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

myokit/formats/axon/_abf.py

@@ -139,23 +139,22 @@
 # Information - but no direct code - from the matlab script get_abf_header.m
 # was also used: http://neurodata.hg.sourceforge.net/hgweb/neurodata/neurodata/
 #------------------------------------------------------------------------------
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
-from collections import OrderedDict
-import numpy as np
-import traceback
 import datetime
 import logging
-import struct
 import os
+import struct
+import traceback
+
+import numpy as np
+
+from collections import OrderedDict
 
 
 # Encoding for text parts of files
 _ENC = 'latin-1'
 
 
-class AbfFile(object):
+class AbfFile:
     """
     Represents a read-only Axon Binary Format file (``.abf``), stored at the
     location pointed to by ``filepath``.
@@ -199,7 +198,6 @@ class AbfFile(object):
     """
     def __init__(self, filepath, is_protocol_file=None):
         # The path to the file and its basename
-        # Ensure it's a `str` for Python2/3 compatibility
         filepath = str(filepath)
         self._filepath = os.path.abspath(filepath)
         self._filename = os.path.basename(filepath)
@@ -254,7 +252,6 @@ class AbfFile(object):
             # cases that trigger this error they should be resolved. At the
             # same time, if it happens to a user we want it to "sort-of work"
             # (an experimental rather than a production setting)
-            logging.basicConfig()
             log = logging.getLogger(__name__)
             log.warning('Unable to read protocol from ' + self._filepath)
             log.warning(traceback.format_exc())
@@ -703,7 +700,6 @@ class AbfFile(object):
             """
             Read and unpack a file section using the given format ``form``.
             """
-            # Form must be a str (so bytes on Python 2)
             form = str(form)
             if offset is not None:
                 f.seek(offset)
@@ -1065,7 +1061,6 @@ class AbfFile(object):
 
                     else:  # pragma: no cover
 
-                        logging.basicConfig()
                         log = logging.getLogger(__name__)
                         log.warning(
                             'Unsupported epoch type: ' + epoch_types(kind))
@@ -1308,14 +1303,14 @@ class AbfFile(object):
                 self._adc_offsets.append(s)
 
 
-class Sweep(object):
+class Sweep:
     """
     Represents a single sweep (also called an 'episode')
 
     A sweep is represented as a fixed-size list of channels.
     """
     def __init__(self, n):
-        super(Sweep, self).__init__()
+        super().__init__()
         n = int(n)
         if n < 0:   # pragma: no cover
             raise ValueError('Number channels cannot be negative.')
@@ -1338,14 +1333,14 @@ class Sweep(object):
         self._channels[key] = value
 
 
-class Channel(object):
+class Channel:
     """
     Represents an analog signal for a single channel.
 
     To obtain this channel's formatted data, use times() and trace()
     """
     def __init__(self, parent_file):
-        super(Channel, self).__init__()
+        super().__init__()
         self._parent_file = parent_file  # The abf file this channel is from
         self._type = TYPE_UNKNOWN   # Type of recording
 
@@ -1388,7 +1383,7 @@ class Channel(object):
     def number(self):
         """
         Returns the channel index used by pClamp. Note that this does not
-        necessarily equal its index in the python sweep data!
+        necessarily equal its index in the Python sweep data!
         """
         return self._numb
 

myokit/formats/axon/_atf.py

@@ -4,20 +4,19 @@
 # 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 collections import OrderedDict
-import numpy as np
 import os
 import re
 
+import numpy as np
+
+from collections import OrderedDict
+
 
 # Format used for any text
 _ENC = 'ascii'
 
 
-class AtfFile(object):
+class AtfFile:
     """
     Represents an Axon Text File (ATF) stored on disk.
 

myokit/formats/axon/_importer.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
 
 

myokit/formats/cellml/__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 CellMLExporter, CellML1Exporter, CellML2Exporter
 from ._ewriter import CellMLExpressionWriter
 from ._importer import CellMLImporter, CellMLImporterError  # noqa

myokit/formats/cellml/_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 lxml import etree
 
 import myokit
@@ -24,8 +21,8 @@ class CellMLExpressionWriter(MathMLExpressionWriter):
     unit names with :meth:`set_unit_function()`.
     """
     def __init__(self, version='1.0'):
-        super(CellMLExpressionWriter, self).__init__()
-        super(CellMLExpressionWriter, self).set_mode(presentation=False)
+        super().__init__()
+        super().set_mode(presentation=False)
 
