myokit 1.35.4__tar.gz → 1.36.1__tar.gz

{myokit-1.35.4 → myokit-1.36.1}/LICENSE.txt

@@ -3,7 +3,7 @@ BSD 3-Clause License
 Copyright (c) 2011-2017 Maastricht University. All rights reserved.
 Copyright (c) 2017-2020 University of Oxford. All rights reserved.
 (University of Oxford means the Chancellor, Masters and Scholars of the University of Oxford, having an administrative office at Wellington Square, Oxford OX1 2JD, UK).
-Copyright (c) 2020-2023 University of Nottingham. All rights reserved.
+Copyright (c) 2020-2024 University of Nottingham. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

{myokit-1.35.4/myokit.egg-info → myokit-1.36.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: myokit
-Version: 1.35.4
+Version: 1.36.1
 Summary: A modeling and simulation tool for cardiac cellular electrophysiology
 Home-page: http://myokit.org
 Author: Michael Clerx
@@ -37,19 +37,19 @@ License-File: LICENSE.txt
 [![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](http://myokit.org/static/img/logo.png)
+![Myokit](https://myokit.org/static/img/logo.png)
 
-[Myokit](http://myokit.org) is a tool for modeling and simulation of cardiac cellular electrophysiology.
+[Myokit](https://myokit.org) is a tool for modeling and simulation of cardiac cellular electrophysiology.
 It's [open-source](https://github.com/myokit/myokit/blob/main/LICENSE.txt), written in Python, hosted on [GitHub](https://github.com/myokit/myokit/) and available on [PyPi](https://pypi.org/project/myokit/).
 For the latest documentation, see [myokit.readthedocs.io](https://myokit.readthedocs.io/).
 
-More information, including examples and an installation guide, is available on [myokit.org](http://myokit.org).
+More information, including examples and an installation guide, is available on [myokit.org](https://myokit.org).
 A list of changes introduced in each Myokit release is provided in the [Changelog](https://github.com/myokit/myokit/blob/main/CHANGELOG.md).
 
 
 ## Install
 
-For full installation details (on linux, mac, or windows), please see [http://myokit.org/install](http://myokit.org/install).
+For full installation details (on linux, mac, or windows), please see [https://myokit.org/install](https://myokit.org/install).
 A shorter installation guide for experienced users is given below.
 
 To install Myokit, using PyQt5 for Myokit's GUI components, run:
@@ -97,12 +97,23 @@ To see what else Myokit can do, type
 
 ## Contributing to Myokit
 
-You can contribute to Myokit by [reporting issues](https://github.com/myokit/myokit/issues), but code contributions (bugfixes, new formats, new features etc.) are also very welcome!
-New features are best discussed in an issue before starting any implementation work, and guidelines for code style (and more) can be found in [CONTRIBUTING.md](https://github.com/myokit/myokit/blob/main/CONTRIBUTING.md).
+Contributing to Myokit is as easy as [asking questions](https://github.com/myokit/myokit/discussions) or posting [issues and feature requests](https://github.com/myokit/myokit/issues), and we have [pledged](./CODE_OF_CONDUCT.md) to make this an inclusive experience.
+
+We are always looking for people to contribute code too!
+Guidelines to help you do this are provided in [CONTRIBUTING.md](./CONTRIBUTING.md), but before diving in please [open an issue](https://github.com/myokit/myokit/issues) so that we can first discuss what needs to be done.
+
+A high-level plan for Myokit's future is provided in the [roadmap](./ROADMAP.md).
+
+
+### Meet the team!
+
+Myokit's development is driven by a [team](https://github.com/orgs/myokit/people) at the Universities of Nottingham, Oxford, and Macao, led by Michael Clerx (Nottingham).
+It is guided by an external advisory board composed of Jordi Heijman (Maastricht University), Trine Krogh-Madsen (Weill Cornell Medicine), and David Gavaghan (Oxford).
 
 
 ## Citing Myokit
 
 If you use Myokit in your research, please cite it using the information in our [CITATION file](https://github.com/myokit/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.
+We like to [keep track of who's using Myokit](https://myokit.org/publications/) for research (based on publications) and teaching (based on peronsal correspondence).
+If you've used Myokit in teaching, we're always happy to hear about it so please get in touch via the [discussion board](https://github.com/myokit/myokit/discussions)!

