ dep }}
+    {% endfor %}
+  imports:
+    - openalea.vmapplet
+  source_files:
+    - test/**
+  commands:
+    - cd test
+    - pytest -v
+
+about:
+  home: {{ home }}
+  summary: {{ description }}
+  license: {{ license }}