Additional Unit Test Fixes

.github/workflows/main.yml

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

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',
@@ -94,6 +80,38 @@ def __init__(self, model=None, result_dir=None, loaddata=False):
 #        return model2
 
 
+    def __eq__(self, other):
+        """ Compare Result object's output for equality. This does _NOT_ compare objects themselves
+
+        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 __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. """
@@ -156,6 +174,7 @@ 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();
+                # Should this ; be here? ^
 
         if timepoints is not None:
             if isinstance(timepoints,float):
@@ -257,7 +276,7 @@ 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 +515,7 @@ 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/test_solver.py

@@ -1,52 +1,9 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # import pickle
-from spatialpy.Model import ModelError
 import unittest
 import spatialpy
 
-# class SimpleDiffusion(spatialpy.Model):
-#     """ Initial condition is a delta function at the center voxel.
-#         The solution should be a Gaussian, up to the point where
-#         the BC becomes important. """
-
-#     def __init__(self, model_name="simple_diffusion"):
-#         spatialpy.Model.__init__(self, model_name)
-#         A = self.add_species(spatialpy.Species(
-#             name="A", diffusion_constant=0.01))
-#         # A unit square
-
-#         # System constants
-#         nxF, nyF = 50, 50     # number of particles in x and y-direction
-#         L = 1         # characteristic lenght of the cavity (= width = height)
-#         nW = 3         # number of wall points
-#         rho0 = 1         # reference fluid density
-
-#         # Compute domain bounds (including the boundary)
-#         dx, dy = L/(nxF-1), L/(nyF-1)
-#         xLim = ((0-(nW-1)*dx), 1+(nW-1)*dx)
-#         yLim = ((0-(nW-1)*dy), 1+(nW-1)*dy)
-
-#         # Discretization
-#         # total number of particles in x-direction (including walls)
-#         nxTot = nxF + 2*(nW-1)
-#         # total number of particles in y-direction (including walls)
-#         nyTot = nyF + 2*(nW-1)
-
-#         # Compute volume and mass per particle
-#         # in 2D simulations, consider z-lenght = 1
-#         vol = (xLim[1]-xLim[0])*(yLim[1]-yLim[0])*1.0
-#         # density * total volume / total number of particles
-#         mPP = rho0*vol/(nxTot*nyTot)
-
-#         self.mesh = spatialpy.Mesh.create_2D_domain(
-#             xlim=xLim, ylim=yLim, nx=nxTot, ny=nyTot, type_id=1, mass=mPP, rho0=rho0, fixed=True)
-#         # Place the A molecules in the voxel nearest the center of the square
-#         # self.set_initial_condition_place_near({A:10000},point=[0.5,0.5])
-#         self.add_initial_condition(spatialpy.ScatterInitialCondition(A, 10000))
-#         self.timestep_size = 1e-4
-#         self.timespan(numpy.linspace(0, 5, 200))
-
 
 class diffusion_debug(spatialpy.Model):
 
@@ -97,32 +54,32 @@ def test_solver_io(self):
     #     A = result.get_species("A", -1)
     #     self.assertFalse((A - model.u0).any())
 
-    # def test_same_seed(self):
-    #     """ Test that the output is the same if the same seed is used, edxplicit solver creation  """
-    #     solver = spatialpy.Solver(self.model)
-    #     result1 = solver.run(seed=1)
-    #     result2 = solver.run(seed=1)
-    #     self.assertEqual(result1, result2)
-
-    # def test_same_seed2(self):
-    #     """ Test that the output is the same if the same seed is used, use model.run()  """
-    #     result1 = self.model.run(seed=1)
-    #     result2 = self.model.run(seed=1)
-    #     self.assertEqual(result1, result2)
-
-    # def test_different_seeds(self):
-    #     """ Test that the output is different if different seeds are used. """
-    #     solver = spatialpy.Solver(self.model)
-    #     result1 = solver.run(seed=1)
-    #     result2 = solver.run(seed=100)
-    #     self.assertNotEqual(result1, result2)
-
-    # def test_default_seed(self):
-    #     """ Test that the output is different if no seed is given (default set on C level). """
-    #     solver = spatialpy.Solver(self.model)
-    #     result1 = solver.run()
-    #     result2 = solver.run()
-    #     self.assertNotEqual(result1, result2)
+    def test_same_seed(self):
+        """ Test that the output is the same if the same seed is used, edxplicit solver creation  """
+        solver = spatialpy.Solver(self.model)
+        result1 = solver.run(seed=1)
+        result2 = solver.run(seed=1)
+        self.assertTrue(result1 == result2)
+
+    def test_same_seed2(self):
+        """ Test that the output is the same if the same seed is used, use model.run()  """
+        result1 = self.model.run(seed=1)
+        result2 = self.model.run(seed=1)
+        self.assertTrue(result1 == result2)
+
+    def test_different_seeds(self):
+        """ Test that the output is different if different seeds are used. """
+        solver = spatialpy.Solver(self.model)
+        result1 = solver.run(seed=1)
+        result2 = solver.run(seed=100)
+        self.assertFalse(result1 == result2)
+
+    def test_default_seed(self):
+        """ Test that the output is different if no seed is given (default set on C level). """
+        solver = spatialpy.Solver(self.model)
+        result1 = solver.run()
+        result2 = solver.run()
+        self.assertFalse(result1 == result2)
 
     # def test_mesh_pickle(self):
     #     meshstr = pickle.dumps(self.model.mesh)