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

myokit/tests/test_expressions.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 pickle
 import unittest
 
@@ -15,12 +12,6 @@ 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
-
 
 # Unit --> See test_units.py
 # Quantity --> See test_units.py

myokit/tests/test_float.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 sys
 import unittest
 
@@ -91,8 +88,7 @@ class FloatTest(unittest.TestCase):
         # Test float to string conversion.
 
         # String should be passed through
-        # Note: convert to str() to test in python 2 and 3.
-        self.assertEqual(myokit.float.str(str('123')), '123')
+        self.assertEqual(myokit.float.str('123'), '123')
 
         # Simple numbers
         self.assertEqual(myokit.float.str(0), '0')

myokit/tests/test_formats.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.formats
 
 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 FormatsTest(unittest.TestCase):
     """

myokit/tests/test_formats_axon.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.formats.axon as axon
 
 from myokit.tests import TemporaryDirectory, DIR_FORMATS
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class AbfTest(unittest.TestCase):
     """

myokit/tests/test_formats_cellml.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 re
 import unittest
@@ -23,18 +20,6 @@ from myokit.tests import TemporaryDirectory, DIR_FORMATS, WarningCollector
 # CellML dir
 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 Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no python 2 cover
-    basestring = str
-
 
 class CellMLExporterTest(unittest.TestCase):
     """

myokit/tests/test_formats_channelml.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 DIR_FORMATS, WarningCollector
 # ChannelML dir
 DIR = os.path.join(DIR_FORMATS, 'channelml')
 
-# 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 ChannelMLTest(unittest.TestCase):
     """ Test ChannelML importing. """

myokit/tests/test_formats_easyml.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
 
@@ -17,17 +14,6 @@ import myokit.formats.easyml
 
 from myokit.tests import TemporaryDirectory, WarningCollector, DIR_DATA
 
-# 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
 
 # Model that requires unit conversion
 units_model = """

myokit/tests/test_formats_exporters.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
 
@@ -16,18 +13,6 @@ import myokit.formats
 
 from myokit.tests import TemporaryDirectory
 
-# 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 ExportTest(unittest.TestCase):
     """
@@ -38,7 +23,7 @@ class ExportTest(unittest.TestCase):
         """ Test a given exporter `e`. """
 
         # Test info method.
-        self.assertIsInstance(e.post_export_info(), basestring)
+        self.assertIsInstance(e.post_export_info(), str)
 
         # Load model, protocol
         m, p = model, protocol

myokit/tests/test_formats_expression_writers.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
@@ -20,19 +17,6 @@ import myokit.formats.python
 import myokit.formats.stan
 
 
-# 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 ExpressionWriterTest(unittest.TestCase):
     """ Test shared expression writer functionality. """
 
@@ -45,7 +29,7 @@ class ExpressionWriterTest(unittest.TestCase):
 
         # Create one of each
         for e in es:
-            self.assertIsInstance(e, basestring)
+            self.assertIsInstance(e, str)
             e = myokit.formats.ewriter(e)
             self.assertTrue(isinstance(e, myokit.formats.ExpressionWriter))
 

myokit/tests/test_formats_html.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.formats.html

myokit/tests/test_formats_importers.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
 
@@ -16,18 +13,6 @@ import myokit.formats as formats
 
 from myokit.tests import DIR_FORMATS
 
-# 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 ImporterTest(unittest.TestCase):
     """ Test shared importer functionality. """
@@ -37,7 +22,7 @@ class ImporterTest(unittest.TestCase):
         ims = myokit.formats.importers()
         self.assertTrue(len(ims) > 0)
         for i in ims:
-            self.assertIsInstance(i, basestring)
+            self.assertIsInstance(i, str)
             i = myokit.formats.importer(i)
             self.assertTrue(isinstance(i, myokit.formats.Importer))
 

myokit/tests/test_formats_mathml_content.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 lxml.etree as etree
 import myokit
 import myokit.formats.mathml as mathml
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class ContentMathMLParserTest(unittest.TestCase):
     """ Tests content MathML parsing. """

myokit/tests/test_formats_mathml_presentation.py

@@ -5,21 +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 re
 import unittest
 
 import myokit
 import myokit.formats.mathml as mathml
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class PresentationMathMLTest(unittest.TestCase):
     """

myokit/tests/test_formats_opencl.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
@@ -15,13 +12,6 @@ import myokit.formats
 import myokit.formats.opencl
 
