myokit 1.34.0__py3-none-any.whl → 1.35.0__py3-none-any.whl

myokit/_datablock.py

@@ -4,15 +4,14 @@
 # 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 array
 import os
 import sys
-import array
-import numpy as np
+
 import myokit
 
+import numpy as np
+
 
 # Readme file for DataBlock1d binary files
 README_SAVE_1D = """
@@ -85,7 +84,7 @@ header, and little-endian:
 ENC = 'utf-8'
 
 
-class DataBlock1d(object):
+class DataBlock1d:
     """
     Container for time-series of 1d rectangular data arrays.
 
@@ -476,17 +475,10 @@ class DataBlock1d(object):
                 'This method requires the ``zlib`` module to be installed.')
 
         # Get size of single and double types on this machine
-        try:
-            dsize = {
-                'd': len(array.array('d', [1]).tobytes()),
-                'f': len(array.array('f', [1]).tobytes()),
-            }
-        except (AttributeError, TypeError):  # pragma: no python 3 cover
-            # List dtype as str for Python 2.7.10 (see #225)
-            dsize = {
-                b'd': len(array.array(b'd', [1]).tostring()),
-                b'f': len(array.array(b'f', [1]).tostring()),
-            }
+        dsize = {
+            'd': len(array.array('d', [1]).tobytes()),
+            'f': len(array.array('f', [1]).tobytes()),
+        }
 
         # Read data from file
         try:
@@ -544,8 +536,6 @@ class DataBlock1d(object):
             nt = int(next(head))
             nx = int(next(head))
             dtype = next(head)[1:-1]
-            # Convert dtype to str for Python 2.7.10 (see #225)
-            dtype = str(dtype)
             if dtype not in dsize:
                 raise myokit.DataBlockReadError(
                     'Unable to read DataBlock1d: Unrecognized data type "'
@@ -573,10 +563,7 @@ class DataBlock1d(object):
                     'Unable to read DataBlock1d: Header indicates larger data'
                     ' than found in the body.')
             data = array.array(dtype)
-            try:
-                data.frombytes(body[start:end])
-            except AttributeError:  # pragma: no python 3 cover
-                data.fromstring(body[start:end])
+            data.frombytes(body[start:end])
             if sys.byteorder == 'big':  # pragma: no cover
                 data.byteswap()
             data = np.array(data)
@@ -597,10 +584,7 @@ class DataBlock1d(object):
                         'Unable to read DataBlock1d: Header indicates larger'
                         ' data than found in the body.')
                 data = array.array(dtype)
-                try:
-                    data.frombytes(body[start:end])
-                except AttributeError:  # pragma: no python 3 cover
-                    data.fromstring(body[start:end])
+                data.frombytes(body[start:end])
                 if sys.byteorder == 'big':  # pragma: no cover
                     data.byteswap()
                 data = np.array(data)
@@ -619,10 +603,7 @@ class DataBlock1d(object):
                         'Unable to read DataBlock1d: Header indicates larger'
                         ' data than found in the body.')
                 data = array.array(dtype)
-                try:
-                    data.frombytes(body[start:end])
-                except AttributeError:  # pragma: no python 3 cover
-                    data.fromstring(body[start:end])
+                data.frombytes(body[start:end])
                 if sys.byteorder == 'big':  # pragma: no cover
                     data.byteswap()
                 data = np.array(data).reshape(nt, nx, order='C')
@@ -680,8 +661,7 @@ class DataBlock1d(object):
                 'This method requires the ``zlib`` module to be installed.')
 
