A large number of unit cleanups and fix numpy wart

The main thing that's done here is that numpy arrays can be given units via the
* operator, rather than relying on the Quantity constructor

e.g.,

>>> import numpy as np
>>> np.zeros(10) * u.angstroms
Quantity(value=array([ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.]), unit=angstrom)

yay!

wrappers/python/simtk/unit/basedimension.py

 #!/bin/env python
-
-
 """
 Module simtk.unit.basedimension
 
@@ -34,6 +32,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import print_function, division
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.6"

wrappers/python/simtk/unit/baseunit.py

@@ -33,6 +33,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import print_function, division, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.6"
@@ -44,6 +45,7 @@ class BaseUnit(object):
     For example, meter_base_unit could be a BaseUnit for the length dimension.
     The BaseUnit class is used internally in the more general Unit class.
     '''
+    __array_priority__ = 100
 
     def __init__(self, base_dim, name, symbol):
         """Creates a new BaseUnit.
@@ -127,7 +129,7 @@ class BaseUnit(object):
         self._conversion_factor_to_by_name[other.name] = factor
         for (unit, cfac) in other._conversion_factor_to.items():
             if unit is self: continue
-            if self._conversion_factor_to.has_key(unit): continue
+            if unit in self._conversion_factor_to: continue
             self._conversion_factor_to[unit] = factor * cfac
             unit._conversion_factor_to[self] = pow(factor * cfac, -1)
             self._conversion_factor_to_by_name[unit.name] = factor * cfac
@@ -138,7 +140,7 @@ class BaseUnit(object):
         other._conversion_factor_to_by_name[self.name] = invFac
         for (unit, cfac) in self._conversion_factor_to.items():
             if unit is other: continue
-            if other._conversion_factor_to.has_key(unit): continue
+            if unit in other._conversion_factor_to: continue
             other._conversion_factor_to[unit] = invFac * cfac
             unit._conversion_factor_to[other] = pow(invFac * cfac, -1)
             other._conversion_factor_to_by_name[unit.name] = invFac * cfac

wrappers/python/simtk/unit/constants.py

@@ -29,13 +29,12 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
-
-from __future__ import division
+from __future__ import print_function, division, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 
-from unit_definitions import *
+from .unit_definitions import *
 
 #################
 ### CONSTANTS ###

wrappers/python/simtk/unit/mymatrix.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import print_function, division, absolute_import
 
 import sys
 
@@ -41,9 +42,9 @@ def eye(size):
      [0, 0, 1]]
     """
     result = []
-    for row in range(0, size):
+    for row in range(size):
         r = []
-        for col in range(0, size):
+        for col in range(size):
             if row == col:
                 r.append(1)
             else:
@@ -63,9 +64,9 @@ def zeros(m, n=None):
     if n is None:
         n = m
     result = []
-    for row in range(0, m):
+    for row in range(m):
         r = []
-        for col in range(0, n):
+        for col in range(n):
             r.append(0)
         result.append(r)
     return MyMatrix(result)
@@ -171,7 +172,7 @@ class MyMatrix(MyVector):
     def __str__(self):
         result = ""
         start_char = "["
-        for m in range(0, self.numRows()):
+        for m in range(self.numRows()):
             result += start_char
             result += str(self[m])
             if m < self.numRows() - 1:
@@ -226,9 +227,9 @@ class MyMatrix(MyVector):
         if self.numCols() != r:
             raise ArithmeticError("Matrix multplication size mismatch (%d vs %d)" % (self.numCols(), r))
         result = zeros(m, n)
-        for i in range(0, m):
-            for j in range(0, n):
-                for k in range(0, r):
+        for i in range(m):
+            for j in range(n):
+                for k in range(r):
                     result[i][j] += self[i][k]*rhs[k][j]
         return result
 
@@ -245,8 +246,8 @@ class MyMatrix(MyVector):
         assert len(rhs) == m
         assert len(rhs[0]) == n
         result = zeros(m,n)
-        for i in range(0,m):
-            for j in range(0,n):
+        for i in range(m):
+            for j in range(n):
                 result[i][j] = self[i][j] + rhs[i][j]
         return result
 
@@ -263,8 +264,8 @@ class MyMatrix(MyVector):
         assert len(rhs) == m
         assert len(rhs[0]) == n
         result = zeros(m,n)
-        for i in range(0,m):
-            for j in range(0,n):
+        for i in range(m):
+            for j in range(n):
                 result[i][j] = self[i][j] - rhs[i][j]
         return result
 
@@ -275,8 +276,8 @@ class MyMatrix(MyVector):
         m = self.numRows()
         n = self.numCols()
         result = zeros(m, n)
-        for i in range(0,m):
-            for j in range(0,n):
+        for i in range(m):
+            for j in range(n):
                 result[i][j] = -self[i][j]
         return result
 