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:  # pragma: no python 3 cover
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
-
 class OpenCLExpressionWriterTest(unittest.TestCase):
     """ Test the OpenCL ewriter class. """
 

myokit/tests/test_formats_sbml.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 @@ import myokit.formats.sbml
 # from shared import DIR_FORMATS, WarningCollector
 from myokit.tests import DIR_FORMATS, 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 SBMLImporterTest(unittest.TestCase):
     """

myokit/tests/test_formats_sympy.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.formats.sympy as mypy
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class SymPyReadWriteTest(unittest.TestCase):
     """

myokit/tests/test_formats_wcp.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.formats.wcp as wcp

myokit/tests/test_io.py

@@ -6,23 +6,15 @@
 # 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, TemporaryDirectory
 
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:
-    basestring = str
-
 
 class LoadSaveMmtTest(unittest.TestCase):
     """Tests load/save functions for mmt files."""
@@ -105,7 +97,7 @@ class LoadSaveMmtTest(unittest.TestCase):
         m, p, x = myokit.load(spath)
         self.assertIsNone(m)
         self.assertIsNone(p)
-        self.assertTrue(isinstance(x, basestring))
+        self.assertTrue(isinstance(x, str))
 
         self.assertRaises(
             myokit.SectionNotFoundError, myokit.load_model, ppath)
@@ -128,7 +120,7 @@ class LoadSaveMmtTest(unittest.TestCase):
         m, p, x = myokit.load('example')
         self.assertIsInstance(m, myokit.Model)
         self.assertIsInstance(p, myokit.Protocol)
-        self.assertTrue(isinstance(x, basestring))
+        self.assertTrue(isinstance(x, str))
 
         # Save all three and reload
         with TemporaryDirectory() as d:
@@ -255,6 +247,12 @@ class LoadSaveMmtTest(unittest.TestCase):
                 text = f.read()
             self.assertEqual(text, myokit.save(model=m, protocol=p, script=x))
 
+        # Save nothing
+        with TemporaryDirectory() as d:
+            opath = d.path('test.mmt')
+            self.assertRaises(ValueError, myokit.save, opath)
+            self.assertFalse(os.path.exists(opath))
+
     def test_save_model(self):
         # Test if the correct parts are saved/loaded from disk using the
         # ``save_model()`` method.
@@ -312,10 +310,10 @@ class LoadSaveMmtTest(unittest.TestCase):
         ipath = os.path.join(DIR_DATA, 'lr-1991.mmt')
         # Test example loading
         x = myokit.load_script('example')
-        self.assertTrue(isinstance(x, basestring))
+        self.assertTrue(isinstance(x, str))
         # Test file loading
         x = myokit.load_script(ipath)
-        self.assertTrue(isinstance(x, basestring))
+        self.assertTrue(isinstance(x, str))
         with TemporaryDirectory() as d:
             opath = d.path('test.mmt')
             myokit.save_script(opath, x)
@@ -327,7 +325,7 @@ class LoadSaveMmtTest(unittest.TestCase):
             self.assertTrue('[[script]]' in text)
             # Test reloading
             xx = myokit.load_script(opath)
-            self.assertTrue(isinstance(xx, basestring))
+            self.assertTrue(isinstance(xx, str))
             self.assertEqual(x, xx)
 
 
@@ -340,22 +338,22 @@ class LoadSaveStateTest(unittest.TestCase):
         with TemporaryDirectory() as d:
             # Test save and load without model
             f = d.path('state.txt')
-            myokit.save_state(f, m.state())
-            self.assertEqual(myokit.load_state(f), m.state())
+            myokit.save_state(f, m.initial_values(True))
+            self.assertEqual(myokit.load_state(f), m.initial_values(True))
 
