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

myokit/__init__.py

@@ -20,24 +20,11 @@ and then a myokit.Simulation which you can .run() to obtain simulated results.
 # Without an explicit __all__, importing * will result in importing all
 # functions and classes described below. No submodules of myokit will be
 # loaded!
-
-
 #
 # GUI and graphical modules should not be auto-included because they define a
 # matplotlib backend to use. If the user requires a different backend, this
 # will generate an error.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
-
-#
-# Configure logging
-#
-import logging  # noqa  (not at top of file)
-logging.basicConfig()
-del logging
-
 
 #
 # Check python version
@@ -52,27 +39,14 @@ del logging
 #
 import sys  # noqa
 if sys.hexversion < 0x03000000:  # pragma: no cover
+    raise Exception('This version of Myokit does not support Python 2.')
+elif sys.hexversion < 0x03070000:  # pragma: no cover
     import logging  # noqa
     log = logging.getLogger(__name__)
     log.warning(
-        'Myokit support for Python 2.7 is nearing the end of its lifetime.'
-        ' Please upgrade as soon as possible! Detected Python version: '
-        + sys.version)
-    del logging, log
-elif sys.hexversion < 0x03060000:  # pragma: no cover
-    import logging  # noqa
-    log = logging.getLogger(__name__)
-    log.warning(
-        'Myokit is not tested on Python 3 versions older than 3.6. Detected'
+        'Myokit is not tested on Python 3 versions older than 3.7. Detected'
         ' Python version: ' + sys.version)
     del logging, log
-
-
-# Exec() that works with Python 2 versions before 2.7.9
-if sys.hexversion < 0x020709F0:     # pragma: no python 3 cover
-    from ._exec_old import _exec    # noqa
-else:
-    from ._exec_new import _exec    # noqa
 del sys
 
 
@@ -295,11 +269,11 @@ DATE_FORMAT = '%Y-%m-%d %H:%M:%S'
 TIME_FORMAT = '%H:%M:%S'
 
 #
-# GUI: Favour PySide or PyQt
+# GUI: Favor PySide or PyQt
 #
+FORCE_PYQT6 = False
 FORCE_PYQT5 = False
-FORCE_PYQT4 = False
-FORCE_PYSIDE = False
+FORCE_PYSIDE6 = False
 FORCE_PYSIDE2 = False
 
 
@@ -341,6 +315,7 @@ from ._err import (  # noqa
     GenerationError,
     IllegalAliasError,
     IllegalReferenceError,
+    IllegalReferenceInInitialValueError,
     ImportError,
     IncompatibleModelError,
     IncompatibleUnitError,
@@ -354,7 +329,6 @@ from ._err import (  # noqa
     MissingRhsError,
     MissingTimeVariableError,
     MyokitError,
-    NonLiteralValueError,
     NumericalError,
     ParseError,
     ProtocolEventError,
@@ -462,6 +436,7 @@ from ._protocol import (  # noqa
     PacingSystem,
     Protocol,
     ProtocolEvent,
+    TimeSeriesProtocol,
 )
 from . import pacing  # noqa
 
@@ -505,6 +480,7 @@ from ._aux import (  # noqa
     default_script,
     ModelComparison,
     numpy_writer,
+    _prepare_bindings,
     python_writer,
     run,
     step,
@@ -564,11 +540,8 @@ from ._sim.opencl import (  # noqa
 )
 from ._sim.cmodel import CModel             # noqa
 from ._sim.cvodessim import Simulation      # noqa
-from ._sim.cvodesim import Simulation as LegacySimulation  # noqa
 from ._sim.cable import Simulation1d        # noqa
 from ._sim.rhs import RhsBenchmarker        # noqa
-from ._sim.icsim import ICSimulation        # noqa
-from ._sim.psim import PSimulation          # noqa
 from ._sim.jacobian import JacobianTracer, JacobianCalculator   # noqa
 from ._sim.openclsim import SimulationOpenCL                    # noqa
 from ._sim.fiber_tissue import FiberTissueSimulation            # noqa

myokit/__main__.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
 
 _line_width = 79
@@ -29,6 +26,55 @@ def colored(color, text):
     return colors[color] + str(text) + colors['normal']
 
