Fixed parameter placement when read from run call

Author: fabriciocravo

for_local_use.py

@@ -2,21 +2,55 @@
 from mobspy import modules
 
 if __name__ == '__main__':
-    from mobspy import *
 
-
-    # Replace parameters using units
-    Color, Location = BaseSpecies()
-    Color.red, Color.blue
-    Location.here, Location.there
-    Something = Color*Location
-
-    2*Something >> 3*Something [lambda r1, r2: 1*u.decimeter**2/u.h if Location(r1) == Location(r2) else 0.5*u.decimeter**2/u.h]
-
-    S = Simulation(Something)
-    S.volume = 1*u.m**2
-    print(S.compile())
-
-    # print(A.get_characteristics())
+    A = BaseSpecies()
+    p1, p2 = ModelParameters([1], [1 / u.hour, 2 / u.hour, 3 / u.hour])
+    A >> Zero[p1 * p2]
+    A(100)
+    S = Simulation(A)
+    S.run(duration=5 * u.hour, plot_data=False, level=-1)
+    print(S.results)
+
+    exit()
+
+    """
+        This is the Tree model from the paper
+        We have a population of Trees
+        The Trees can die, age, have different colors and be in two different forests
+        The colors can change randomly from time to time
+        All old Trees can reproduce, but the Three is born green and young 
+    """
+    Ager, Mortal, Colored, Location = BaseSpecies()
+    Colored.green, Colored.yellow, Colored.brown
+    Location.dense, Location.sparse
+    Ager.young >> Ager.old[1 / 10 / u.year]
+    Mortal >> Zero [lambda r1: 0.1 / u.year if r1.old else 0]
+    Tree = Ager * Colored * Mortal * Location
+
+    # replication
+    Tree.old >> Tree + Tree.green.young[0.1/u.year]
+
+    # competition
+    Tree.dense.old + Tree.dense.young >> Tree.dense.old[1e-10 * u.decimeter ** 2 / u.year]
+
+    # reproduction
+    bf = 1e-10 * u.decimeter ** 2 / u.year
+    rep_r = lambda t1, t2: 5 * bf if (Location(t1) == Location(t2) and Colored(t1) == Colored(t2)) else bf
+    2 * Tree >> 2 * Tree + Tree.yound[rep_r]
+
+    # color cycling
+    colors = ['green', 'yellow', 'brown']
+    for color, next_color in zip(colors, colors[1:] + colors[:1]):
+        Tree.c(color) >> Tree.c(next_color)[10/u.year]
+
+    # initial conditions
+    Tree.dense(50), Tree.dense.old(50), Tree.sparse(50), Tree.sparse.old(50)
+    # initial conditions
+    Tree.dense(50), Tree.dense.old(50), Tree.sparse(50), Tree.sparse.old(50)
+    MySim = Simulation(Tree)
+    MySim.run(volume = 1 * u.meter ** 2, unit_x='year',
+              duration=100 * u.years, repetitions=3, output_concentration=False,
+              simulation_method='stochastic', save_data=False, plot_data=False)
+    MySim.plot_stochastic(Tree.dense, Tree.sparse, Tree.brown)
 
 

local_debug_script.py

@@ -346,14 +346,6 @@ def run(self, duration=None, volume=None, dimension=None,
             :param save_data: (bool) save data or not
             :param plot_data: (bool) plot data or not
         """
-        # Level needs to be set before compilation
-        if level is not None:
-            self.level = level
-
-        # Base case - If there are no events we compile the model here
-        if self._species_for_sbml is None:
-            self.compile(verbose=False)
-
         # This is only here so the ide gives the users tips about the function argument.
         # I wish there was a way to loop over all argument without args and kargs
         pr_manually_process_each_parameter(self, duration, volume, dimension,
@@ -362,6 +354,14 @@ def run(self, duration=None, volume=None, dimension=None,
                                            jobs, unit_x, unit_y, output_concentration, output_event,
                                            output_file, save_data, plot_data, rate_type, plot_type)
 
+        # Level needs to be set before compilation
+        if level is not None:
+            self.level = level
+
+        # Base case - If there are no events we compile the model here
+        if self._species_for_sbml is None:
+            self.compile(verbose=False)
+
         self._assemble_multi_simulation_structure()
 
         simlog.debug('Starting Simulator')

mobspy/simulation.py

@@ -11,13 +11,20 @@
 from copy import deepcopy
 import sys
 import os
-
+import re
 
 # Compare results with expected file
 def compare_model(comp_results, file_name):
-    with open(file_name, 'r') as file:
+    def normalize(text):
+        """ Normalize text by removing extra spaces, tabs, and Unicode variations. """
+        text = text.strip()  # Remove leading/trailing spaces
+        text = re.sub(r'\s+', ' ', text)  # Replace multiple spaces/tabs/newlines with a single space
+        return text
+
+    with open(file_name, 'r', encoding='utf-8') as file:
         for r, line in zip(comp_results.split('\n'), file.readlines()):
-            line = line.replace('\n', '')
+            line = normalize(line)
+            r = normalize(r)
 
             if r != line:
                 print('file: ' + line)
@@ -1411,6 +1418,7 @@ def test_double_parameters_with_units():
     A(100)
     S = Simulation(A)
     S.run(duration=5 * u.hour, plot_data=False, level=-1)
+
     assert compare_model(str(S.results), 'test_tools/model_45.txt')