         # Units lookup method
         self._funits = None
@@ -54,7 +51,7 @@ class CellMLExpressionWriter(MathMLExpressionWriter):
         self._funits = f
 
     def _ex_number(self, e, t):
-        x = super(CellMLExpressionWriter, self)._ex_number(e, t)
+        x = super()._ex_number(e, t)
         unit = e.unit()
         if self._funits is not None and unit is not None:
             units = self._funits(e.unit())

myokit/formats/cellml/_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 myokit
 import myokit.lib.guess
 
@@ -18,7 +15,7 @@ class CellMLExporter(myokit.formats.Exporter):
     This:class:`Exporter <myokit.formats.Exporter>` creates a CellML model.
     """
     def __init__(self):
-        super(CellMLExporter, self).__init__()
+        super().__init__()
 
     def model(self, path, model, protocol=None, version='1.0'):
         """
@@ -69,7 +66,7 @@ class CellML1Exporter(CellMLExporter):
     This:class:`Exporter <myokit.formats.Exporter>` creates a CellML 1.0 model.
     """
     def model(self, path, model, protocol=None):
-        super(CellML1Exporter, self).model(path, model, protocol, '1.0')
+        super().model(path, model, protocol, '1.0')
 
 
 class CellML2Exporter(CellMLExporter):
@@ -77,5 +74,5 @@ class CellML2Exporter(CellMLExporter):
     This:class:`Exporter <myokit.formats.Exporter>` creates a CellML 2.0 model.
     """
     def model(self, path, model, protocol=None):
-        super(CellML2Exporter, self).model(path, model, protocol, '2.0')
+        super().model(path, model, protocol, '2.0')
 

myokit/formats/cellml/_importer.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
-
 from lxml import etree
 
 import myokit
@@ -28,7 +25,7 @@ class CellMLImporter(myokit.formats.Importer):
     from CellML.
     """
     def __init__(self, verbose=False):
-        super(CellMLImporter, self).__init__()
+        super().__init__()
 
     def model(self, path):
         """

myokit/formats/cellml/v1/__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
     AnnotatableElement,
     CellMLError,
@@ -22,7 +19,6 @@ from ._api import (     # noqa
     is_valid_identifier,
 )
 
-
 from ._parser import (  # noqa
     parse_file,
     parse_string,

myokit/formats/cellml/v1/_api.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 re
 import warnings
@@ -116,7 +113,7 @@ def create_unit_name(unit):
     return name
 
 
-class AnnotatableElement(object):
+class AnnotatableElement:
     """
     Represents a CellML 1.0 or 1.1 element that can have a cmeta:id.
 
@@ -187,7 +184,7 @@ class UnsupportedBaseUnitsError(UnitsError):
     """
     def __init__(self, units):
         self.units = units
-        super(UnsupportedBaseUnitsError, self).__init__(
+        super().__init__(
             'Unsupported base units "' + units + '".')
 
 
@@ -196,7 +193,7 @@ class UnsupportedUnitOffsetError(UnitsError):
     Raised when units with non-zero offsets are used.
     """
     def __init__(self):
-        super(UnsupportedUnitOffsetError, self).__init__(
+        super().__init__(
             'Units with non-zero offsets are not supported.')
 
 
@@ -206,7 +203,7 @@ class Component(AnnotatableElement):
     :meth:`Model.add_component()`.
     """
     def __init__(self, model, name):
-        super(Component, self).__init__(model)
+        super().__init__(model)
 
         # Store model
         self._model = model
@@ -474,7 +471,7 @@ class Model(AnnotatableElement):
 
     """
     def __init__(self, name, version='1.0'):
-        super(Model, self).__init__(self)
+        super().__init__(self)
 
         # Check and store name
         if not is_valid_identifier(name):
@@ -898,7 +895,7 @@ class Model(AnnotatableElement):
                 # Promote states and set rhs and initial value
                 elif variable.is_state():
                     v.set_is_state(True)
-                    v.set_initial_value(variable.state_value())
+                    v.set_initial_value(variable.initial_value(True))
                     v.set_rhs(rhs)
 
                 # Store literals (single number) in initial value
@@ -1165,7 +1162,7 @@ class Model(AnnotatableElement):
         return self._version
 
 
-class Units(object):
+class Units:
     """
     Represents a CellML units definition, should not be created directly but
     only via :meth:`Model.add_units()` or :meth:`Component.add_units()`.
@@ -1470,7 +1467,7 @@ class Variable(AnnotatableElement):
     """
     def __init__(self, component, name, units, public_interface='none',
                  private_interface='none'):
-        super(Variable, self).__init__(component.model())
+        super().__init__(component.model())
 
