Add windows (#12)

jvail · Sep 3, 2023 · cf7c273 · cf7c273
1 parent 3e4ed26
commit cf7c273
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Showing 5 changed files with 90 additions and 80 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,8 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        os: ['ubuntu-latest', 'macos-latest']
-        # os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ["3.10"]
     runs-on: ${{ matrix.os }}
 

diff --git a/notebooks/simple_simulation.ipynb b/notebooks/simple_simulation.ipynb
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "f4e4ddad-ba3d-40c8-9ecc-28740c010452",
    "metadata": {
     "tags": []
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "89991d0d-2539-478d-8bb5-fe63a9a8095a",
    "metadata": {
     "tags": []
@@ -73,7 +73,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "8f50dd49",
    "metadata": {
     "tags": []
@@ -86,7 +86,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "b243f0f4-cf7c-4c35-8fa3-a6e894c36e8b",
    "metadata": {
     "tags": []
@@ -100,12 +100,53 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "64f4118d-93ff-4d43-99ed-f919d820003c",
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "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()"
    ]

diff --git a/vmapplet/__init__.py b/vmapplet/__init__.py
@@ -3,7 +3,6 @@
 if TYPE_CHECKING:
     from pgljupyter import SceneWidget
 
-# from ._cppyy import *  # noqa
 from .simulation import Simulation
 from .options import Options
 

diff --git a/vmapplet/organs/metamer.py b/vmapplet/organs/metamer.py
@@ -10,7 +10,6 @@
     second_moment_of_area_annular_section,
     reaction_wood_target,
     second_moment_of_area_circle,
-    second_moment_of_area_circular_section,
 )
 from ..srandom import boolean_event
 from ..enums import Zone, FruitState, LeafState
@@ -519,67 +518,6 @@ def leaf_mass(self):
         return self.leaf.mass
 
 
-def reaction_wood_target(up, heading, previous_heading):
-    r"""Reaction wood target
-
-    The reaction wood is proportional to the change in inclination
-    over a season (Almeras, 2001). Hypothesis: The reaction wood is
-    also proportional to the inclination from gravity.
-
-    .. math::
-
-        P_r = 0.1635 - 0.1778 \theta_s
-
-    where :math:`P_r` is the radial portion of the outermost cambial layer that
-    become reaction wood and :math:`\theta_s` is the change in inclination of the
-    internode over the season (i.e., the cahnge in :math:`\vec{H}`, the heading
-    vector of the HLU frame since the start of the spring.
-
-    In order to also take into account the gravity, The firs term in the equation above
-    must be multiply by a coefficient that varies with the angle between the internode and
-    :math:`\vec{u}` a unit vector opposite to  :math:`-\vec{g}`
-
-    :param Vector3 up:
-    :param heading: vector3
-    :param previous_heading: vector3
-    :returns: reaction_wood (double)
-    """
-
-    # multiply by gravity normalised
-    cos_gh = Vector3(0.0, 0.0, 1.0) * heading
-    cos_pu = previous_heading * up
-    cos_ph = previous_heading * heading
-
-    if cos_pu * cos_ph >= 0.0:
-        try:
-            inclination = acos(cos_ph / 1.0001)
-        except Exception:
-            print("Problem with acos(cos_ph) where cos_ph=%f" % cos_ph)
-            inclination = 0.0
-    else:
-        try:
-            inclination = -acos(cos_ph)
-        except Exception:
-            tol = 1e-6
-            try:
-                inclination = -acos(cos_ph - tol)
-                ValueError("try again with tol set %s %s" % (cos_ph, cos_ph - 1.0))
-            except Exception:
-                print("cos+_pu=", cos_pu, " cos_ph=", cos_ph, "cosgh=", cos_gh)
-                print(cos_ph - 1.0)
-                raise ValueError("Problem with acos(cos_ph) where cos_ph=%f" % cos_ph)
-
-    percentage = 0.1635 * (1.0 - cos_gh) - 0.1778 * inclination
-    r = constants.two_pi * percentage
-
-    if r < 0.0:
-        r = 0.0
-    elif r > constants.pi:
-        r = constants.pi
-
-    return r
-
-
 def _clamp_if_near_zero(data, tol=0.0001):
     if data < tol and data > -tol:
         return 0

diff --git a/vmapplet/physics.py b/vmapplet/physics.py
@@ -32,30 +32,63 @@
 
 
 def reaction_wood_target(up, heading, previous_heading):
+    r"""Reaction wood target
+
+    The reaction wood is proportional to the change in inclination
+    over a season (Almeras, 2001). Hypothesis: The reaction wood is
+    also proportional to the inclination from gravity.
+
+    .. math::
+
+        P_r = 0.1635 - 0.1778 \theta_s
+
+    where :math:`P_r` is the radial portion of the outermost cambial layer that
+    become reaction wood and :math:`\theta_s` is the change in inclination of the
+    internode over the season (i.e., the cahnge in :math:`\vec{H}`, the heading
+    vector of the HLU frame since the start of the spring.
+
+    In order to also take into account the gravity, The firs term in the equation above
+    must be multiply by a coefficient that varies with the angle between the internode and
+    :math:`\vec{u}` a unit vector opposite to  :math:`-\vec{g}`
+
+    :param Vector3 up:
+    :param heading: vector3
+    :param previous_heading: vector3
+    :returns: reaction_wood (double)
+    """
+
+    # multiply by gravity normalised
     cos_gh = pgl.Vector3(0.0, 0.0, 1.0) * heading
     cos_pu = previous_heading * up
     cos_ph = previous_heading * heading
+    inclination = 0.0
 
-    inclination = 0
     if cos_pu * cos_ph >= 0.0:
         try:
-            inclination = acos(cos_ph)
+            inclination = acos(cos_ph / 1.0001)
         except Exception:
-            pass
-            # print(str(cos_ph))
+            print("Problem with acos(cos_ph) where cos_ph=%f" % cos_ph)
+            inclination = 0.0
     else:
         try:
             inclination = -acos(cos_ph)
         except Exception:
-            pass
-            # print(str(cos_ph))
+            tol = 1e-6
+            try:
+                inclination = -acos(cos_ph - tol)
+                ValueError("try again with tol set %s %s" % (cos_ph, cos_ph - 1.0))
+            except Exception:
+                print("cos+_pu=", cos_pu, " cos_ph=", cos_ph, "cosgh=", cos_gh)
+                print(cos_ph - 1.0)
+                raise ValueError("Problem with acos(cos_ph) where cos_ph=%f" % cos_ph)
+
     percentage = 0.1635 * (1.0 - cos_gh) - 0.1778 * inclination
-    r = 3.14159 * 2.0 * percentage
+    r = constants.two_pi * percentage
 
     if r < 0.0:
         r = 0.0
-    elif r > 3.14159:
-        r = 3.141459
+    elif r > constants.pi:
+        r = constants.pi
 
     return r