myokit 1.37.1__tar.gz → 1.37.3__tar.gz

{myokit-1.37.1 → myokit-1.37.3}/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) 2020-2024 University of Nottingham. All rights reserved.
+Copyright (c) 2020-2025 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-1.37.1/myokit.egg-info → myokit-1.37.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: myokit
-Version: 1.37.1
+Version: 1.37.3
 Summary: A modeling and simulation tool for cardiac cellular electrophysiology
 Home-page: http://myokit.org
 Author: Michael Clerx
@@ -22,13 +22,28 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: configparser
+Requires-Dist: lxml
+Requires-Dist: matplotlib>=2.2
+Requires-Dist: numpy
+Requires-Dist: setuptools
 Provides-Extra: docs
+Requires-Dist: sphinx>=1.7.4; extra == "docs"
 Provides-Extra: dev
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: flake8>=3; extra == "dev"
 Provides-Extra: optional
+Requires-Dist: scipy; extra == "optional"
+Requires-Dist: sympy; extra == "optional"
 Provides-Extra: gui
+Requires-Dist: pyqt6; extra == "gui"
+Requires-Dist: sip; extra == "gui"
 Provides-Extra: pyqt
+Requires-Dist: pyqt6; extra == "pyqt"
+Requires-Dist: sip; extra == "pyqt"
 Provides-Extra: pyside
-License-File: LICENSE.txt
+Requires-Dist: pyside6; extra == "pyside"
 
 [![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)

{myokit-1.37.1 → myokit-1.37.3}/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) 2020-2024 University of Nottingham. All rights reserved.
+Copyright (c) 2020-2025 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) 2020-2024 University of Nottingham. All rights
+    <br />Copyright (c) 2020-2025 University of Nottingham. All rights
     reserved.</br></p>
 <p>
     Redistribution and use in source and binary forms, with or without

{myokit-1.37.1 → myokit-1.37.3}/myokit/_datalog.py

@@ -329,23 +329,27 @@ class DataLog(OrderedDict):
         """
         Creates a copy of the log, split with the given ``period``.
 
-        Split signals are given indexes so that "current" becomes "0.current",
-        "1.current", "2.current", etc.
+        Split signals are given indexes so that ``current`` becomes
+        ``0.current``, ``1.current``, ``2.current``, etc.
 
         If the logs entries do not divide well by ``period``, the remainder
         will be ignored. This happens commonly due to rounding point errors (in
         which case the remainder is a single entry). To disable this behavior,
         set ``discard_remainder=False``.
+
+        To split a log into a list of logs, use :meth:`DataLog.split_periodic`.
         """
         # Note: Using closed intervals can lead to logs of unequal length, so
         # it should be disabled here to ensure a valid log
         logs = self.split_periodic(period, adjust=True, closed_intervals=False)
+
         # Discard remainder if present
         if discard_remainder:
             if len(logs) > 1:
                 n = logs[0].length()
                 if logs[-1].length() < n:
                     logs = logs[:-1]
+
         # Create new log with folded data
         out = myokit.DataLog()
         out._time = self._time
@@ -1305,10 +1309,12 @@ class DataLog(OrderedDict):
 
     def split_periodic(self, period, adjust=False, closed_intervals=True):
         """
-        Splits this log into multiple logs, each covering an equal period of
-        time. For example a log covering the time span ``[0, 10000]`` can be
-        split with period ``1000`` to obtain ten logs covering ``[0, 1000]``,
-        ``[1000, 2000]`` etc.
+        Splits this log into multiple logs, returning a list of
+        :class:`DataLog` objects.
+
+        Each returned log covers an equal ``period`` of time. For example a log
+        covering the time span ``[0, 10000]`` split with period ``1000`` will
+        result in a list of ten logs ``[0, 1000]``, ``[1000, 2000]`` etc.
 
         The split log files can be returned as-is, or with the time variable's
         value adjusted so that all logs appear to cover the same span. To
@@ -1319,6 +1325,9 @@ class DataLog(OrderedDict):
         the duplication of some data points. To disable this behavior and
         return half-closed endpoints (containing only the left point), set
         ``closed_intervals`` to ``False``.
+
+        To return a single log with entries ``x`` split as ``x.0``, ``x.1``,
+        etc., use :meth:`DataLog.fold`.
         """
         # Validate log before starting
         self.validate()

{myokit-1.37.1 → myokit-1.37.3}/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, 37, 1
+__version_tuple__ = 1, 37, 3
 
 # String version of the version number
 __version__ = '.'.join([str(x) for x in __version_tuple__])

{myokit-1.37.1 → myokit-1.37.3}/myokit/_sim/cvodessim.py

@@ -695,9 +695,9 @@ class Simulation(myokit.CModule):
             An optional fixed size log interval. Must be ``None`` if
             ``log_times`` is used. If both are ``None`` every step is logged.
         ``log_times``
-            An optional set of pre-determined logging times. Must be ``None``
-            if ``log_interval`` is used. If both are ``None`` every step is
-            logged.
+            An optional sequence (e.g. a list or a numpy array) of
+            pre-determined logging times. Must be ``None`` if ``log_interval``
+            is used. If both are ``None`` every step is logged.
         ``sensitivities``
             An optional list-of-lists to append the calculated sensitivities
             to.

{myokit-1.37.1 → myokit-1.37.3}/myokit/_unit.py

@@ -487,56 +487,55 @@ class Unit:
         return self.__rtruediv__(other)
 
     @staticmethod
-    def register(name, unit, quantifiable=False, output=False):
+    def register(name, unit, quantifiable=False,
+                 preferred_representation=False):
         """
-        Registers a unit name with the Unit class. Registered units will be
-        recognised by the parse() method.
+        Registers a unit name with the :class:`Unit` class so that it will be
+        recognised when parsing.
 
