Additional Unit Test Fixes

.github/workflows/main.yml

@@ -9,7 +9,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  unit-tests:
     runs-on: ubuntu-latest
 
     steps:

examples/coral_reef/coral.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import os
 import numpy
 import sys

examples/coral_reef/old/coral.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import math
 import matplotlib.pyplot as plt
 import numpy

examples/cylinderDemo/SpatialPy_cylinderDemo3D.ipynb

@@ -223,23 +223,6 @@
     "%time result = sol.run()\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 60,
-   "metadata": {},
-   "outputs": [
-    {
-     "output_type": "stream",
-     "name": "stdout",
-     "text": [
-      "{'Status': 'Success'}\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(result)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 12,

examples/cylinderDemo/old/cylinder_demo3D.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ pyURDME model file for the annihilation cylinder 3D example. """
 
 import os

examples/cylinderDemo/old/ensemble_test.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 from cylinder_demo3D import cylinderDemo3D
 from pyurdme.nsmsolver import NSMSolver
 import matplotlib.pyplot as plt

examples/cylinderDemo/old/pickle_test.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 from cylinder_demo3D import cylinderDemo3D
 from pyurdme.nsmsolver import NSMSolver
 import matplotlib.pyplot as plt

examples/mincde/old/mincde.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import numpy
 import os.path

examples/simple_diffusion/simple_diffusion2.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ PyURDME model with one species diffusing in the unit circle and one
     species diffusing on the boundary of the circle. Subdomains are 
     here handled by Dolfin's native subdomain model. """

examples/yeast_polarization/G_protein_cycle.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ pyURDME model file for the polarization 1D example. """
 
 import os

examples/yeast_polarization/polarisome_model.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ pyURDME model file for the model found in Lawson et al. PloS Comp Bio (2013). """
 
 import os

spatialpy/Result.py

@@ -1,28 +1,14 @@
+import filecmp
+import math
 import os
-import re
+import pickle
 import shutil
 import subprocess
-import sys
-import tempfile
-import types
-import warnings
-import uuid
-
 
 import numpy
-import scipy.io
-import scipy.sparse
 
-from spatialpy.VTKReader import VTKReader
 from spatialpy.Model import *
-
-import inspect
-
-import pickle
-import json
-import math
-
-
+from spatialpy.VTKReader import VTKReader
 
 common_rgb_values=['#1f77b4','#ff7f0e','#2ca02c','#d62728','#9467bd','#8c564b','#e377c2','#7f7f7f',
                    '#bcbd22','#17becf','#ff0000','#00ff00','#0000ff','#ffff00','#00ffff','#ff00ff',
@@ -94,16 +80,37 @@ def __init__(self, model=None, result_dir=None, loaddata=False):
 #        return model2
 
 
-    def __getstate__(self):
-        """ Used by pickle to get state when pickling. We need to read the contents of the
-        output file since we can't pickle file objects. """
-        #TODO
-        raise Exception('TODO: spatialpy.Result.__getstate__()');
+    def __eq__(self, other):
+        """ Compare Result object's output for equality. This does _NOT_ compare objects themselves
 
-    def __setstate__(self, state):
-        """ Used by pickle to set state when unpickling. """
-        #TODO
-        raise Exception('TODO: spatialpy.Result.__setstate__()');
+        Params:
+            self: Results object
+            other: Results object to compare against
+        Return:
+            bool """
+
+        if isinstance(other, Result) and self.result_dir != None and other.result_dir != None:
+                # Compare contents, not shallow compare
+                filecmp.cmpfiles.__defaults__ = (False,)
+                dircmp = filecmp.dircmp(self.result_dir, other.result_dir)
+                # Raise exception if funny_files
+                assert not dircmp.funny_files
+                if not (dircmp.left_only or dircmp.right_only or dircmp.funny_files or dircmp.diff_files):
+                    return True
+                return False
+        return NotImplemented
+
+    def __ne__(self, other):
+        """ Compare Result object's output for inequality. This does _NOT_ compare objects themselves.
+            This inverts the logic in __eq__().
+
+        Params:
+            self: Results object
+            other: Results object to compare against
+        Return:
+            bool """
+
+        return not self.__eq__(other)
 
 
     def read_step(self, step_num, debug=False):
@@ -155,7 +162,7 @@ def get_species(self, species, timepoints=None, concentration=False, determinist
 
         #t_index_arr = numpy.linspace(0,self.model.num_timesteps,
         #                    num=self.model.num_timesteps+1, dtype=int)
-        t_index_arr = self.get_timespan();
+        t_index_arr = self.get_timespan()
 
         if timepoints is not None:
             if isinstance(timepoints,float):
@@ -257,7 +264,7 @@ def plot_species(self, species, t_ndx=0, concentration=False, deterministic=Fals
 
         if use_matplotlib:
             import matplotlib.pyplot as plt
-            
+
             if (deterministic or not concentration):
                 d = data[spec_name]
             else:
@@ -496,7 +503,7 @@ def plot_property(self, property_name, t_ndx=0, p_ndx=0, width=500, height=500,
 
         if use_matplotlib:
             import matplotlib.pyplot as plt
-            
+
             if (property_name == 'v'):
                 d = data[property_name]
                 d = [d[i][p_ndx] for i in range(0,len(d))]

test/ioperformance.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ PyURDME model with one species diffusing in the unit circle and one
     species diffusing on the boundary of the circle. Subdomains are 
     here handled by Dolfin's native subdomain model. """

test/models/mincde.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 from spatialpy.Model import SpeciesError
 import numpy

test/models/mincde_5r.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ spatialpy model file for the MinCDE example. """
 
 import os.path

test/test_mincde.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 from models.mincde import mincde
 from models.mincde_5r import MinCDE5R