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

myokit/tests/test_protocol_floating_point.py

@@ -26,21 +26,12 @@
 # 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
 
 from myokit.tests.ansic_event_based_pacing import AnsicEventBasedPacing
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class ProtocolFloatingPointTest(unittest.TestCase):
 
@@ -125,7 +116,7 @@ class ProtocolFloatingPointTest(unittest.TestCase):
 
 class PacingSystemFloatingPointTest(unittest.TestCase):
     """
-    Test float behaviour in the Python PacingSystem implementation, using the
+    Test float behavior in the Python PacingSystem implementation, using the
     log_for_interval method.
     """
 

myokit/tests/test_protocol_time_series.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+#
+# Tests the time series protocol class
+#
+# This file is part of Myokit.
+# See http://myokit.org for copyright, sharing, and licensing details.
+#
+import unittest
+import pickle
+
+import myokit
+
+
+class TimeSeriesProtocolTest(unittest.TestCase):
+    """
+    Tests the TimeSeriesProtocol class.
+    """
+
+    def test_eq(self):
+        # Equality testing
+        p1 = myokit.TimeSeriesProtocol([1, 2], [2, 4])
+        p2 = myokit.TimeSeriesProtocol([1, 2], [2, 4])
+        self.assertEqual(p1, p2)
+        self.assertNotEqual(p1, 1)
+        self.assertEqual(p1, p1)
+
+    def test_pickle(self):
+        # Pickling and unpickling
+        p1 = myokit.TimeSeriesProtocol([1, 2], [2, 4])
+        p2 = pickle.loads(pickle.dumps(p1))
+        self.assertEqual(p1, p2)
+
+    def test_constructor(self):
+        p = myokit.TimeSeriesProtocol([1], [2])
+        self.assertEqual(p.times(), [1])
+        self.assertEqual(p.values(), [2])
+
+        p = myokit.TimeSeriesProtocol([1, 2], [1, 2])
+        self.assertEqual(p.times(), [1, 2])
+        self.assertEqual(p.values(), [1, 2])
+
+        p = myokit.TimeSeriesProtocol([2, 1], [2, 1])
+        self.assertEqual(p.times(), [1, 2])
+        self.assertEqual(p.values(), [1, 2])
+
+        self.assertRaises(  # No specific error from class!!
+            TypeError, myokit.TimeSeriesProtocol, 1, 2)
+        self.assertRaisesRegex(
+            ValueError, 'same size', myokit.TimeSeriesProtocol, [1, 2], [2])
+        self.assertRaisesRegex(
+            ValueError, 'nknown interpolation', myokit.TimeSeriesProtocol,
+            [1, 2], [2, 4], method='cubic'
+        )
+
+    def test_values(self):
+        values = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
+        times = [0, 0, 1, 1, 1, 2, 2, 2, 3, 4, 5, 7]
+        values = list(range(len(times)))
+        pacing = myokit.TimeSeriesProtocol(times, values)
+
+        def test(value, index):
+            self.assertEqual(pacing.pace(value), index)
+
+        test(-1, 0)
+        test(0, 1)
+        test(1, 4)
+        test(2, 7)
+        test(3, 8)
+        test(4, 9)
+        test(5, 10)
+        test(7, 11)
+        test(8, 11)
+        test(1.5, 4.5)
+        test(1.75, 4.75)
+        test(6, 10.5)
+        test(5.5, 10.25)
+
+
+if __name__ == '__main__':
+    import warnings
+    warnings.simplefilter('always')
+    unittest.main()

myokit/tests/test_pype.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
@@ -15,12 +12,6 @@ import myokit.pype
 
 from myokit.tests import TemporaryDirectory
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class PypeTest(unittest.TestCase):
 

myokit/tests/test_quantity.py

@@ -5,19 +5,10 @@
 # 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
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class QuantityTest(unittest.TestCase):
     """

myokit/tests/test_rhs_benchmarker.py

@@ -5,20 +5,12 @@
 # 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 numpy as np
 