         Arguments:
 
         ``name``
-            The unit name. A variable will be created using this name.
+            The unit name. This must be a valid myokit name, i.e.
+            ``myokit.check_name(name)`` should not raise any errors.
         ``unit``
             A valid unit object
         ``quantifiable``
             ``True`` if this unit should be registered with the unit class as a
-            quantifiable unit. Typically this should only be done for the
-            unquantified symbol notation of SI or SI derived units. For example
-            m, g, Hz, N but not meter, kg, hertz or forthnight.
-        ``output``
-            ``True`` if this units name should be used to display this unit in.
-            This should be set for all common units (m, kg, nm, Hz) but not for
-            more obscure units (furlong, parsec). Having ``output`` set to
-            ``False`` will cause one-way behavior: Myokit will recognise the
-            unit name but never use it in output.
-            Setting this to ``True`` will also register the given name as a
-            preferred representation format.
-
-        """
-        if not isinstance(name, str):
-            raise TypeError('Given name must be a string.')
+            _quantifiable_ unit, i.e. a unit that can be preceded by an SI
+            prefix such as "m" or "G". Typically this should only be done
+            for the unquantified symbol notation of SI or SI derived units. For
+            example "m", "g", or "Hz" but not "km", "meter", or "bushel".
+        ``preferred_representation``
+            Set to ``True`` to also register ``name`` as the preferred
+            representation for ``unit``.
+
+        """
+        name = myokit.check_name(name)
         if not isinstance(unit, Unit):
             raise TypeError('Given unit must be myokit.Unit')
         Unit._units[name] = unit
         if quantifiable:
             # Overwrite existing entries without warning
             Unit._quantifiable.add(name)
-        if output:
+        if preferred_representation:
             # Overwrite existing entries without warning
             Unit._preferred_representations[unit] = name
 
     @staticmethod
     def register_preferred_representation(rep, unit):
         """
-        Registers a preferred representation for the given unit without
-        registering it as a new type. This method can be used to register
-        common representations such as "umol/L" and "km/h".
+        Sets the preferred representation for the a unit, in terms of already
+        defined units.
+
+        This method can be used to register common representations such as
+        "umol/L" and "km/h". The given representation should be parseable by
+        Myokit, with the result equalling ``unit``.
 
         Arguments:
 
         ``rep``
-            A string, containing the preferred name for this unit. This should
-            be something that Myokit can parse.
+            A string containing the preferred representation for this unit.
         ``unit``
             The unit to register a notation for.
 
@@ -545,9 +544,14 @@ class Unit:
         # Overwrite existing entries without warning
         if not isinstance(unit, myokit.Unit):
             raise ValueError(
-                'Second argument to register_preferred_representation must be'
-                ' a myokit.Unit')
-        Unit._preferred_representations[unit] = str(rep)
+                'The second argument to register_preferred_representation must'
+                ' be a myokit.Unit')
+        rep = str(rep)
+        if not myokit.parse_unit(rep) == unit:
+            raise ValueError(
+                f'The representation [{rep}] does not equal {unit._str(True)}'
+                ' when parsed.')
+        Unit._preferred_representations[unit] = rep
 
     def __repr__(self):
         """
@@ -616,7 +620,8 @@ class Unit:
 
     def __str__(self):
 
-        # Strategy 1: Try simple look-up (using float.eq comparison)
+        # Strategy 1: Try simple look-up (using hash based on _str() followed
+        # by check of exponents in __eq__ for comparison
         try:
             return '[' + Unit._preferred_representations[self] + ']'
         except KeyError:
@@ -629,8 +634,8 @@ class Unit:
                 rep = '[' + test + ']'
                 break
 
-        # Strategy 3: Try finding a representation for the exponent and adding
-        # a multiplier to that.
+        # Strategy 3: Try finding a representation for the exponent (without a
+        # multiplier) and adding a multiplier to that.
         if rep is None:
 
             # Because kilos are defined with a multiplier of 1000, the
@@ -640,17 +645,20 @@ class Unit:
             u = Unit(list(self._x), m)
             rep = Unit._preferred_representations.get(u, None)
 
-            # Add multiplier part
+            # Add multiplier part:
             if rep is not None:
-                m = myokit.float.cround(self._m - m)
-                m = 10**m
-                if m >= 1:
-                    m = myokit.float.cround(m)
-                if m < 1e6:
-                    m = str(m)
+                if '(' in rep:
+                    rep = None
                 else:
-                    m = '{:<1.0e}'.format(m)
-                rep = '[' + rep + ' (' + m + ')]'
+                    m = myokit.float.cround(self._m - m)
+                    m = 10**m
+                    if m >= 1:
+                        m = myokit.float.cround(m)
+                    if m < 1e6:
+                        m = str(m)
+                    else:
+                        m = '{:<1.0e}'.format(m)
+                    rep = '[' + rep + ' (' + m + ')]'
 
         # Strategy 4: Build a new representation
         if rep is None:

{myokit-1.37.1 → myokit-1.37.3}/myokit/formats/heka/__init__.py

@@ -9,7 +9,10 @@ from ._patchmaster import ( # noqa
     AmplifierSeries,
     AmplifierState,
     AmplifierStateRecord,
+    CSlowRange,
     EndianAwareReader,
+    Filter1Setting,
+    Filter2Type,
     Group,
     NoSupportedDAChannelError,
     PatchMasterFile,
@@ -22,6 +25,7 @@ from ._patchmaster import ( # noqa
     Stimulus,
     StimulusChannel,
     StimulusFile,
+    StimulusFilterSetting,
     Sweep,
     Trace,
     TreeNode,