myokit 1.33.9__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
 
 
@@ -52,7 +51,7 @@ def create_state_dependency_matrix(model, direct=False, knockout=None):
             v = model.get(v, class_filter=myokit.Variable)
             if not v.is_state():
                 raise ValueError('Knockout variables must be states.')
-            iknock.append(v.indice())
+            iknock.append(v.index())
 
     # Create matrix of direct dependencies
     m = []
@@ -61,7 +60,7 @@ def create_state_dependency_matrix(model, direct=False, knockout=None):
         if i not in iknock:
             for dep in deep[var.lhs()]:
                 if dep.var().is_state():
-                    j = dep.var().indice()
+                    j = dep.var().index()
                     if j not in iknock:
                         row[j] = 1
         m.append(row)
@@ -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()
@@ -455,7 +454,7 @@ class DiGraph(object):
         for n_runs in range(max_runs):
             change = False
             for i, layer in enumerate(layers):
-                # Set nodes to median of neighbours
+                # Set nodes to median of neighbors
                 for j, node in enumerate(layer):
                     n = len(node.edgi) + len(node.edgo)
                     if n > 0:
@@ -493,8 +492,8 @@ class DiGraph(object):
                             x2 = None
                             for k in range(j + 1, n):
                                 if abs(layer[k].x - node.x) >= too_close:
-                                    x2 = layer[k].x
-                                    break
+                                    x2 = layer[k].x     # pragma: no cover
+                                    break               # pragma: no cover
                                 eq.append(layer[k])
                             if x2 is None:
                                 x2 = 1.0
@@ -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
 
 
@@ -392,7 +391,7 @@ def membrane_potential(model):
     # Common units for the membrane potential
     common_units = [myokit.units.V]
 
-    # Non-dimensionalised (e.g. Mitchell-Schaeffer) use [1]
+    # Non-dimensionalized (e.g. Mitchell-Schaeffer) use [1]
     # But this causes too many false positives
     # common_units.append(myokit.units.dimensionless)
 
@@ -581,7 +580,7 @@ def stimulus_current(model):
         myokit.units.A / myokit.units.m**2,
     ]
 
-    # Non-dimensionalised (e.g. Mitchell-Schaeffer) use [mS/uF]
+    # Non-dimensionalized (e.g. Mitchell-Schaeffer) use [mS/uF]
     # But this causes too many false positives
     # common_units.append(myokit.units.S / myokit.units.F)
 

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`.
@@ -29,7 +27,8 @@ class HHModel(object):
     The model variables to treat as parameter are specified by the user when
     the model is created. Any other variables, for example state variables such
     as intercellular calcium or constants such as temperature, are fixed when
-    the current model is created and can no longer be changed.
+    the current model is created and can no longer be changed. Initial values
+    written as expressions are evaluated when the model is made.
 
     The current variable is optional.
 
@@ -83,7 +82,7 @@ class HHModel(object):
         # Load a model from disk
         model = myokit.load_model('some-model.mmt')
 
-        # Extract a markov model
+        # Extract a Hodgkin-Huxley style channel model
         mm = hh.HHModel.from_component(model.get('ina'))
 
     """
@@ -93,7 +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
@@ -183,15 +182,18 @@ class HHModel(object):
                 'The membrane potential should not be the current variable.')
         del vm
 
+        # Get values of all states
+        # Note: Do this _before_ changing the model!
+        s = self._model.initial_values(True)
+        self._model.set_initial_values(s)  # Remove expressions
+        self._default_state = np.array(
+            [v.initial_value(True) for v in self._states])
+
         #
         # Demote unnecessary states and remove bindings
         #
-        # Get values of all states
-        # Note: Do this _before_ changing the model!
-        self._default_state = np.array([v.state_value() for v in self._states])
 
         # Freeze remaining, non-current-model states
-        s = self._model.state()   # Get state values before changing anything!
         # Note: list() cast is required so that we iterate over a static list,
         # otherwise we can get issues because the iterator depends on the model
         # (which we're changing).
@@ -346,19 +348,19 @@ class HHModel(object):
 
     def default_membrane_potential(self):
         """
-        Returns this markov model's default membrane potential value.
+        Returns this HH model's default membrane potential value.
         """
         return self._default_inputs[0]
 
     def default_parameters(self):
         """
-        Returns this markov model's default parameter values
+        Returns this HH model's default parameter values
         """
         return list(self._default_inputs[1:])
 
     def default_state(self):
         """
-        Returns this markov model's default state values.
+        Returns this HH model's default state values.
         """
         return list(self._default_state)
 
@@ -389,8 +391,8 @@ class HHModel(object):
             # Get state variables
             states = [x for x in component.variables(state=True)]
 
-            # Sort by state indice
-            states.sort(key=lambda x: x.indice())
+            # Sort by state index
+            states.sort(key=lambda x: x.index())
 
         else:
 
@@ -529,7 +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.
@@ -579,7 +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`.
@@ -37,7 +35,8 @@ class LinearModel(object):
     The model variables to treat as parameter are specified by the user when
     the model is created. Any other variables, for example state variables such
     as intercellular calcium or constants such as temperature, are fixed when
-    the markov model is created and can no longer be changed.
+    the markov model is created and can no longer be changed. Initial values
+    written as expressions are evaluated when the model is made.
 