@@ -358,7 +359,7 @@ class MyMatrix(MyVector):
                 ipiv[icol] += 1
                 # We now have the pivot element, so we interchange rows...
                 if irow != icol:
-                    for l in range(0,n):
+                    for l in range(n):
                         temp = a[irow][l]
                         a[irow][l] = a[icol][l]
                         a[icol][l] = temp
@@ -368,20 +369,20 @@ class MyMatrix(MyVector):
                     raise ArithmeticError("Cannot invert singular matrix")
                 pivinv = 1.0/a[icol][icol]
                 a[icol][icol] = 1.0
-                for l in range(0,n):
+                for l in range(n):
                     a[icol][l] *= pivinv
-                for ll in range(0,n): # next we reduce the rows
+                for ll in range(n): # next we reduce the rows
                     if ll == icol:
                         continue # except the pivot one, of course
                     dum = a[ll][icol]
                     a[ll][icol] = 0.0
-                    for l in range(0,n):
+                    for l in range(n):
                         a[ll][l] -= a[icol][l]*dum
             # Unscramble the permuted columns
             for l in range(n-1, -1, -1):
                 if indxr[l] == indxc[l]:
                     continue
-                for k in range(0,n):
+                for k in range(n):
                     temp = a[k][indxr[l]]
                     a[k][indxr[l]] = a[k][indxc[l]]
                     a[k][indxc[l]] = temp
@@ -415,7 +416,7 @@ class MyMatrixTranspose(MyMatrix):
             return MyVector(result)
 
     def __setitem__(self, key, rhs):
-        for n in range(0, len(self.data)):
+        for n in range(len(self.data)):
             self.data[n][key] = rhs[n]
 
     def __str__(self):
@@ -423,11 +424,11 @@ class MyMatrixTranspose(MyMatrix):
             return "[[]]"
         start_char = "["
         result = ""
-        for m in range(0, len(self.data[0])):
+        for m in range(len(self.data[0])):
             result += start_char
             result += "["
             sep_char = ""
-            for n in range(0, len(self.data)):
+            for n in range(len(self.data)):
                 result += sep_char
                 result += str(self.data[n][m])
                 sep_char = ", "
@@ -443,11 +444,11 @@ class MyMatrixTranspose(MyMatrix):
             return "MyMatrixTranspose([[]])"
         start_char = "["
         result = 'MyMatrixTranspose('
-        for m in range(0, len(self.data[0])):
+        for m in range(len(self.data[0])):
             result += start_char
             result += "["
             sep_char = ""
-            for n in range(0, len(self.data)):
+            for n in range(len(self.data)):
                 result += sep_char
                 result += repr(self.data[n][m])
                 sep_char = ", "

wrappers/python/simtk/unit/prefix.py

@@ -29,12 +29,13 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import print_function, division, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.6"
 
-from baseunit import BaseUnit
-from unit import Unit, ScaledUnit
+from .baseunit import BaseUnit
+from .unit import Unit, ScaledUnit
 import sys
 
 ###################

wrappers/python/simtk/unit/quantity.py

@@ -67,8 +67,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
-
-from __future__ import division
+from __future__ import division, print_function, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
@@ -76,8 +75,8 @@ __version__ = "0.5"
 
 import math
 import copy
-from standard_dimensions import *
-from unit import Unit, is_unit, dimensionless
+from .standard_dimensions import *
+from .unit import Unit, is_unit, dimensionless
 
 class Quantity(object):
     """Physical quantity, such as 1.3 meters per second.
@@ -92,17 +91,6 @@ class Quantity(object):
             Note - unit conversions will cause tuples to be converted to lists
       4 - lists of tuples of numbers, lists of lists of ... etc. of numbers
       5 - numpy.arrays
-
-    Create numpy.arrays with units using the Quantity constructor, not the
-    multiply operator.  e.g.
-
-      Quantity(numpy.array([1,2,3]), centimeters) # correct
-
-        *NOT*
-
-      numpy.array([1,2,3]) * centimeters # won't work
-
-    because numpy.arrays already overload the multiply operator for EVERYTHING.
     """
 
     def __init__(self, value=None, unit=None):
@@ -136,7 +124,7 @@ class Quantity(object):
                     if len(value) < 1:
                         unit = dimensionless
                     else:
-                        first_item = iter(value).next()
+                        first_item = next(iter(value))
                         # Avoid infinite recursion for string, because a one-character
                         # string is its own first element
                         try:
@@ -613,6 +601,9 @@ class Quantity(object):
         """
         return bool(self._value)
 
+    def __bool__(self):
+        return self.__nonzero__()
+
     def __complex__(self):
         return Quantity(complex(self._value), self.unit)
     def __float__(self):
@@ -713,7 +704,7 @@ class Quantity(object):
                     else:
                         for i in range(len(value)):
                             value[i] = factor*value[i]
-            except TypeError as ex:
+            except TypeError:
                 if isinstance(value, tuple):
                     value = tuple([self._scale_sequence(x, factor, post_multiply) for x in value])
                 else:

wrappers/python/simtk/unit/standard_dimensions.py

@@ -31,11 +31,12 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import division, print_function, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.6"
 
