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

myokit/formats/python/__init__.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
-
 from ._exporter import PythonExporter
 from ._ewriter import PythonExpressionWriter, NumPyExpressionWriter
 

myokit/formats/python/_ewriter.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.formats
 
 
@@ -17,7 +14,7 @@ class PythonExpressionWriter(myokit.formats.ExpressionWriter):
     equivalent.
     """
     def __init__(self):
-        super(PythonExpressionWriter, self).__init__()
+        super().__init__()
 
         self._flhs = None
         self.set_lhs_function(lambda v: str(v))
@@ -192,7 +189,7 @@ class NumPyExpressionWriter(PythonExpressionWriter):
     intended for use in NumPy arrays.
     """
     def __init__(self):
-        super(NumPyExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = 'numpy.'
     #def _ex_name(self, e):
     #def _ex_derivative(self, e):

myokit/formats/python/_exporter.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 os
 
 import myokit.formats

myokit/formats/python/template/sim.py

@@ -45,7 +45,7 @@ w.set_lhs_function(v)
 e = w.eq
 
 # Process bindings
-bound_variables = model.prepare_bindings({
+bound_variables = myokit._prepare_bindings(model, {
     'time' : 'engine.time',
     'pace' : 'engine.pace',
     })
@@ -73,7 +73,7 @@ for comp in components:
     w.set_lhs_function(lambda x: v(x, comp))
 
     ?>
-class <?= names[1] ?>(object):
+class <?= names[1] ?>:
     def __init__(self):
 <?
     for var in comp.variables(deep=True):
@@ -96,9 +96,9 @@ class <?= names[1] ?>(object):
         Resets the state variables to their initial values
         """
 <?
-    for eq in model.inits():
-        if eq.lhs.var().parent() == comp:
-            print(tab2 + e(eq))
+    for var, value in zip(model.states(), model.initial_values(True)):
+        if var.parent() == comp:
+            print(tab2 + v(var, comp) + ' = ' + myokit.float.str(value))
     ?>    def update(self):
         """
         Re-calculates all values for the current time and state
@@ -118,7 +118,7 @@ class <?= names[1] ?>(object):
 #
 # Engine component
 #
-class Engine(object):
+class Engine:
     """
     Calculates the derivatives in the current state
     """
@@ -213,10 +213,10 @@ def test_step():
 #
 # Pacing
 #
-class Protocol(object):
+class Protocol:
     """ Holds an ordered set of ProtocolEvent objects """
     def __init__(self):
-        super(Protocol, self).__init__()
+        super().__init__()
         self.head = None
     def add(self, e):
         """ Schedules an event """
@@ -238,9 +238,11 @@ class Protocol(object):
         if self.head is not None:
             self.head = self.head.next
         return e
-class ProtocolEvent(object):
+
+
+class ProtocolEvent:
     def __init__(self, level, start, duration, period=0, multiplier=0):
-        super(ProtocolEvent, self).__init__()
+        super().__init__()
         self.level = float(level)
         self.start = float(start)
         self.duration = float(duration)
@@ -256,6 +258,7 @@ class ProtocolEvent(object):
             raise Exception('Non-periodic event cannot occur more than once')
         self.next = None
 
+
 def pacing_protocol():
     pacing = Protocol()
 <?
@@ -377,10 +380,7 @@ if __name__ == '__main__':
         except ArithmeticError as e:
             print('Arithmetic error occurred')
             y = 'Continue with smaller stepsize? (y/n): '
-            try:
-                y = raw_input(y)    # Python 2
-            except NameError:
-                y = input(y)        # Python 3
+            y = input(y)
             if y.lower()[0:1] == 'y':
                 small /= 2
                 large /= 2

myokit/formats/sbml/__init__.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
-
 from ._api import (  # noqa
     Compartment,
     CSymbolVariable,

myokit/formats/sbml/_api.py

@@ -1,3 +1,9 @@
+#
+# SBML API
+#
+# This file is part of Myokit.
+# See http://myokit.org for copyright, sharing, and licensing details.
+#
 import collections
 import warnings
 import re
@@ -16,7 +22,7 @@ class SBMLError(Exception):
     """Raised if something goes wrong when working with an SBML model."""
 
