About to release v0.6.7

bjodah · Apr 4, 2018 · a8447b9 · a8447b9
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commit a8447b9
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Showing 10 changed files with 16 additions and 9 deletions.
diff --git a/.gitignore b/.gitignore
@@ -25,3 +25,4 @@ build/
 .ipython/
 .jupyter/*
 !.jupyter/jupyter_notebook_config.py
+.*cache/
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,7 @@
+v0.6.7
+======
+- Updated manuscript for JOSS.
+
 v0.6.6
 ======
 - Support for containers in ``chempy.units.unit_of``.

diff --git a/chempy/chemistry.py b/chempy/chemistry.py
@@ -125,7 +125,7 @@ def molar_mass(self, units=None):
         --------
         >>> nh4p = Substance.from_formula('NH4+')  # simpler
         >>> from chempy.units import default_units as u
-        >>> nh4p.molar_mass(u)
+        >>> nh4p.molar_mass(u)  # doctest: +ELLIPSIS
         array(18.0384511...) * g/mol
 
         """

diff --git a/chempy/kinetics/ode.py b/chempy/kinetics/ode.py
@@ -159,8 +159,8 @@ def get_odesys(rsys, include_params=True, substitutions=None, SymbolicSys=None,
     >>> odesys, extra = get_odesys(rsys)
     >>> init_conc = {'Fe+3': 1.0, 'SCN-': .3, 'FeSCN+2': 0}
     >>> tout, Cout, info = odesys.integrate(5, init_conc)
-    >>> Cout[-1, :].round(4)
-    array([ 0.7042,  0.0042,  0.2958])
+    >>> Cout[-1, :].round(4)  # doctest: +NORMALIZE_WHITESPACE
+    array([0.7042, 0.0042, 0.2958])
 
     """
     if SymbolicSys is None:

diff --git a/chempy/reactionsystem.py b/chempy/reactionsystem.py
@@ -50,8 +50,8 @@ class ReactionSystem(object):
     >>> from chempy import Reaction
     >>> r1 = Reaction({'R1': 1}, {'P1': 1}, 42.0)
     >>> rsys = ReactionSystem([r1], 'R1 P1')
-    >>> rsys.as_per_substance_array({'R1': 2, 'P1': 3})
-    array([ 2.,  3.])
+    >>> rsys.as_per_substance_array({'R1': 2, 'P1': 3})  # doctest: +NORMALIZE_WHITESPACE
+    array([2., 3.])
 
     Raises
     ------

diff --git a/chempy/units.py b/chempy/units.py
@@ -558,8 +558,8 @@ class Backend(object):
     >>> np.sum([1000*pq.metre/pq.kilometre, 1])
     1001.0
     >>> be_np = Backend(np)
-    >>> be_np.sum([[1000*pq.metre/pq.kilometre, 1], [3, 4]], axis=1)
-    array([ 2.,  7.])
+    >>> be_np.sum([[1000*pq.metre/pq.kilometre, 1], [3, 4]], axis=1)  # doctest: +NORMALIZE_WHITESPACE
+    array([2., 7.])
 
     """
 

diff --git a/chempy/util/stoich.py b/chempy/util/stoich.py
@@ -62,8 +62,8 @@ def decompose_yields(yields, rxns, atol=1e-10):
     >>> from chempy import Reaction
     >>> h2a = Reaction({'H2O': 1}, {'H2': 1, 'O': 1})
     >>> h2b = Reaction({'H2O': 1}, {'H2': 1, 'H2O2': 1}, inact_reac={'H2O': 1})
-    >>> decompose_yields({'H2': 3, 'O': 2, 'H2O2': 1}, [h2a, h2b])
-    array([ 2.,  1.])
+    >>> decompose_yields({'H2': 3, 'O': 2, 'H2O2': 1}, [h2a, h2b])  # doctest: +NORMALIZE_WHITESPACE
+    array([2., 1.])
 
     Raises
     ------

diff --git a/examples/kinetics.png b/examples/kinetics.png
diff --git a/scripts/generate_docs.sh b/scripts/generate_docs.sh
@@ -25,6 +25,7 @@ sed -i "s/$MATCH/$NEW/g" doc/conf.py
 sed -i "s/alabaster/sphinx_rtd_theme/g" doc/conf.py
 if [[ $NARGS -eq 3 ]]; then
 cat <<EOF>>doc/conf.py
+
 context = {
     'conf_py_path': '/doc/',
     'github_user': '$1',

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,6 @@
 [tool:pytest]
 norecursedirs = .* _* build dist conda-recipe scripts benchmarks doc deploy venv
+doctest_optionflags= NORMALIZE_WHITESPACE
 pep8maxlinelength=119
 pep8ignore =
     doc/conf.py ALL  # conf.py is a generated file