{myokit-1.35.4 → myokit-1.36.1}/README.md

@@ -5,19 +5,19 @@
 [![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](http://myokit.org/static/img/logo.png)
+![Myokit](https://myokit.org/static/img/logo.png)
 
-[Myokit](http://myokit.org) is a tool for modeling and simulation of cardiac cellular electrophysiology.
+[Myokit](https://myokit.org) is a tool for modeling and simulation of cardiac cellular electrophysiology.
 It's [open-source](https://github.com/myokit/myokit/blob/main/LICENSE.txt), written in Python, hosted on [GitHub](https://github.com/myokit/myokit/) and available on [PyPi](https://pypi.org/project/myokit/).
 For the latest documentation, see [myokit.readthedocs.io](https://myokit.readthedocs.io/).
 
-More information, including examples and an installation guide, is available on [myokit.org](http://myokit.org).
+More information, including examples and an installation guide, is available on [myokit.org](https://myokit.org).
 A list of changes introduced in each Myokit release is provided in the [Changelog](https://github.com/myokit/myokit/blob/main/CHANGELOG.md).
 
 
 ## Install
 
-For full installation details (on linux, mac, or windows), please see [http://myokit.org/install](http://myokit.org/install).
+For full installation details (on linux, mac, or windows), please see [https://myokit.org/install](https://myokit.org/install).
 A shorter installation guide for experienced users is given below.
 
 To install Myokit, using PyQt5 for Myokit's GUI components, run:
@@ -65,12 +65,23 @@ To see what else Myokit can do, type
 
 ## Contributing to Myokit
 
-You can contribute to Myokit by [reporting issues](https://github.com/myokit/myokit/issues), but code contributions (bugfixes, new formats, new features etc.) are also very welcome!
-New features are best discussed in an issue before starting any implementation work, and guidelines for code style (and more) can be found in [CONTRIBUTING.md](https://github.com/myokit/myokit/blob/main/CONTRIBUTING.md).
+Contributing to Myokit is as easy as [asking questions](https://github.com/myokit/myokit/discussions) or posting [issues and feature requests](https://github.com/myokit/myokit/issues), and we have [pledged](./CODE_OF_CONDUCT.md) to make this an inclusive experience.
+
+We are always looking for people to contribute code too!
+Guidelines to help you do this are provided in [CONTRIBUTING.md](./CONTRIBUTING.md), but before diving in please [open an issue](https://github.com/myokit/myokit/issues) so that we can first discuss what needs to be done.
+
+A high-level plan for Myokit's future is provided in the [roadmap](./ROADMAP.md).
+
+
+### Meet the team!
+
+Myokit's development is driven by a [team](https://github.com/orgs/myokit/people) at the Universities of Nottingham, Oxford, and Macao, led by Michael Clerx (Nottingham).
+It is guided by an external advisory board composed of Jordi Heijman (Maastricht University), Trine Krogh-Madsen (Weill Cornell Medicine), and David Gavaghan (Oxford).
 
 
 ## Citing Myokit
 
 If you use Myokit in your research, please cite it using the information in our [CITATION file](https://github.com/myokit/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.
+We like to [keep track of who's using Myokit](https://myokit.org/publications/) for research (based on publications) and teaching (based on peronsal correspondence).
+If you've used Myokit in teaching, we're always happy to hear about it so please get in touch via the [discussion board](https://github.com/myokit/myokit/discussions)!

{myokit-1.35.4 → myokit-1.36.1}/myokit/__init__.py

@@ -79,7 +79,7 @@ Copyright (c) 2017-2020 University of Oxford. All rights reserved.
  (University of Oxford means the Chancellor, Masters and Scholars of the
   University of Oxford, having an administrative office at Wellington Square,
   Oxford OX1 2JD, UK).
-Copyright (c) 2020-2023 University of Nottingham. All rights reserved.
+Copyright (c) 2020-2024 University of Nottingham. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
@@ -118,7 +118,7 @@ LICENSE_HTML = """
     <br />(University of Oxford means the Chancellor, Masters and Scholars of
     the University of Oxford, having an administrative office at Wellington
     Square, Oxford OX1 2JD, UK).
-    <br />Copyright (c) 2020-2023 University of Nottingham. All rights
+    <br />Copyright (c) 2020-2024 University of Nottingham. All rights
     reserved.</br></p>
 <p>
     Redistribution and use in source and binary forms, with or without
@@ -220,8 +220,10 @@ DEBUG_WG = False
 DEBUG_SC = False
 # Show C debug Messages when running compiled code:
 DEBUG_SM = False
-# Show C Profiling information when running compiled code:
+# Show C profiling information when running compiled code:
 DEBUG_SP = False
+# Show C detailed simulator stats when running simulations
+DEBUG_SS = False
 
