myokit 1.36.1__py3-none-any.whl → 1.37.0__py3-none-any.whl

myokit/__init__.py

@@ -336,29 +336,12 @@ from ._err import (  # noqa
     SimulationCancelledError,
     SimulationError,
     SimultaneousProtocolEventError,
+    TypeError,
     UnresolvedReferenceError,
     UnusedVariableError,
     VariableMappingError,
 )
 
-# Check if all errors imported
-# Dynamically importing them doesn't seem to be possible, and forgetting to
-#  import an error creates a hard to debug bug (something needs to go wrong
-#  before the interpreter reaches the code raising the error and notices it's
-#  not there).
-if not __release__:
-    from . import _err  # noqa
-    import inspect  # noqa
-    _globals = globals()
-    ex, name, clas = None, None, None
-    for ex in inspect.getmembers(_err):
-        name, clas = ex
-        if type(clas) == type(MyokitError) and issubclass(clas, MyokitError):
-            if name not in _globals:    # pragma: no cover
-                raise Exception('Failed to import exception: ' + name)
-    del ex, name, clas, _globals, inspect  # Prevent public visibility
-    del _err
-
 # Tools
 from . import float  # noqa
 from . import tools  # noqa
@@ -386,6 +369,7 @@ from ._expressions import (  # noqa
     And,
     ASin,
     ATan,
+    BinaryComparison,
     Ceil,
     Condition,
     Cos,
@@ -411,6 +395,8 @@ from ._expressions import (  # noqa
     Multiply,
     Name,
     Number,
+    NumericalInfixExpression,
+    NumericalPrefixExpression,
     Not,
     NotEqual,
     Or,
@@ -418,7 +404,6 @@ from ._expressions import (  # noqa
     Piecewise,
     Plus,
     Power,
-    PrefixCondition,
     PrefixExpression,
     PrefixMinus,
     PrefixPlus,
@@ -427,6 +412,8 @@ from ._expressions import (  # noqa
     Sin,
     Sqrt,
     Tan,
+    UnaryNumericalFunction,
+    UnaryNumericalDimensionlessFunction,
 )
 
 # Unit and quantity

myokit/_datablock.py

@@ -121,16 +121,19 @@ class DataBlock1d:
         if w < 1:
             raise ValueError('Minimum w is 1.')
         self._nx = w
+
         # Time
-        time = np.array(time, copy=copy)
+        time = np.array(time) if copy else np.asarray(time)
         if len(time.shape) != 1:
             raise ValueError('Time must be a sequence.')
         if np.any(np.diff(time) < 0):
             raise ValueError('Time must be non-decreasing.')
         self._time = time
         self._nt = len(time)
+
         # 0d variables
         self._0d = {}
+
         # 1d variables
         self._1d = {}
 
@@ -235,7 +238,7 @@ class DataBlock1d:
             return 0
 
         # Get times in seconds, lengths in cm
-        t = np.array(t, copy=False) * time_multiplier
+        t = np.asarray(t) * time_multiplier
         x = np.arange(i1, 1 + i2, dtype=float) * length
 
         # Use linear least squares to find the conduction velocity
@@ -287,8 +290,7 @@ class DataBlock1d:
             if d not in (0, 1):
                 raise ValueError(
                     'The given simulation log should only contain 0d or 1d'
-                    ' variables. Found <' + str(name) + '> with d = '
-                    + str(d) + '.')
+                    f' variables. Found <{name}> with d = {d}.')
             if d == 1:
                 if size is None:
                     size = info.size()
@@ -322,7 +324,7 @@ class DataBlock1d:
                 data = data.reshape((nt, nx), order='F')
                 # If this is a view of existing data, make a copy!
                 if data.base is not None:
-                    data = np.array(data)
+                    data = np.copy(data)
                 block.set1d(name, data, copy=False)
 
