Fix a typo (#61)

* fixes on PR #60 
* typo fixes
* Update MANIFEST.in

MANIFEST.in

@@ -1,5 +1,5 @@
 include *.rst
-recursive-include src/alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out *.xvg
+recursive-include src/alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out *.xvg *.npy
 include README.rst
 include LICENSE
 include versioneer.py

docs/generic.rst

@@ -28,18 +28,18 @@ The usage is like this ::
     >>> import numpy as np
     >>> from pymbar import MBAR
     >>> from alchemtest.generic import load_MBAR_BGFS
-    >>> u_kn = np.load(load_MBAR_BGFS()['data']['u_kn'])
+    >>> u_nk = np.load(load_MBAR_BGFS()['data']['u_nk'])
     >>> N_k = np.load(load_MBAR_BGFS()['data']['N_k'])
     >>> solver_options = {"maximum_iterations":10000,"verbose":True}
     >>> solver_protocol = {"method":"adaptive","options":solver_options}
-    >>> mbar = MBAR(u_kn, N_k, solver_protocol=(solver_protocol,))
+    >>> mbar = MBAR(u_nk, N_k, solver_protocol=(solver_protocol,))
     >>> results, errors = mbar.getFreeEnergyDifferences()
 
 Which will give the :class:`pymbar.utils.ParameterError` ::
 
     >>> solver_options = {"maximum_iterations":10000,"verbose":True}
     >>> solver_protocol = {"method":"BFGS","options":solver_options}
-    >>> mbar = MBAR(u_kn, N_k, solver_protocol=(solver_protocol,))
+    >>> mbar = MBAR(u_nk, N_k, solver_protocol=(solver_protocol,))
     >>> results, errors = mbar.getFreeEnergyDifferences()
 
 Which will work.

src/alchemtest/generic/BFGS/descr.rst

@@ -2,7 +2,7 @@ generic: MBAR solver stability test
 ==============================================
 
 
-u_kn and N_k files that could be calculated with MBAR using BGFS method but not
+u_nk and N_k files that could be calculated with MBAR using BGFS method but not
 the adaptive method.
 
 Notes

src/alchemtest/generic/access.py

@@ -18,11 +18,11 @@ def load_MBAR_BGFS():
     data: Bunch
         Dictionary-like object, the interesting attributes are:
 
-        - 'data' : the data files for u_kn and N_k
+        - 'data' : the data files for u_nk and N_k
 
     """
     module_path = dirname(__file__)
-    data = {'u_kn': join(module_path, 'BFGS/u_kn.npy'),
+    data = {'u_nk': join(module_path, 'BFGS/u_nk.npy'),
             'N_k': join(module_path, 'BFGS/N_k.npy'),}
 
     with open(join(module_path, 'BFGS', 'descr.rst')) as rst_file:

src/alchemtest/tests/test_generic.py

@@ -7,7 +7,7 @@
 
 class TestGeneric(BaseDatasetTest):
     @pytest.fixture(scope="class",
-                    params = [(load_MBAR_BGFS, ('u_kn', 'N_k'), (1, 1)),
+                    params = [(load_MBAR_BGFS, ('u_nk', 'N_k'), (1, 1)),
                               ])
     def dataset(self, request):
         return super(TestGeneric, self).dataset(request)