 
-class Quantity(object):
+class Quantity:
     """
     Base class for anything that has a numerical value in an SBML model, and
     can be set by rules, reactions, or initial assignments.
@@ -52,8 +58,8 @@ class Quantity(object):
         """
         if not isinstance(value, myokit.Expression):
             raise SBMLError(
-                '<' + str(value) + '> needs to be an instance of '
-                'myokit.Expression.')
+                '<' + str(value) + '> needs to be an instance of'
+                ' myokit.Expression.')
 
         self._initial_value = value
 
@@ -75,8 +81,8 @@ class Quantity(object):
         """
         if not isinstance(value, myokit.Expression):
             raise SBMLError(
-                '<' + str(value) + '> needs to be an instance of '
-                'myokit.Expression.')
+                '<' + str(value) + '> needs to be an instance of'
+                ' myokit.Expression.')
 
         self._value = value
         self._is_rate = bool(is_rate)
@@ -89,7 +95,7 @@ class Quantity(object):
         return self._value
 
 
-class CSymbolVariable(object):
+class CSymbolVariable:
     """
     Represents a CSymbol that can appear in SBML expressions, but which has a
     predetermind value and/or meaning, e.g. "time".
@@ -122,12 +128,12 @@ class Compartment(Quantity):
 
     """
     def __init__(self, model, sid):
-        super(Compartment, self).__init__()
+        super().__init__()
 
         if not isinstance(model, Model):
             raise SBMLError(
-                '<' + str(model) + '> needs to be an instance of '
-                'myokit.formats.sbml.Model.')
+                '<' + str(model) + '> needs to be an instance of'
+                ' myokit.formats.sbml.Model.')
 
         self._model = model
         self._sid = str(sid)
@@ -185,7 +191,7 @@ class Compartment(Quantity):
         return '<Compartment ' + self._sid + '>'
 
 
-class Model(object):
+class Model:
     """
     Represents a model in SBML.
 
@@ -280,7 +286,7 @@ class Model(object):
         if not isinstance(compartment, Compartment):
             raise SBMLError(
                 '<' + compartment + '> needs to be instance of'
-                'myokit.formats.sbml.Compartment')
+                ' myokit.formats.sbml.Compartment')
 
         sid = str(sid) if sid else sid
         self._register_sid(sid)
@@ -427,7 +433,7 @@ class Model(object):
         if not isinstance(factor, Parameter):
             raise SBMLError(
                 '<' + str(factor) + '> needs to be instance of'
-                'myokit.formats.sbml.Parameter.')
+                ' myokit.formats.sbml.Parameter.')
 
         self._conversion_factor = factor
 
@@ -581,12 +587,12 @@ class Parameter(Quantity):
 
     """
     def __init__(self, model, sid):
-        super(Parameter, self).__init__()
+        super().__init__()
 
         if not isinstance(model, Model):
             raise SBMLError(
-                '<' + str(model) + '> needs to be an instance of '
-                'myokit.formats.sbml.Model.')
+                '<' + str(model) + '> needs to be an instance of'
+                ' myokit.formats.sbml.Model.')
 
         self._model = model
         self._sid = str(sid)
@@ -612,7 +618,7 @@ class Parameter(Quantity):
         return self._units
 
 
-class Reaction(object):
+class Reaction:
     """
     Represents an SBML reaction; to create a reaction use
     :meth:`Model.add_reaction()`.
@@ -629,8 +635,8 @@ class Reaction(object):
 
         if not isinstance(model, Model):
             raise SBMLError(
-                '<' + str(model) + '> needs to be an instance of '
-                'myokit.formats.sbml.Model.')
+                '<' + str(model) + '> needs to be an instance of'
+                ' myokit.formats.sbml.Model.')
 
         self._model = model
         self._sid = str(sid)
@@ -650,8 +656,8 @@ class Reaction(object):
         """Adds a modifier to this reaction and returns the created object."""
         if not isinstance(species, Species):
             raise SBMLError(
-                '<' + str(species) + '> needs to be an instance of '
-                'myokit.formats.sbml.Species')
+                '<' + str(species) + '> needs to be an instance of'
+                ' myokit.formats.sbml.Species')
 
         sid = str(sid) if sid else sid
         if sid is not None:
@@ -668,8 +674,8 @@ class Reaction(object):
         """
         if not isinstance(species, Species):
             raise SBMLError(
-                '<' + str(species) + '> needs to be an instance of '
-                'myokit.formats.sbml.Species')
+                '<' + str(species) + '> needs to be an instance of'
+                ' myokit.formats.sbml.Species')
 
         sid = str(sid) if sid else sid
         if sid is not None:
@@ -685,8 +691,8 @@ class Reaction(object):
         """Adds a reactant to this reaction and returns the created object."""
         if not isinstance(species, Species):
             raise SBMLError(
-                '<' + str(species) + '> needs to be an instance of '
-                'myokit.formats.sbml.Species')
+                '<' + str(species) + '> needs to be an instance of'
+                ' myokit.formats.sbml.Species')
 
         sid = str(sid) if sid else sid
         if sid is not None:
@@ -731,8 +737,8 @@ class Reaction(object):
         """
         if not isinstance(expression, myokit.Expression):
             raise SBMLError(
-                '<' + str(expression) + '> needs to be an instance of '
-                'myokit.Expression.')
+                '<' + str(expression) + '> needs to be an instance of'
+                ' myokit.Expression.')
 