 import myokit
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class RhsBenchmarkerTest(unittest.TestCase):
     """

myokit/tests/test_sbml_api.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
@@ -18,18 +15,6 @@ from myokit.formats.sbml._api import _MyokitConverter as X
 
 from myokit.tests import WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:  # pragma: no python 3 cover
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no python 2 cover
-    basestring = str
-
 
 class TestCompartment(unittest.TestCase):
     """
@@ -1214,7 +1199,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         c.set_initial_value(myokit.Name(p))
         mm = sm.myokit_model()
         self.assertTrue(mm.has_component('comp'))
-        self.assertEqual(mm.get('comp.size').rhs().code(), 'myokit.parameter')
+        self.assertEqual(mm.get('comp.size').rhs().code(), 'global.parameter')
         self.assertFalse(mm.get('comp.size').is_state())
 
         # Check setting size as value
@@ -1241,7 +1226,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         c.set_value(myokit.Name(p))
         mm = sm.myokit_model()
         self.assertTrue(mm.has_component('comp'))
-        self.assertEqual(mm.get('comp.size').rhs().code(), 'myokit.parameter')
+        self.assertEqual(mm.get('comp.size').rhs().code(), 'global.parameter')
         self.assertFalse(mm.get('comp.size').is_state())
 
         # Check setting size as rate
@@ -1289,9 +1274,9 @@ class SBMLTestMyokitModel(unittest.TestCase):
         m = m.myokit_model()
 
         # Check that model created parameters in 'global' component
-        self.assertTrue(m.has_variable('myokit.z'))
-        self.assertTrue(m.has_variable('myokit.boat'))
-        self.assertTrue(m.has_variable('myokit.c'))
+        self.assertTrue(m.has_variable('global.z'))
+        self.assertTrue(m.has_variable('global.boat'))
+        self.assertTrue(m.has_variable('global.c'))
 
         # Check that total number of parameters is 4 (3 parameters and time)
         self.assertEqual(m.count_variables(), 4)
@@ -1303,7 +1288,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         p = m.add_parameter('param')
         p.set_initial_value(myokit.Number(7))
         mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertFalse(pp.is_state())
         self.assertEqual(pp.rhs(), myokit.Number(7))
 
@@ -1311,7 +1296,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         self.assertIsNone(pp.unit())
         p.set_units(myokit.units.pF)
         mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertFalse(pp.is_state())
         self.assertEqual(pp.rhs(), myokit.Number(7))
         self.assertEqual(pp.unit(), myokit.units.pF)
@@ -1331,7 +1316,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         p = m.add_parameter('param')
         p.set_value(myokit.Plus(myokit.Number(7), myokit.Number(3)))
         mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertFalse(pp.is_state())
         self.assertEqual(
             pp.rhs(), myokit.Plus(myokit.Number(7), myokit.Number(3)))
@@ -1340,7 +1325,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         self.assertIsNone(pp.unit())
         p.set_units(myokit.units.pF)
         mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertFalse(pp.is_state())
         self.assertEqual(pp.rhs().code(), '7 + 3')
         self.assertEqual(pp.unit(), myokit.units.pF)
@@ -1361,24 +1346,24 @@ class SBMLTestMyokitModel(unittest.TestCase):
         p.set_value(myokit.Number(3.2), is_rate=True)
         with WarningCollector():
             mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertTrue(pp.is_state())
         self.assertEqual(pp.rhs(), myokit.Number(3.2))
-        self.assertEqual(pp.state_value(), 0)
+        self.assertEqual(pp.initial_value(as_float=True), 0)
 
         # With initial value
         p.set_initial_value(myokit.Number(1))
         mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertTrue(pp.is_state())
         self.assertEqual(pp.rhs(), myokit.Number(3.2))
-        self.assertEqual(pp.state_value(), 1)
+        self.assertEqual(pp.initial_value(as_float=True), 1)
 