 #
 # Compatibility settings: Some users report problems with output capturing.

{myokit-1.35.4 → myokit-1.36.1}/myokit/__main__.py

@@ -924,10 +924,8 @@ def add_reset_parser(subparsers):
 # Run
 #
 
-def run(source, debug_sg, debug_wg, debug_sc, debug_sm, debug_sp):
-    """
-    Runs an mmt file script.
-    """
+def run(source, debug_sg, debug_wg, debug_sc, debug_sm, debug_sp, debug_ss):
+    """ Runs an mmt file script. """
     import sys
     import myokit
 
@@ -942,6 +940,8 @@ def run(source, debug_sg, debug_wg, debug_sc, debug_sm, debug_sp):
     myokit.DEBUG_SM = myokit.DEBUG_SM or debug_sm
     # Show profiling information when running compiled code
     myokit.DEBUG_SP = myokit.DEBUG_SP or debug_sp
+    # Show CVODES stats
+    myokit.DEBUG_SS = myokit.DEBUG_SS or debug_ss
 
     # Read mmt file
     try:
@@ -1011,31 +1011,31 @@ def add_run_parser(subparsers):
         '--debug-sg',
         action='store_true',
         help='Show the generated code instead of executing it.',
-        #metavar='debug_sg',
     )
     parser.add_argument(
         '--debug-wg',
         action='store_true',
         help='Write the generated code to file(s) instead of executing it.',
-        #metavar='debug_wg',
     )
     parser.add_argument(
         '--debug-sc',
         action='store_true',
         help='Show compiler output.',
-        #metavar='debug_sc',
     )
     parser.add_argument(
         '--debug-sm',
         action='store_true',
         help='Show debug messages when executing compiled code.',
-        #metavar='debug_sm',
     )
     parser.add_argument(
         '--debug-sp',
         action='store_true',
         help='Show profiling information when executing compiled code.',
-        #metavar='debug_sp',
+    )
+    parser.add_argument(
+        '--debug-ss',
+        action='store_true',
+        help='Show CVODES stats when running simulations.',
     )
     parser.set_defaults(func=run)
 
@@ -1239,11 +1239,6 @@ def add_test_parser(subparsers):
         help='Test documentation cover, building, and doc tests.')
     doc_parser.set_defaults(testfunc=test_documentation)
 
-    # Example notebooks
-    example_parser = subparsers.add_parser(
-        'examples', help='Test example notebooks.')
-    example_parser.set_defaults(testfunc=test_examples)
-
     # Style tests
     style_parser = subparsers.add_parser('style', help='Run code style tests.')
     style_parser.set_defaults(testfunc=test_style)
@@ -1643,151 +1638,6 @@ def test_doc_coverage_index(modules, classes, functions):
     return n == 0
 