         self._kinetic_law = expression
 
@@ -772,12 +778,12 @@ class Species(Quantity):
 
     """
     def __init__(self, compartment, sid, is_amount, is_constant, is_boundary):
-        super(Species, self).__init__()
+        super().__init__()
 
         if not isinstance(compartment, Compartment):
             raise SBMLError(
                 '<' + compartment + '> needs to be instance of'
-                'myokit.formats.sbml.Compartment')
+                ' myokit.formats.sbml.Compartment')
         if not isinstance(is_amount, bool):
             raise SBMLError(
                 'Is_amount <' + str(is_amount) + '> needs to be a boolean.')
@@ -853,7 +859,7 @@ class Species(Quantity):
         if not isinstance(factor, Parameter):
             raise SBMLError(
                 '<' + str(factor) + '> needs to be instance of'
-                'myokit.formats.sbml.Parameter.')
+                ' myokit.formats.sbml.Parameter.')
 
         self._conversion_factor = factor
 
@@ -867,8 +873,8 @@ class Species(Quantity):
         """
         if not isinstance(value, myokit.Expression):
             raise SBMLError(
-                '<' + str(value) + '> needs to be an instance of '
-                'myokit.Expression.')
+                '<' + str(value) + '> needs to be an instance of'
+                ' myokit.Expression.')
         if (in_amount is not None) and (not isinstance(in_amount, bool)):
             raise SBMLError(
                 '<in_amount> needs to be an instance of bool or None.')
@@ -914,12 +920,12 @@ class SpeciesReference(Quantity):
     MODIFIER = 2
 
     def __init__(self, species, sid=None):
-        super(SpeciesReference, self).__init__()
+        super().__init__()
 
         if not isinstance(species, Species):
             raise SBMLError(
                 '<' + species + '> needs to be instance of'
-                'myokit.formats.sbml.Species')
+                ' myokit.formats.sbml.Species')
 
         self._species = species
         self._sid = str(sid) if sid else sid
@@ -936,16 +942,16 @@ class SpeciesReference(Quantity):
         return '<SpeciesReference ' + self._sid + '>'
 
 
-class ModifierSpeciesReference(object):
+class ModifierSpeciesReference:
     """Represents a reference to a modifier species in an SBML reaction."""
 
     def __init__(self, species, sid=None):
-        super(ModifierSpeciesReference, self).__init__()
+        super().__init__()
 
         if not isinstance(species, Species):
             raise SBMLError(
                 '<' + species + '> needs to be instance of'
-                'myokit.formats.sbml.Species')
+                ' myokit.formats.sbml.Species')
 
         self._species = species
         self._sid = str(sid) if sid else sid
@@ -971,7 +977,7 @@ def convert_name(name):
     return name
 
 
-class _MyokitConverter(object):
+class _MyokitConverter:
     """
     Converts SBML Models to Myokit models.
     """
@@ -1058,7 +1064,7 @@ class _MyokitConverter(object):
 
     @staticmethod
     def add_global_component(
-            myokit_model, component_references, name='myokit'):
+            myokit_model, component_references, name='global'):
         """
         Creates a component used to store global parameters and the time
         variable.
@@ -1298,7 +1304,7 @@ class _MyokitConverter(object):
                         'with an initial value. Default is set to 1.')
 
                 # Promote size to state variable
-                var.promote(state_value=state_value)
+                var.promote(state_value)
 
             # Set RHS
             # (assignmentRule overwrites initialAssignment)
@@ -1383,7 +1389,7 @@ class _MyokitConverter(object):
                         'value. Default is set to 0.')
 
                 # Promote size to state variable
-                var.promote(state_value=state_value)
+                var.promote(state_value)
                 var.set_rhs(myokit.Number(0))
 
             if (not var.rhs().is_literal()) or var.rhs().eval():
@@ -1473,7 +1479,7 @@ class _MyokitConverter(object):
                         'value. Default is set to 0.')
 
                 # Promote size to state variable
-                var.promote(state_value=state_value)
+                var.promote(state_value)
                 var.set_rhs(myokit.Number(0))
 
             if (not var.rhs().is_literal()) or var.rhs().eval():
@@ -1546,7 +1552,7 @@ class _MyokitConverter(object):
                         'value. Default is set to 0.')
 
                 # Promote size to state variable
-                var.promote(state_value=state_value)
+                var.promote(state_value)
 
             # Set RHS (reactions are dealt with elsewhere)
             expr = species.value()
@@ -1607,7 +1613,7 @@ class _MyokitConverter(object):
                         ' initial value. Default is set to 1.')
 