         # Test units
         self.assertIsNone(pp.unit())
         p.set_units(myokit.units.pF)
         mm = m.myokit_model()
-        pp = mm.get('myokit.param')
+        pp = mm.get('global.param')
         self.assertTrue(pp.is_state())
         self.assertEqual(pp.rhs(), myokit.Number(3.2))
         self.assertEqual(pp.unit(), myokit.units.pF)
@@ -1478,7 +1463,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         mm = m.myokit_model()
         ms = mm.get('comp.spec_1_amount')
         self.assertFalse(ms.is_state())
-        self.assertEqual(ms.rhs().code(), 'myokit.p1')
+        self.assertEqual(ms.rhs().code(), 'global.p1')
 
         # Species in concentration: unreferenced parameter
         p2 = sbml.Parameter(m, 'p2')
@@ -1542,13 +1527,13 @@ class SBMLTestMyokitModel(unittest.TestCase):
         ms = mm.get('comp.spec_1_amount')
         self.assertTrue(ms.is_state())
         self.assertEqual(ms.rhs(), myokit.Number(3))
-        self.assertEqual(ms.state_value(), 0)
+        self.assertEqual(ms.initial_value(as_float=True), 0)
         s1.set_initial_value(myokit.Number(7))
         mm = m.myokit_model()
         ms = mm.get('comp.spec_1_amount')
         self.assertTrue(ms.is_state())
         self.assertEqual(ms.rhs(), myokit.Number(3))
-        self.assertEqual(ms.state_value(), 7)
+        self.assertEqual(ms.initial_value(as_float=True), 7)
 
         # Species in concentration
         s2 = m.add_species(c, 'spec_2', is_amount=False)
@@ -1562,7 +1547,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         sa = mm.get('comp.spec_2_amount')
         self.assertTrue(sa.is_state())
         self.assertEqual(sa.rhs().code(), '4 * comp.size')
-        self.assertEqual(sa.state_value(), 0)
+        self.assertEqual(sa.initial_value(as_float=True), 0)
 
         # I: Set compartment size
         m = sbml.Model()
@@ -1577,13 +1562,13 @@ class SBMLTestMyokitModel(unittest.TestCase):
         ms = mm.get('comp.spec_1_amount')
         self.assertTrue(ms.is_state())
         self.assertEqual(ms.rhs(), myokit.Number(3))
-        self.assertEqual(ms.state_value(), 0)
+        self.assertEqual(ms.initial_value(as_float=True), 0)
         s1.set_initial_value(myokit.Number(7))
         mm = m.myokit_model()
         ms = mm.get('comp.spec_1_amount')
         self.assertTrue(ms.is_state())
         self.assertEqual(ms.rhs(), myokit.Number(3))
-        self.assertEqual(ms.state_value(), 7)
+        self.assertEqual(ms.initial_value(as_float=True), 7)
 
         # Species in concentration
         s2 = m.add_species(c, 'spec_2', is_amount=False)
@@ -1599,7 +1584,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         sa = mm.get('comp.spec_2_amount')
         self.assertTrue(sa.is_state())
         self.assertEqual(sa.rhs().code(), '4 * comp.size')
-        self.assertEqual(sa.state_value(), 6 * 2)
+        self.assertEqual(sa.initial_value(as_float=True), 6 * 2)
 
     def test_species_units(self):
         # Tests whether species units are set properly.
@@ -1968,7 +1953,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         self.assertEqual(var.eval(), 5)
 
         var = mm.get('c.sr2')
-        self.assertEqual(var.state_value(), 0)
+        self.assertEqual(var.initial_value(as_float=True), 0)
         self.assertEqual(var.eval(), 3.82)
 
     def test_reaction_stoichiometries_exist(self):
@@ -2061,7 +2046,7 @@ class SBMLTestMyokitModel(unittest.TestCase):
         self.assertEqual(var.eval(), 15.23)
 
         var = mm.get('c.sr2')
-        self.assertEqual(var.state_value(), 3.5)
+        self.assertEqual(var.initial_value(as_float=True), 3.5)
         self.assertEqual(var.eval(), 9.23)
 
