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

myokit/tests/test_aux.py

@@ -5,25 +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 io
 import os
 import re
 import unittest
 
-# StringIO in Python 2 and 3
-try:
-    from cStringIO import StringIO
-except ImportError:  # pragma: no python 2 cover
-    from io import StringIO
-
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 import myokit
 
 from myokit.tests import DIR_DATA, WarningCollector
@@ -87,7 +73,7 @@ class AuxTest(unittest.TestCase):
 
         # Test without a model
         script = myokit.default_script()
-        self.assertTrue(isinstance(script, basestring))
+        self.assertTrue(isinstance(script, str))
         self.assertIn('run(1000)', script)
 
         # Test adapting the time unit
@@ -95,29 +81,29 @@ class AuxTest(unittest.TestCase):
         t = model.add_component('c').add_variable('t')
         t.set_rhs(0)
         script = myokit.default_script(model)
-        self.assertTrue(isinstance(script, basestring))
+        self.assertTrue(isinstance(script, str))
         self.assertIn('run(1000)', script)
 
         t.set_binding('time')
         script = myokit.default_script(model)
-        self.assertTrue(isinstance(script, basestring))
+        self.assertTrue(isinstance(script, str))
         self.assertIn('run(1000)', script)
 
         t.set_unit('s')
         script = myokit.default_script(model)
-        self.assertTrue(isinstance(script, basestring))
+        self.assertTrue(isinstance(script, str))
         self.assertIn('run(1.0)', script)
 
         t.set_unit('ms')
         script = myokit.default_script(model)
-        self.assertTrue(isinstance(script, basestring))
+        self.assertTrue(isinstance(script, str))
         self.assertIn('run(1000)', script)
 
         # Test plotting membrane potential
         v = model.get('c').add_variable('v')
         v.set_label('membrane_potential')
         script = myokit.default_script(model)
-        self.assertTrue(isinstance(script, basestring))
+        self.assertTrue(isinstance(script, str))
         self.assertIn("var = 'c.v'", script)
 
         # TODO: Run with tiny model?
@@ -163,6 +149,7 @@ class AuxTest(unittest.TestCase):
             '[1] Missing User function <g(1)>.',
             '[x] Mismatched Time variable: [1]<engine.time> [2]<engine.toim>',
             '[x] Mismatched Initial value for <ina.h>',
+            '[x] Mismatched Initial value for <ina.j>',
             '[x] Mismatched State at position 5: [1]<isi.d> [2]<isiz.d>',
             '[x] Mismatched State at position 6: [1]<isi.f> [2]<isiz.f>',
             '[2] Missing state at position 7',
@@ -193,9 +180,6 @@ class AuxTest(unittest.TestCase):
             '  ' + str(len(differences)) + ' differences found',
         ]
 
-        # Show massive diff messages
-        self.maxDiff = None
-
         caught_differences = set(capture.text().splitlines())
         live = set(live)
         self.assertEqual(live, caught_differences)
@@ -276,8 +260,6 @@ class AuxTest(unittest.TestCase):
             'import myokit',
             'm = get_model()',  # Test magic methods
             'p = get_protocol()',
-            's = myokit.Simulation(m, p)',
-            's.run(200)',
         ])
         with myokit.tools.capture():
             myokit.run(m, p, x)
@@ -287,7 +269,7 @@ class AuxTest(unittest.TestCase):
 
         # Test with stringio
         x = "print('Hi there')"
-        s = StringIO()
+        s = io.StringIO()
         with myokit.tools.capture() as c:
             myokit.run(m, p, x, stderr=s, stdout=s)
         self.assertEqual(c.text(), '')
@@ -513,6 +495,9 @@ class AuxTest(unittest.TestCase):
         # Test positive/negative zero comparison
         m1 = myokit.Model()
         c = m1.add_component('c')
+        t = c.add_variable('t')
+        t.set_binding('time')
+        t.set_rhs(0)
         x = c.add_variable('x')
         x.promote(1)
         x.set_rhs('-0.0')
@@ -564,7 +549,7 @@ class AuxTest(unittest.TestCase):
 