         return block
@@ -426,7 +428,7 @@ class DataBlock1d:
             z = np.reshape(z, (self._nt, self._nx), order='C')
         # If z is a view, create a copy
         if z.base is not None:
-            z = np.array(z, copy=True)
+            z = np.copy(z)
         return x, y, z
 
     def keys0d(self):
@@ -667,12 +669,12 @@ class DataBlock1d:
         head_str = []
         head_str.append(str(self._nt))
         head_str.append(str(self._nx))
-        head_str.append('"' + dtype + '"')
+        head_str.append(f'"{dtype}"')
         for name in self._0d:
-            head_str.append('"' + name + '"')
+            head_str.append(f'"{name}"')
         head_str.append(str(1))
         for name in self._1d:
-            head_str.append('"' + name + '"')
+            head_str.append(f'"{name}"')
         head_str = '\n'.join(head_str)
 
         # Create body
@@ -714,10 +716,9 @@ class DataBlock1d:
         name = str(name)
         if not name:
             raise ValueError('Name cannot be empty.')
-        data = np.array(data, copy=copy)
+        data = np.array(data) if copy else np.asarray(data)
         if data.shape != (self._nt,):
-            raise ValueError(
-                'Data must be sequence of length ' + str(self._nt) + '.')
+            raise ValueError(f'Data must be sequence of length {self._nt}.')
         self._0d[name] = data
 
     def set1d(self, name, data, copy=True):
@@ -734,10 +735,10 @@ class DataBlock1d:
         name = str(name)
         if not name:
             raise ValueError('Name cannot be empty.')
-        data = np.array(data, copy=copy)
+        data = np.array(data) if copy else np.asarray(data)
         shape = (self._nt, self._nx)
         if data.shape != shape:
-            raise ValueError('Data must have shape ' + str(shape) + '.')
+            raise ValueError(f'Data must have shape {shape}.')
         self._1d[name] = data
 
     def shape(self):
@@ -761,14 +762,16 @@ class DataBlock1d:
 
         The data will be copied, unless ``copy`` is set to ``False``.
         """
+        array = np.array if copy else np.asarray
+
         d = myokit.DataLog()
         d.set_time_key('time')
-        d['time'] = np.array(self._time, copy=copy)
+        d['time'] = array(self._time)
         for k, v in self._0d.items():
-            d[k] = np.array(v, copy=copy)
+            d[k] = array(v)
         for k, v in self._1d.items():
             for i in range(self._nx):
-                d[str(i) + '.' + k] = np.array(v[:, i], copy=copy)
+                d[f'{i}.{k}'] = array(v[:, i])
         return d
 
     def trace(self, variable, x):
@@ -823,7 +826,7 @@ class DataBlock2d:
         self._ny = h
         self._nx = w
         # Time
-        time = np.array(time, copy=copy)
+        time = np.array(time) if copy else np.asarray(time)
         if len(time.shape) != 1:
             raise ValueError('Time must be a sequence.')
         if not np.all(np.diff(time) >= 0):
@@ -951,8 +954,7 @@ class DataBlock2d:
             x1, y1 = [int(i) for i in pos1]
             if x1 < 0 or y1 < 0:
                 raise ValueError(
-                    'Negative indices not supported: pos1=('
-                    + str(x1) + ', ' + str(y1) + ').')
+                    f'Negative indices not supported: pos1=({x1}, {y1}).')
         else:
             x1, y1 = 0, 0
 
@@ -960,8 +962,7 @@ class DataBlock2d:
             x2, y2 = [int(i) for i in pos2]
             if x2 < 0 or y2 < 0:
                 raise ValueError(
-                    'Negative indices not supported: pos2=('
-                    + str(x2) + ', ' + str(y2) + ').')
+                    f'Negative indices not supported: pos2=({x2}, {y2}).')
         else:
             x2, y2 = x1 + w1, 0
 