 
+def qtforce(pyqt6=False, pyqt5=False, pyside6=False, pyside2=False):
+    """ Enforce a chosen Qt version. """
+
+    if pyqt6 or pyqt5 or pyside6 or pyside2:
+        import myokit
+
+        myokit.FORCE_PYQT6 = False
+        myokit.FORCE_PYQT5 = False
+        myokit.FORCE_PYSIDE6 = False
+        myokit.FORCE_PYSIDE2 = False
+
+        if pyqt6:
+            myokit.FORCE_PYQT6 = True
+        elif pyside6:
+            myokit.FORCE_PYSIDE6 = True
+        elif pyqt5:
+            myokit.FORCE_PYQT5 = True
+        elif pyside2:
+            myokit.FORCE_PYSIDE2 = True
+
+        import myokit.gui
+        print('Using backend: ' + myokit.gui.backend)
+
+
+def add_qtforce_arguments(parser):
+    """ Updates a parser with arguments to force a Qt version. """
+
+    parser.add_argument(
+        '--pyqt6',
+        action='store_true',
+        help='Run using the PyQt6 backend.',
+    )
+    parser.add_argument(
+        '--pyqt5',
+        action='store_true',
+        help='Run using the PyQt5 backend.',
+    )
+    parser.add_argument(
+        '--pyside6',
+        action='store_true',
+        help='Run using the PySide6 backend.',
+    )
+    parser.add_argument(
+        '--pyside2',
+        action='store_true',
+        help='Run using the PySide2 backend.',
+    )
+
+
 def main():
     """
     Parses command line arguments.
@@ -88,36 +134,13 @@ def main():
 #
 # Data block viewer
 #
-
-def block(filename, pyqt4=False, pyqt5=False, pyside=False, pyside2=False):
+def block(filename, pyqt6=False, pyqt5=False, pyside6=False, pyside2=False):
     """
     Runs the DataBlock viewer.
     """
-    import myokit
-    if pyqt5:
-        myokit.FORCE_PYQT5 = True
-        myokit.FORCE_PYQT4 = False
-        myokit.FORCE_PYSIDE = False
-        myokit.FORCE_PYSIDE2 = False
-    elif pyqt4:
-        myokit.FORCE_PYQT5 = False
-        myokit.FORCE_PYQT4 = True
-        myokit.FORCE_PYSIDE = False
-        myokit.FORCE_PYSIDE2 = False
-    elif pyside:
-        myokit.FORCE_PYQT5 = False
-        myokit.FORCE_PYQT4 = False
-        myokit.FORCE_PYSIDE = True
-        myokit.FORCE_PYSIDE2 = False
-    elif pyside2:
-        myokit.FORCE_PYQT5 = False
-        myokit.FORCE_PYQT4 = False
-        myokit.FORCE_PYSIDE = False
-        myokit.FORCE_PYSIDE2 = True
-    import myokit.gui
+    qtforce(pyqt6, pyqt5, pyside6, pyside2)
+
     import myokit.gui.datablock_viewer
-    if pyqt5 or pyqt4 or pyside or pyside2:
-        print('Using backend: ' + myokit.gui.backend)
     myokit.gui.run(myokit.gui.datablock_viewer.DataBlockViewer, filename)
 
