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

myokit/_parsing.py

@@ -4,22 +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 os
 import re
-#import unicodedata
+
 from collections import OrderedDict
 
 import myokit
-from myokit import ParseError, ProtocolParseError
 
-# Strings in Python2 and Python3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
+from myokit import ParseError, ProtocolParseError
 
 
 def parse(source):
@@ -34,7 +26,7 @@ def parse(source):
     """
     # Get raw stream
     raw = source
-    if isinstance(raw, basestring):
+    if isinstance(raw, str):
         raw = raw.splitlines()
     raw = iter(raw)
 
@@ -78,7 +70,7 @@ def parse_model(source):
     """
     # Get raw stream
     raw = source
-    if isinstance(raw, basestring):
+    if isinstance(raw, str):
         raw = raw.splitlines()
     raw = iter(raw)
 
@@ -100,7 +92,7 @@ def parse_protocol(source):
     """
     # Get raw stream
     raw = source
-    if isinstance(raw, basestring):
+    if isinstance(raw, str):
         raw = raw.splitlines()
     raw = iter(raw)
 
@@ -122,7 +114,7 @@ def parse_script(source):
     """
     # Get raw stream
     raw = source
-    if isinstance(raw, basestring):
+    if isinstance(raw, str):
         raw = raw.splitlines()
     raw = iter(raw)
 
@@ -162,7 +154,7 @@ def parse_state(state):
     """
     # Get raw stream
     raw = state
-    if isinstance(raw, basestring):
+    if isinstance(raw, str):
         raw = raw.splitlines()
     raw = iter(raw)
 
@@ -205,7 +197,7 @@ def split(source):
     """
     # Get raw stream
     raw = source
-    if isinstance(raw, basestring):
+    if isinstance(raw, str):
         raw = raw.splitlines()
     raw = iter(raw)
     segments = ['', '', '']
@@ -317,7 +309,7 @@ def unexpected_token(token, expected):
     # Parse expected token(s) or string
     if type(expected) == int:
         expected = [expected]
-    if not isinstance(expected, basestring):
+    if not isinstance(expected, str):
         if len(expected) > 2:
             expected = 'one of [' \
                 + ', '.join([token_str[i] for i in expected]) + ']'
@@ -348,7 +340,7 @@ def reg_token(info, token, obj):
         d[token[3]] = (token, obj)
 
 
-class ParseInfo(object):
+class ParseInfo:
     def __init__(self):
         self.model = None
         self.initial_values = OrderedDict()
@@ -1071,7 +1063,7 @@ def strip_expression_units(model_text, skip_literals=True):
     This method will raise a :class:`myokit.ParseError` if the given code
     cannot be parsed to a valid model.
     """
-    if isinstance(model_text, basestring):
+    if isinstance(model_text, str):
         lines = model_text.splitlines()
     else:
         lines = model_text
@@ -1267,7 +1259,7 @@ _COMPEQ = '=!><'
 _COMPEQ_MAP = [EQEQUAL, NOTEQUAL, MOREEQUAL, LESSEQUAL]
 
 
-class Tokenizer(object):
+class Tokenizer:
     """
     Takes a stream of lines as input and provides a stream interface returning
     tokens.
@@ -1312,7 +1304,7 @@ class Tokenizer(object):
         self._catcheri = 0
 
         # String given instead of stream of lines? Convert
-        if isinstance(stream_of_lines, basestring):
+        if isinstance(stream_of_lines, str):
             stream_of_lines = iter(stream_of_lines.splitlines())
 
         # Create tokenizer
@@ -1965,7 +1957,7 @@ def format_parse_error(ex, source=None):
     line = None
 
     if ex.line > 0 and source is not None:
-        if isinstance(source, basestring) and os.path.isfile(source):
+        if isinstance(source, str) and os.path.isfile(source):
             # Re-open file, find line
             with open(source, 'r') as f:
                 for i in range(0, ex.line):
@@ -2015,7 +2007,7 @@ def format_parse_error(ex, source=None):
     return '\n'.join(out)
 
 
-class NudParser(object):
+class NudParser:
     """
     Expression parser for nud operators.
 
@@ -2084,7 +2076,7 @@ class FunctionParser(NudParser):
     Parser for function calls.
     """
     def __init__(self):
-        super(FunctionParser, self).__init__()
+        super().__init__()
         self._rbp = myokit.Function._rbp
 
     def parse(self, stream, info):
@@ -2125,7 +2117,7 @@ class FunctionParser(NudParser):
         return (func, ops, (name,))
 
 
-class LedParser(object):
+class LedParser:
     """
     Expression parser for led operators.
 

myokit/_progress.py

@@ -4,15 +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 timeit
 
 import myokit
 
 
-class ProgressReporter(object):
+class ProgressReporter:
     """
     Interface for progress updates in Simulations. Also allows some job types
     to be cancelled by the user.
@@ -62,7 +59,7 @@ class ProgressReporter(object):
         """
         pass
 
