Changes to support Python 3

wrappers/python/setup.py

@@ -69,6 +69,11 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            build_info=BUILD_INFO):
     from distutils.core import Extension
     setupKeywords = {}
+    try:
+        from distutils.command.build_py import build_py_2to3 as build_py
+    except ImportError:
+        from distutils.command.build_py import build_py
+    setupKeywords["cmdclass"]          = {'build_py': build_py}
     setupKeywords["name"]              = "OpenMM"
     setupKeywords["version"]           = "%s.%s.%s" % (major_version_num,
                                                        minor_version_num,
@@ -158,11 +163,11 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     outputString = ''
     firstTab     = 40
     secondTab    = 60
-    for key in sorted( setupKeywords.iterkeys() ):
+    for key in sorted(iter(setupKeywords)):
          value         = setupKeywords[key]
          outputString += key.rjust(firstTab) + str( value ).rjust(secondTab) + "\n"
     
-    print "%s" % outputString
+    sys.stdout.write("%s" % outputString)
 
     return setupKeywords
     
@@ -170,8 +175,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
 def main():
     if sys.version_info < (2, 6):
         reportError("OpenMM requires Python 2.6 or better.")
-    if sys.version_info >= (3,):
-        reportError("OpenMM has not been tested with Python 3.0 or higher.")
     if platform.system() == 'Darwin':
         macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
         if tuple(macVersion) < (10, 5):

wrappers/python/simtk/unit/basedimension.py

@@ -44,15 +44,15 @@ class BaseDimension(object):
             BaseDimension._next_unused_index += 1
         self._index = BaseDimension._index_by_name[name]
         
-    def __cmp__(self, other):
+    def __lt__(self, other):
         """
         The implicit order of BaseDimensions is the order in which they were created.
         This method is used for using BaseDimensions as hash keys, and also affects
         the order in which units appear in multi-dimensional Quantities.
         
-        Returns 0 if self == other, -1 if self < other, and 1 if self > other.
+        Returns True if self < other, False otherwise.
         """
-        return cmp(self._index, other._index)
+        return self._index < other._index
         
     def __hash__(self):
         """

wrappers/python/simtk/unit/baseunit.py

@@ -37,15 +37,15 @@ class BaseUnit(object):
         self._conversion_factor_to_by_name = {}
         self._conversion_factor_to_by_name[self.name] = 1.0
     
-    def __cmp__(self, other):
+    def __lt__(self, other):
         """
         Comparison function that sorts BaseUnits by BaseDimension
         """
         # First sort on dimension
-        c = cmp(self.dimension, other.dimension)
-        if c != 0: return c
+        if self.dimension != other.dimension:
+            return self.dimension < other.dimension
         # Second on conversion factor
-        return cmp(self.conversion_factor_to(other), 1.0)
+        return self.conversion_factor_to(other) < 1.0
 
     def iter_base_dimensions(self):
         """

wrappers/python/simtk/unit/constants.py

@@ -3,6 +3,8 @@
 Module simtk.unit.constants
 """
 
+from __future__ import division
+
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 

wrappers/python/simtk/unit/mymatrix.py

@@ -8,7 +8,7 @@ def eye(size):
     """
     Returns identity matrix.
     
-    >>> print eye(3)
+    >>> print(eye(3))
     [[1, 0, 0]
      [0, 1, 0]
      [0, 0, 1]]
@@ -28,7 +28,7 @@ def zeros(m, n=None):
     """
     Returns matrix of zeroes
     
-    >>> print zeros(3)
+    >>> print(zeros(3))
     [[0, 0, 0]
      [0, 0, 0]
      [0, 0, 0]]
@@ -94,13 +94,13 @@ class MyMatrix(MyVector):
     Pure python linear algebra matrix for internal matrix inversion in UnitSystem.
     
