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

myokit/_sim/pacing.h

@@ -353,9 +353,7 @@ ESys_Populate(ESys sys, PyObject* protocol)
     if (protocol != Py_None) {
 
         // Get PyList from protocol (will need to decref!)
-        // Cast to (char*) happens because CallMethod accepts a mutable char*
-        // This should have been const char* and has been fixed in python 3
-        PyObject* list = PyObject_CallMethod(protocol, (char*)"events", NULL); // Returns a new reference
+        PyObject* list = PyObject_CallMethod(protocol, "events", NULL); // Returns a new reference
         if(list == NULL) return ESys_POPULATE_INVALID_PROTOCOL;
         if(!PyList_Check(list)) {
             Py_DECREF(list);
@@ -368,7 +366,7 @@ ESys_Populate(ESys sys, PyObject* protocol)
         // since they are tested by the Python code already!
         if(n > 0) {
             PyObject *item, *attr;
-            events = (ESys_Event)malloc((size_t)n*sizeof(struct ESys_Event_mem));
+            events = (ESys_Event)malloc((size_t)n * sizeof(struct ESys_Event_mem));
             e = events;
             for(i=0; i<n; i++) {
                 item = PyList_GetItem(list, i); // Don't decref!
@@ -620,6 +618,7 @@ typedef int FSys_Flag;
 #define FSys_POPULATE_INVALID_TIMES_DATA    -24
 #define FSys_POPULATE_INVALID_VALUES_DATA   -25
 #define FSys_POPULATE_DECREASING_TIMES_DATA -26
+#define FSys_POPULATE_INVALID_PROTOCOL      -27
 
 /*
  * Sets a python exception based on a fixed-form pacing error flag.
@@ -647,6 +646,9 @@ FSys_SetPyErr(FSys_Flag flag)
         PyErr_SetString(PyExc_Exception, "F-Pacing error: Pacing system not populated.");
         break;
     // Populate
+    case FSys_POPULATE_INVALID_PROTOCOL:
+        PyErr_SetString(PyExc_Exception, "F-Pacing error: Invalid protocol python object passed.");
+        break;
     case FSys_POPULATE_INVALID_TIMES:
         PyErr_SetString(PyExc_Exception, "F-Pacing error: Invalid times array passed.");
         break;
@@ -750,28 +752,34 @@ FSys_Destroy(FSys sys)
  * Returns a fixed-form pacing error flag.
  */
 FSys_Flag
-FSys_Populate(FSys sys, PyObject* times_list, PyObject* values_list)
+FSys_Populate(FSys sys, PyObject* protocol)
 {
     int i;
     Py_ssize_t n;
+    PyObject *times_list, *values_list;
 
     // Check ESys
     if(sys == 0) return FSys_INVALID_SYSTEM;
     if (sys->n_points != -1) return FSys_POPULATED_SYSTEM;
+    if (protocol == Py_None) return FSys_POPULATE_INVALID_PROTOCOL;
+
+    // Get PyList from protocol (will need to decref!)
+    times_list = PyObject_CallMethod(protocol, "times", NULL); // Returns a new reference
+    if(times_list == NULL) return FSys_POPULATE_INVALID_PROTOCOL;
+    if(!PyList_Check(times_list)) {
+        Py_DECREF(times_list);
+        return FSys_POPULATE_INVALID_TIMES;
+    }
 