             # Test save and load with model argument
-            myokit.save_state(f, m.state(), m)
-            self.assertEqual(myokit.load_state(f, m), m.state())
+            myokit.save_state(f, m.initial_values(True), m)
+            self.assertEqual(myokit.load_state(f, m), m.initial_values(True))
 
             # Save without, load with model
-            myokit.save_state(f, m.state())
-            self.assertEqual(myokit.load_state(f, m), m.state())
+            myokit.save_state(f, m.initial_values(True))
+            self.assertEqual(myokit.load_state(f, m), m.initial_values(True))
 
             # Save with model, load without
             # Loaded version is dict!
-            myokit.save_state(f, m.state(), m)
-            dct = dict(zip([v.qname() for v in m.states()], m.state()))
-            self.assertEqual(myokit.load_state(f), dct)
+            myokit.save_state(f, m.initial_values(True), m)
+            self.assertEqual(myokit.load_state(f), dict(zip(
+                [v.qname() for v in m.states()], m.initial_values(True))))
 
     def test_load_save_state_bin(self):
         # Test loading/saving state in binary format.
@@ -364,13 +362,15 @@ class LoadSaveStateTest(unittest.TestCase):
 
             # Test save and load with double precision
             f = d.path('state.bin')
-            myokit.save_state_bin(f, m.state())
-            self.assertEqual(myokit.load_state_bin(f), m.state())
+            myokit.save_state_bin(f, m.initial_values(True))
+            self.assertEqual(myokit.load_state_bin(f), m.initial_values(True))
 
             # Test save and load with single precision
             f = d.path('state.bin')
-            myokit.save_state_bin(f, m.state(), myokit.SINGLE_PRECISION)
-            d = np.array(myokit.load_state_bin(f)) - np.array(m.state())
+            myokit.save_state_bin(
+                f, m.initial_values(True), myokit.SINGLE_PRECISION)
+            d = np.array(myokit.load_state_bin(f))
+            d -= np.array(m.initial_values(True))
             self.assertTrue(np.all(np.abs(d) < 1e-5))   # Not very precise!
 
 

myokit/tests/test_jacobian_calculator.py

@@ -5,23 +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
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class JacobianCalculatorTest(unittest.TestCase):
     """
@@ -37,16 +29,16 @@ class JacobianCalculatorTest(unittest.TestCase):
 
         # Test if still runs with initial x all zero
         # (But does cause a linear algebra issue in this case)
-        x = np.zeros(len(m.state()))
+        x = np.zeros(m.count_states())
         c.newton_root(x, damping=0.01, max_iter=50)
 
         # Test if still works with a single zero (Enno's bug)
-        x = np.array(m.state())
+        x = np.array(m.initial_values(True))
         x[1] = 0
         x, f, j, e = c.newton_root(x, damping=0.01, max_iter=50)
 
         # Test quick return
-        x = np.array(m.state())
+        x = np.array(m.initial_values(True))
         x[0] = 0
         x2, f, j, e = c.newton_root(damping=0.01, max_iter=1)
         self.assertTrue(np.sum((x2 - x)**2) > 10)
@@ -58,12 +50,12 @@ class JacobianCalculatorTest(unittest.TestCase):
             ValueError, 'Damping', c.newton_root, damping=1.1)
 
         # Missing a state
-        x = m.state()[:-1]
+        x = m.initial_values(True)[:-1]
         self.assertRaisesRegex(
             ValueError, 'must have length', c.calculate, x)
 
         # Non-numbers in state
-        x = m.state()
+        x = m.initial_values(True)
         x[0] = 'Hello'
         self.assertRaisesRegex(
             ValueError, 'floats', c.calculate, x)

myokit/tests/test_jacobian_tracer.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 JacobianTracerTest(unittest.TestCase):
     """

myokit/tests/test_lib_deps.py

@@ -5,21 +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 random
 import unittest
 
 import myokit
 import myokit.lib.deps as deps
 
-# Unit testing in Python 2 and 3
-try:
-    unittest.TestCase.assertRaisesRegex
-except AttributeError:
-    unittest.TestCase.assertRaisesRegex = unittest.TestCase.assertRaisesRegexp
-
 
 class LibDepsTest(unittest.TestCase):