myokit 1.33.9__py3-none-any.whl → 1.35.0__py3-none-any.whl

myokit/tests/test_lib_guess.py

@@ -5,20 +5,11 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import unittest
 
 import myokit
 import myokit.lib.guess as guess
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class LibGuessTest(unittest.TestCase):
     """

myokit/tests/test_lib_hh.py

@@ -5,11 +5,9 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 import unittest
+
 import numpy as np
 
 import myokit
@@ -17,12 +15,6 @@ import myokit.lib.hh as hh
 
 from myokit.tests import DIR_DATA
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 MODEL = """
 [[model]]
@@ -365,13 +357,13 @@ class HHDetectionTest(unittest.TestCase):
         a = m2.get('ikr.a')
         rl = hh.get_rl_expression(a, myokit.Name(dt))
         a1 = rl.eval()
-        a2 = a.state_value() + dt.eval() * a.rhs().eval()
+        a2 = a.initial_value(True) + dt.eval() * a.rhs().eval()
         self.assertAlmostEqual(a1, a2)
         # And for r
         r = m2.get('ikr.r')
         rl = hh.get_rl_expression(r, myokit.Name(dt))
         r1 = rl.eval()
-        r2 = r.state_value() + dt.eval() * r.rhs().eval()
+        r2 = r.initial_value(True) + dt.eval() * r.rhs().eval()
         self.assertAlmostEqual(r1, r2)
 
         # Dt must be an expression
@@ -608,7 +600,7 @@ class HHModelTest(unittest.TestCase):
         # Test if derivatives are zero
         for k, x in enumerate(['ina.m', 'ina.h', 'ina.j']):
             x = model.get(x)
-            x.set_state_value(ss[k])
+            x.set_initial_value(ss[k])
             self.assertAlmostEqual(x.eval(), 0)
 
         # Test arguments
@@ -645,6 +637,20 @@ class HHModelTest(unittest.TestCase):
 
         self.assertEqual(len(m.states()), 3)
 
+    def test_initial_value_conversion(self):
+        # Tests that initial value expressions are converted to floats
+
+        model = myokit.parse_model(MODEL)
+        model.get('ikr.a').set_initial_value('1 / sqrt(7)')
+        model.get('ikr.r').set_initial_value('log(binding.koff, 10)')
+        m = hh.HHModel.from_component(model.get('ikr'))
+        x0 = m.default_state()
+        self.assertEqual(len(x0), 2)
+        self.assertIsInstance(x0[0], float)
+        self.assertIsInstance(x0[1], float)
+        self.assertAlmostEqual(x0[0], 0.377964473)
+        self.assertAlmostEqual(x0[1], -5)
+
 
 class AnalyticalSimulationTest(unittest.TestCase):
     """

myokit/tests/test_lib_markov.py

@@ -5,11 +5,9 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 import unittest
+
 import numpy as np
 
 import myokit
@@ -17,12 +15,6 @@ import myokit.lib.markov as markov
 
 from myokit.tests import DIR_DATA, WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class LinearModelTest(unittest.TestCase):
     """
@@ -155,8 +147,8 @@ class LinearModelTest(unittest.TestCase):
 
         # States must sum to 1
         m2 = model.clone()
-        m2.get(states[0]).set_state_value(0.6)
-        m2.get(states[1]).set_state_value(0.6)
+        m2.get(states[0]).set_initial_value(0.6)
+        m2.get(states[1]).set_initial_value(0.6)
         self.assertRaisesRegex(
             markov.LinearModelError, 'sum of states',
             markov.LinearModel, m2, states, parameters, current)
@@ -283,7 +275,7 @@ class LinearModelTest(unittest.TestCase):
 
         # Check that derivatives with ss are close to zero
         ss = list(ss)
-        model.set_state(ss + ss)    # Model has 2 ina's
+        model.set_initial_values(ss + ss)    # Model has 2 ina's
         derivs = model.evaluate_derivatives()
         for i in range(len(ss)):
             self.assertAlmostEqual(0, derivs[i])
@@ -310,7 +302,7 @@ class LinearModelTest(unittest.TestCase):
         self.assertTrue(np.all(ss <= 1))
 
         # Check that derivatives with ss are close to zero
-        model.set_state(ss)
+        model.set_initial_values(ss)
         derivs = model.evaluate_derivatives()
         for i in range(len(ss)):
             self.assertAlmostEqual(0, derivs[i])
@@ -331,6 +323,22 @@ class LinearModelTest(unittest.TestCase):
             ValueError, 'Illegal parameter vector size',
             m.rates, parameters=[0.01] * 22)
 
+    def test_initial_value_conversion(self):
+        # Tests that initial value expressions are converted to floats
+
+        fname = os.path.join(DIR_DATA, 'clancy-1999-fitting.mmt')
+        model = myokit.load_model(fname)
+        model.get('ina.C3').set_initial_value('1 / sqrt(7)')
+        model.get('ina.C2').set_initial_value('-1 / log(ina_ref.p)')
+        model.get('ina.C1').set_initial_value(0.5134619065149598)
+        m = markov.LinearModel.from_component(model.get('ina'))
+        x0 = m.default_state()
+        self.assertEqual(len(x0), 6)
+        self.assertIsInstance(x0[0], float)
+        self.assertIsInstance(x0[1], float)
+        self.assertAlmostEqual(x0[0], 0.3779644730092272)
+        self.assertAlmostEqual(x0[1], 0.10857362047581297)
+
 
 class AnalyticalSimulationTest(unittest.TestCase):
     """

myokit/tests/test_lib_multi.py

@@ -5,9 +5,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 import unittest
 
@@ -15,12 +12,6 @@ import myokit
 
 from myokit.tests import DIR_DATA, WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 # Path to multi-model testing files
 DIR_MULTI = os.path.join(DIR_DATA, 'multi')
 

myokit/tests/test_lib_plots.py

@@ -6,16 +6,13 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 import unittest
 
 import myokit
 import myokit.lib.plots as plots
 
-from myokit.tests import DIR_DATA
+from myokit.tests import DIR_DATA, WarningCollector
 
 
 class LibPlotTest(unittest.TestCase):
@@ -176,20 +173,28 @@ class LibPlotTest(unittest.TestCase):
         plt.close(fig)
         plt.show()
 
-        # Normalise currents
+        # Normalize currents
         fig = plt.figure()
-        plots.cumulative_current(d, currents, normalise=True)
+        plots.cumulative_current(d, currents, normalize=True)
         plt.legend()
         plt.close(fig)
         plt.show()
 
-        # Normalise currents and set maximum number of currents shown
+        # Normalize currents and set maximum number of currents shown
         fig = plt.figure()
-        plots.cumulative_current(d, currents, normalise=True, max_currents=3)
+        plots.cumulative_current(d, currents, normalize=True, max_currents=3)
         plt.legend()
         plt.close(fig)
         plt.show()
 
+        with WarningCollector() as w:
+            fig = plt.figure()
+            plots.cumulative_current(d, currents, normalise=True)
+            plt.legend()
+            plt.close(fig)
+            plt.show()
+        self.assertIn('deprecated', w.text())
+
 
 if __name__ == '__main__':
     unittest.main()

myokit/tests/test_meta.py

@@ -5,9 +5,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import unittest
 
 import myokit