myokit 1.34.0__tar.gz → 1.35.0__tar.gz

{myokit-1.34.0/myokit.egg-info → myokit-1.35.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: myokit
-Version: 1.34.0
+Version: 1.35.0
 Summary: A simple interface to cardiac cellular electrophysiology
 Home-page: http://myokit.org
 Author: Michael Clerx
@@ -13,7 +13,6 @@ 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
@@ -21,6 +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

{myokit-1.34.0 → myokit-1.35.0}/myokit/__init__.py

@@ -20,16 +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
-
 
 #
 # Check python version
@@ -44,27 +39,14 @@ from __future__ import print_function, unicode_literals
 #
 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
 
 
@@ -289,9 +271,9 @@ TIME_FORMAT = '%H:%M:%S'
 #
 # GUI: Favor PySide or PyQt
 #
+FORCE_PYQT6 = False
 FORCE_PYQT5 = False
-FORCE_PYQT4 = False
-FORCE_PYSIDE = False
+FORCE_PYSIDE6 = False
 FORCE_PYSIDE2 = False
 
 

{myokit-1.34.0 → 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)
 
 
@@ -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:
@@ -1329,7 +1283,7 @@ def test_coverage(args):
     try:
         print('Gathering coverage data')
         p = subprocess.Popen([
-            'python3',
+            sys.executable,
             '-m',
             'coverage',
             'run',
@@ -1353,7 +1307,7 @@ def test_coverage(args):
 
         print('Generating coverage report.')
         p = subprocess.Popen([
-            'python3',
+            sys.executable,
             '-m',
             'coverage',
             'report',
@@ -1784,8 +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')

{myokit-1.34.0 → myokit-1.35.0}/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.
 
@@ -520,9 +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
@@ -555,7 +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

{myokit-1.34.0 → myokit-1.35.0}/myokit/_config.py

@@ -5,27 +5,18 @@
 # 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
-
-# Load Myokit, at least, the bit that's been setup so far. This just means
-# this method will add a link to the myokit module already being loaded
-# into this method's namespace. This allows us to use the constants defined
-# before this method was called.
-import myokit
-
-# Load standard library modules
+import configparser
 import logging
 import os
 import platform
 import sys
 import warnings
 
-# ConfigParser in Python 2 and 3
-try:
-    from ConfigParser import ConfigParser
-except ImportError:
-    from configparser import RawConfigParser as ConfigParser
+# Load Myokit, at least, the bit that's been setup so far. This just means
+# this method will add a link to the myokit module already being loaded
+# into this method's namespace. This allows us to use the constants defined
+# before this method was called.
+import myokit
 
 
 def _create(path):
@@ -37,7 +28,7 @@ def _create(path):
     system = platform.system()
 
     # Create config parser
-    config = ConfigParser(allow_no_value=True)
+    config = configparser.RawConfigParser(allow_no_value=True)
 
     # Make the parser case sensitive (need for unix paths!)
     config.optionxform = str
@@ -71,12 +62,12 @@ def _create(path):
     # GUI Backend
     config.add_section('gui')
     config.set('gui', '# Backend to use for graphical user interface.')
-    config.set('gui', '# Valid options are pyqt5, pyqt4, pyside2 and pyside.')
+    config.set('gui', '# Valid options are pyqt6, pyqt5, pyside6 and pyside2.')
     config.set('gui', '# Leave unset for automatic selection.')
+    config.set('gui', '#backend = pyqt6')
     config.set('gui', '#backend = pyqt5')
-    config.set('gui', '#backend = pyqt4')
+    config.set('gui', '#backend = pyside6')
     config.set('gui', '#backend = pyside2')
-    config.set('gui', '#backend = pyside')
 
     # Locations of sundials library
     config.add_section('sundials')
@@ -223,7 +214,7 @@ def _load():
         del lines, inline_comment
 
     # Create the config parser (no value allows comments)
-    config = ConfigParser(allow_no_value=True)
+    config = configparser.RawConfigParser(allow_no_value=True)
 
     # Make the parser case sensitive (need for unix paths!)
     config.optionxform = str
@@ -270,30 +261,30 @@ def _load():
     # GUI Backend
     if config.has_option('gui', 'backend'):
         x = config.get('gui', 'backend').strip().lower()
-        if x == 'pyqt' or x == 'pyqt4':
-            myokit.FORCE_PYQT4 = True
+        if x == 'pyqt6':
+            myokit.FORCE_PYQT6 = True
             myokit.FORCE_PYQT5 = False
-            myokit.FORCE_PYSIDE = False
+            myokit.FORCE_PYSIDE6 = False
             myokit.FORCE_PYSIDE2 = False
         elif x == 'pyqt5':
-            myokit.FORCE_PYQT4 = False
+            myokit.FORCE_PYQT6 = False
             myokit.FORCE_PYQT5 = True
-            myokit.FORCE_PYSIDE = False
+            myokit.FORCE_PYSIDE6 = False
             myokit.FORCE_PYSIDE2 = False
-        elif x == 'pyside':
-            myokit.FORCE_PYQT4 = False
+        elif x == 'pyside6':
+            myokit.FORCE_PYQT6 = False
             myokit.FORCE_PYQT5 = False
-            myokit.FORCE_PYSIDE = True
+            myokit.FORCE_PYSIDE6 = True
             myokit.FORCE_PYSIDE2 = False
         elif x == 'pyside2':
-            myokit.FORCE_PYQT4 = False
+            myokit.FORCE_PYQT6 = False
             myokit.FORCE_PYQT5 = False
-            myokit.FORCE_PYSIDE = False
+            myokit.FORCE_PYSIDE6 = False
             myokit.FORCE_PYSIDE2 = True
         elif x != '':
             warnings.warn(
                 'Invalid setting in myokit.ini. Expected values for backend'
-                ' are pyqt, pyqt4, pyqt5, pyside, or pyside2. Got: ' + x)
+                ' are pyqt6, pyqt5, pyside6, or pyside2. Got: ' + x)
 
     # Sundials libraries, header files, and version
     if config.has_option('sundials', 'lib'):