         # Data type
-        # Create dtype as str for Python 2.7.10 (see #225)
-        dtype = str('d')     # Only supporting doubles right now
+        dtype = 'd'     # Only supporting doubles right now
 
         # Create header
         head_str = []
@@ -706,10 +686,7 @@ class DataBlock1d(object):
         if sys.byteorder == 'big':  # pragma: no cover
             for ar in body_str:
                 ar.byteswap()
-        try:
-            body_str = b''.join([ar.tobytes() for ar in body_str])
-        except AttributeError:  # pragma: no python 3 cover
-            body_str = b''.join([ar.tostring() for ar in body_str])
+        body_str = b''.join([ar.tobytes() for ar in body_str])
 
         # Write
         head = zipfile.ZipInfo('header_block1d.txt')
@@ -803,7 +780,7 @@ class DataBlock1d(object):
         return self._1d[variable][:, x]
 
 
-class DataBlock2d(object):
+class DataBlock2d:
     """
     Container for time-series of 2d rectangular data arrays.
 
@@ -1274,17 +1251,10 @@ class DataBlock2d(object):
                 'This method requires the ``zlib`` module to be installed.')
 
         # Get size of single and double types on this machine
-        try:
-            dsize = {
-                'd': len(array.array('d', [1]).tobytes()),
-                'f': len(array.array('f', [1]).tobytes()),
-            }
-        except (AttributeError, TypeError):  # pragma: no python 3 cover
-            # List dtype as str for Python 2.7.10 (see #225)
-            dsize = {
-                b'd': len(array.array(b'd', [1]).tostring()),
-                b'f': len(array.array(b'f', [1]).tostring()),
-            }
+        dsize = {
+            'd': len(array.array('d', [1]).tobytes()),
+            'f': len(array.array('f', [1]).tobytes()),
+        }
 
         # Read data from file
         try:
@@ -1353,8 +1323,7 @@ class DataBlock2d(object):
             nx = int(next(head))
 
             # Get dtype
-            # Convert dtype to str for Python 2.7.10 (see #225)
-            dtype = str(next(head))[1:-1]
+            dtype = next(head)[1:-1]
             if dtype not in dsize:
                 raise myokit.DataBlockReadError(
                     'Unable to read DataBlock2d: Unrecognized data type "'
@@ -1384,10 +1353,7 @@ class DataBlock2d(object):
                     ' than found in the body.')
 
             data = array.array(dtype)
-            try:
-                data.frombytes(body[start:end])
-            except AttributeError:  # pragma: no python 3 cover
-                data.fromstring(body[start:end])
+            data.frombytes(body[start:end])
             if sys.byteorder == 'big':  # pragma: no cover
                 data.byteswap()
             data = np.array(data)
@@ -1408,10 +1374,7 @@ class DataBlock2d(object):
                         'Unable to read DataBlock2d: Header indicates larger'
                         ' data than found in the body.')
                 data = array.array(dtype)
-                try:
-                    data.frombytes(body[start:end])
-                except AttributeError:  # pragma: no python 3 cover
-                    data.fromstring(body[start:end])
+                data.frombytes(body[start:end])
                 if sys.byteorder == 'big':  # pragma: no cover
                     data.byteswap()
                 data = np.array(data)
@@ -1430,10 +1393,7 @@ class DataBlock2d(object):
                         'Unable to read DataBlock2d: Header indicates larger'
                         ' data than found in the body.')
                 data = array.array(dtype)
-                try:
-                    data.frombytes(body[start:end])
-                except AttributeError:  # pragma: no python 3 cover
-                    data.fromstring(body[start:end])
+                data.frombytes(body[start:end])
                 if sys.byteorder == 'big':  # pragma: no cover
                     data.byteswap()
                 data = np.array(data).reshape(nt, ny, nx, order='C')
@@ -1496,8 +1456,7 @@ class DataBlock2d(object):
                 'This method requires the ``zlib`` module to be installed.')
 
