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

myokit/formats/cuda/_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/easyml/__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 EasyMLExporter
 from ._ewriter import EasyMLExpressionWriter
 

myokit/formats/easyml/_ewriter.py

@@ -4,12 +4,10 @@
 # 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 warnings
 
 import myokit
+
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -19,7 +17,7 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
     equations for variables in EasyML syntax.
     """
     def __init__(self):
-        super(EasyMLExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
 
     #def _ex_name(self, e):
@@ -39,7 +37,7 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
         if isinstance(e[1], myokit.Exp) and isinstance(e[0], myokit.Number):
             if e[0].eval() == 1:
                 return '-expm1(' + self.ex(e[1][0]) + ')'
-        return super(EasyMLExpressionWriter, self)._ex_minus(e)
+        return super()._ex_minus(e)
 
     #def _ex_multiply(self, e):
     #def _ex_divide(self, e):
@@ -58,23 +56,23 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
 
     def _ex_sin(self, e):
         warnings.warn('Potentially unsupported function: sin()')
-        return super(EasyMLExpressionWriter, self)._ex_sin(e)
+        return super()._ex_sin(e)
 
     #def _ex_cos(self, e):
 
     def _ex_tan(self, e):
         warnings.warn('Potentially unsupported function: tan()')
-        return super(EasyMLExpressionWriter, self)._ex_tan(e)
+        return super()._ex_tan(e)
 
     def _ex_asin(self, e):
         warnings.warn('Potentially unsupported function: asin()')
-        return super(EasyMLExpressionWriter, self)._ex_asin(e)
+        return super()._ex_asin(e)
 
     #def _ex_acos(self, e):
 
     def _ex_atan(self, e):
         warnings.warn('Potentially unsupported function: atan()')
-        return super(EasyMLExpressionWriter, self)._ex_atan(e)
+        return super()._ex_atan(e)
 
     #def _ex_exp(self, e):
 
@@ -87,11 +85,11 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
 
     def _ex_floor(self, e):
         warnings.warn('Potentially unsupported function: floor()')
-        return super(EasyMLExpressionWriter, self)._ex_floor(e)
+        return super()._ex_floor(e)
 
     def _ex_ceil(self, e):
         warnings.warn('Potentially unsupported function: ceil()')
-        return super(EasyMLExpressionWriter, self)._ex_ceil(e)
+        return super()._ex_ceil(e)
 
     def _ex_abs(self, e):
         return self._ex_function(e, 'fabs')

myokit/formats/easyml/_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 collections
 import os
 import warnings

myokit/formats/html/__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 HTMLExporter
 from ._flatten import html2ascii    # noqa
 

myokit/formats/html/_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
-
 from lxml import etree
 
 import myokit

myokit/formats/html/_flatten.py

@@ -4,19 +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 html
+import html.parser
 import re
-import sys
 import textwrap
 
-# HTML Parser in Python 2 and 3
-try:
-    from HTMLParser import HTMLParser
-except ImportError:
-    from html.parser import HTMLParser
-
 
 def html2ascii(html, width=79, indent='  '):
     """
@@ -32,21 +24,13 @@ def html2ascii(html, width=79, indent='  '):
     return f.get_text()
 
 
-class Asciifier(HTMLParser):
+class Asciifier(html.parser.HTMLParser):
     INDENT = 1
     DEDENT = -1
     WHITE = [' ', '\t', '\f', '\r', '\n']
 
     def __init__(self, line_width=79, indent='  '):
-        if sys.hexversion < 0x03000000:     # pragma: no python 3 cover
-            # HTMLParser requires old-school constructor
-            HTMLParser.__init__(self)
-        else:                               # pragma: no python 2 cover
-            super(Asciifier, self).__init__(convert_charrefs=False)
-
-            # Unescape method is deprecated
-            import html
-            self.unescape = html.unescape
+        super().__init__(convert_charrefs=False)
 
         # In <head> yes/no
         self.inhead = False
@@ -226,7 +210,7 @@ class Asciifier(HTMLParser):
             return
 
         # Convert html characters
-        data = self.unescape('&' + name + ';')
+        data = html.unescape('&' + name + ';')
 
         # Convert to ascii and back to strip out non-ascii content
         data = data.encode('ascii', 'ignore').decode('ascii')

myokit/formats/latex/__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 PdfExporter, PosterExporter
 from ._ewriter import LatexExpressionWriter
 

myokit/formats/latex/_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
 
 
@@ -16,7 +13,7 @@ class LatexExpressionWriter(myokit.formats.ExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to their Tex equivalent.
     """
     def __init__(self):
-        super(LatexExpressionWriter, self).__init__()
+        super().__init__()
 