     >>> m = MyMatrix([[1,0,],[0,1,]])
-    >>> print m
+    >>> print(m)
     [[1, 0]
      [0, 1]]
-    >>> print ~m
+    >>> print(~m)
     [[1.0, 0.0]
      [0.0, 1.0]]
-    >>> print eye(5)
+    >>> print(eye(5))
     [[1, 0, 0, 0, 0]
      [0, 1, 0, 0, 0]
      [0, 0, 1, 0, 0]
@@ -111,18 +111,18 @@ class MyMatrix(MyVector):
     1
     >>> m[1:4]
     MyMatrixTranspose([[0, 0, 0],[1, 0, 0],[0, 1, 0],[0, 0, 1],[0, 0, 0]])
-    >>> print m[1:4]
+    >>> print(m[1:4])
     [[0, 0, 0]
      [1, 0, 0]
      [0, 1, 0]
      [0, 0, 1]
      [0, 0, 0]]
-    >>> print m[1:4][0:2]
+    >>> print(m[1:4][0:2])
     [[0, 1]
      [0, 0]
      [0, 0]]
     >>> m[1:4][0:2] = [[9,8],[7,6],[5,4]]
-    >>> print m
+    >>> print(m)
     [[1, 0, 0, 0, 0]
      [9, 8, 0, 0, 0]
      [7, 6, 1, 0, 0]
@@ -182,13 +182,13 @@ class MyMatrix(MyVector):
         
         >>> a = MyMatrix([[1,2],[3,4]])
         >>> b = MyMatrix([[5,6],[7,8]])
-        >>> print a
+        >>> print(a)
         [[1, 2]
          [3, 4]]
-        >>> print b
+        >>> print(b)
         [[5, 6]
          [7, 8]]
-        >>> print a*b
+        >>> print(a*b)
         [[19, 22]
          [43, 50]]
         
@@ -209,7 +209,7 @@ class MyMatrix(MyVector):
         """
         Matrix addition.
         
-        >>> print MyMatrix([[1, 2],[3, 4]]) + MyMatrix([[5, 6],[7, 8]])
+        >>> print(MyMatrix([[1, 2],[3, 4]]) + MyMatrix([[5, 6],[7, 8]]))
         [[6, 8]
          [10, 12]]
         """
@@ -227,7 +227,7 @@ class MyMatrix(MyVector):
         """
         Matrix subtraction.
         
-        >>> print MyMatrix([[1, 2],[3, 4]]) - MyMatrix([[5, 6],[7, 8]])
+        >>> print(MyMatrix([[1, 2],[3, 4]]) - MyMatrix([[5, 6],[7, 8]]))
         [[-4, -4]
          [-4, -4]]
         """
@@ -256,32 +256,32 @@ class MyMatrix(MyVector):
     def __invert__(self):
         """
         >>> m = MyMatrix([[1,1],[0,1]])
-        >>> print m
+        >>> print(m)
         [[1, 1]
          [0, 1]]
-        >>> print ~m
+        >>> print(~m)
         [[1.0, -1.0]
          [0.0, 1.0]]
-        >>> print m*~m
+        >>> print(m*~m)
         [[1.0, 0.0]
          [0.0, 1.0]]
-        >>> print ~m*m
+        >>> print(~m*m)
         [[1.0, 0.0]
          [0.0, 1.0]]
         >>> m = MyMatrix([[1,0,0],[0,0,1],[0,-1,0]])
-        >>> print m
+        >>> print(m)
         [[1, 0, 0]
          [0, 0, 1]
          [0, -1, 0]]
-        >>> print ~m
+        >>> print(~m)
         [[1.0, 0.0, 0.0]
          [0.0, 0.0, -1.0]
          [0.0, 1.0, 0.0]]
-        >>> print m*~m
+        >>> print(m*~m)
         [[1.0, 0.0, 0.0]
          [0.0, 1.0, 0.0]
          [0.0, 0.0, 1.0]]
-        >>> print ~m*m
+        >>> print(~m*m)
         [[1.0, 0.0, 0.0]
          [0.0, 1.0, 0.0]
          [0.0, 0.0, 1.0]]

wrappers/python/simtk/unit/quantity.py

@@ -39,6 +39,8 @@ Two possible enhancements that have not been implemented are
   2) Incorporate offsets for celsius <-> kelvin conversion
 """
 
