myokit 1.34.0__py3-none-any.whl → 1.35.0__py3-none-any.whl

myokit/gui/vargrapher.py

@@ -4,23 +4,13 @@
 # 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
-
-# Standard library imports
-
-# Myokit
 import myokit
+import myokit.gui
 
-# Qt imports
 from myokit.gui import QtGui, QtWidgets
 
-# NumPy
 import numpy as np
 
-# GUI components
-import myokit.gui
-
 # Matplotlib (must be imported _after_ gui has had chance to set backend)
 import matplotlib
 import matplotlib.figure
@@ -50,7 +40,7 @@ class VarGrapher(QtWidgets.QDialog):
     *Extends:* ``QtWidgets.QDialog``
     """
     def __init__(self, parent, title, var, func, args):
-        super(VarGrapher, self).__init__(parent)
+        super().__init__(parent)
         self.setFixedSize(700, 600)
         self.setWindowTitle(title)
 

myokit/lib/deps.py

@@ -5,12 +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 random
 import collections
+import random
+
 import myokit
+
 # Don't import pyplot yet, this will crash if no window environment is loaded
 
 
@@ -174,7 +173,7 @@ def plot_state_dependency_matrix(
     return a
 
 
-class DiGraph(object):
+class DiGraph:
     """
     A simple directed graph implementation.
 
@@ -182,7 +181,7 @@ class DiGraph(object):
     for example ``matrix=[[0, 1, 1], [0, 1, 0], [0, 0, 0]]``
     """
     def __init__(self, matrix=None):
-        super(DiGraph, self).__init__()
+        super().__init__()
         if isinstance(matrix, DiGraph):
             # Clone
             self.nodes = collections.OrderedDict()
@@ -526,7 +525,7 @@ class DiGraph(object):
         return test
 
 
-class Node(object):
+class Node:
     """
     Defines a node in a graph
     """
@@ -534,7 +533,7 @@ class Node(object):
         """
         Creates a new, graphless node with the given identifier
         """
-        super(Node, self).__init__()
+        super().__init__()
         self.graph = None
         self.uid = uid
         self.edgo = set()

myokit/lib/guess.py

@@ -5,9 +5,8 @@
 # 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 collections
+
 import myokit
 
 

myokit/lib/hh.py

@@ -4,14 +4,12 @@
 # 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 numpy as np
+
 import myokit
 
 
-class HHModel(object):
+class HHModel:
     """
     Represents a Hodgkin-Huxley (HH)-style model of an ion channel, extracted
     from a :class:`myokit.Model`.
@@ -94,7 +92,7 @@ class HHModel(object):
     # A HHModel can return a function to calculate state values, but it never
     # updates its internal state in any way.
     def __init__(self, model, states, parameters=None, current=None, vm=None):
-        super(HHModel, self).__init__()
+        super().__init__()
 
         #
         # Check input
@@ -533,7 +531,7 @@ class HHModel(object):
         return self._steady_state_function(*inputs)
 
 
-class AnalyticalSimulation(object):
+class AnalyticalSimulation:
     """
     Analytically evaluates a :class:`HHModel`'s state for a given set of points
     in time.
@@ -583,7 +581,7 @@ class AnalyticalSimulation(object):
 
     """
     def __init__(self, model, protocol=None):
-        super(AnalyticalSimulation, self).__init__()
+        super().__init__()
 
         # Check model
         if not isinstance(model, HHModel):

myokit/lib/markov.py

@@ -4,16 +4,14 @@
 # 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 collections
+
 import numpy as np
 
 import myokit
 
 
-class LinearModel(object):
+class LinearModel:
     """
     Represents a linear Markov model of an ion channel extracted from a
     :class:`myokit.Model`.
@@ -120,7 +118,7 @@ class LinearModel(object):
     # for its default values or newly passed in values, but it never updates
     # its internal state in any way!
     def __init__(self, model, states, parameters=None, current=None, vm=None):
-        super(LinearModel, self).__init__()
+        super().__init__()
 
         # Get a clone of the model, with all markov models written in full ODE
         # form.
@@ -389,7 +387,7 @@ class LinearModel(object):
         globl = {'numpy': np, 'n': n}
         local = {}
 
-        myokit._exec(code, globl, local)
+        exec(code, globl, local)
         self._matrix_function = local['matrix_function']
 
         #
@@ -408,7 +406,7 @@ class LinearModel(object):
         code = head + '\n' + '\n'.join(['    ' + line for line in body])
         globl = {'numpy': np}
         local = {}
-        myokit._exec(code, globl, local)
+        exec(code, globl, local)
         self._rate_list_function = local['rate_list_function']
 
     def current(self):
@@ -635,7 +633,7 @@ class LinearModel(object):
         return x
 
