Add JOSS paper template, github actions and update openalea dependenc…

…ies (#10)

.github/workflows/draft-pdf.yml

@@ -0,0 +1,25 @@
+name: Draft JOOS PDF
+
+on:
+  push:
+    branches:
+      - master
+      - main
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          path: paper/paper.pdf

.github/workflows/test.yml

@@ -0,0 +1,30 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - master
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          generate-run-shell: true
+          environment-file: binder/environment.yml
+      - name: Test with pytest
+        run: |
+          pytest --disable-pytest-warnings
+        shell: micromamba-shell {0}

CHANGES.md

@@ -1,6 +1,6 @@
 # 0.1.0
 
-Major changes compared to the original `MAppleT`:
+Major changes compared to the original `MAppleT/StocaTree`:
 
 - support Python 3 and updated dependencies
 - support Jupyter notebooks

README.md

@@ -1,11 +1,11 @@
 # VMAppleT
 
-A refactored implementation and maintenance release of MAppleT. Original sources copied and modified from [openalea/incubator](https://github.com/openalea-incubator/MAppleT).
+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)
 
 
-## Major changes compared to MAppleT
+## 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 * Build system and dependencies: All outdated and unmaintained dependencies have been removed or replaced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

binder/environment.yml

@@ -3,21 +3,22 @@ channels:
   - fredboudon
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.10
   - jupyterlab=4.0
   - jupyterlab_widgets=3.0
   - ipywidgets=8.0
-  - toml=0.10
-  - matplotlib=3.7
-  - scipy=1.10
-  - boost=1.74
-  - boost-cpp=1.74
+  - toml
+  - matplotlib
+  - scipy
+  - boost
+  - boost-cpp
   - cppyy=2.4
   - openalea.lpy
-  - openalea.plantgl=3.14
-  - openalea.mtg=2.0
-  - xlrd=2.0
-  - pip=23.0
+  - openalea.plantgl=3.20.1
+  - openalea.mtg
+  - xlrd
+  - pip
+  - numpy>=1.22
   - flake8
   - mypy
   - black

notebooks/simple_simulation.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "c53a8105-14b5-437b-91ce-604152bb9c61",
    "metadata": {
     "tags": []
@@ -17,36 +17,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "b74cb80a-cac4-4d6f-ae18-165a52517072",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ddfba628792b452a9dd2cceff6ee0224",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "SceneWidget(scenes=[{'id': 'dQ6u5Pg13qMfGtHHPX8NPxVF2', 'data': b'x\\xdaSLrw\\xf5\\xf7e`Pp\\xe0\\xe5RPVVd\\x00\\x020\\…"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "widget = SceneWidget()\n",
     "widget"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "f4e4ddad-ba3d-40c8-9ecc-28740c010452",
    "metadata": {
     "tags": []
@@ -60,7 +44,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "89991d0d-2539-478d-8bb5-fe63a9a8095a",
    "metadata": {
     "tags": []
@@ -73,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "8f50dd49",
    "metadata": {
     "tags": []
@@ -86,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "b243f0f4-cf7c-4c35-8fa3-a6e894c36e8b",
    "metadata": {
     "tags": []
@@ -100,65 +84,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "64f4118d-93ff-4d43-99ed-f919d820003c",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['edge_type',\n",
-       " 'label',\n",
-       " '_axial_id',\n",
-       " 'growth_units',\n",
-       " 'year',\n",
-       " 'inflorescence',\n",
-       " 'number',\n",
-       " 'closest_apex',\n",
-       " 'farthest_apex',\n",
-       " 'sons_nb',\n",
-       " 'observation',\n",
-       " 'parent_observation',\n",
-       " 'parent_unit_id',\n",
-       " 'parent_fbr_id',\n",
-       " 'parent_tree_id',\n",
-       " 'zone',\n",
-       " 'cumulated_mass',\n",
-       " 'radius',\n",
-       " 'offset',\n",
-       " 'developped',\n",
-       " 'phyllotactic_angle',\n",
-       " 'branching_angle',\n",
-       " 'rigidity',\n",
-       " 'age',\n",
-       " 'length',\n",
-       " 'trunk',\n",
-       " 'fruit_age',\n",
-       " 'fruit_mass',\n",
-       " 'leaf_age',\n",
-       " 'leaf_mass',\n",
-       " 'leaf_area']"
-      ]
-     },
-     "execution_count": 7,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "tree.property_names()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1d1b6f74-217b-4ef9-adee-6c4452458970",
-   "metadata": {},
    "outputs": [],
    "source": [
-    "tree.display()"
+    "tree.property_names()"
    ]
   },
   {
@@ -186,7 +119,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.10.12"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