-    // Check input lists
-    if(!PyList_Check(times_list)) return FSys_POPULATE_INVALID_TIMES;
-    if(!PyList_Check(values_list)) return FSys_POPULATE_INVALID_VALUES;
+    // Check and convert times list
     n = PyList_Size(times_list);
-    if (n != PyList_Size(values_list)) return FSys_POPULATE_SIZE_MISMATCH;
-    if (n < 2) return FSys_POPULATE_NOT_ENOUGH_DATA;
-
-    // Convert and check times list
-    sys->times = (double*)malloc((size_t)n*sizeof(double));
+    sys->times = (double*)malloc((size_t)n * sizeof(double));
     for(i=0; i<n; i++) {
         // GetItem and convert --> Borrowed reference so ok not to decref!
         sys->times[i] = PyFloat_AsDouble(PyList_GetItem(times_list, i));
     }
+    Py_DECREF(times_list);  // Finished with the times_list
+
     if (PyErr_Occurred()) {
         free(sys->times); sys->times = NULL;
         return FSys_POPULATE_INVALID_TIMES_DATA;
@@ -783,12 +791,24 @@ FSys_Populate(FSys sys, PyObject* times_list, PyObject* values_list)
         }
     }
 
-    // Convert values list
-    sys->values = (double*)malloc((size_t)n*sizeof(double));
+    // Check and convert values list
+    values_list = PyObject_CallMethod(protocol, (char*)"values", NULL); // Returns a new reference
+    if(values_list == NULL) {
+        free(sys->times); sys->times = NULL;
+        return FSys_POPULATE_INVALID_PROTOCOL;
+    }
+    if(!PyList_Check(values_list) || PyList_Size(values_list) != n) {
+        free(sys->times); sys->times = NULL;
+        Py_DECREF(values_list);
+        return FSys_POPULATE_INVALID_VALUES;
+    }
+    sys->values = (double*)malloc((size_t)n * sizeof(double));
     for(i=0; i<n; i++) {
         // GetItem and convert --> Borrowed reference so ok not to decref!
         sys->values[i] = PyFloat_AsDouble(PyList_GetItem(values_list, i));
     }
+    Py_DECREF(values_list); // Finished with the values list
+
     if (PyErr_Occurred()) {
         free(sys->times); sys->times = NULL;
         free(sys->values); sys->values = NULL;
@@ -832,7 +852,7 @@ FSys_GetLevel(FSys sys, double time, FSys_Flag* flag)
     }
 
     // Find the highest index `i` of sorted array `times` such that
-    // `times[i] <= time`, or `-1` if no such indice can be found.
+    // `times[i] <= time`, or `-1` if no such index can be found.
     // A guess can be given, which will be used to speed things up
 
     // Get left point, check value

myokit/_sim/rhs.c

@@ -49,9 +49,9 @@ tab = '    '
 
 # Process bindings, remove unsupported bindings, get map of bound variables to
 # internal names
-bound_variables = model.prepare_bindings({
+bound_variables = myokit._prepare_bindings(model, {
     'time' : 'engine_time',
-    })
+})
 
 # Get equations
 equations = model.solvable_order()
@@ -135,15 +135,12 @@ log_extract(PyObject* data, const char* name, const int position, double* var)
     PyObject* key;
     PyObject* list;
     PyObject* item;
-    char errstr[1000];
 
     // Get sequence from dict
     key = PyUnicode_FromString(name);
     if (!PyDict_Contains(data, key)) {
         Py_DECREF(key);
-        // Raise exception
-        sprintf(errstr, "Variable %s not found in log.", name);
-        PyErr_SetString(PyExc_Exception, errstr);
+        PyErr_Format(PyExc_Exception, "Variable %s not found in log.", name);
         return 0;
     }
     list = PyDict_GetItem(data, key); // Borrowed ref, don't decref
@@ -154,9 +151,7 @@ log_extract(PyObject* data, const char* name, const int position, double* var)
     item = PySequence_GetItem(list, position); // New reference, decref
     if (item == NULL) {
         Py_DECREF(key);
-        // Raise exception
-        sprintf(errstr, "No item found at position %i of log for %s.", position, name);
-        PyErr_SetString(PyExc_Exception, errstr);
+        PyErr_Format(PyExc_Exception, "No item found at position %i of log for %s.", position, name);
         return 0;
     }
     Py_DECREF(key);
@@ -164,9 +159,7 @@ log_extract(PyObject* data, const char* name, const int position, double* var)
     // Get double from float
     if (!PyFloat_Check(item)) {
         Py_XDECREF(item);
-        // Raise exception
-        sprintf(errstr, "Log for %s can only contain floats (error at index %i).", name, position);
-        PyErr_SetString(PyExc_Exception, errstr);
+        PyErr_Format(PyExc_Exception, "Log for %s can only contain floats (error at index %i).", name, position);
         return 0;
     }
 