         # Store component
         self._component = component

myokit/formats/cellml/v1/_parser.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 warnings
 
@@ -60,10 +57,10 @@ class CellMLParsingError(myokit.ImportError):
                 message = 'Error on line ' + line + '. ' + message
             except AttributeError:
                 pass
-        super(CellMLParsingError, self).__init__(message)
+        super().__init__(message)
 
 
-class CellMLParser(object):
+class CellMLParser:
     """
     Parses CellML 1.0 and 1.1 documents, and performs (partial) validation of a
     CellML document.

myokit/formats/cellml/v1/_writer.py

@@ -4,21 +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
-
 from lxml import etree
+from urllib.parse import quote
 
 import myokit
 import myokit.formats.cellml as cellml
 
-# Quoting URI strings in Python2 and Python3
-try:
-    from urllib.parse import quote
-except ImportError:     # pragma: no python 3 cover
-    # Python 2
-    from urllib import quote
-
 
 # Left-over from old exporter. Not sure if this had any function.
 # Add name in 'tmp-documentation' format
@@ -45,7 +36,7 @@ def write_string(model):
     return CellMLWriter().write_string(model)
 
 
-class CellMLWriter(object):
+class CellMLWriter:
     """
     Writes CellML 1.0 or 1.1 documents.
     """

myokit/formats/cellml/v2/__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
     AnnotatableElement,
     CellMLError,

myokit/formats/cellml/v2/_api.py

@@ -4,21 +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 collections
 import re
 import warnings
 
 import myokit
 
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 # Data types
 _cellml_identifier = re.compile(r'^[a-zA-Z][a-zA-Z0-9_]*$')
@@ -142,7 +133,7 @@ def create_unit_name(unit):
     return name
 
 
-class AnnotatableElement(object):
+class AnnotatableElement:
     """
     Represents a CellML 2.0 element that can be annotated (using a public dict
     ``meta`` that stores key:value pairs).
@@ -167,7 +158,7 @@ class Component(AnnotatableElement):
     :meth:`Model.add_component()`.
     """
     def __init__(self, model, name):
-        super(Component, self).__init__()
+        super().__init__()
 
         # Store model
         self._model = model
@@ -323,7 +314,7 @@ class Model(AnnotatableElement):
 
     """
     def __init__(self, name, version='2.0'):
-        super(Model, self).__init__()
+        super().__init__()
 
         # Check and store name
         if not is_identifier(name):
@@ -802,7 +793,7 @@ class Model(AnnotatableElement):
 
                 # Promote states and set rhs and initial value
                 elif variable.is_state():
-                    v.set_initial_value(variable.state_value())
+                    v.set_initial_value(variable.initial_value(True))
                     v.set_equation(myokit.Equation(lhs, rhs))
 
                 # Store literals (single number) in initial value
@@ -1068,7 +1059,7 @@ class Model(AnnotatableElement):
         return self._version
 
 
-class Units(object):
+class Units:
     """
     Represents a CellML units definition; should not be created directly but
     only via :meth:`Model.add_units()` or :meth:`Component.add_units()`.
@@ -1359,7 +1350,7 @@ class Variable(AnnotatableElement):
 
     """
     def __init__(self, component, name, units, interface='none'):
-        super(Variable, self).__init__()
+        super().__init__()
 
         # Store model and component
         self._model = component.model()
@@ -1615,7 +1606,7 @@ class Variable(AnnotatableElement):
         if value is not None:
 
             # Check value is a real number string
-            if isinstance(value, basestring):
+            if isinstance(value, str):
                 if is_real_number_string(value):
                     value = float(value)
                 else:
@@ -1642,7 +1633,7 @@ class Variable(AnnotatableElement):
         return self._units
 
 
-class ConnectedVariableSet(object):
+class ConnectedVariableSet:
     """
     Represents a set of connected variables.
 

myokit/formats/cellml/v2/_parser.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 warnings
 
 from lxml import etree
@@ -59,10 +56,10 @@ class CellMLParsingError(myokit.ImportError):
                 message = 'Error on line ' + line + '. ' + message
             except AttributeError:
                 pass
-        super(CellMLParsingError, self).__init__(message)
+        super().__init__(message)
 
 
-class CellMLParser(object):
+class CellMLParser:
     """
     Parses CellML 2.0 documents, and performs (partial) validation.
 