         # Default time variable
         self._time = None

myokit/formats/latex/_exporter.py

@@ -4,12 +4,10 @@
 # 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
+
 from ._ewriter import LatexExpressionWriter
 
 
@@ -19,7 +17,7 @@ class PdfExporter(myokit.formats.Exporter):
     a simple latex document.
     """
     def __init__(self):
-        super(PdfExporter, self).__init__()
+        super().__init__()
 
     def _clean(self, text):
         """
@@ -111,7 +109,7 @@ class PosterExporter(myokit.formats.Exporter):
     beholders.
     """
     def __init__(self):
-        super(PosterExporter, self).__init__()
+        super().__init__()
 
     def post_export_info(self):
         return '\n'.join((

myokit/formats/mathml/__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 ._ewriter import MathMLExpressionWriter
 from ._parser import (   # noqa
     MathMLError,

myokit/formats/mathml/_ewriter.py

@@ -4,19 +4,10 @@
 # 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 lxml import etree
 
 import myokit.formats
 
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 class MathMLExpressionWriter(myokit.formats.ExpressionWriter):
     """
@@ -25,7 +16,7 @@ class MathMLExpressionWriter(myokit.formats.ExpressionWriter):
     Presentation MathML.
     """
     def __init__(self):
-        super(MathMLExpressionWriter, self).__init__()
+        super().__init__()
 
         # Default mode
         self._pres = False
@@ -33,7 +24,7 @@ class MathMLExpressionWriter(myokit.formats.ExpressionWriter):
         # Default lhs conversion function
         def flhs(lhs):
             var = lhs.var()
-            if isinstance(var, basestring):
+            if isinstance(var, str):
                 # This can happen with time variable of derivative if the
                 # proper variable isn't set!
                 return var

myokit/formats/mathml/_parser.py

@@ -4,10 +4,8 @@
 # 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.xml import split
 
 
@@ -63,10 +61,10 @@ class MathMLError(myokit.ImportError):
                 message = 'Error on line ' + line + '. ' + message
             except AttributeError:
                 pass
-        super(MathMLError, self).__init__(message)
+        super().__init__(message)
 
 
-class MathMLParser(object):
+class MathMLParser:
     """
     Parses MathML expressions into :class:`myokit.Expression` objects.
 

myokit/formats/matlab/__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 MatlabExporter
 from ._ewriter import MatlabExpressionWriter
 

myokit/formats/matlab/_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
-
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -16,7 +13,7 @@ class MatlabExpressionWriter(PythonExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to a Matlab syntax.
     """
     def __init__(self):
-        super(MatlabExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
         self._fcond = 'ifthenelse'
 

myokit/formats/matlab/_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/opencl/__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 OpenCLExporter, OpenCLRLExporter
 from ._ewriter import OpenCLExpressionWriter
 from myokit.formats import ansic

myokit/formats/opencl/_ewriter.py

@@ -4,10 +4,8 @@
 # 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
 
 
@@ -17,7 +15,7 @@ class OpenCLExpressionWriter(PythonExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to OpenCL syntax.
     """
     def __init__(self, precision=myokit.SINGLE_PRECISION, native_math=True):
-        super(OpenCLExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
         self._sp = (precision == myokit.SINGLE_PRECISION)
         self._nm = bool(native_math)

myokit/formats/opencl/_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/__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

@@ -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):
@@ -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.
@@ -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".
@@ -122,7 +128,7 @@ class Compartment(Quantity):
 
     """
     def __init__(self, model, sid):
-        super(Compartment, self).__init__()
+        super().__init__()
 
         if not isinstance(model, Model):
             raise SBMLError(
@@ -185,7 +191,7 @@ class Compartment(Quantity):
         return '<Compartment ' + self._sid + '>'
 
 
-class Model(object):
+class Model:
     """
     Represents a model in SBML.
 
@@ -581,7 +587,7 @@ class Parameter(Quantity):
 
     """
     def __init__(self, model, sid):
-        super(Parameter, self).__init__()
+        super().__init__()
 
         if not isinstance(model, Model):
             raise SBMLError(
@@ -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()`.
@@ -772,7 +778,7 @@ 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(
@@ -914,7 +920,7 @@ class SpeciesReference(Quantity):
     MODIFIER = 2
 
     def __init__(self, species, sid=None):
-        super(SpeciesReference, self).__init__()
+        super().__init__()
 
         if not isinstance(species, Species):
             raise SBMLError(
@@ -936,11 +942,11 @@ 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(
@@ -971,7 +977,7 @@ def convert_name(name):
     return name
 
 
-class _MyokitConverter(object):
+class _MyokitConverter:
     """
     Converts SBML Models to Myokit models.
     """

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.