@@ -250,7 +243,7 @@ bench(PyObject* self, PyObject* args, void (*fnc)(void))
         return 0;
     }
     if (start < 0) {
-        PyErr_SetString(PyExc_Exception, "Invalid log position selection: Negative list indice given.");
+        PyErr_SetString(PyExc_Exception, "Invalid log position selection: Negative list index given.");
         return 0;
     }
 

myokit/_sim/rhs.py

@@ -4,20 +4,11 @@
 # 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 os
-import timeit
-import myokit
 import platform
+import timeit
 
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
+import myokit
 
 # Location of C source file
 SOURCE_FILE = 'rhs.c'
@@ -33,7 +24,7 @@ class RhsBenchmarker(myokit.CModule):
     be selected.
 
     By default, the given list of variables are the only variables included in
-    a partial simulation. This behaviour can be inverted by setting
+    a partial simulation. This behavior can be inverted by setting
     ``exclude_selected=True``. With this setting, all variables except those in
     the given list will be tested.
 
@@ -42,7 +33,7 @@ class RhsBenchmarker(myokit.CModule):
     _index = 0  # Unique id for the generated module
 
     def __init__(self, model, variables=None, exclude_selected=False):
-        super(RhsBenchmarker, self).__init__()
+        super().__init__()
 
         # Require a valid model
         model.validate()
@@ -201,7 +192,7 @@ class RhsBenchmarker(myokit.CModule):
         else:
             self._variables = set()
             for var in variables:
-                if isinstance(var, basestring):
+                if isinstance(var, str):
                     # String? Then get variable from model
                     var = self._model.get(var)
                 else:

myokit/_sim/sundials.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 os
 
 import myokit
@@ -32,7 +29,7 @@ class Sundials(myokit.CModule):
     _version = None
 
     def __init__(self):
-        super(Sundials, self).__init__()
+        super().__init__()
         # Create and cache back-end
         Sundials._index += 1
 

myokit/_system.py

@@ -4,13 +4,10 @@
 # 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 importlib
 import os
-import sys
 import platform
-import importlib
+import sys
 
 import myokit
 
@@ -28,7 +25,7 @@ def system(live_printing=False):
         out = []
     else:
         # Create fake list interface that just prints
-        class Out(object):
+        class Out:
             def append(self, x):
                 print(x)
 
@@ -68,25 +65,22 @@ def system(live_printing=False):
     out.append('== GUI ==')
 
     try:    # pragma: no cover
-        from PyQt5.QtCore import QT_VERSION_STR
-        out.append('PyQt5: ' + QT_VERSION_STR)
+        from PyQt6.QtCore import QT_VERSION_STR
+        out.append('PyQt6: ' + QT_VERSION_STR)
         out.append('  Sip: ' + _module_version('sip'))
         del QT_VERSION_STR
     except ImportError:
-        out.append('PyQt5: Not found')
+        out.append('PyQt6: Not found')
 
     try:    # pragma: no cover
-        from PyQt4.QtCore import QT_VERSION_STR
-        out.append('PyQt4: ' + QT_VERSION_STR)
+        from PyQt5.QtCore import QT_VERSION_STR
+        out.append('PyQt5: ' + QT_VERSION_STR)
         out.append('  Sip: ' + _module_version('sip'))
         del QT_VERSION_STR
     except ImportError:
-        out.append('PyQt4: Not found')
-    except RuntimeError:    # pragma: no cover
-        # Happens if PyQt5 was also found
-        out.append('PyQt4: OK')
+        out.append('PyQt5: Not found')
 
-    out.append('PySide: ' + _module_version('PySide'))
+    out.append('PySide6: ' + _module_version('PySide6'))
     out.append('PySide2: ' + _module_version('PySide2'))
     out.append('')
 

myokit/_unit.py

@@ -5,21 +5,12 @@
 # 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 math
 
 import myokit
 
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no python 2 cover
-    basestring = str
-
 
-class Unit(object):
+class Unit:
     """
     Represents a unit.
 