         # Data type
-        # Create dtype as str for Python 2.7.10 (see #225)
-        dtype = str('d')  # Only supporting doubles right now
+        dtype = 'd'     # Only supporting doubles right now
 
         # Create header
         head_str = []
@@ -1523,10 +1482,7 @@ class DataBlock2d(object):
         if sys.byteorder == 'big':  # pragma: no cover
             for ar in body_str:
                 ar.byteswap()
-        try:
-            body_str = b''.join([ar.tobytes() for ar in body_str])
-        except AttributeError:  # pragma: no python 3 cover
-            body_str = b''.join([ar.tostring() for ar in body_str])
+        body_str = b''.join([ar.tobytes() for ar in body_str])
 
         # Write
         head = zipfile.ZipInfo('header_block2d.txt')
@@ -1671,7 +1627,7 @@ class DataBlock2d(object):
         return self._2d[variable][:, y, x]
 
 
-class ColorMap(object):
+class ColorMap:
     """
     *Abstract class*
 

myokit/_datalog.py

@@ -4,22 +4,16 @@
 # 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 re
 import sys
 import array
+
 import numpy as np
+
 from collections import OrderedDict
-import myokit
 
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no python 2 cover
-    basestring = str
+import myokit
 
 
 # Function to split keys into dimension-key,qname-key pairs
@@ -101,11 +95,11 @@ class DataLog(OrderedDict):
     def __init__(self, other=None, time=None):
         if other is None:
             # Create new
-            super(DataLog, self).__init__()
+            super().__init__()
             self._time = None
         else:
             # Clone
-            super(DataLog, self).__init__(other)
+            super().__init__(other)
             try:
                 self._time = str(other._time)
             except Exception:
@@ -216,10 +210,10 @@ class DataLog(OrderedDict):
         return log
 
     def __contains__(self, key):
-        return super(DataLog, self).__contains__(self._parse_key(key))
+        return super().__contains__(self._parse_key(key))
 
     def __delitem__(self, key):
-        return super(DataLog, self).__delitem__(self._parse_key(key))
+        return super().__delitem__(self._parse_key(key))
 
     def extend(self, other):
         """
@@ -328,7 +322,7 @@ class DataLog(OrderedDict):
         return out
 
     def __getitem__(self, key):
-        return super(DataLog, self).__getitem__(self._parse_key(key))
+        return super().__getitem__(self._parse_key(key))
 
     def has_nan(self):
         """
@@ -517,17 +511,10 @@ class DataLog(OrderedDict):
                 'This method requires the ``zlib`` module to be installed.')
 
         # Get size of single and double types on this machine
-        try:
-            dsize = {
-                'd': len(array.array('d', [1]).tobytes()),
-                'f': len(array.array('f', [1]).tobytes()),
-            }
-        except (AttributeError, TypeError):  # pragma: no python 3 cover
-            # List dtype as str for Python 2.7.10 (see #225)
-            dsize = {
-                b'd': len(array.array(b'd', [1]).tostring()),
-                b'f': len(array.array(b'f', [1]).tostring()),
-            }
+        dsize = {
+            'd': len(array.array('d', [1]).tobytes()),
+            'f': len(array.array('f', [1]).tobytes()),
+        }
 
         # Read data
         try:
@@ -563,7 +550,7 @@ class DataLog(OrderedDict):
         head = iter(head.splitlines())
         n = int(next(head))
         data_size = int(next(head))
-        data_type = str(next(head))  # Cast to str for Python 2.7.10 (see #225)
+        data_type = next(head)
         time = next(head)
         if time:
             # Note, this field doesn't have to be present in the log!
@@ -604,10 +591,7 @@ class DataLog(OrderedDict):
 
                 # Read data
                 ar = array.array(data_type)
-                try:
-                    ar.frombytes(body[start:end])
-                except AttributeError:  # pragma: no python 3 cover
-                    ar.fromstring(body[start:end])
+                ar.frombytes(body[start:end])
                 if sys.byteorder == 'big':  # pragma: no cover
                     ar.byteswap()
                 log[field] = ar
@@ -638,8 +622,7 @@ class DataLog(OrderedDict):
         filename = os.path.expanduser(filename)
 
         # Typecode dependent on precision
-        # Typecode must be str for Python 2.7.10 (see #225)
-        typecode = str('d' if precision == myokit.DOUBLE_PRECISION else 'f')
+        typecode = 'd' if precision == myokit.DOUBLE_PRECISION else 'f'
 
         # Error raising function
         def e(line, char, msg):
@@ -647,16 +630,9 @@ class DataLog(OrderedDict):
                 'Syntax error on line ' + str(line) + ', character '
                 + str(1 + char) + ': ' + msg)
 