 
-def test_examples(args):
-    """
-    Tests the example notebooks.
-    """
-    books = test_examples_list('examples')
-    print(books)
-
-    print('Found ' + str(len(books)) + ' notebook(s).')
-    test_examples_index('examples', books)
-    test_examples_all('examples', books)
-
-
-def test_examples_index(root, books):
-    """ Check that every notebook is included in the index. """
-    import os
-    import sys
-
-    print('Checking index...')
-
-    # Index file is in ./examples/README.md
-    index_file = os.path.join(root, 'README.md')
-    with open(index_file, 'r') as f:
-        index_contents = f.read()
-
-    # Find which are not indexed
-    not_indexed = [book for book in books if book not in index_contents]
-
-    # Report any failures
-    if len(not_indexed) > 0:
-        print('FAIL: Unindexed notebooks')
-        for book in sorted(not_indexed):
-            print('  ' + str(book))
-        sys.exit(1)
-    else:
-        print('ok: All (' + str(len(books)) + ') notebooks are indexed.')
-
-
-def test_examples_list(root, recursive=True):
-    """ Returns a list of all notebooks in a directory. """
-    import os
-
-    def scan(root, recursive, notebooks):
-        for filename in os.listdir(root):
-            path = os.path.join(root, filename)
-
-            # Add notebook
-            if os.path.splitext(path)[1] == '.ipynb':
-                notebooks.append(path)
-
-            # Recurse into subdirectories
-            elif recursive and os.path.isdir(path):
-                # Ignore hidden directories
-                if filename[:1] == '.':
-                    continue
-                scan(path, recursive, notebooks)
-        return notebooks
-
-    notebooks = []
-    scan(root, recursive, notebooks)
-    notebooks = [os.path.relpath(book, root) for book in notebooks]
-
-    return notebooks
-
-
-def test_examples_single(root, path):
-    """ Tests a notebook in a subprocess, exists if it doesn't finish. """
-    import myokit
-    import nbconvert
-    import os
-    import subprocess
-    import sys
-
-    b = myokit.tools.Benchmarker()
-    print('Running ' + path + ' ... ', end='')
-    sys.stdout.flush()
-
-    # Load notebook, convert to python
-    e = nbconvert.exporters.PythonExporter()
-    code, _ = e.from_filename(os.path.join(root, path))
-
-    # Remove coding statement, if present
-    code = '\n'.join([x for x in code.splitlines() if x[:9] != '# coding'])
-
-    # Tell matplotlib not to produce any figures
-    env = os.environ.copy()
-    env['MPLBACKEND'] = 'Template'
-
-    # Run in subprocess
-    cmd = [sys.executable, '-c', code]
-    curdir = os.getcwd()
-    try:
-        os.chdir(root)
-        p = subprocess.Popen(
-            cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env
-        )
-        stdout, stderr = p.communicate(timeout=3600)
-        if p.returncode != 0:
-            # Show failing code, output and errors before returning
-            print('ERROR')
-            print('-- script ' + '-' * (79 - 10))
-            for i, line in enumerate(code.splitlines()):
-                j = str(1 + i)
-                print(j + ' ' * (5 - len(j)) + line)
-            print('-- stdout ' + '-' * (79 - 10))
-            print(stdout)
-            print('-- stderr ' + '-' * (79 - 10))
-            print(stderr)
-            print('-' * 79)
-            return False
-    except KeyboardInterrupt:
-        p.terminate()
-        print('ABORTED')
-        sys.exit(1)
-    finally:
-        os.chdir(curdir)
-
-    # Successfully run
-    print('ok (' + b.format(b.time()) + ')')
-    return True
-
-
-def test_examples_all(root, books):
-    """ Runs all notebooks, and exits if one fails. """
-    import sys
-
-    # Ignore books with deliberate errors, but check they still exist
-    ignore_list = [
-    ]
-    books = set(books) - set(ignore_list)
-
-    # Scan and run
-    print('Testing notebooks')
-    failed = []
-    for book in books:
-        if not test_examples_single(root, book):
-            failed.append(book)
-    if failed:
-        print('FAIL: Errors encountered in notebooks')
-        for book in failed:
-            print('  ' + str(book))
-        sys.exit(1)
-    else:
-        print('ok: Successfully ran all (' + str(len(books)) + ') notebooks.')
-
-
 def test_examples_web(args):
     """
     Runs all web examples, exits if one of them fails.

{myokit-1.35.4 → myokit-1.36.1}/myokit/_config.py

@@ -139,7 +139,7 @@ def _create(path):
         config.set('opencl', 'lib', ';'.join([
             c64 + 'Intel\\OpenCL SDK\\6.3\\lib\\x64',
             c64 + 'AMD APP SDK\\2.9\\bin\\x64',
-            c64 + 'NVIDIA GPU Computing Toolkit\CUDA\\v11.8\\lib\\x64',
+            c64 + 'NVIDIA GPU Computing Toolkit\\CUDA\\v11.8\\lib\\x64',
         ]))
     else:
         # Linux and mac
@@ -199,7 +199,7 @@ def _load():
             lines = f.readlines()
 
         import re
-        inline_comment = re.compile('[\w]+[\s]*=[\s]*.+?\s+(;)')
+        inline_comment = re.compile(r'[\w]+[\s]*=[\s]*.+?\s+(;)')
         for i, line in enumerate(lines):
             m = inline_comment.match(line)
             if m is not None:

{myokit-1.35.4 → myokit-1.36.1}/myokit/_expressions.py

@@ -665,8 +665,8 @@ class Expression:
 
         # Create function text
         args = [w.ex(x) for x in self._references]
-        c = 'def ex_pyfunc_generated(' + ','.join(args) + '):\n    return ' \
-            + w.ex(self)
+        c = ('def ex_pyfunc_generated(' + ','.join(sorted(args))
+             + '):\n    return ' + w.ex(self))
 
         # Create function
         local = {}
@@ -682,8 +682,8 @@ class Expression:
         """
         Returns a string representing this expression in Python syntax.
 