myokit/formats/cellml/v2/_writer.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
@@ -27,7 +24,7 @@ def write_string(model):
     return CellMLWriter().write_string(model)
 
 
-class CellMLWriter(object):
+class CellMLWriter:
     """
     Writes CellML 2.0 documents.
     """

myokit/formats/channelml/__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 ._importer import ChannelMLImporter, ChannelMLError  # noqa
 
 

myokit/formats/channelml/_importer.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
-
+import io
 import os
 import textwrap
+import warnings
 import xml.dom
 import xml.dom.minidom
 
-import warnings
-
-try:
-    # Python 2
-    from cStringIO import StringIO
-except ImportError:
-    # Python3
-    from io import StringIO
-
 import myokit
 from myokit import formats
 from myokit import Name, Number, Minus, Multiply, Divide, Power
@@ -71,7 +61,7 @@ class ChannelMLImporter(formats.Importer):
     from the ChannelML format.
     """
     def __init__(self, verbose=False):
-        super(ChannelMLImporter, self).__init__()
+        super().__init__()
         self.generated_name_index = 0
 
     def component(self, path, model):
@@ -147,7 +137,7 @@ class ChannelMLImporter(formats.Importer):
                 ' supported.')
 
         # Add channel component
-        name = self._sanitise_name(root.getAttribute('name'))
+        name = self._sanitize_name(root.getAttribute('name'))
         if name in model:
             name_root = name
             i = 2
@@ -200,7 +190,7 @@ class ChannelMLImporter(formats.Importer):
         # Add gates
         gvars = []
         for gate in cvr.getElementsByTagName('gate'):
-            gname = self._sanitise_name(gate.getAttribute('name'))
+            gname = self._sanitize_name(gate.getAttribute('name'))
             gvar = component.add_variable(gname)
             gvar.promote(0)
             cstate = gate.getElementsByTagName('closed_state')
@@ -242,7 +232,7 @@ class ChannelMLImporter(formats.Importer):
                         + gname + '>')
 
                 # Add closed-to-open transition
-                tname = self._sanitise_name(tco.getAttribute('name'))
+                tname = self._sanitize_name(tco.getAttribute('name'))
                 tcovar = gvar.add_variable(tname)
                 expr = str(tco.getAttribute('expr'))
                 try:
@@ -255,7 +245,7 @@ class ChannelMLImporter(formats.Importer):
                     tcovar.meta['expression'] = str(expr)
 
                 # Add open-to-closed transition
-                tname = self._sanitise_name(toc.getAttribute('name'))
+                tname = self._sanitize_name(toc.getAttribute('name'))
                 tocvar = gvar.add_variable(tname)
                 expr = str(toc.getAttribute('expr'))
                 try:
@@ -284,7 +274,7 @@ class ChannelMLImporter(formats.Importer):
                 tc = tc[0]
 
                 # Add steady-state variable
-                ssname = self._sanitise_name(ss.getAttribute('name'))
+                ssname = self._sanitize_name(ss.getAttribute('name'))
                 ssvar = gvar.add_variable(ssname)
                 expr = str(ss.getAttribute('expr'))
                 try:
@@ -296,7 +286,7 @@ class ChannelMLImporter(formats.Importer):
                     ssvar.meta['expression'] = str(expr)
 
                 # Add time course variable
-                tcname = self._sanitise_name(tc.getAttribute('name'))
+                tcname = self._sanitize_name(tc.getAttribute('name'))
                 tcvar = gvar.add_variable(tcname)
                 expr = str(tc.getAttribute('expr'))
                 try:
@@ -373,7 +363,7 @@ class ChannelMLImporter(formats.Importer):
         if not root.hasAttribute('xmlns:meta'):
             return None
         ns = root.getAttribute('xmlns:meta')
-        b = StringIO()
+        b = io.StringIO()
 
         def scan(parent):
             kid = dom_child(parent)
@@ -412,7 +402,7 @@ class ChannelMLImporter(formats.Importer):
         return textwrap.fill(
             str('\n'.join(text(node))), 70, replace_whitespace=False)
 
-    def _sanitise_name(self, name):
+    def _sanitize_name(self, name):
         """
         Tests if a name is a valid myokit name. Adapts it if it isn't.
         """

myokit/formats/cpp/__init__.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.formats.ansic
+
 from ._ewriter import CppExpressionWriter
 
 

myokit/formats/cpp/_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.ansic import AnsiCExpressionWriter