         # Bad value
@@ -2168,10 +2153,10 @@ class SBMLTestMyokitModel(unittest.TestCase):
         m = m.myokit_model()
 
         # Check that time variable exists
-        self.assertTrue(m.has_variable('myokit.time'))
+        self.assertTrue(m.has_variable('global.time'))
 
         # Check that unit is set
-        var = m.get('myokit.time')
+        var = m.get('global.time')
         self.assertEqual(var.unit(), myokit.units.ampere)
 
         # Check that initial value is set
@@ -2189,10 +2174,10 @@ class SBMLTestMyokitModel(unittest.TestCase):
         p = s.add_parameter('param')
         p.set_value(myokit.Plus(myokit.Number(1), myokit.Name(s.time())))
         m = s.myokit_model()
-        t = m.get('myokit.time')
+        t = m.get('global.time')
         self.assertEqual(t.unit(), myokit.units.ms)
         self.assertEqual(
-            m.get('myokit.param').rhs(),
+            m.get('global.param').rhs(),
             myokit.Plus(myokit.Number(1), myokit.Name(m.time())))
 
 

myokit/tests/test_sbml_parser.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
@@ -17,18 +14,6 @@ from myokit.formats.sbml import SBMLParser, SBMLParsingError
 
 from myokit.tests import WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:  # pragma: no python 3 cover
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no python 2 cover
-    basestring = str
-
 
 class TestSBMLParser(unittest.TestCase):
     """
@@ -913,12 +898,12 @@ class TestSBMLParser(unittest.TestCase):
         # Check species reactions (no unecessary zeros and all terms present)
         model_mmt = m.myokit_model().code()
         S1_rhs = \
-            'dot(S1_amount) = -(r1 * (size * myokit.k1 * S1_concentration)) ' \
-            + '- size * myokit.k1 * S1_concentration'
+            'dot(S1_amount) = -(r1 * (size * global.k1 * S1_concentration)) ' \
+            + '- size * global.k1 * S1_concentration'
         self.assertTrue(S1_rhs in model_mmt)
-        S2_rhs = 'dot(S2_amount) = r2 * (size * myokit.k1 * S1_concentration)'
+        S2_rhs = 'dot(S2_amount) = r2 * (size * global.k1 * S1_concentration)'
         self.assertTrue(S2_rhs in model_mmt)
-        S3_rhs = 'dot(S3_amount) = size * myokit.k1 * S1_concentration'
+        S3_rhs = 'dot(S3_amount) = size * global.k1 * S1_concentration'
         self.assertTrue(S3_rhs in model_mmt)
 
     def test_parse_rule(self):

myokit/tests/test_simulation_1d.py

@@ -5,24 +5,15 @@
 # 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
 
 from myokit.tests import DIR_DATA, CancellingReporter
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-
 # Show simulation output
 debug = False
 
@@ -31,6 +22,7 @@ class Simulation1dTest(unittest.TestCase):
     """
     Test the non-parallel 1d simulation.
     """
+
     def test_basic(self):
         # Test basic usage.
 
@@ -42,23 +34,24 @@ class Simulation1dTest(unittest.TestCase):
         s = myokit.Simulation1d(m, p, ncells=ncells)
         s.set_step_size(0.05)
 
+        x0 = m.initial_values(True)
         self.assertEqual(s.time(), 0)
-        self.assertEqual(s.state(0), m.state())
-        self.assertEqual(s.default_state(0), m.state())
+        self.assertEqual(s.state(0), x0)
+        self.assertEqual(s.default_state(0), x0)
         d = s.run(5, log_interval=1)
         self.assertEqual(s.time(), 5)
-        self.assertNotEqual(s.state(0), m.state())
-        self.assertEqual(s.default_state(0), m.state())
+        self.assertNotEqual(s.state(0), x0)
+        self.assertEqual(s.default_state(0), x0)
 