@@ -516,13 +507,13 @@ class Unit(object):
             ``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 behaviour: Myokit will recognise the
+            ``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, basestring):
+        if not isinstance(name, str):
             raise TypeError('Given name must be a string.')
         if not isinstance(unit, Unit):
             raise TypeError('Given unit must be myokit.Unit')
@@ -679,7 +670,7 @@ class Unit(object):
             self._m - other._m)
 
 
-class Quantity(object):
+class Quantity:
     """
     Represents a quantity with a :class:`unit <myokit.Unit>`. Can be used to
     perform unit-safe arithmetic.

myokit/float.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 sys
 
 import myokit

myokit/formats/__init__.py

@@ -4,15 +4,13 @@
 # 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 os
 import sys
 import traceback
 import warnings
 
+import myokit
+
 # Constants
 DIR_FORMATS = os.path.join(myokit.DIR_MYOKIT, 'formats')
 
@@ -23,12 +21,12 @@ _EWRITERS = None
 
 
 # Classes & methods
-class Exporter(object):
+class Exporter:
     """
     Abstract base class for exporters.
     """
     def __init__(self):
-        super(Exporter, self).__init__()
+        super().__init__()
 
     def post_export_info(self):
         """
@@ -106,7 +104,7 @@ def exporters():
     return sorted(_EXPORTERS.keys())
 
 
-class ExpressionWriter(object):
+class ExpressionWriter:
     """
     Base class for expression writers, that take myokit expressions as input
     and convert them to text or other formats.
@@ -322,12 +320,12 @@ def ewriters():
     return sorted(_EWRITERS.keys())
 
 
-class Importer(object):
+class Importer:
     """
     Abstract base class for importers.
     """
     def __init__(self):
-        super(Importer, self).__init__()
+        super().__init__()
 
     def component(self, path, model):
         """
@@ -411,7 +409,7 @@ class TemplatedRunnableExporter(Exporter):
     protocol) into a runnable chunk of code.
     """
     def __init__(self):
-        super(TemplatedRunnableExporter, self).__init__()
+        super().__init__()
 
     def runnable(self, path, model, protocol=None, *args):
         """

myokit/formats/ansic/__init__.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
-
 from ._exporter import AnsiCExporter, AnsiCCableExporter, AnsiCEulerExporter
 from ._ewriter import AnsiCExpressionWriter
 

myokit/formats/ansic/_ewriter.py

@@ -4,10 +4,8 @@
 # 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
+
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -17,7 +15,7 @@ class AnsiCExpressionWriter(PythonExpressionWriter):
     equations for variables in a C-style syntax.
     """
     def __init__(self):
-        super(AnsiCExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
         self._fcond = None
 

myokit/formats/ansic/_exporter.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 os
 
 import myokit.formats
@@ -121,7 +118,7 @@ class AnsiCCableExporter(myokit.formats.TemplatedRunnableExporter):
     ``pace``
         The value of the pacing variable, implemented using the given protocol.
     ``diffusion_current``
-        The current flowing from each cell to its neighbours. This will be
+        The current flowing from each cell to its neighbors. This will be
         positive if the cell is acting as a source, negative when it's acting
         as a sink.
 

myokit/formats/ansic/template/cable.c

@@ -23,11 +23,11 @@ model.create_unique_names()
 w = ansic.AnsiCExpressionWriter()
 