 
@@ -137,26 +160,7 @@ def add_block_parser(subparsers):
         metavar='filename',
         help='The DataBlock zip file to open (optional).',
     )
-    parser.add_argument(
-        '--pyqt5',
-        action='store_true',
-        help='Run the DataBlock Viewer using the PyQt5 backend.',
-    )
-    parser.add_argument(
-        '--pyqt4',
-        action='store_true',
-        help='Run the DataBlock Viewer using the PyQt4 backend.',
-    )
-    parser.add_argument(
-        '--pyside',
-        action='store_true',
-        help='Run the DataBlock Viewer using the PySide backend.',
-    )
-    parser.add_argument(
-        '--pyside2',
-        action='store_true',
-        help='Run the DataBlock Viewer using the PySide2 backend.',
-    )
+    add_qtforce_arguments(parser)
     parser.set_defaults(func=block)
 
 
@@ -240,7 +244,7 @@ def add_compiler_parser(subparsers):
 
 def debug(source, variable, deps=False):
     """
-    Shows how a single variable is calculated from the initial conditions.
+    Shows how a single variable is calculated from the initial values.
     """
     import myokit
 
@@ -261,8 +265,8 @@ def add_debug_parser(subparsers):
     parser = subparsers.add_parser(
         'debug',
         description='Shows how a single variable is calculated from the '
-                    'initial conditions. The variable\'s equation and value'
-                    ' are displayed, along with the value and formula of any'
+                    ' initial values. The variable\'s equation and value are'
+                    ' displayed, along with the value and formula of any'
                     ' nested variables and the values of all dependencies.',
         help='Shows how a single variable is calculated.',
     )
@@ -421,10 +425,7 @@ def install():
     if plat == 'Linux':
         yesno = \
             'Install launcher icons and file type associations for Gnome/KDE? '
-        try:
-            yesno = raw_input(yesno)
-        except NameError:   # pragma: no python 2 cover
-            yesno = input(yesno)
+        yesno = input(yesno)
         yesno = (yesno.strip().lower())[:1] == 'y'
 
         if yesno:
@@ -432,10 +433,7 @@ def install():
 
     elif plat == 'Windows':
         yesno = 'Install start menu shortcuts? '
-        try:
-            yesno = raw_input(yesno)
-        except NameError:   # pragma: no python 2 cover
-            yesno = input(yesno)
+        yesno = input(yesno)
         yesno = (yesno.strip().lower())[:1] == 'y'
 
         if yesno:
@@ -587,38 +585,17 @@ def add_icon_parser(subparsers):
 # IDE
 #
 
-def ide(filename, pyqt4=False, pyqt5=False, pyside=False, pyside2=False):
+def ide(filename, pyqt6=False, pyqt5=False, pyside6=False, pyside2=False):
     """
     Runs the Myokit IDE.
     """
+    qtforce(pyqt6, pyqt5, pyside6, pyside2)
+
     import os
-    import myokit
-    if pyqt5:
-        myokit.FORCE_PYQT5 = True
-        myokit.FORCE_PYQT4 = False
-        myokit.FORCE_PYSIDE = False
-        myokit.FORCE_PYSIDE2 = False
-    elif pyqt4:
-        myokit.FORCE_PYQT5 = False
-        myokit.FORCE_PYQT4 = True
-        myokit.FORCE_PYSIDE = False
-        myokit.FORCE_PYSIDE2 = False
-    elif pyside:
-        myokit.FORCE_PYQT5 = False
-        myokit.FORCE_PYQT4 = False
-        myokit.FORCE_PYSIDE = True
-        myokit.FORCE_PYSIDE2 = False
-    elif pyside2:
-        myokit.FORCE_PYQT5 = False
-        myokit.FORCE_PYQT4 = False
-        myokit.FORCE_PYSIDE = False
-        myokit.FORCE_PYSIDE2 = True
-    import myokit.gui
-    import myokit.gui.ide
-    if pyqt5 or pyqt4 or pyside or pyside2:
-        print('Using backend: ' + myokit.gui.backend)
     if filename is not None:
         filename = os.path.abspath(os.path.expanduser(filename))
+
+    import myokit.gui.ide
     myokit.gui.run(myokit.gui.ide.MyokitIDE, filename)
 