+from __future__ import division
+
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 
@@ -232,25 +234,23 @@ class Quantity(object):
         """
         if not is_quantity(other):
             return False
-        else:
-            return NotImplemented # punt to cmp
+        if not self.unit.is_compatible(other.unit):
+            return False
+        return self.value_in_unit(other.unit) == other._value
             
     def __ne__(self, other):
         """
         """
-        if not is_quantity(other):
-            return True
-        else:
-            return NotImplemented # punt to cmp
+        return not self.__eq__(other)
 
-    def __cmp__(self, other):
+    def __lt__(self, other):
         """Compares two quantities.
         
         Raises TypeError if the Quantities are of different dimension (e.g. length vs. mass)
         
-        Returns -1 if self < other, 0 if self == other, and 1 if self > other.
+        Returns True if self < other, False otherwise.
         """
-        return cmp(self._value, (other.value_in_unit(self.unit)))       
+        return self._value < other.value_in_unit(self.unit)
 
     def __ge__(self, other):
         return self._value >= (other.value_in_unit(self.unit))     
@@ -363,7 +363,7 @@ class Quantity(object):
             return self._change_units_with_factor(self.unit, other, post_multiply=True)
             # return Quantity(other * self._value, self.unit)
         
-    def __div__(self, other):
+    def __truediv__(self, other):
         """Divide a Quantity by another object
 
         Returns a new Quantity, unless the resulting unit type is dimensionless,
@@ -383,16 +383,16 @@ class Quantity(object):
             return self * pow(other, -1.0)
             # return Quantity(self._value / other, self.unit)
 
-    def __rdiv__(self, other):
+    def __rtruediv__(self, other):
         """Divide a scalar by a quantity.
         
         Returns a new Quantity.  The resulting units are the inverse of the self argument units.
         """
         if is_unit(other):
             # print "R unit / quantity"
-            raise NotImplementedError('programmer is surprised __rdiv__ was called instead of __div__')
+            raise NotImplementedError('programmer is surprised __rtruediv__ was called instead of __truediv__')
         elif is_quantity(other):
-            raise NotImplementedError('programmer is surprised __rdiv__ was called instead of __div__')
+            raise NotImplementedError('programmer is surprised __rtruediv__ was called instead of __truediv__')
         else:
             # print "R scalar / quantity"
             return other * pow(self, -1.0)

wrappers/python/simtk/unit/unit.py

@@ -5,6 +5,8 @@ Module simtk.unit
 Contains classes Unit and ScaledUnit.
 """
 
+from __future__ import division
+
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 
@@ -149,17 +151,16 @@ class Unit(object):
     def __ne__(self, other):
         return not self.__eq__(other)
 
-    def __cmp__(self, other):
+    def __lt__(self, other):
         """Compare two Units.
         
         Raises a TypeError if the units have different dimensions.
         
-        Returns 0 if the Units are equal, -1 if the first Unit is smaller, 
-        and returns 1 if the first Unit is larger.
+        Returns True if self < other, False otherwise.
         """
         if not self.is_compatible(other):
             raise TypeError('Unit "%s" is not compatible with Unit "%s".', (self, other))
-        return cmp(self.conversion_factor_to(other), 1.0)
+        return self.conversion_factor_to(other) < 1.0
 
     def __hash__(self):
         """
@@ -175,7 +176,7 @@ class Unit(object):
     # def __mul__(self, other):
     # See unit_operators.py for Unit.__mul__ operator
     
-    def __div__(self, other):
+    def __truediv__(self, other):
         """Divide a Unit by another object.
         