 # Process bindings, remove unsupported bindings
-bound_variables = model.prepare_bindings({
+bound_variables = myokit._prepare_bindings(model, {
     'time'         : 't',
     'pace'         : 'pace',
     'diffusion_current' : 'current'
-    }).keys()
+}).keys()
 
 if model.binding('diffusion_current') is None:
     raise Exception('This exporter requires a variable to be bound to'
@@ -155,8 +155,8 @@ static void
 Cell_set_initial_state(Cell *cell)
 {
 <?
-for eq in model.inits():
-    print(tab + w.eq(eq) + ';')
+for var, init in zip(model.states(), model.initial_values(True)):
+    print(tab + v(var) + ' = ' + myokit.float.str(init) + ';')
 ?>}
 
 /*

myokit/formats/ansic/template/euler.c

@@ -29,10 +29,10 @@ model.create_unique_names()
 
 # Process bindings, remove unsupported bindings, get map of bound variables to
 # internal names
-bound_variables = model.prepare_bindings({
+bound_variables = myokit._prepare_bindings(model, {
     'time' : 'time',
     'pace' : 'pace',
-    })
+})
 
 # Get equations
 equations = model.solvable_order()
@@ -95,7 +95,7 @@ def v(var):
     if var in bound_variables:
         return bound_variables[var]
     if var.is_state():
-        return pre + 'state[' + str(var.indice()) + ']'
+        return pre + 'state[' + str(var.index()) + ']'
     elif var.is_constant():
         return pre + 'C_' + var.uname()
     else:
@@ -126,7 +126,7 @@ typedef double Real;
 #define N_STATE <?= model.count_states() ?>
 <?
 for var in model.states():
-    print('#define S_' + var.uname() + ' state[' + str(var.indice()) + ']')
+    print('#define S_' + var.uname() + ' state[' + str(var.index()) + ']')
 ?>
 
 /* Define constants, calculated constants */
@@ -220,7 +220,7 @@ int main()
     Real state[N_STATE];
 <?
 for var in model.states():
-    print(tab + v(var) + ' = ' + myokit.float.str(var.state_value()) + ';')
+    print(tab + v(var) + ' = ' + myokit.float.str(var.initial_value(True)) + ';')
 
 ?>
 

myokit/formats/ansic/template/sim.c

@@ -22,11 +22,11 @@ model.create_unique_names()
 # Define lhs function
 def v(var):
     if isinstance(var, myokit.Derivative):
-        return 'NV_Ith_S(ydot, ' + str(var.var().indice()) + ')'
+        return 'NV_Ith_S(ydot, ' + str(var.var().index()) + ')'
     elif isinstance(var, myokit.Name):
         var = var.var()
     if var.is_state():
-        return 'NV_Ith_S(y, ' + str(var.indice()) + ')'
+        return 'NV_Ith_S(y, ' + str(var.index()) + ')'
     elif var.is_constant():
         return 'AC_' + var.uname()
     else:
@@ -38,10 +38,10 @@ w.set_lhs_function(v)
 
 # Process bindings, remove unsupported bindings, get map of bound variables to
 # internal names
-bound_variables = model.prepare_bindings({
+bound_variables = myokit._prepare_bindings(model, {
     'time' : 't',
     'pace' : 'pace',
-    })
+})
 
 # Tab
 tab = '    '
@@ -131,8 +131,8 @@ static void
 default_initial_values(N_Vector y)
 {
 <?
-for eq in model.inits():
-    print(tab + w.eq(eq) + ';')
+for var, init in zip(model.states(), model.initial_values(True)):
+    print(tab + v(var) + ' = ' + myokit.float.str(init) + ';')
 ?>
 }
 

myokit/formats/axon/__init__.py

@@ -4,13 +4,11 @@
 # 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
-
 from ._abf import AbfFile, Sweep, Channel  # noqa
 from ._atf import AtfFile, load_atf, save_atf  # noqa
 from ._importer import AbfImporter
 
+
 # Importers
 _importers = {
     'abf': AbfImporter,