-        def uopen(filename):
-            # Open a filename in 'universal newline' mode, python 2 and 3
-            try:
-                return open(filename, 'r', newline=None)
-            except TypeError:   # pragma: no python 3 cover
-                return open(filename, 'U')
-
         quote = '"'
         delim = ','
-        with uopen(filename) as f:
+        with open(filename, 'r', newline=None) as f:
             # Read header
             keys = []   # The log keys, in order of appearance
 
@@ -936,8 +912,7 @@ class DataLog(OrderedDict):
                 'This method requires the `zlib` module to be installed.')
 
         # Data type
-        # dtype must be str for Python 2.7.10 (see #225)
-        dtype = str('d' if precision == myokit.DOUBLE_PRECISION else 'f')
+        dtype = 'd' if precision == myokit.DOUBLE_PRECISION else 'f'
 
         # Create data strings
         head_str = []
@@ -959,10 +934,7 @@ class DataLog(OrderedDict):
             ar = array.array(dtype, v)
             if sys.byteorder == 'big':  # pragma: no cover
                 ar.byteswap()
-            try:
-                body_str.append(ar.tobytes())
-            except AttributeError:   # pragma: no python 3 cover
-                body_str.append(ar.tostring())
+            body_str.append(ar.tobytes())
         head_str = '\n'.join(head_str)
         body_str = b''.join(body_str)
 
@@ -1006,7 +978,7 @@ class DataLog(OrderedDict):
             If a precision argument (for example ``myokit.DOUBLE_PRECISION``)
             is given, the output will be stored in such a way that this amount
             of precision is guaranteed to be present in the string. If the
-            precision argument is set to ``None`` python's default formatting
+            precision argument is set to ``None`` Python's default formatting
             is used, which may lead to smaller files.
         ``order``
             To specify the ordering of the log's arguments, pass in a sequence
@@ -1107,7 +1079,7 @@ class DataLog(OrderedDict):
         self._time = None if key is None else str(key)
 
     def __setitem__(self, key, value):
-        return super(DataLog, self).__setitem__(
+        return super().__setitem__(
             self._parse_key(key), value)
 
     def split(self, value):
@@ -1422,7 +1394,7 @@ class DataLog(OrderedDict):
         return infos
 
 
-class LoggedVariableInfo(object):
+class LoggedVariableInfo:
     """
     Contains information about the log entries for each variable. These objects
     should only be created by :meth:`DataLog.variable_info()`.
@@ -1629,9 +1601,7 @@ def prepare_log(
     be specified using the ``precision`` argument.
     """
     # Typecode dependent on precision
-    # Note: Cast to str() here makes it work with older versions of 2.7.x,
-    # where unicode isn't accepted (Python 3 of course doesn't accept bytes)
-    typecode = str('d' if precision == myokit.DOUBLE_PRECISION else 'f')
+    typecode = 'd' if precision == myokit.DOUBLE_PRECISION else 'f'
 
     # Get all options for dimensionality
     if dims is None:
@@ -1874,7 +1844,7 @@ def prepare_log(
             'Argument `log` has unexpected type. Expecting None, integer flag,'
             ' sequence of names, dict or DataLog.')
 
-    if isinstance(log, basestring):
+    if isinstance(log, str):
         raise ValueError(
             'String passed in as `log` argument, should be list'
             ' or other sequence containing strings.')