     To create a :class:`Markov`, pass in a :class:`myokit.Model` and select a
     list of states. All other states will be fixed at their current value and
@@ -119,7 +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.
@@ -205,15 +204,17 @@ class LinearModel(object):
                 'The membrane potential should not be the current variable.')
         del vm
 
+        # Get values of all states
+        # Note: Do this _before_ changing the model!
+        s = self._model.initial_values(True)
+        self._default_state = np.array(
+            [v.initial_value(True) for v in self._states])
+
         #
         # Demote unnecessary states, remove bindings and validate model.
         #
-        # Get values of all states
-        # Note: Do this _before_ changing the model!
-        self._default_state = np.array([v.state_value() for v in self._states])
 
         # Freeze remaining, non-markov-model states
-        s = self._model.state()   # Get state values before changing anything!
         for k, state in enumerate(self._model.states()):
             if state not in self._states:
                 state.demote()
@@ -386,7 +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']
 
         #
@@ -405,7 +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):
@@ -460,8 +461,8 @@ class LinearModel(object):
             # Get state variables
             states = [x for x in component.variables(state=True)]
 
-            # Sort by state indice
-            states.sort(key=lambda x: x.indice())
+            # Sort by state index
+            states.sort(key=lambda x: x.index())
 
         else:
 
@@ -632,7 +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.
@@ -686,7 +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`.')
@@ -1090,7 +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.
@@ -1225,7 +1226,7 @@ class DiscreteSimulation(object):
                 ' equal 1.')
         y = np.round(x * self._nchannels)
         # To make sure it always sums to 1, correct the value found at the
-        # indice with the biggest rounding error.
+        # index with the biggest rounding error.
         i = np.argmax(np.abs(x - y))
         y[i] = 0
         y[i] = self._nchannels - np.sum(y)
@@ -1560,7 +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
@@ -1701,7 +1702,7 @@ def _split_factor(term, variables):
                 'Non-linear function of ' + str(name) + ' found in '
                 + str(term) + '.')
 
-    # Finalise multiplier
+    # Finalize multiplier
     if m is None:
         m = myokit.Number(1)
     if not positive:

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.
 
@@ -265,7 +263,8 @@ def current_arrows(log, voltage, currents, axes=None):
 
 def cumulative_current(
         log, currents, axes=None, labels=None, colors=None, integrate=False,
-        normalise=False, max_currents=None, line_args={}, fill_args={}):
+        normalize=False, max_currents=None, line_args={}, fill_args={},
+        normalise=None):
     """
     Plots a number of currents, one on top of the other, with the positive and
     negative parts of the current plotted separately.
@@ -291,8 +290,8 @@ def cumulative_current(
         current.
     ``integrate``
         Set this to ``True`` to plot total carried charge instead of currents.
-    ``normalise``
-        Set this to ``True`` to normalise the graph at every point, so that the
+    ``normalize``
+        Set this to ``True`` to normalize the graph at every point, so that the
         relative contribution of each current is shown.
     ``max_currents``
         Set this to any integer n to display only the first n currents, and
@@ -310,6 +309,15 @@ def cumulative_current(
     import matplotlib
     import matplotlib.pyplot as plt
 
+    # Deprecated on 2023-06-7
+    if normalize is not None:
+        import warnings
+        warnings.warn(
+            'The keyword argument `normalise` is deprecated. Please use'
+            ' `normalize` instead.')
+        normalize = normalise
+    del normalise
+
     # Get axes
     if axes is None:
         axes = plt.gca()
@@ -330,8 +338,8 @@ def cumulative_current(
     neg = np.minimum(pos, 0)
     pos = np.maximum(pos, 0)
 
-    # Normalise
-    if normalise:
+    # Normalize
+    if normalize:
         pos /= np.maximum(np.sum(pos, axis=0), 1e-99)
         neg /= -np.minimum(np.sum(neg, axis=0), -1e-99)
 
@@ -350,7 +358,10 @@ def cumulative_current(
             colors.extend(colors)
     else:
         # Colormap
-        cmap = matplotlib.cm.get_cmap(name='tab20')
+        try:
+            cmap = matplotlib.colormaps['tab20']
+        except AttributeError:  # pragma: no cover
+            cmap = matplotlib.cm.get_cmap(name='tab20')
         colors = [cmap(i) for i in range(nc)]
 
     # Line drawing keyword arguments

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
@@ -24,8 +21,8 @@ class AnsicFixedFormPacing(myokit.CModule):
     """
     _index = 0
 
-    def __init__(self, times=None, values=None):
-        super(AnsicFixedFormPacing, self).__init__()
+    def __init__(self, protocol):
+        super().__init__()
 
         # Unique id
         AnsicFixedFormPacing._index += 1
@@ -43,7 +40,7 @@ class AnsicFixedFormPacing(myokit.CModule):
         self._sys = self._compile(module_name, fname, args, libs, libd, incd)
 
         # Initialize
-        self._sys.init(times, values)
+        self._sys.init(protocol)
 
     def pace(self, time):
         return self._sys.pace(time)

myokit/tests/data/beeler-1977-model-compare-b.mmt

@@ -2,7 +2,7 @@
 name: beeler-1977-with-differences
 desc: """
     The 1997 Beeler Reuter model of the AP in ventricular myocytes.
-    
+
     This test version has some differences
 
     Reference:
@@ -18,7 +18,7 @@ membrane.V  = -84.622
 calcium.Cai = 2e-7
 ina.m       = 0.01
 ina.h       = 1.0
-ina.j       = 0.98
+ina.j       = 0.97 + 0.01
 isiz.d       = 0.003
 isiz.f       = 1.0
 

myokit/tests/data/clancy-1999-fitting.mmt

@@ -143,6 +143,7 @@ dot(O)  = -O  * (a2  + b13     ) + C1 * a13 + IF * b2
 dot(IF) = -IF * (a4  + b2  + a3) + IS * b4  + O  * a2  + C1 * b3
 dot(IS) = -IS * (b4            ) + IF * a4
 i = gmax * O * (V - E)
+p = 1e-4
 
 [[protocol]]
 # Level  Start    Length   Period   Multiplier