         # Test full state getting and reset
-        self.assertEqual(s.default_state(), m.state() * ncells)
-        self.assertNotEqual(s.state(), m.state() * ncells)
+        self.assertEqual(s.default_state(), x0 * ncells)
+        self.assertNotEqual(s.state(), x0 * ncells)
         s.reset()
         self.assertEqual(s.state(), s.default_state())
 
         # Test pre updates the default state.
         s.pre(1)
-        self.assertNotEqual(s.default_state(0), m.state())
+        self.assertNotEqual(s.default_state(0), x0)
 
         # Test running without a protocol
         s.set_protocol(None)
@@ -103,6 +96,31 @@ class Simulation1dTest(unittest.TestCase):
         s.set_time(100)
         self.assertEqual(s.time(), 100)
 
+    def test_initial_value_expressions(self):
+        # Test if initial value expressions are converted to floats
+        m = myokit.parse_model('''
+            [[model]]
+            c.x = 1 + sqrt(3)
+            c.y = 1 / c.p
+            c.z = 3
+
+            [c]
+            t = 0 bind time
+            dot(x) = 1 label membrane_potential
+            dot(y) = 2
+            dot(z) = 3
+            p = log(3)
+            q = 0 bind diffusion_current
+        ''')
+        s = myokit.Simulation1d(m, ncells=2)
+        x = s.state()
+        self.assertIsInstance(x[0], float)
+        self.assertIsInstance(x[1], float)
+        self.assertIsInstance(x[2], float)
+        self.assertEqual(x[:3], x[3:])
+        self.assertEqual(x, m.initial_values(True) * 2)
+        self.assertEqual(x, s.default_state())
+
     def test_with_progress_reporter(self):
         # Test running with a progress reporter.
         m, p, _ = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
@@ -130,7 +148,8 @@ class Simulation1dTest(unittest.TestCase):
         n = 4
 
         s = myokit.Simulation1d(m, p, n)
-        self.assertEqual(s.state(), m.state() * n)
+        x0 = m.initial_values(True)
+        self.assertEqual(s.state(), x0 * n)
 
         # Test setting a full state
         sx = [0] * 8 * n
@@ -142,8 +161,8 @@ class Simulation1dTest(unittest.TestCase):
         sx = [0] * 8
         s.set_state(sx)
         self.assertEqual(s.state(), sx * n)
-        s.set_state(m.state())
-        self.assertEqual(s.state(), m.state() * n)
+        s.set_state(x0)
+        self.assertEqual(s.state(), x0 * n)
 
         # Test setting a single state
         j = 1
@@ -152,7 +171,7 @@ class Simulation1dTest(unittest.TestCase):
             if i == j:
                 self.assertEqual(s.state(i), sx)
             else:
-                self.assertEqual(s.state(i), m.state())
+                self.assertEqual(s.state(i), x0)
 
         # Invalid cell index
         s.set_state(sx, 0)
@@ -167,7 +186,7 @@ class Simulation1dTest(unittest.TestCase):
         n = 4
 
         s = myokit.Simulation1d(m, p, n)
-        self.assertEqual(s.state(), m.state() * n)
+        self.assertEqual(s.state(), m.initial_values(True) * n)
 
         # Test setting a full state
         sx = [0] * 8 * n
@@ -179,8 +198,9 @@ class Simulation1dTest(unittest.TestCase):
         sx = [0] * 8
         s.set_default_state(sx)
         self.assertEqual(s.default_state(), sx * n)
-        s.set_default_state(m.state())
-        self.assertEqual(s.default_state(), m.state() * n)
+        sy = m.initial_values(True)
+        s.set_default_state(sy)
+        self.assertEqual(s.default_state(), sy * n)
 
         # Test setting a single state
         j = 1
@@ -189,7 +209,7 @@ class Simulation1dTest(unittest.TestCase):
             if i == j:
                 self.assertEqual(s.default_state(i), sx)
             else:
-                self.assertEqual(s.default_state(i), m.state())
+                self.assertEqual(s.default_state(i), sy)
 
         # Invalid cell index
         s.set_default_state(sx, 0)