                 # Promote size to state variable
-                var.promote(state_value=state_value)
+                var.promote(state_value)
 
             # Set RHS
             # (assignmentRule overwrites initialAssignment)
@@ -1673,7 +1679,7 @@ class _MyokitConverter(object):
                             ' 1.')
 
                     # Promote size to state variable
-                    var.promote(state_value=state_value)
+                    var.promote(state_value)
 
                 # Set RHS
                 # (assignmentRule overwrites initialAssignment)

myokit/formats/sbml/_importer.py

@@ -7,9 +7,6 @@
 # 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.formats
 
 
@@ -22,7 +19,7 @@ class SBMLImporter(myokit.formats.Importer):
     :class:`myokit.formats.sbml.SBMLParser`.
     """
     def __init__(self):
-        super(SBMLImporter, self).__init__()
+        super().__init__()
 
     def supports_model(self):
         """Returns ``True``."""

myokit/formats/sbml/_parser.py

@@ -8,9 +8,6 @@
 # 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 warnings
 
@@ -76,10 +73,10 @@ class SBMLParsingError(myokit.ImportError):
                 message = 'Error on line ' + line + '. ' + message
             except AttributeError:  # pragma: no cover
                 pass
-        super(SBMLParsingError, self).__init__(message)
+        super().__init__(message)
 
 
-class SBMLParser(object):
+class SBMLParser:
     """
     Parses SBML models, creating an SBML Model structure that can be converted
     to a :class:`myokit.Model` object.

myokit/formats/stan/__init__.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
-
 from ._exporter import StanExporter
 from ._ewriter import StanExpressionWriter
 

myokit/formats/stan/_ewriter.py

@@ -6,10 +6,8 @@
 # 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 myokit
+
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -19,7 +17,7 @@ class StanExpressionWriter(PythonExpressionWriter):
     Myokit:class:`expressions <myokit.Expression>` to a Stan syntax.
     """
     def __init__(self):
-        super(StanExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
 
         self._fcond = None

myokit/formats/stan/_exporter.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 os
 
 import myokit.formats
@@ -61,7 +58,7 @@ class StanExporter(myokit.formats.TemplatedRunnableExporter):
             ion current).
 
         """
-        super(StanExporter, self).runnable(
+        super().runnable(
             path, model, protocol, parameters, output)
 
     def _vars(self, model, protocol, parameters, output):
@@ -109,7 +106,7 @@ class StanExporter(myokit.formats.TemplatedRunnableExporter):
         ew.set_lhs_function(v)
 
         # Process bound variables
-        bound_variables = model.prepare_bindings({
+        bound_variables = myokit._prepare_bindings(model, {
             'time': 'time',
             'pace': 'pace',
         })

myokit/formats/stan/template/cell.stan

@@ -21,7 +21,7 @@ functions{
    *
    * @param x The value to search for.
    * @param sorted A sorted (non-decreasing) vector of values to search in.
-   * @return The greatest array indice `i` such that `sorted[i] <= x`
+   * @return The greatest array index `i` such that `sorted[i] <= x`
    */
   int find_interval_elem(real x, vector sorted) {
 
@@ -83,10 +83,10 @@ functions{
     vector[n] times  = to_vector(xr[1:n]);
     vector[n] values = to_vector(xr[(n + 1):(2 * n)]);
 
-    // Find indice for current time
+    // Find index for current time
     int i = find_interval_elem(time, values);
 
-    // Return pacing value
+    // Return pacing valueo
     return (i == 0) ? values[1] : values[i];
   }
 

myokit/formats/sympy/__init__.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
-
 from ._ereader import SymPyExpressionReader
 from ._ewriter import SymPyExpressionWriter
 

myokit/formats/sympy/_ereader.py

@@ -4,14 +4,11 @@
 # 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 myokit
 import myokit.formats
 
 
-class SymPyExpressionReader(object):
+class SymPyExpressionReader:
     """
     Converts Sympy expressions to Myokit expressions.
 

myokit/formats/sympy/_ewriter.py

@@ -4,16 +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
+import myokit.formats
 
 try:
     import sympy as sp
 except ImportError:
     pass
 
-import myokit.formats
-
 
 class SymPyExpressionWriter(myokit.formats.ExpressionWriter):
     """
@@ -23,7 +20,7 @@ class SymPyExpressionWriter(myokit.formats.ExpressionWriter):
     The returned type is a SymPy object, not a string!
     """
     def __init__(self):
-        super(SymPyExpressionWriter, self).__init__()
+        super().__init__()
 
         self._flhs = None
         self.set_lhs_function(lambda lhs: str(lhs))

myokit/formats/wcp/__init__.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
-
 from ._wcp import WcpFile  # noqa
 # Importers
 # Exporters