 
@@ -638,26 +615,7 @@ def add_ide_parser(subparsers):
         metavar='filename',
         help='The mmt file to open (optional).',
     )
-    parser.add_argument(
-        '--pyqt5',
-        action='store_true',
-        help='Run the IDE using the PyQt5 backend.',
-    )
-    parser.add_argument(
-        '--pyqt4',
-        action='store_true',
-        help='Run the IDE using the PyQt4 backend.',
-    )
-    parser.add_argument(
-        '--pyside',
-        action='store_true',
-        help='Run the IDE using the PySide backend.',
-    )
-    parser.add_argument(
-        '--pyside2',
-        action='store_true',
-        help='Run the DataBlock Viewer using the PySide2 backend.',
-    )
+    add_qtforce_arguments(parser)
     parser.set_defaults(func=ide)
 
 
@@ -741,11 +699,12 @@ def add_import_parser(subparsers):
 # Log viewer
 #
 
-def log(filenames):
+def log(filenames, pyqt6=False, pyqt5=False, pyside6=False, pyside2=False):
     """
     Runs the DataLog Viewer.
     """
-    import myokit.gui
+    qtforce(pyqt6, pyqt5, pyside6, pyside2)
+
     import myokit.gui.datalog_viewer
     myokit.gui.run(myokit.gui.datalog_viewer.DataLogViewer, *filenames)
 
@@ -761,6 +720,7 @@ def add_log_parser(subparsers):
         description='Runs the DataLog Viewer (PROTOTYPE).',
         help='Runs the DataLog Viewer (PROTOTYPE).',
     )
+    add_qtforce_arguments(parser)
     parser.add_argument(
         'filenames',
         default=None,
@@ -867,10 +827,7 @@ def opencl_select():
     try:
         while True:
             x = 'Select device: '
-            try:
-                x = raw_input(x)
-            except NameError:   # pragma: no python 2 cover
-                x = input(x)    # lgtm [py/use-of-input]
+            x = input(x)
             x = x.strip()
             if x == '':
                 x = None
@@ -932,10 +889,7 @@ def reset(force=False):
         remove = True
     else:
         yesno = 'Remove all Myokit settings files? '
-        try:
-            yesno = raw_input(yesno)
-        except NameError:           # pragma: no python 2 cover
-            yesno = input(yesno)    # lgtm [py/use-of-input]
+        yesno = input(yesno)
         yesno = yesno.strip().lower()
         remove = (yesno[:1] == 'y')
     if remove:
@@ -1290,11 +1244,6 @@ def add_test_parser(subparsers):
         'examples', help='Test example notebooks.')
     example_parser.set_defaults(testfunc=test_examples)
 
-    # Publication examples
-    pub_parser = subparsers.add_parser(
-        'pub', help='Run publication examples.')
-    pub_parser.set_defaults(testfunc=test_examples_pub)
-
     # Style tests
     style_parser = subparsers.add_parser('style', help='Run code style tests.')
     style_parser.set_defaults(testfunc=test_style)
@@ -1334,7 +1283,7 @@ def test_coverage(args):
     try:
         print('Gathering coverage data')
         p = subprocess.Popen([
-            'python3',
+            sys.executable,
             '-m',
             'coverage',
             'run',
@@ -1358,7 +1307,7 @@ def test_coverage(args):
 
         print('Generating coverage report.')
         p = subprocess.Popen([
-            'python3',
+            sys.executable,
             '-m',
             'coverage',
             'report',
@@ -1789,8 +1738,7 @@ def test_examples_single(root, path):
         p = subprocess.Popen(
             cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env
         )
-        stdout, stderr = p.communicate()
-        # TODO: Use p.communicate(timeout=3600) if Python3 only
+        stdout, stderr = p.communicate(timeout=3600)
         if p.returncode != 0:
             # Show failing code, output and errors before returning
             print('ERROR')
@@ -1840,23 +1788,6 @@ def test_examples_all(root, books):
         print('ok: Successfully ran all (' + str(len(books)) + ') notebooks.')
 