-        By default, built-in functions such as 'exp' are converted to the
-        Python version 'math.exp'. To use the numpy versions, set
+        By default, built-in functions such as ``exp`` are converted to the
+        Python version ``math.exp``. To use the numpy versions, set
         ``numpy=True``.
         """
         # Get expression writer
@@ -810,7 +810,6 @@ class Expression:
 class Number(Expression):
     """
     Represents a number with an optional unit for use in Myokit expressions.
-    All numbers used in Myokit expressions are floating point.
 
     >>> import myokit
     >>> x = myokit.Number(10)
@@ -821,11 +820,12 @@ class Number(Expression):
     >>> print(x)
     5 [V]
 
+    All numbers used in Myokit expressions are floating point.
+
     Arguments:
 
     ``value``
         A numerical value (something that can be converted to a ``float``).
-        Number objects are immutable so no clone constructor is provided.
     ``unit``
         A unit to associate with this number. If no unit is specified the
         number's unit will be left undefined.

{myokit-1.35.4 → myokit-1.36.1}/myokit/_model_api.py

@@ -10,6 +10,8 @@ import re
 
 from collections import OrderedDict
 
+import numpy
+
 import myokit
 
 
@@ -1406,11 +1408,13 @@ class Model(ObjectWithMetaData, VarProvider):
                         value = float('nan')
                     values[eq.lhs] = value
         else:
-            for group in order.values():
-                for eq in group:
-                    if eq.lhs in values:
-                        continue
-                    values[eq.lhs] = eq.rhs.eval(values, precision=precision)
+            with numpy.errstate(all='raise'):
+                for group in order.values():
+                    for eq in group:
+                        if eq.lhs in values:
+                            continue
+                        values[eq.lhs] = eq.rhs.eval(
+                            values, precision=precision)
 
         # Return calculated state
         return [values[state.lhs()] for state in self._state_vars]
@@ -1571,7 +1575,7 @@ class Model(ObjectWithMetaData, VarProvider):
         ``derivatives=None``
             An optional list or other sequence of evaluated derivatives. If not
             given, the values will be calculed from ``state`` using
-            :meth:`eval_derivatives()`.
+            :meth:`evaluate_derivatives()`.
         ``precision=myokit.DOUBLE_PRECISION``
             An optional precision argument to use when evaluating the state
             derivatives, and to pass into :meth:`myokit.float.str` when
@@ -2196,7 +2200,7 @@ class Model(ObjectWithMetaData, VarProvider):
         """
         # Deprecated since 2023-02-22
         import warnings
-        warnings.warn('The method `load_state` is deprecated.')
+        warnings.warn('The method `Model.load_state` is deprecated.')
         self.set_initial_values(myokit.load_state(filename, self))
 
     def map_component_dependencies(

{myokit-1.35.4 → myokit-1.36.1}/myokit/_myokit_version.py

@@ -14,7 +14,7 @@ __release__ = True
 #    incompatibility
 #  - Changes to revision indicate bugfixes, tiny new features
 #  - There is no significance to odd/even numbers
-__version_tuple__ = 1, 35, 4
+__version_tuple__ = 1, 36, 1
 
 # String version of the version number
 __version__ = '.'.join([str(x) for x in __version_tuple__])

{myokit-1.35.4 → myokit-1.36.1}/myokit/_protocol.py

@@ -858,6 +858,10 @@ class TimeSeriesProtocol:
     Protocols can be compared with ``==``, which will check if the sequence of
     time value pairs is the same, and the interpolation method is the same.
     Protocols can be serialized with ``pickle``.
+
+    **Note**: Time series protocols cannot be used to represent signals
+    containing discontinuities, as these will be smoothed out by the
+    interpolation.
     """
 
     def __init__(self, times, values, method=None):

{myokit-1.35.4 → myokit-1.36.1}/myokit/_sim/__init__.py

@@ -150,6 +150,7 @@ class CModule:
                 if platform.system() == 'Linux':
                     carg.extend([
                         '-Wextra',
+                        #'-Wpedantic',
                         '-Wstrict-prototypes',
                         '-Wold-style-definition',
                         #'-Wmissing-prototypes',