         # Raw version
         raw = myokit.version(raw=True)
-        self.assertIsInstance(raw, basestring)
+        self.assertIsInstance(raw, str)
         parts = raw.split('.')
         self.assertTrue(len(parts) in [3, 4])
 

myokit/tests/test_cellml_v1_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
@@ -15,18 +12,6 @@ import myokit.formats.cellml.v1 as cellml
 
 from myokit.tests import WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 class TestCellML1AnnotatedElement(unittest.TestCase):
     """ Tests for cellml.AnnotatableElement. """
@@ -730,8 +715,8 @@ class TestCellML1ModelConversion(unittest.TestCase):
         # Recreate myokit model and test states
         mm = cm.myokit_model()
         mm.validate()
-        state_1 = m.state()
-        state_2 = mm.state()
+        state_1 = m.initial_values(True)
+        state_2 = mm.initial_values(True)
         states_1 = [x.name() for x in m.states()]
         states_2 = [x.name() for x in mm.states()]
         state_2 = [state_2[states_2.index(x)] for x in states_1]
@@ -830,7 +815,7 @@ class TestCellML1ModelConversion(unittest.TestCase):
 
         # Check state
         self.assertTrue(mx.is_state())
-        self.assertEqual(mx.state_value(), 0.123)
+        self.assertEqual(mx.initial_value(True), 0.123)
 
         # Check binding
         self.assertEqual(mt.binding(), 'time')
@@ -1503,7 +1488,7 @@ class TestCellML1Units(unittest.TestCase):
         names = [x for x in cellml.Units.si_unit_names()]
         self.assertTrue(len(names) > 10)
         for name in names:
-            self.assertTrue(isinstance(name, basestring))
+            self.assertTrue(isinstance(name, str))
             if name == 'celsius':
                 continue
             self.assertTrue(

myokit/tests/test_cellml_v1_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 os
 import unittest
 
@@ -20,18 +17,6 @@ from myokit.tests import TemporaryDirectory, DIR_FORMATS, WarningCollector
 # CellML directory
 DIR = os.path.join(DIR_FORMATS, 'cellml')
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 class TestCellMLParser(unittest.TestCase):
     """ Tests the CellML 1.0/1.1 parser (mostly for errors). """

myokit/tests/test_cellml_v1_writer.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 re
 import unittest
 
@@ -16,12 +13,6 @@ import myokit.formats.cellml.v1 as cellml
 
 from myokit.tests import TemporaryDirectory, WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class TestCellMLWriter(unittest.TestCase):
     """ Tests for cellml.Writer. """

myokit/tests/test_cellml_v2_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
@@ -15,18 +12,6 @@ import myokit.formats.cellml.v2 as cellml
 
 from myokit.tests import WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 class TestCellML2AnnotatableElement(unittest.TestCase):
     """ Tests for ``cellml.v2.AnnotatableElement``. """
@@ -909,8 +894,8 @@ class TestCellML2ModelConversion(unittest.TestCase):
         # Recreate myokit model and test states
         mm = cm.myokit_model()
         mm.validate()
-        state_1 = m.state()
-        state_2 = mm.state()
+        state_1 = m.initial_values(True)
+        state_2 = mm.initial_values(True)
         states_1 = [x.name() for x in m.states()]
         states_2 = [x.name() for x in mm.states()]
         state_2 = [state_2[states_2.index(x)] for x in states_1]
@@ -1013,7 +998,7 @@ class TestCellML2ModelConversion(unittest.TestCase):
 
         # Check state
         self.assertTrue(mx.is_state())
-        self.assertEqual(mx.state_value(), 0.123)
+        self.assertEqual(mx.initial_value(True), 0.123)
 
         # Check binding
         self.assertEqual(mt.binding(), 'time')
@@ -1810,7 +1795,7 @@ class TestCellML2Units(unittest.TestCase):
         names = [x for x in cellml.Units.si_unit_names()]
         self.assertTrue(len(names) > 10)
         for name in names:
-            self.assertTrue(isinstance(name, basestring))
+            self.assertTrue(isinstance(name, str))
             self.assertTrue(
                 isinstance(cellml.Units.find_units(name), cellml.Units))
 

myokit/tests/test_cellml_v2_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 os
 import unittest
 
@@ -19,18 +16,6 @@ from myokit.tests import TemporaryDirectory, DIR_FORMATS, WarningCollector
 # CellML directory
 DIR = os.path.join(DIR_FORMATS, 'cellml')
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 class TestCellMLParser(unittest.TestCase):
     """ Tests the CellML 2.0 parser (mostly for errors / model validation). """

myokit/tests/test_cellml_v2_writer.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 re
 import unittest
 
