Updated examples to work with changes made for unit tests.

StochSS · Dec 8, 2021 · b6fe71e · b6fe71e
1 parent 96ccc18
commit b6fe71e
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Showing 5 changed files with 60 additions and 14,786 deletions.
diff --git a/examples/Bistable_Biochem_Elf_Ehrenberg/Bistable_Biochem_Elf_Ehrenberg.ipynb b/examples/Bistable_Biochem_Elf_Ehrenberg/Bistable_Biochem_Elf_Ehrenberg.ipynb
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -79,8 +79,8 @@
     "        R8 = spatialpy.Reaction(reactants={EBA:1}, products={EB:1, A:1}, rate=Kd)\n",
     "        R9 = spatialpy.Reaction(reactants={EBA:1, A:1}, products={EBA2:1}, rate=Ka)\n",
     "        R10 = spatialpy.Reaction(reactants={EBA2:1}, products={EBA:1, A:1}, rate=Kd)\n",
-    "        R11 = spatialpy.Reaction(reactants={B:1}, products=None, rate=K4)\n",
-    "        R12 = spatialpy.Reaction(reactants={A:1}, products=None, rate=K4)\n",
+    "        R11 = spatialpy.Reaction(reactants={B:1}, products={}, rate=K4)\n",
+    "        R12 = spatialpy.Reaction(reactants={A:1}, products={}, rate=K4)\n",
     "        self.add_reaction([R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, R12])\n",
     "\n",
     "        self.add_initial_condition(spatialpy.ScatterInitialCondition(EA, 200, [1]))\n",
@@ -93,7 +93,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -378716,7 +378716,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -378730,7 +378730,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.2"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/examples/cylinderDemo/SpatialPy_cylinderDemo3D-ResultsCheck.ipynb b/examples/cylinderDemo/SpatialPy_cylinderDemo3D-ResultsCheck.ipynb
@@ -28,7 +28,7 @@
     {
      "data": {
       "text/plain": [
-       "'../../spatialpy/__init__.py'"
+       "'/Users/bryanrumsey/Documents/SpatialPy/examples/cylinderDemo/../../spatialpy/__init__.py'"
       ]
      },
      "execution_count": 3,
@@ -133,11 +133,11 @@
     "\n",
     "\n",
     "        # Define Reactions\n",
-    "        R1 = spatialpy.Reaction(reactants=None, products={A:1}, \n",
+    "        R1 = spatialpy.Reaction(reactants={}, products={A:1}, \n",
     "                                rate=k_creat1, restrict_to=2)\n",
-    "        R2 = spatialpy.Reaction(reactants=None, products={B:1}, \n",
+    "        R2 = spatialpy.Reaction(reactants={}, products={B:1}, \n",
     "                              rate=k_creat2, restrict_to=3)\n",
-    "        R3 = spatialpy.Reaction(reactants={A:1, B:1}, products=None, \n",
+    "        R3 = spatialpy.Reaction(reactants={A:1, B:1}, products={}, \n",
     "                              rate=k_react)\n",
     "        self.add_reaction([R1, R2, R3])\n",
     "        \n",
@@ -39648,7 +39648,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -39662,7 +39662,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.2"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/examples/cylinderDemo/SpatialPy_cylinderDemo3D.ipynb b/examples/cylinderDemo/SpatialPy_cylinderDemo3D.ipynb
diff --git a/examples/cylinderDemo/cylinder_demo.py b/examples/cylinderDemo/cylinder_demo.py
@@ -60,11 +60,11 @@ def __init__(self, model_name="cylinder_demo3d"):
 
 
         # Define Reactions
-        R1 = spatialpy.Reaction(reactants=None, products={A:1},
+        R1 = spatialpy.Reaction(reactants={}, products={A:1},
                                 rate=k_creat1, restrict_to=2)
-        R2 = spatialpy.Reaction(reactants=None, products={B:1},
+        R2 = spatialpy.Reaction(reactants={}, products={B:1},
                               rate=k_creat2, restrict_to=3)
-        R3 = spatialpy.Reaction(reactants={A:1, B:1}, products=None,
+        R3 = spatialpy.Reaction(reactants={A:1, B:1}, products={},
                               rate=k_react)
         self.add_reaction([R1, R2, R3])
 

diff --git a/examples/yeast_polarization/Polarisome_1D.ipynb b/examples/yeast_polarization/Polarisome_1D.ipynb
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +125,7 @@
     "        self.add_initial_condition(spatialpy.ScatterInitialCondition(Actinc,40))\n",
     "\n",
     "        #self.timespan(range(0,3601,30))\n",
-    "        self.timespan(range(0,201,10))"
+    "        self.timespan(range(0,201,10), timestep_size=1)"
    ]
   },
   {
@@ -137,7 +137,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -757,7 +757,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -771,7 +771,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.2"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,