paper/paper.bib

@@ -0,0 +1,18 @@
+@Article{Costes:2008,
+author={Costes, Evelyne
+and Smith, Colin
+and Renton, Michael
+and Gu{\'e}don, Yann
+and Prusinkiewicz, Przemyslaw
+and Godin, Christophe},
+title={MAppleT: simulation of apple tree development using mixed stochastic and biomechanical models},
+journal={Functional Plant Biology},
+year={2008},
+volume={35},
+number={10},
+pages={936-950},
+keywords={biomechanics, functional--structural plant model, Malus{\thinspace}{\texttimes}{\thinspace}domestica, Markov model, tree simulation.},
+abstract={Construction of tree architectural databases over years is time consuming and cannot easily capture event dynamics, especially when both tree topology and geometry are considered. The present project aimed to bring together models of topology and geometry in a single simulation such that the architecture of an apple tree may emerge from process interactions. This integration was performed using L-systems. A mixed approach was developed based on stochastic models to simulate plant topology and mechanistic model for the geometry. The succession of growth units (GUs) along axes and their branching structure were jointly modelled by a hierarchical hidden Markov model. A biomechanical model, derived from previous studies, was used to calculate stem form at the metamer scale, taking into account the intra-year dynamics of primary, secondary and fruit growth. Outputs consist of 3-D mock-ups -- geometric models representing the progression of tree form over time. To asses these models, a sensitivity analysis was performed and descriptors were compared between simulated and digitised trees, including the total number of GUs in the entire tree, descriptors of shoot geometry (basal diameter, length), and descriptors of axis geometry (inclination, curvature). In conclusion, despite some limitations, MAppleT constitutes a useful tool for simulating development of apple trees in interaction with gravity.},
+doi={10.1071/FP08081},
+url={https://doi.org/10.1071/FP08081}
+}

paper/paper.md

@@ -0,0 +1,34 @@
+---
+title: 'VMAppleT: Apple Tree simulations based on StocaTree'
+tags:
+  - Python
+  - biology
+  - FSPM
+authors:
+  - name: Frédéric Boudon
+    affiliation: 1
+  - name: Jan Vaillant
+    affiliation: 3
+  - name: Evelyne Costes
+    affiliation: 2
+affiliations:
+ - name: CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
+   index: 1
+ - name: French National Institute for Agriculture, Food, and Environment (INRAE)
+   index: 2
+ - name: Independent Researcher, France
+   index: 3
+date: 2 September 2023
+bibliography: paper.bib
+---
+
+# Summary
+
+VMAppleT is a greatly refactored, modernized and updated implementation of StocaTree/MappleT [@Costes:2008] with
+support for running simulations in Jupyter notebooks to improve accessibility, extensibility and customization of the model.
+
+
+# Acknowledgements
+
+
+# References

pyproject.toml

@@ -14,7 +14,7 @@ authors = [
 ]
 description = "Apple Tree simulation using Markov Chains based on MAppleT"
 readme = "README.md"
-requires-python = "~=3.9.0"
+requires-python = "~=3.10.0"
 
 [tool.setuptools]
 packages = ["vmapplet"]

vmapplet/optimisation.py

@@ -4,14 +4,21 @@
 
 from .frame import Frame
 
-rotate = cppyy.gbl.optimization.rotate
 second_moment_of_area_annular_section = (
     cppyy.gbl.optimization.second_moment_of_area_annular_section
 )
 second_moment_of_area_circle = cppyy.gbl.optimization.second_moment_of_area_circle
 get_new_radius = cppyy.gbl.optimization.get_new_radius
 # _reaction_wood_target = cppyy.gbl.optimization.reaction_wood_target
 
+
+def rotate(
+    v3x: float, v3y: float, v3z: float, angle: float, vx: float, vy: float, vz: float
+):
+    # pgl can not handle the vector: wrap in list
+    return list(cppyy.gbl.optimization.rotate(v3x, v3y, v3z, angle, vx, vy, vz))
+
+
 import openalea.plantgl.all as pgl