@@ -16,12 +13,6 @@ import myokit.formats.cellml.v2 as cellml
 
 from myokit.tests import TemporaryDirectory, WarningCollector
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class TestCellMLWriter(unittest.TestCase):
     """ Tests for cellml.Writer. """

myokit/tests/test_cmodel.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
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class CModelTest(unittest.TestCase):
     """
@@ -33,7 +24,10 @@ class CModelTest(unittest.TestCase):
         m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
         cls.model = m
         cls.sensitivities = (['ik1.gK1', 'ikp.IKp'], ['cell.K_o', 'ikp.gKp'])
-        cls.cmodel = myokit.CModel(cls.model, cls.sensitivities)
+        cls.pacing_labels = {}
+        cls.cmodel = myokit.CModel(
+            cls.model, cls.pacing_labels, cls.sensitivities
+        )
 
     def test_sensitivities(self):
         # Test instantiation of cmodel with sensitivities
@@ -41,14 +35,14 @@ class CModelTest(unittest.TestCase):
         # Bad type
         sens = 'Bad type'
         with self.assertRaisesRegex(ValueError, 'The argument `sensitivities'):
-            myokit.CModel(self.model, sens)
+            myokit.CModel(self.model, self.pacing_labels, sens)
 
         # Empty deps or indeps
         sens = ([], ['some parameter'])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertFalse(m.has_sensitivities)
         sens = (['some state'], [])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertFalse(m.has_sensitivities)
 
         # Provide sensitivies as Variables
@@ -57,14 +51,14 @@ class CModelTest(unittest.TestCase):
         p1 = self.model.get('cell.K_o')
         p2 = self.model.get('ikp.gKp')
         sens = ([s1, s2], [p1, p2])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertTrue(m.has_sensitivities)
 
         # Provide sensitivities as Names
         sens = (
             [myokit.Name(s1), myokit.Name(s2)],
             [myokit.Name(p1), myokit.Name(p2)])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertTrue(m.has_sensitivities)
 
         # Sensitivity of derivative
@@ -72,13 +66,13 @@ class CModelTest(unittest.TestCase):
         sens = (
             [myokit.Derivative(myokit.Name(s3)), myokit.Name(s2)],
             [myokit.Name(p1), myokit.Name(p2)])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertTrue(m.has_sensitivities)
         s3 = 'dot(ik.x)'
         sens = (
             [s3, myokit.Name(s2)],
             [myokit.Name(p1), myokit.Name(p2)])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertTrue(m.has_sensitivities)
 
         # Sensitivity of derivative of non-state
@@ -86,21 +80,21 @@ class CModelTest(unittest.TestCase):
             [myokit.Derivative(myokit.Name(s1)), myokit.Name(s2)],
             [myokit.Name(p1), myokit.Name(p2)])
         with self.assertRaisesRegex(ValueError, 'Sensitivity of '):
-            myokit.CModel(self.model, sens)
+            myokit.CModel(self.model, self.pacing_labels, sens)
 
         # Sensitivity of bound variable
         sens = (
             ['engine.time', myokit.Name(s2)],
             [myokit.Name(p1), myokit.Name(p2)])
         with self.assertRaisesRegex(ValueError, 'Sensitivities cannot'):
-            myokit.CModel(self.model, sens)
+            myokit.CModel(self.model, self.pacing_labels, sens)
 
         # Sensitivity w.r.t. Initial value
         s3 = self.model.get('ik.x')
         sens = (
             [s3, myokit.Name(s2)],
             [myokit.Name(p1), myokit.InitialValue(myokit.Name(s3))])
-        m = myokit.CModel(self.model, sens)
+        m = myokit.CModel(self.model, self.pacing_labels, sens)
         self.assertTrue(m.has_sensitivities)
 
         # Sensitivity w.r.t. initial value of non-state
@@ -108,14 +102,14 @@ class CModelTest(unittest.TestCase):
             [myokit.Name(s1), myokit.Name(s2)],
             [myokit.Name(p1), myokit.InitialValue(myokit.Name(p2))])
         with self.assertRaisesRegex(ValueError, 'Sensitivity with respect to'):
-            myokit.CModel(self.model, sens)
+            myokit.CModel(self.model, self.pacing_labels, sens)
 
         # Sensitivity w.r.t. non-literal
         sens = (
             [myokit.Name(s1), myokit.Name(s2)],
             [myokit.Name(p1), 'ik.E'])
         with self.assertRaisesRegex(ValueError, 'Sensitivity with respect to'):
-            myokit.CModel(self.model, sens)
+            myokit.CModel(self.model, self.pacing_labels, sens)
 
 
 if __name__ == '__main__':

myokit/tests/test_compiler_detection.py

@@ -5,28 +5,18 @@
 # 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
 
 
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
-
 class CompilerDetectionTest(unittest.TestCase):
     """
     Tests the compiler detection.
     """
     def test_compiler(self):
         # Test the compiler detection.
-        self.assertIsInstance(myokit.Compiler.info(), basestring)
+        self.assertIsInstance(myokit.Compiler.info(), str)
 
 
 if __name__ == '__main__':