Merge branch 'master' of github.com:SimTk/openmm

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.

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -180,6 +180,7 @@ UNITS = {
 ("*", "getParticleMass") : ("unit.amu", ()),
 ("*", "getPlatform") : (None, ()),
 ("*", "getPlatformByName") : (None, ()),
+("*", "getPluginLoadFailures"): (None, ()),
 ("*", "getRandomNumberSeed") : (None, ()),
 ("*", "getReactionFieldDielectric") : (None, ()),
 ("*", "getSoluteDielectric") : (None, ()),
@@ -413,7 +414,8 @@ UNITS = {
 ("Platform", "getSpeed") : (None, ()),
 ("RBTorsionForce", "getTorsionParameters")
  : (None, (None, None, None, None,
-           None, None, None, None, None, None)),
+           'unit.kilojoules_per_mole', 'unit.kilojoules_per_mole', 'unit.kilojoules_per_mole',
+           'unit.kilojoules_per_mole', 'unit.kilojoules_per_mole', 'unit.kilojoules_per_mole')),
 ("System", "getConstraintParameters") : (None, (None, None, 'unit.nanometer')),
 ("System", "getForce") : (None, ()),
 ("System", "getVirtualSite") : (None, ()),

wrappers/python/tests/TestUnits.py

@@ -448,7 +448,7 @@ class TestUnits(QuantityTestCase):
         self.assertAlmostEqualQuantities(n, 2.05834818672e-17 * u.mole)
         self.assertAlmostEqualQuantities(V, 5.2359833333333e-19 * u.meters**3)
         self.assertEqual(str(T), '310.0 K')
-        self.assertEqual(str(u.MOLAR_GAS_CONSTANT_R), '8.31447247122 J/(K mol)')
+        self.assertEqual(str(1*u.joules/u.kelvin/u.mole), '1 J/(K mol)')
         self.assertTrue(u.is_quantity(V))
         # Checks trouble with complicated unit conversion factors
         p1 = 1.0 * u.atmospheres
@@ -638,6 +638,7 @@ class TestUnits(QuantityTestCase):
         self.assertEqual(str(u.meters*u.meters), 'meter**2')
         self.assertEqual(str(u.meter*u.meter), 'meter**2')
 
+@unittest.skipIf(np is None, 'Skipping numpy units tests')
 class TestNumpyUnits(QuantityTestCase):
 
     def testNumpyQuantity(self):
@@ -686,6 +687,14 @@ class TestNumpyUnits(QuantityTestCase):
         b = a.reshape((5, 2))
         self.assertTrue(u.is_quantity(b))
 
-if np is None:
-    # Support lack of numpy
-    del TestNumpyUnits
+    def testMultiplication(self):
+        """ Tests that units override numpy.ndarray multiplication """
+        self.assertIsInstance(np.arange(10)*u.angstroms, u.Quantity)
+        # This only works with versions of numpy > 1.7 due to a bug in older
+        # versions. Since Travis-CI installs Python 1.6.1 from aptitude, and we
+        # don't want it to report test failures *every time*, just disable this
+        # particular test for the numpy versions known to be bad.
+        if np.version.version > '1.7':
+            x = np.array([1]) * u.liters
+            self.assertIsInstance(x, u.Quantity)
+            self.assertIsInstance(np.arange(10) * x, u.Quantity)