         Returns a composite Unit if other is another Unit.
@@ -186,8 +187,8 @@ class Unit(object):
         """
         return self * pow(other, -1)
 
-    # def __rdiv__(self, other):
-    # Because rdiv returns a Quantity, look in quantity.py for definition of Unit.__rdiv__
+    # def __rtruediv__(self, other):
+    # Because rtruediv returns a Quantity, look in quantity.py for definition of Unit.__rtruediv__
 
     _pow_cache = {}
 
@@ -522,6 +523,11 @@ class ScaledUnit(object):
         else:
             other_u = Unit({other: 1.0})
         return self.factor * Unit(u).conversion_factor_to(other_u)
+
+    def __lt__(self, other):
+        """Compare two ScaledUnits.
+        """
+        return hash(self) < hash(other)
         
     def __str__(self):
         """Returns a string with the name of this ScaledUnit
@@ -569,7 +575,7 @@ class UnitSystem(object):
                 to_base_units[m][n] = power
         try:
             self.from_base_units = ~to_base_units
-        except ArithmeticError, e:
+        except ArithmeticError as e:
         # for compatibility between python 2.5 and python 3.0,
         # try replacing line above with the following two lines:
         # except ArithmeticError:

wrappers/python/simtk/unit/unit_definitions.py

@@ -4,6 +4,8 @@ Module simtk.unit.unit_definitions
 
 """
 
+from __future__ import division
+
 __author__ = "Christopher M. Bruns"
 __version__ = "0.6"
 

wrappers/python/simtk/unit/unit_math.py

@@ -5,6 +5,8 @@ Module simtk.unit.math
 Arithmetic methods on Quantities and Units
 """
 
+from __future__ import division
+
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 
@@ -69,7 +71,7 @@ def acos(x):
     """
     >>> acos(1.0)
     Quantity(value=0.0, unit=radian)
-    >>> print acos(1.0)
+    >>> print(acos(1.0))
     0.0 rad
     """
     return math.acos(x) * radians
@@ -100,7 +102,7 @@ def sqrt(val):
     """
     >>> sqrt(9.0)
     3.0
-    >>> print sqrt(meter*meter)
+    >>> print(sqrt(meter*meter))
     meter
     >>> sqrt(9.0*meter*meter)
     Quantity(value=3.0, unit=meter)

wrappers/python/simtk/unit/unit_operators.py

@@ -36,14 +36,14 @@ def _unit_class_rdiv(self, other):
     of the inverse of self.
     """
     if is_unit(other):
-        raise NotImplementedError('programmer is surprised __rdiv__ was called instead of __div__')
+        raise NotImplementedError('programmer is surprised __rtruediv__ was called instead of __truediv__')
     else:
         # print "R scalar / unit"
         unit = pow(self, -1.0)
         value = other
         return Quantity(value, unit).reduce_unit(self)
 
-Unit.__rdiv__ = _unit_class_rdiv
+Unit.__rtruediv__ = _unit_class_rdiv
 
 
 def _unit_class_mul(self, other):

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -188,7 +188,7 @@ class SwigInputBuilder:
 
     def writeGlobalConstants(self):
         self.fOut.write("/* Global Constants */\n\n")
-        node = (x for x in findNodes(self.doc.getroot(), "compounddef", kind="namespace") if x.findtext("compoundname") == "OpenMM").next()
+        node = next((x for x in findNodes(self.doc.getroot(), "compounddef", kind="namespace") if x.findtext("compoundname") == "OpenMM"))
         for section in findNodes(node, "sectiondef", kind="var"):
             for memberNode in findNodes(section, "memberdef", kind="variable", mutable="no", prot="public", static="yes"):
                 vDef = stripOpenmmPrefix(getText("definition", memberNode))

wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i

@@ -250,9 +250,9 @@ def stripUnits(args):
     newArgList=[]
     for arg in args:
         if unit.is_quantity(arg):
-	    # JDC: Ugly workaround for OpenMM using 'bar' for fundamental pressure unit.
+            # JDC: Ugly workaround for OpenMM using 'bar' for fundamental pressure unit.
             if arg.unit.is_compatible(unit.bar):
-	        arg = arg / unit.bar
+                arg = arg / unit.bar
             else:
                 arg=arg.value_in_unit_system(unit.md_unit_system)                
             # JDC: End workaround.