myokit/_err.py

@@ -4,8 +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
 
 
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
@@ -24,7 +22,7 @@ class MyokitError(Exception):
     *Extends:* ``Exception``
     """
     def __init__(self, message):
-        super(MyokitError, self).__init__(message)
+        super().__init__(message)
 
 
 class IntegrityError(MyokitError):
@@ -37,7 +35,7 @@ class IntegrityError(MyokitError):
     *Extends:* :class:`myokit.MyokitError`
     """
     def __init__(self, message, token=None):
-        super(IntegrityError, self).__init__(message)
+        super().__init__(message)
         self._token = token
 
     def token(self):
@@ -77,7 +75,7 @@ class CyclicalDependencyError(IntegrityError):
         # Set token: First item in cycle is model's defining lhs
         tok = cycle[0].var()._token
         # Raise
-        super(CyclicalDependencyError, self).__init__(msg, tok)
+        super().__init__(msg, tok)
 
 
 class DataBlockReadError(MyokitError):
@@ -167,7 +165,7 @@ class IllegalReferenceError(IntegrityError):
     *Extends:* :class:`myokit.IntegrityError`
     """
     def __init__(self, reference, owner):
-        super(IllegalReferenceError, self).__init__(
+        super().__init__(
             'Illegal reference: The referenced variable <' + reference.qname()
             + '> is outside the scope of <' + owner.qname() + '>.')
 
@@ -179,7 +177,7 @@ class IllegalReferenceInInitialValueError(IllegalReferenceError):
     The only way this can occur is if the reference is to a nested variable.
     """
     def __init__(self, reference, owner):
-        super(IllegalReferenceError, self).__init__(
+        super(IntegrityError, self).__init__(
             'Illegal reference made in initial value: The referenced variable'
             ' <' + reference.qname() + '> is nested.')
 
@@ -203,7 +201,7 @@ class IncompatibleModelError(MyokitError):
         if model_name:
             msg += ' <' + str(model_name) + '>'
         msg += ': ' + str(message)
-        super(IncompatibleModelError, self).__init__(msg)
+        super().__init__(msg)
 
 
 class IncompatibleUnitError(MyokitError):
@@ -213,7 +211,7 @@ class IncompatibleUnitError(MyokitError):
     *Extends:* :class:`myokit.MyokitError`.
     """
     def __init__(self, message, token=None):
-        super(MyokitError, self).__init__(message)
+        super().__init__(message)
         self._token = token
 
     def token(self):
@@ -288,7 +286,7 @@ class MissingRhsError(IntegrityError):
     def __init__(self, var):
         msg = 'No rhs set for <' + var.qname() + '>.'
         tok = var._token
-        super(MissingRhsError, self).__init__(msg, tok)
+        super().__init__(msg, tok)
 
 
 class MissingTimeVariableError(IntegrityError):
@@ -300,7 +298,7 @@ class MissingTimeVariableError(IntegrityError):
     def __init__(self):
         msg = 'No variable bound to time. At least one of the model\'s' \
               ' variables must be bound to "time".'
-        super(MissingTimeVariableError, self).__init__(msg)
+        super().__init__(msg)
 
 
 class NumericalError(MyokitError):
@@ -339,7 +337,7 @@ class ParseError(MyokitError):
         self.desc = str(desc)
         self.value += ': ' + self.desc
         self.cause = cause
-        super(ParseError, self).__init__(self.value)
+        super().__init__(self.value)
 
 
 class ProtocolEventError(MyokitError):
@@ -383,7 +381,7 @@ class SimulationCancelledError(MyokitError):
     *Extends:* :class:`myokit.MyokitError`
     """
     def __init__(self, message='Operation cancelled by user.'):
-        super(SimulationCancelledError, self).__init__(message)
+        super().__init__(message)
 
 
 class SimultaneousProtocolEventError(MyokitError):
@@ -402,7 +400,7 @@ class UnresolvedReferenceError(IntegrityError):
     *Extends:* :class:`myokit.IntegrityError`
     """
     def __init__(self, reference, extra_message=None):
-        super(UnresolvedReferenceError, self).__init__(
+        super().__init__(
             'Unknown variable: <' + reference + '>.'
             + ((' ' + extra_message) if extra_message else '')
         )
@@ -419,7 +417,7 @@ class UnusedVariableError(IntegrityError):
     def __init__(self, var):
         msg = 'Unused variable: <' + var.qname() + '>.'
         tok = var.lhs()._token
-        super(UnusedVariableError, self).__init__(msg, tok)
+        super().__init__(msg, tok)
 
 
 class VariableMappingError(MyokitError):