added unittest for one-species-crn

tests/test_solver.py

@@ -0,0 +1,60 @@
+
+import os
+import imp
+import unittest
+from argparse import ArgumentParser
+
+from crnsimulator.reactiongraph import ReactionGraph, ReactionNode
+from crnsimulator.crn_parser import parse_crn_string
+from crnsimulator.odelib_template import add_integrator_args
+
+
+class testSolver(unittest.TestCase):
+  def setUp(self):
+    parser = ArgumentParser()
+    add_integrator_args(parser)
+    self.args = parser.parse_args([])
+    self.filename = 'test_file.py'
+    self.executable = 'test_file.pyc'
+
+  def tearDown(self):
+    ReactionNode.rid = 0
+    os.remove(self.filename)
+    os.remove(self.executable)
+
+  def test_crn(self):
+    # At some pont the simulator had troubles with CRNs that have
+    # only one species...
+    crn = "2X <=> 3X; X -> [k=0.1]"
+    crn, _ = parse_crn_string(crn, process=True)
+
+    # Split CRN into irreversible reactions
+    new = []
+    for [r, p, k] in crn :
+      if None in k :
+        k[:] = [x if x != None else 1 for x in k]
+      if len(k) == 2:
+        new.append([r,p,k[0]])
+        new.append([p,r,k[1]])
+      else :
+        new.append([r,p,k[0]])
+    crn = new
+
+    RG = ReactionGraph(crn)
+
+    filename, odename = RG.write_ODE_lib(filename=self.filename)
+    _temp = imp.load_source(odename, filename)
+    integrate = getattr(_temp, 'integrate')
+
+    self.args.p0 = ['1=0.5']
+    self.args.t_log = 10
+    self.args.t0 = 0.1
+    self.args.t8 = 10
+    simu = integrate(self.args)
+
+    first = simu[0]
+    last = simu[-1]
+
+    self.assertEqual(first, (0.10000000000000001, 0.5))
+    self.assertEqual(last, (10.0, 0.88535344232897151))
+