myokit 1.33.9__tar.gz → 1.35.0__tar.gz

{myokit-1.33.9/myokit.egg-info → myokit-1.35.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: myokit
-Version: 1.33.9
+Version: 1.35.0
 Summary: A simple interface to cardiac cellular electrophysiology
 Home-page: http://myokit.org
 Author: Michael Clerx
@@ -9,12 +9,10 @@ License: BSD 3-clause license
 Project-URL: Bug Tracker, https://github.com/MichaelClerx/myokit/issues
 Project-URL: Documentation, http://docs.myokit.org
 Project-URL: Source Code, https://github.com/MichaelClerx/myokit
-Platform: UNKNOWN
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 2.7
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
@@ -22,6 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Mathematics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 Provides-Extra: docs
 Provides-Extra: dev
@@ -31,10 +30,10 @@ Provides-Extra: pyqt
 Provides-Extra: pyside
 License-File: LICENSE.txt
 
-[![Ubuntu unit tests](https://github.com/MichaelClerx/myokit/workflows/Ubuntu%20unit%20tests/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"Ubuntu+unit+tests")
-[![MacOS unit tests](https://github.com/MichaelClerx/myokit/workflows/MacOS%20unit%20tests/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"MacOS+unit+tests")
-[![Windows unit tests](https://github.com/MichaelClerx/myokit/workflows/Windows%20unit%20tests/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"Windows+unit+tests")
-[![Windows Miniconda test](https://github.com/MichaelClerx/myokit/workflows/Windows%20Miniconda%20test/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"Windows+Miniconda+test")
+[![Ubuntu unit tests](https://github.com/myokit/myokit/actions/workflows/unit-tests-ubuntu.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-ubuntu.yml)
+[![MacOS unit tests](https://github.com/myokit/myokit/actions/workflows/unit-tests-macos.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-macos.yml)
+[![Windows unit tests](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows.yml)
+[![Windows Miniconda test](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows-miniconda.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows-miniconda.yml)
 [![codecov](https://codecov.io/gh/myokit/myokit/branch/main/graph/badge.svg)](https://codecov.io/gh/myokit/myokit)
 [![Documentation Status](https://readthedocs.org/projects/myokit/badge/?version=latest)](https://myokit.readthedocs.io/?badge=latest)
 
@@ -107,5 +106,3 @@ New features are best discussed in an issue before starting any implementation w
 If you use Myokit in your research, please cite it using the information in our [CITATION file](https://github.com/MichaelClerx/myokit/blob/main/CITATION).
 
 I like to [keep track of who's using Myokit](http://myokit.org/publications/) (for my CV!). If you are using Myokit for teaching, I'd love to hear about it. You can drop me a line at michael[at]myokit.org.
-
-

{myokit-1.33.9 → myokit-1.35.0}/README.md

@@ -1,7 +1,7 @@
-[![Ubuntu unit tests](https://github.com/MichaelClerx/myokit/workflows/Ubuntu%20unit%20tests/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"Ubuntu+unit+tests")
-[![MacOS unit tests](https://github.com/MichaelClerx/myokit/workflows/MacOS%20unit%20tests/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"MacOS+unit+tests")
-[![Windows unit tests](https://github.com/MichaelClerx/myokit/workflows/Windows%20unit%20tests/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"Windows+unit+tests")
-[![Windows Miniconda test](https://github.com/MichaelClerx/myokit/workflows/Windows%20Miniconda%20test/badge.svg)](https://github.com/MichaelClerx/myokit/actions?query=workflow%3A"Windows+Miniconda+test")
+[![Ubuntu unit tests](https://github.com/myokit/myokit/actions/workflows/unit-tests-ubuntu.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-ubuntu.yml)
+[![MacOS unit tests](https://github.com/myokit/myokit/actions/workflows/unit-tests-macos.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-macos.yml)
+[![Windows unit tests](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows.yml)
+[![Windows Miniconda test](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows-miniconda.yml/badge.svg)](https://github.com/myokit/myokit/actions/workflows/unit-tests-windows-miniconda.yml)
 [![codecov](https://codecov.io/gh/myokit/myokit/branch/main/graph/badge.svg)](https://codecov.io/gh/myokit/myokit)
 [![Documentation Status](https://readthedocs.org/projects/myokit/badge/?version=latest)](https://myokit.readthedocs.io/?badge=latest)
 

{myokit-1.33.9 → myokit-1.35.0}/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-1.33.9 → myokit-1.35.0}/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()