-from basedimension import BaseDimension
+from .basedimension import BaseDimension
 
 ##################
 ### DIMENSIONS ###

wrappers/python/simtk/unit/unit.py

@@ -31,8 +31,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
-
-from __future__ import division
+from __future__ import division, print_function, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
@@ -40,15 +39,18 @@ __version__ = "0.5"
 
 import math
 import sys
-from mymatrix import MyMatrix, zeros
-from basedimension import BaseDimension
-from baseunit import BaseUnit
-from standard_dimensions import *
+from .mymatrix import MyMatrix, zeros
+from .basedimension import BaseDimension
+from .baseunit import BaseUnit
+from .standard_dimensions import *
 
 class Unit(object):
     """
     Physical unit such as meter or ampere.
     """
+
+    __array_priority__ = 100
+
     def __init__(self, base_or_scaled_units):
         """Create a new Unit.
 
@@ -495,6 +497,8 @@ class ScaledUnit(object):
     ScaledUnit and BaseUnit are both used in the internals of Unit.  They
     should only be used during the construction of Units.
     """
+    __array_priority__ = 100
+
     def __init__(self, factor, master, name, symbol):
         self.factor = factor
         # Convert to one base_unit per dimension
@@ -576,6 +580,14 @@ class ScaledUnit(object):
                 + ", symbol=" + repr(self.symbol) + ")"
 
 class UnitSystem(object):
+    """
+    A complete system of units defining the *base* unit in each dimension
+
+    Parameters
+    ----------
+    units: ``list``
+        List of base units from which to construct the unit system
+    """
     def __init__(self, units):
         self.units = units
         self._unit_conversion_cache = {}

wrappers/python/simtk/unit/unit_definitions.py

@@ -30,16 +30,16 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 
-from __future__ import division
+from __future__ import division, print_function, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.6"
 
-from baseunit import BaseUnit
-from standard_dimensions import *
-from unit import Unit, ScaledUnit, UnitSystem, dimensionless
-from unit_operators import * ; # needed for manipulation of units
-from prefix import *
+from .baseunit import BaseUnit
+from .standard_dimensions import *
+from .unit import Unit, ScaledUnit, UnitSystem, dimensionless
+from .unit_operators import * ; # needed for manipulation of units
+from .prefix import *
 import math
 import sys
 
@@ -303,20 +303,20 @@ mmHg = Unit({mmHg_base_unit: 1.0})
 
 ampere_base_unit = ScaledUnit(1.0, coulomb/second, "ampere", "A")
 
-si_unit_system = UnitSystem([\
-        meter_base_unit,\
-        kilogram_base_unit,\
-        second_base_unit,\
+si_unit_system = UnitSystem([
+        meter_base_unit,
+        kilogram_base_unit,
+        second_base_unit,
         ampere_base_unit,
         kelvin_base_unit,
         mole_base_unit,
         candela_base_unit,
         radian_base_unit])
 
-cgs_unit_system = UnitSystem([\
-        centimeter_base_unit,\
-        gram_base_unit,\
-        second_base_unit,\
+cgs_unit_system = UnitSystem([
+        centimeter_base_unit,
+        gram_base_unit,
+        second_base_unit,
         ampere_base_unit,
         kelvin_base_unit,
         mole_base_unit,
@@ -324,10 +324,10 @@ cgs_unit_system = UnitSystem([\
 
 dalton_base_unit = ScaledUnit(1.0, gram/mole, "dalton", "Da")
 
-md_unit_system = UnitSystem([\
-        nanometer_base_unit,\
+md_unit_system = UnitSystem([
+        nanometer_base_unit,
         dalton_base_unit,
-        picosecond_base_unit,\
+        picosecond_base_unit,
         elementary_charge_base_unit,
         kelvin_base_unit,
         mole_base_unit,

wrappers/python/simtk/unit/unit_math.py

@@ -31,16 +31,15 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
-
-from __future__ import division
+from __future__ import division, print_function, absolute_import
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 
 
 import math
-from quantity import is_quantity
-from unit_definitions import *
+from .quantity import is_quantity
+from .unit_definitions import *
 
 ####################
 ### TRIGONOMETRY ###

wrappers/python/simtk/unit/unit_operators.py

@@ -46,12 +46,13 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import print_function, absolute_import, division
 
 __author__ = "Christopher M. Bruns"
 __version__ = "0.5"
 
-from unit import Unit, is_unit
-from quantity import Quantity, is_quantity
+from .unit import Unit, is_unit
+from .quantity import Quantity, is_quantity
 
 # Attach methods of Unit class that return a Quantity to Unit class.
 # I put them here to avoid circular dependence in imports.