 
-class AnalyticalSimulation(object):
+class AnalyticalSimulation:
     """
     Analytically evaluates a :class:`LinearModel`'s state over a given set of
     points in time.
@@ -689,7 +687,7 @@ class AnalyticalSimulation(object):
 
     """
     def __init__(self, model, protocol=None):
-        super(AnalyticalSimulation, self).__init__()
+        super().__init__()
         # Check model
         if not isinstance(model, LinearModel):
             raise ValueError('First parameter must be a `LinearModel`.')
@@ -1093,7 +1091,7 @@ class AnalyticalSimulation(object):
         return list(self._state)
 
 
-class DiscreteSimulation(object):
+class DiscreteSimulation:
     """
     Performs stochastic simulations of a :class:`LinearModel`'s behavior for a
     finite number of channels.
@@ -1563,7 +1561,7 @@ class DiscreteSimulation(object):
         return list(self._state)
 
 
-class MarkovModel(object):
+class MarkovModel:
     """
     **Deprecated**: This class has been replaced by the classes
     :class:`LinearModel` and :class:`AnalyticalSimulation`. Please update your

myokit/lib/multi.py

@@ -4,11 +4,9 @@
 # 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 myokit
-import os
 
 
 #

myokit/lib/plots.py

@@ -5,10 +5,8 @@
 # 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 numpy as np
+
 # Don't import pyplot yet, this will cause a crash if no window environment
 # is loaded.
 

myokit/pacing.py

@@ -4,9 +4,6 @@
 # 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 myokit
 """
 This module contains factory methods to create Protocol objects

myokit/pype.py

@@ -4,25 +4,14 @@
 # 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 ast
+import io
 import re
 import sys
 import traceback
 
-import myokit
-
-try:
-    # Python 2
-    from cStringIO import StringIO
-except ImportError:
-    # Python3
-    from io import StringIO
-
 
-class TemplateEngine(object):
+class TemplateEngine:
     """
     A tiny templating engine using a php style syntax.
 
@@ -40,7 +29,7 @@ class TemplateEngine(object):
     stream specified by the user.
     """
     def __init__(self):
-        super(TemplateEngine, self).__init__()
+        super().__init__()
         self.stream = None
         self.error = None
 
@@ -71,8 +60,8 @@ class TemplateEngine(object):
         script = self._convert(filename)
 
         # Get or create output stream
-        stdout = self.stream if self.stream else StringIO()
-        stderr = StringIO()
+        stdout = self.stream if self.stream else io.StringIO()
+        stderr = io.StringIO()
 
         # Run and handle errors
         error = None
@@ -84,7 +73,7 @@ class TemplateEngine(object):
                 syserr = sys.stderr
                 sys.stdout = stdout
                 sys.stderr = stderr
-                myokit._exec(script, variables)
+                exec(script, variables)
             except Exception:
                 error = sys.exc_info()
             finally:
@@ -245,5 +234,5 @@ class PypeError(Exception):
     *Extends:* Exception
     """
     def __init__(self, message):
-        super(PypeError, self).__init__(message)
+        super().__init__(message)
 

myokit/tests/__init__.py

@@ -8,9 +8,6 @@
 # The TemporaryDirectory class was adapted from Pints
 # See: https://github.com/pints-team/pints
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 import tempfile
 import warnings
@@ -43,14 +40,14 @@ if OpenCL_FOUND:
     del info
 
 
-class TemporaryDirectory(object):
+class TemporaryDirectory:
     """
     ContextManager that provides a temporary directory to create temporary
     files in. Deletes the directory and its contents when the context is
     exited.
     """
     def __init__(self):
-        super(TemporaryDirectory, self).__init__()
+        super().__init__()
         self._dir = None
 
     def __enter__(self):
@@ -138,7 +135,7 @@ class CancellingReporter(myokit.ProgressReporter):
         return self.okays >= 0
 
 
-class WarningCollector(object):
+class WarningCollector:
     """
     Wrapper around warnings.catch_warnings() that gathers all messages into a
     single string.

myokit/tests/ansic_event_based_pacing.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 myokit
@@ -26,7 +23,7 @@ class AnsicEventBasedPacing(myokit.CModule):
     _index = 0
 
     def __init__(self, protocol):
-        super(AnsicEventBasedPacing, self).__init__()
+        super().__init__()
 
         # Unique id
         AnsicEventBasedPacing._index += 1

myokit/tests/ansic_fixed_form_pacing.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 myokit
@@ -25,7 +22,7 @@ class AnsicFixedFormPacing(myokit.CModule):
     _index = 0
 
     def __init__(self, protocol):
-        super(AnsicFixedFormPacing, self).__init__()
+        super().__init__()
 
         # Unique id
         AnsicFixedFormPacing._index += 1

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?
@@ -283,7 +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(), '')
@@ -563,7 +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. """
@@ -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``. """
@@ -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):
     """