-    class _Job(object):
+    class _Job:
         def __init__(self, parent, msg):
             self._parent = parent
             self._msg = msg
@@ -97,7 +94,7 @@ class ProgressPrinter(ProgressReporter):
     status every ten percent.
     """
     def __init__(self, digits=1):
-        super(ProgressPrinter, self).__init__()
+        super().__init__()
         self._b = myokit.tools.Benchmarker()
         self._f = None
         self._d = int(digits)
@@ -138,7 +135,7 @@ class Timeout(ProgressReporter):
     Progress reporter that cancels a simulation after ``timeout`` seconds.
     """
     def __init__(self, timeout):
-        super(Timeout, self).__init__()
+        super().__init__()
         self._timeout = float(timeout)
 
     def enter(self, msg=None):

myokit/_protocol.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 numpy as np
@@ -14,7 +11,7 @@ import numpy as np
 from bisect import bisect_right
 
 
-class Protocol(object):
+class Protocol:
     """
     Represents a pacing protocol as a sequence of :class:`events
     <ProtocolEvent>`.
@@ -49,7 +46,7 @@ class Protocol(object):
     ``pickle``.
     """
     def __init__(self):
-        super(Protocol, self).__init__()
+        super().__init__()
         self._head = None
 
     def add(self, e):
@@ -536,7 +533,7 @@ class Protocol(object):
         return [p.advance(t) for t in times]
 
 
-class ProtocolEvent(object):
+class ProtocolEvent:
     """
     Describes an event occurring as part of a protocol.
     """
@@ -719,7 +716,7 @@ class ProtocolEvent(object):
         return self.in_words()
 
 
-class PacingSystem(object):
+class PacingSystem:
     """
     This class uses a :class:`myokit.Protocol` to update the value of a
     pacing variable over time.
@@ -853,7 +850,7 @@ class NotAnUnbrokenSequenceError(myokit.MyokitError):
     pass
 
 
-class TimeSeriesProtocol(object):
+class TimeSeriesProtocol:
     """
     Represents a pacing protocol as a sequence of time value pairs and an
     interpolation method (currently only linear interpolation is supported).
@@ -870,7 +867,7 @@ class TimeSeriesProtocol(object):
     """
 
     def __init__(self, times, values, method=None):
-        super(TimeSeriesProtocol, self).__init__()
+        super().__init__()
 
         if len(times) != len(values):
             raise ValueError('Times and values array must have same size.')

myokit/_sim/__init__.py

@@ -5,10 +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
-
-# Library imports
 import os
 import platform
 import sys
@@ -36,36 +32,23 @@ if platform.system() == 'Windows':  # pragma: no linux cover
             ).stdin
     os.popen = _ospop
 
-
-# Setuptools imports
 from setuptools import setup, Extension  # noqa
 
-
-# Myokit imports
 import myokit       # noqa
 import myokit.pype  # noqa
 
 
-# Dynamic module finding and loading in Python 3.5+ and younger
-if sys.hexversion >= 0x03050000:
-    import importlib.machinery
+def load_module(name, path):
+    """ Dynamically find and load a module (Python 3.5+). """
     import importlib
+    import importlib.machinery
 
-    def load_module(name, path):
-        spec = importlib.machinery.PathFinder.find_spec(name, [path])
-        module = importlib.util.module_from_spec(spec)
-        return module
-
-else:  # pragma: no python 3 cover
-    import imp
-
-    def load_module(name, path):
-        (f, pathname, description) = imp.find_module(name, [path])
-        f.close()
-        return imp.load_dynamic(name, pathname)
+    spec = importlib.machinery.PathFinder.find_spec(name, [path])
+    module = importlib.util.module_from_spec(spec)
+    return module
 
 
-class CModule(object):
+class CModule:
     """
     Abstract base class for classes that dynamically create and compile a
     back-end C-module.

myokit/_sim/cable.c

@@ -367,9 +367,7 @@ sim_init(PyObject *self, PyObject *args)
     for(i_state=0; i_state<ncells * N_STATE; i_state++) {
         flt = PyList_GetItem(state_in, i_state);    /* Borrowed reference */
         if (!PyFloat_Check(flt)) {
-            char errstr[200];
-            sprintf(errstr, "Item %d in state vector is not a float.", i_state);
-            PyErr_SetString(PyExc_Exception, errstr);
+            PyErr_Format(PyExc_Exception, "Item %d in state vector is not a float.", i_state);
             return sim_clean();
         }
     }

myokit/_sim/cable.py

@@ -4,13 +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 os
-import myokit
 import platform
 
+import myokit
+
 # Location of source file
 SOURCE_FILE = 'cable.c'
 
@@ -101,7 +99,7 @@ class Simulation1d(myokit.CModule):
     _index = 0      # Unique id for generated module
 
     def __init__(self, model, protocol=None, ncells=50, rl=False):
-        super(Simulation1d, self).__init__()
+        super().__init__()
 
