Remove cpp optimizations (#12)

jvail · Sep 3, 2023 · 3e4ed26 · 3e4ed26
1 parent 1ecea95
commit 3e4ed26
Show file tree

Hide file tree

Showing 16 changed files with 185 additions and 544 deletions.
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -10,9 +10,6 @@ dependencies:
   - toml
   - matplotlib
   - scipy
-  - boost
-  - boost-cpp
-  - cppyy=2.4
   - openalea.lpy
   - openalea.plantgl=3.20.1
   - openalea.mtg

diff --git a/notebooks/simple_simulation.ipynb b/notebooks/simple_simulation.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "c53a8105-14b5-437b-91ce-604152bb9c61",
    "metadata": {
     "tags": []
@@ -17,12 +17,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "b74cb80a-cac4-4d6f-ae18-165a52517072",
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "47503da9c36d4478af4b36964c741add",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "SceneWidget(scenes=[{'id': 'XaKImpeVjzSwKnKEkcfVxz8VN', 'data': b'x\\xdaSLrw\\xf5\\xf7e`Pp\\xe0\\xe5RPVVd\\x00\\x020\\…"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "widget = SceneWidget()\n",
     "widget"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,10 +1,5 @@
 [build-system]
-requires = [
-    "setuptools>=58",
-    "scikit-build>=0.17",
-    "cmake>=3.18",
-    "ninja",
-]
+requires = ["setuptools>=58"]
 build-backend = "setuptools.build_meta"
 
 [project]

diff --git a/test/notebooks/README.md b/test/notebooks/README.md
diff --git a/test/notebooks/optimization.ipynb b/test/notebooks/optimization.ipynb
diff --git a/test/test_metamer.py b/test/test_metamer.py
@@ -2,12 +2,11 @@
 
 from vmapplet import Simulation, Options
 from vmapplet.organs.metamer import MetamerData, CambialLayer
-from vmapplet.optimisation import reaction_wood_target
 from vmapplet.organs.wood import Wood
 from vmapplet.organs.fruit import AppleFruit
 from vmapplet.organs.leaf import AppleLeaf
 from vmapplet.organs.internode import Internode
-from vmapplet.physics import Frame
+from vmapplet.physics import Frame, reaction_wood_target
 from vmapplet.enums import FruitState
 
 

diff --git a/test/test_physics.py b/test/test_physics.py
@@ -8,7 +8,6 @@
     second_moment_of_area_circular_section,
     Frame,
     rotate_frame_at_branch,
-    reorient_frame,
 )
 
 
@@ -52,13 +51,3 @@ def test_rotate_frame_at_branch():
     v3 = Vector3(1, 1, 2)
     frame = Frame(v1, v2, v3)
     rotate_frame_at_branch(frame, 45, 45)
-
-
-def test_reorient_frame():
-    v1 = Vector3(2, 1, 1)
-    v2 = Vector3(1, 2, 1)
-    v3 = Vector3(1, 1, 2)
-    rotation_velocity = Vector3(1, 1, 1)
-    length = 1
-    frame = Frame(v1, v2, v3)
-    reorient_frame(frame, rotation_velocity, length)
diff --git a/vmapplet/__init__.py b/vmapplet/__init__.py
@@ -1,13 +1,14 @@
-from typing import Optional
+from typing import Optional, TYPE_CHECKING
 
-from pgljupyter import SceneWidget
+if TYPE_CHECKING:
+    from pgljupyter import SceneWidget
 
-from ._cppyy import *  # noqa
+# from ._cppyy import *  # noqa
 from .simulation import Simulation
 from .options import Options
 
 
-def run(simulation: Simulation, scene_widget: Optional[SceneWidget] = None):
+def run(simulation: Simulation, scene_widget: Optional["SceneWidget"] = None):
     """ """
 
     date_start = simulation.options.general.date_start

diff --git a/vmapplet/_cppyy.py b/vmapplet/_cppyy.py
diff --git a/vmapplet/lpy/mechanics_backward.lpy b/vmapplet/lpy/mechanics_backward.lpy
@@ -1,10 +1,10 @@
 import openalea.plantgl.all as pgl
 
 from vmapplet import (
-    constants,
-    optimisation
+    constants
 )
 from vmapplet.enums import LeafState
+from vmapplet.physics import *
 
 gravity = pgl.Vector3(0.0, 0.0, -9.81)
 
@@ -28,10 +28,10 @@ root() >> metamer(m):
     tree.fruit_load = tree.fruits / tree.trunk_cross_sectional_area
 
 metamer(m) >> SB() branch() metamer(mb) EB() metamer(mr):
-    radius = optimisation.get_new_radius(mb.radius, mr.radius)
+    radius = get_new_radius(mb.radius, mr.radius)
     if m.leaf.state == LeafState.GROWING:
-        radius = optimisation.get_new_radius(radius, m.leaf.petiole_radius)
-    m.radius = optimisation.max(radius, m.radius);
+        radius = get_new_radius(radius, m.leaf.petiole_radius)
+    m.radius = max(radius, m.radius);
     # update last layer thickness
     m.layers[-1].thickness = m.radius - m.layers[-1].radius
     m.compute_mass(mr, mb)
@@ -49,8 +49,8 @@ metamer(m) >> SB() branch() metamer(mb) EB() metamer(mr):
 metamer(m) >> metamer(mr):
     radius = mr.radius
     if m.leaf.state == LeafState.GROWING:
-        radius = optimisation.get_new_radius(mr.radius, m.leaf.petiole_radius)
-    m.radius = optimisation.max(radius, m.radius)
+        radius = get_new_radius(mr.radius, m.leaf.petiole_radius)
+    m.radius = max(radius, m.radius)
     m.layers[-1].thickness = m.radius - m.layers[-1].radius
     m.compute_mass(mr)
     if options.general.mechanics:
@@ -66,8 +66,8 @@ metamer(m) >> apex(a):
     # wood.density, m.fruit_mass are units objects
     radius = a.radius
     if m.leaf.state == LeafState.GROWING:
-        radius = optimisation.get_new_radius(a.radius, m.leaf.petiole_radius)
-    m.radius = optimisation.max(radius, m.radius)
+        radius = get_new_radius(a.radius, m.leaf.petiole_radius)
+    m.radius = max(radius, m.radius)
     m.layers[-1].thickness = m.radius - m.layers[-1].radius
     m.compute_mass()
     m.cumulated_torque = cross( m.hlu.heading * m.length, tree.tropism)