logspace10 -> logspace_from_lin

CHANGES.rst

@@ -1,3 +1,10 @@
+v0.4.1
+======
+- Fixes for enhanced robustness:
+  - ``.kinetics.ode.get_odesys``
+  - ``.chemistry.as_per_substance_array``
+- Minor changes.
+
 v0.4.0
 ======
 - Multiple fixes throughout

chempy/chemistry.py

@@ -1301,7 +1301,7 @@ def as_per_substance_array(self, cont, dtype='float64', unit=None, raise_on_unk=
                         raise KeyError("Unkown substance key: %s" % k)
             cont = [cont[k] for k in substance_keys]
 
-        cont = np.asarray(cont, dtype=dtype)
+        cont = np.atleast_1d(np.asarray(cont, dtype=dtype).squeeze())
         if cont.shape[-1] != self.ns:
             raise ValueError("Incorrect size")
         return cont*(unit if unit is not None else 1)

chempy/kinetics/rates.py

@@ -107,7 +107,7 @@ class _Radiolytic(RadiolyticBase):
         parameter_keys = (doserate_name, 'density')
         print_name = 'Radiolytic' if doserate_name == 'doserate' else ('Radiolytic{'+doserate_name+'}')
 
-        def g_value(self, variables, backend):  # for subclasses
+        def g_value(self, variables, backend=math):  # for subclasses
             return self.arg(variables, 0, backend=backend)
 
         def __call__(self, variables, backend=math):

chempy/tests/test_chemistry.py

@@ -187,8 +187,7 @@ def test_ReactionSystem__as_per_substance_array_dict():
     m = default_units.metre
     M = default_units.molar
     rs = ReactionSystem([], [Substance('H2O')])
-    c = rs.as_per_substance_array({'H2O': 1*M},
-                                  unit=M)
+    c = rs.as_per_substance_array({'H2O': 1*M}, unit=M)
     assert c.dimensionality == M.dimensionality
     assert abs(c[0]/(1000*mol/m**3) - 1) < 1e-16
 

chempy/tests/test_units.py

@@ -11,7 +11,7 @@
 
 from ..util.testing import requires
 from ..units import (
-    allclose, get_derived_unit, is_unitless, linspace, logspace10,
+    allclose, get_derived_unit, is_unitless, linspace, logspace_from_lin,
     SI_base_registry, unitless_in_registry, format_string, get_physical_quantity,
     to_unitless, magnitude, default_unit_in_registry, Backend, latex_of_unit,
     unit_of, unit_registry_to_human_readable, units_library,
@@ -104,6 +104,7 @@ def test_to_unitless():
     assert abs(to_unitless(3/(u.second*u.molar),
                            u.metre**3/u.mole/u.second) - 3e-3) < 1e-12
     assert abs(to_unitless(2*u.dm3, u.cm3) - 2000) < 1e-12
+    assert abs(to_unitless(2*u.m3, u.dm3) - 2000) < 1e-12
     assert (float(to_unitless(UncertainQuantity(2, u.dm3, .3), u.cm3)) - 2000) < 1e-12
 
     g1 = UncertainQuantity(4.46, u.per100eV, 0)
@@ -138,8 +139,8 @@ def test_linspace():
 
 
 @requires(units_library)
-def test_logspace10():
-    ls = logspace10(2*u.second, 3*u.second)
+def test_logspace_from_lin():
+    ls = logspace_from_lin(2*u.second, 3*u.second)
     assert abs(to_unitless(ls[0], u.hour) - 2/3600.) < 1e-15
     assert abs(to_unitless(ls[-1], u.hour) - 3/3600.) < 1e-15
 

chempy/units.py

@@ -5,20 +5,21 @@
 - ``chempy.units.default_constants``
 - ``chempy.units.SI_base_registry``
 
+together with some functions.
+
 Currently `quantities <https://pypi.python.org/pypi/quantities>`_ is used as
 the underlying package to handle units. If it is possible you should try to
-only use the `chempy.units` module (in case ``ChemPy`` changes this backend).
+only use the `chempy.units` module (in case ``ChemPy`` changes this backend),
+and avoid relying on any attributes of the Quantity instances (and rather use
+functions in `chempy.units`).
 
 """
 from __future__ import (absolute_import, division, print_function)
 
 from functools import reduce
-from math import log10
 from operator import mul
 
 from ._util import NameSpace
-# Currently we use quantities for units. This may change, therefore use this
-# file for all units. A requirement is first-class numpy support.
 
 units_library = 'quantities'  # info used for selective testing.
 
@@ -41,6 +42,7 @@
     default_units = NameSpace(pq)
     default_units.decimetre = pq.UnitQuantity(
         'decimetre',  default_units.m / 10.0, u_symbol='dm')
+    default_units.m3 = default_units.metre**3
     default_units.dm3 = default_units.decimetre**3
     default_units.cm3 = default_units.centimetre**3
     if not hasattr(default_units, 'molar'):
@@ -321,7 +323,15 @@ def allclose(a, b, rtol=1e-8, atol=None):
 
 
 def linspace(start, stop, num=50):
-    """ Analogous to ``numpy.linspace``. """
+    """ Analogous to ``numpy.linspace``.
+
+    Examples
+    --------
+    >>> abs(linspace(2, 8, num=3)[1] - 5) < 1e-15
+    True
+
+    """
+
     # work around for quantities v0.10.1 and NumPy
     import numpy as np
     unit = unit_of(start)
@@ -330,13 +340,20 @@ def linspace(start, stop, num=50):
     return np.linspace(start_, stop_, num)*unit
 
 
-def logspace10(start, stop, num=50):
-    """ Logarithmically spaced data points """
+def logspace_from_lin(start, stop, num=50):
+    """ Logarithmically spaced data points
+
+    Examples
+    --------
+    >>> abs(logspace_from_lin(2, 8, num=3)[1] - 4) < 1e-15
+    True
+
+    """
     import numpy as np
     unit = unit_of(start)
-    start_ = log10(to_unitless(start, unit))
-    stop_ = log10(to_unitless(stop, unit))
-    return 10**np.linspace(start_, stop_, num)*unit
+    start_ = np.log2(to_unitless(start, unit))
+    stop_ = np.log2(to_unitless(stop, unit))
+    return np.exp2(np.linspace(start_, stop_, num))*unit
 
 
 def _sum(iterable):

chempy/util/bkh.py

@@ -8,7 +8,7 @@
 from itertools import chain
 
 from chempy.kinetics.ode import get_odesys
-from chempy.units import to_unitless, linspace, logspace10
+from chempy.units import to_unitless, linspace, logspace_from_lin
 
 
 def integration_with_sliders(
@@ -36,7 +36,7 @@ def integration_with_sliders(
     if x_axis_type == 'linear':
         tout = linspace(tend*0, tend)
     elif x_axis_type == 'log':
-        tout = logspace10(tend*1e-9, tend)
+        tout = logspace_from_lin(tend*1e-9, tend)
     else:
         raise NotImplementedError("Unknown x_axis_type: %s" % x_axis_type)