         # Require a valid model
         model.validate()

myokit/_sim/cmodel.h

@@ -918,9 +918,7 @@ for eqs in s_output_equations:
  * Private method: Add a variable to the logging lists. Returns 1 if
  * successful.
  *
- * Note: The variable names are all ascii compatible. In Python2, the strings
- * inside log_dict are either unicode or bytes, but they can be matched
- * without conversion.
+ * Note: The variable names are all ascii compatible.
  *
  * Arguments
  *  log_dict : A dictionary mapping variable names to sequences.

myokit/_sim/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 traceback
 
@@ -21,7 +18,7 @@ import myokit.pype
 SOURCE_FILE = 'cmodel.h'
 
 
-class CModel(object):
+class CModel:
     """
     Generates ansi-C code for a model.
 

myokit/_sim/compiler.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
@@ -32,7 +29,7 @@ class Compiler(myokit.CModule):
     _compiler = None
 
     def __init__(self):
-        super(Compiler, self).__init__()
+        super().__init__()
         # Create and cache back-end
         Compiler._index += 1
 

myokit/_sim/cvodessim.c

@@ -173,11 +173,8 @@ void
 ErrorHandler(int error_code, const char *module, const char *function,
              char *msg, void *eh_data)
 {
-    char errstr[1024];
     if (error_code > 0) {
-        sprintf(errstr, "CVODES: %s", msg);
-        PyErr_WarnEx(PyExc_RuntimeWarning, errstr, 1);
-        /* Python 3.2+: PyErr_WarnFormat(PyExc_RuntimeWarning, 1, "CVODES: %s", msg); */
+        PyErr_WarnFormat(PyExc_RuntimeWarning, 1, "CVODES: %s", msg);
     }
 }
 

myokit/_sim/cvodessim.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 platform
 import tempfile
@@ -152,7 +149,7 @@ class Simulation(myokit.CModule):
     _index = 0  # Simulation id
 
     def __init__(self, model, protocol=None, sensitivities=None, path=None):
-        super(Simulation, self).__init__()
+        super().__init__()
 
         # Require a valid model
         if not model.is_valid():

myokit/_sim/fiber_tissue.c

@@ -542,9 +542,7 @@ sim_init(PyObject* self, PyObject* args)
     for(i=0; i < nfx * nfy * n_state_f; i++) {
         flt = PyList_GetItem(state_in_f, i);    // Don't decref!
         if(!PyFloat_Check(flt)) {
-            char errstr[200];
-            sprintf(errstr, "Item %u in fiber state vector is not a float.", (unsigned int)i);
-            PyErr_SetString(PyExc_Exception, errstr);
+            PyErr_Format(PyExc_Exception, "Item %u in fiber state vector is not a float.", (unsigned int)i);
             return sim_clean();
         }
         rvec_state_f[i] = (Real)PyFloat_AsDouble(flt);
@@ -558,9 +556,7 @@ sim_init(PyObject* self, PyObject* args)
     for(i=0; i < ntx * nty * n_state_t; i++) {
         flt = PyList_GetItem(state_in_t, i);
         if(!PyFloat_Check(flt)) {
-            char errstr[200];
-            sprintf(errstr, "Item %u in tissue state vector is not a float.", (unsigned int)i);
-            PyErr_SetString(PyExc_Exception, errstr);
+            PyErr_Format(PyExc_Exception, "Item %u in tissue state vector is not a float.", (unsigned int)i);
             return sim_clean();
         }
         rvec_state_t[i] = (Real)PyFloat_AsDouble(flt);

myokit/_sim/fiber_tissue.py

@@ -4,13 +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 os
-import myokit
 import platform
 
+import myokit
+
 # Location of C and OpenCL sources
 SOURCE_FILE = 'fiber_tissue.c'
 KERNEL_FILE = 'openclsim.cl'
@@ -122,7 +120,7 @@ class FiberTissueSimulation(myokit.CModule):
             ncells_fiber=(128, 2), ncells_tissue=(128, 128), nx_paced=5,
             g_fiber=(9, 6), g_tissue=(9, 6), g_fiber_tissue=9,
             dt=0.005, precision=myokit.SINGLE_PRECISION, native_maths=False):
-        super(FiberTissueSimulation, self).__init__()
+        super().__init__()
 
         # Deprecated since 2021-05-28
         # Un-deprecated on 2022-04-20, following Adam's request

myokit/_sim/jacobian.py

@@ -4,14 +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 os
-import myokit
-import numpy as np
 import platform
 
+import numpy as np
+
+import myokit
+
 # Location of C source file
 SOURCE_FILE = 'jacobian.cpp'
 
@@ -45,7 +44,7 @@ class JacobianTracer(myokit.CppModule):
     _index = 0  # Unique id
 
     def __init__(self, model):
-        super(JacobianTracer, self).__init__()
+        super().__init__()
 
         # Require a valid model
         model.validate()
@@ -216,7 +215,7 @@ class JacobianCalculator(myokit.CppModule):
     _index = 0  # Unique id
 
     def __init__(self, model):
-        super(JacobianCalculator, self).__init__()
+        super().__init__()
         # Require a valid model
         model.validate()