 
-def test_examples_pub(args):
-    """
-    Runs all publication examples, exits if one of them fails.
-    """
-    import os
-    import sys
-    import myokit
-
-    # Get publications directory
-    path = os.path.join(myokit.DIR_MYOKIT, 'tests', 'publications')
-
-    # PBMB 2016. Myokit: A simple interface to cardiac cellular
-    # electrophysiology
-    if test_mmt_files(os.path.join(path, 'pbmb-2016')):
-        sys.exit(1)
-
-
 def test_examples_web(args):
     """
     Runs all web examples, exits if one of them fails.
@@ -2209,4 +2140,7 @@ def add_video_parser(subparsers):
 
 
 if __name__ == '__main__':
+    import logging
+    logging.basicConfig()
+
     main()

myokit/_aux.py

@@ -6,9 +6,6 @@
 # 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 sys
@@ -29,7 +26,7 @@ class Benchmarker(myokit.tools.Benchmarker):
         warnings.warn(
             'The class `myokit.Benchmarker` is deprecated.'
             ' Please use `myokit.tools.Benchmarker` instead.')
-        super(Benchmarker, self).__init__()
+        super().__init__()
 
 
 def date():
@@ -150,7 +147,7 @@ def format_path(path, root='.'):
     return myokit.tools.format_path(path, root)
 
 
-class ModelComparison(object):
+class ModelComparison:
     """
     Compares two models.
 
@@ -281,12 +278,12 @@ class ModelComparison(object):
 
     def _state(self, m1, m2):
         """
-        Compares two models' states.
+        Compares two models' states and initial values.
         """
         s1 = iter([v.qname() for v in m1.states()])
         s2 = iter([v.qname() for v in m2.states()])
-        c1 = m1.state()
-        c2 = m2.state()
+        c1 = m1.initial_values()
+        c2 = m2.initial_values()
         for k, v1 in enumerate(s1):
             try:
                 v2 = next(s2)
@@ -298,7 +295,7 @@ class ModelComparison(object):
                     '[x] Mismatched State at position ' + str(k) + ': [1]<'
                     + v1 + '> [2]<' + v2 + '>')
                 continue
-            if c1[k] != c2[k]:
+            if c1[k].code() != c2[k].code():
                 self._write('[x] Mismatched Initial value for <' + v1 + '>')
         n = m2.count_states()
         for k, v2 in enumerate(s2):
@@ -434,6 +431,50 @@ def python_writer():
     return _pywriter_
 
 
+def _prepare_bindings(model, labels):
+    """
+    Takes a mapping of binding labels to internal references and returns a map
+    from variable instances to the same internal references.
+
+    This method also modifies ``model``: All bindings that are not mapped to
+    an internal reference will be removed.
+
+    The argument ``mapping`` should take the form::
+
+        labels = {
+            binding_label_1 : internal_name_1,
+            binding_label_2 : internal_name_2,
+            ...
+            }
+
+    The returned dictionary will have the form::
+
+        variables = {
+            variable_x : internal_name_1,
+            variable_y : internal_name_2,
+            ...
+            }
+
+    Unsupported bindings (i.e. bindings not appearing in ``labels``) will
+    be ignored.
+    """
+    unused = []
+    variables = {}
+    for label, var in model.bindings():
+        try:
+            variables[var] = labels[label]
+        except KeyError:
+            unused.append(var)
+            continue
+        # TODO: Remove this line; https://github.com/myokit/myokit/issues/320
+        var.set_rhs(0)
+
+    for var in unused:
+        var.set_binding(None)
+
+    return variables
+
+
 def run(model, protocol, script, stdout=None, stderr=None, progress=None):
     """
     Runs a python ``script`` using the given ``model`` and ``protocol``.
@@ -476,9 +517,9 @@ def run(model, protocol, script, stdout=None, stderr=None, progress=None):
     script = '\n' + script
 