@@ -1091,8 +1092,7 @@ class DataBlock2d:
             if d not in (0, 2):
                 raise ValueError(
                     'The given simulation log should only contain 0d or 2d'
-                    ' variables. Found <' + str(name) + '> with d = '
-                    + str(d) + '.')
+                    f' variables. Found <{name}> with d = {d}.')
             if d == 2:
                 if size is None:
                     size = info.size()
@@ -1122,7 +1122,7 @@ class DataBlock2d:
                 data = data.reshape((nt, ny, nx), order='F')
                 # If this is a view of existing data, make a copy!
                 if data.base is not None:
-                    data = np.array(data)
+                    data = np.copy(data)
                 block.set2d(name, data, copy=False)
         return block
 
@@ -1164,9 +1164,7 @@ class DataBlock2d:
         return frames
 
     def is_square(self):
-        """
-        Returns True if this data block's grid is square.
-        """
+        """ Returns True if this data block's grid is square. """
         return self._nx == self._ny
 
     def items0d(self):
@@ -1467,12 +1465,12 @@ class DataBlock2d:
         head_str.append(str(self._nt))
         head_str.append(str(self._ny))
         head_str.append(str(self._nx))
-        head_str.append('"' + dtype + '"')
+        head_str.append(f'"{dtype}"')
         for name in self._0d:
-            head_str.append('"' + name + '"')
+            head_str.append(f'"{name}"')
         head_str.append(str(2))
         for name in self._2d:
-            head_str.append('"' + name + '"')
+            head_str.append(f'"{name}"')
         head_str = '\n'.join(head_str)
 
         # Create body
@@ -1514,7 +1512,7 @@ class DataBlock2d:
         delimy = '\n'
         data = self._2d[name]
         data = data[frame]
-        text = [delimx.join('"' + str(x) + '"' for x in [xname, yname, zname])]
+        text = [delimx.join(f'"{x}"' for x in [xname, yname, zname])]
         for y, row in enumerate(data):
             for x, z in enumerate(row):
                 text.append(delimx.join([str(x), str(y), myokit.float.str(z)]))
@@ -1559,10 +1557,9 @@ class DataBlock2d:
         name = str(name)
         if not name:
             raise ValueError('Name cannot be empty.')
-        data = np.array(data, copy=copy)
+        data = np.array(data) if copy else np.asarray(data)
         if data.shape != (self._nt,):
-            raise ValueError(
-                'Data must be sequence of length ' + str(self._nt) + '.')
+            raise ValueError(f'Data must be sequence of length {self._nt}.')
         self._0d[name] = data
 
     def set2d(self, name, data, copy=True):
@@ -1579,10 +1576,10 @@ class DataBlock2d:
         name = str(name)
         if not name:
             raise ValueError('Name cannot be empty.')
-        data = np.array(data, copy=copy)
+        data = np.array(data) if copy else np.asarray(data)
         shape = (self._nt, self._ny, self._nx)
         if data.shape != shape:
-            raise ValueError('Data must have shape ' + str(shape) + '.')
+            raise ValueError(f'Data must have shape {shape}.')
         self._2d[name] = data
 
     def shape(self):
@@ -1606,20 +1603,20 @@ class DataBlock2d:
 
         The data will be copied, unless ``copy`` is set to ``False``.
         """
+        array = np.array if copy else np.asarray
         d = myokit.DataLog()
 
         # Add 0d vectors
         d.set_time_key('time')
-        d['time'] = np.array(self._time, copy=copy)
+        d['time'] = array(self._time)
         for k, v in self._0d.items():
-            d[k] = np.array(v, copy=copy)
+            d[k] = array(v)
 
         # Add 2d fields
         for k, v in self._2d.items():
             for x in range(self._nx):
-                s = str(x) + '.'
                 for y in range(self._ny):
-                    d[s + str(y) + '.' + k] = np.array(v[:, y, x], copy=copy)
+                    d[f'{x}.{y}.{k}'] = array(v[:, y, x])
         return d
 
     def trace(self, variable, x, y):
@@ -1673,20 +1670,16 @@ class ColorMap:
 