     # Class to run scripts
-    class Runner(object):
+    class Runner:
         def __init__(self, model, protocol, script, stdout, stderr, progress):
-            super(Runner, self).__init__()
+            super().__init__()
             self.model = model
             self.protocol = protocol
             self.script = script
@@ -511,7 +552,7 @@ def run(model, protocol, script, stdout=None, stderr=None, progress=None):
                     'get_model': get_model,
                     'get_protocol': get_protocol,
                 }
-                myokit._exec(self.script, environment)
+                exec(self.script, environment)
             finally:
                 if oldstdout is not None:
                     sys.stdout = oldstdout
@@ -549,7 +590,7 @@ def step(model, initial=None, reference=None, ignore_errors=False):
     """
     # Get initial state
     if initial is None:
-        initial = model.state()
+        initial = model.initial_values(as_floats=True)
 
     # Get evaluation at initial state
     values = model.evaluate_derivatives(
@@ -620,8 +661,13 @@ def step(model, initial=None, reference=None, ignore_errors=False):
             # Large error, small error, or no error
             else:
                 mark_error = False
-                threshold = 13
-                if xx[:threshold] != yy[:threshold]:
+                abs_err = abs(x - y)
+                if abs_err:
+                    rel_err = abs(x - y) / max(abs(x), abs(y))
+                    n_eps = rel_err / sys.float_info.epsilon
+                else:
+                    n_eps = rel_err = 0
+                if n_eps > 1e6:
                     # "Large" error
                     errors += 1
                     line += ' X'
@@ -664,7 +710,7 @@ def step(model, initial=None, reference=None, ignore_errors=False):
         if warnings > 0:
             log.append('Found (' + str(warnings) + ') small mismatches.')
 
-    # Finalise and return
+    # Finalize and return
     log.append('-' * line_width)
     return '\n'.join(log)
 

myokit/_bin/example.mmt

@@ -3,7 +3,6 @@ name: Luo-Rudy 1991
 desc: """
 Implementation of the Luo-Rudy model I for the ventricular myocyte.
 Based on an updated formulation downloaded from http://rudylab.wustl.edu
-and licensed under a GNU GPL license version 2.
 """
 # Initial conditions
 membrane.V = -84.5286
@@ -19,7 +18,7 @@ ica.Ca_i   = 0.0002
 desc: """
 Membrane potential and stimulus
 """
-C = 1.0 [uF/cm^2]
+C = 1 [uF/cm^2]
     in [uF/cm^2]
 dot(V) = - (1/C) * (i_ion + i_diff + i_stim) in [mV]
     label membrane_potential

myokit/_bin/install-win/menu.json

@@ -9,13 +9,6 @@ icons = icons.replace('\\', '/')
     "menu_name": "Myokit",
     "menu_items":
         [
-            {
-                "name": "Myokit IDE",
-                "script": "${PYTHON_SCRIPTS}/myokit.exe",
-                "scriptarguments": ["ide"],
-                "workdir": "${PREFIX}",
-                "icon": "<?=icons?>/icon-ide.ico"
-            },
             {
                 "name": "DataLog viewer",
                 "script": "${PYTHON_SCRIPTS}/myokit.exe",
@@ -29,6 +22,13 @@ icons = icons.replace('\\', '/')
                 "scriptarguments": ["block"],
                 "workdir": "${PREFIX}",
                 "icon": "<?=icons?>/icon-datablock-viewer.ico"
+            },
+            {
+                "name": "Myokit IDE",
+                "script": "${PYTHON_SCRIPTS}/myokit.exe",
+                "scriptarguments": ["ide"],
+                "workdir": "${PREFIX}",
+                "icon": "<?=icons?>/icon-ide.ico"
             }
         ]
 }