     @staticmethod
     def exists(name):
-        """
-        Returns True if the given name corresponds to a colormap.
-        """
+        """ Returns True if the given name corresponds to a colormap. """
         return name in ColorMap._colormaps
 
     @staticmethod
     def get(name):
-        """
-        Returns the colormap method indicated by the given name.
-        """
+        """ Returns the colormap method indicated by the given name. """
         try:
             return ColorMap._colormaps[name]()
         except KeyError:
-            raise KeyError('Non-existent ColorMap "' + str(name) + '".')
+            raise KeyError(f'Non-existent ColorMap "{name}".')
 
     @staticmethod
     def hsv_to_rgb(h, s, v):
@@ -1712,12 +1705,9 @@ class ColorMap:
         r[idx], g[idx], b[idx] = t[idx], p[idx], v[idx]
         idx = (i == 5)
         r[idx], g[idx], b[idx] = v[idx], p[idx], q[idx]
-        out = (
-            np.array(r * 255, dtype=np.uint8, copy=False),
-            np.array(g * 255, dtype=np.uint8, copy=False),
-            np.array(b * 255, dtype=np.uint8, copy=False),
-        )
-        return out
+        return (np.array(r * 255, dtype=np.uint8),
+                np.array(g * 255, dtype=np.uint8),
+                np.array(b * 255, dtype=np.uint8))
 
     @staticmethod
     def image(name, x, y):
@@ -1746,7 +1736,7 @@ class ColorMap:
         Normalizes the given float data based on the specified lower and upper
         bounds.
         """
-        floats = np.array(floats, copy=True)
+        floats = np.copy(floats)
         # Enforce lower and upper bounds
         floats[floats < lower] = lower
         floats[floats > upper] = upper

myokit/_datalog.py

@@ -829,7 +829,7 @@ class DataLog(OrderedDict):
 
             # Guess time variable
             for key in keys:
-                x = np.array(log[key], copy=False)
+                x = np.asarray(log[key])
                 y = x[1:] - x[:-1]
                 if np.all(y > 0):
                     log.set_time_key(key)
@@ -1305,7 +1305,7 @@ class DataLog(OrderedDict):
 
         # No splitting needed? Return clone!
         if nlogs < 2:
-            return self.clone()
+            return [self.clone()]
 
         # Find split points
         tstarts = tmin + np.arange(nlogs) * period

myokit/_err.py

@@ -27,10 +27,19 @@ class MyokitError(Exception):
 
 class IntegrityError(MyokitError):
     """
-    Raised if an integrity error is found in a model.
+    Raised if an "integrity" issue is found or created in a model or its
+    components and variables, for example missing parents or children, or
+    invalid references.
 
-    The error message is stored in the property ``message``. An optional parser
-    token may be obtained with :meth:`token()`.
+    Integrity errors are usually raised by the ``validate`` method, but can
+    also arise from certain manipulations, e.g. deleting or moving a variable
+    or component. Integrity errors can also be raised if they are detected
+    during some other operation.
+
+    The error message is stored in the property ``message``.
+
+    Integrity errors detected during parsing may set a token (pointing to the
+    position in the parsed text) retrievable with :meth:`token()`.
 
     *Extends:* :class:`myokit.MyokitError`
     """
@@ -393,6 +402,20 @@ class SimultaneousProtocolEventError(MyokitError):
     """
 
 
+class TypeError(IntegrityError):
+    """
+    Raised by the expression system if expressions of one type are required but
+    others are found.
+
+    For example, when a Derivative is created with an argument that is not a
+    Name, when a condition is given as input to a numerical operator (e.g.
+    ``log(1 == 2)``), or when a conditional operator is applied to a number
+    (e.g. ``and(1, 2)``).
+
+    *Extends:* :class:`myokit.IntegrityError`
+    """
+
+
 class UnresolvedReferenceError(IntegrityError):
     """
     Raised when a reference to a variable cannot be resolved.