add amber TI energy output files for testing (#6)

* add amber TI output file for testing
* modify the MANIFEST.in to include the amber energy output files
* add license info in amber descr.rst file and clean up the empty line
* update the docs folder with amber dataset info
* fixes #5

MANIFEST.in

@@ -1,4 +1,4 @@
 include *.rst
-recursive-include src/alchemtest *.gz *.bz2 *.zip *.rst *.txt
+recursive-include src/alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out
 include README.rst
 include LICENSE

docs/amber.rst

@@ -0,0 +1,22 @@
+.. _amber:
+
+================
+Amber datasets
+================
+.. automodule:: alchemtest.amber
+
+The :mod:`alchemlyb.amber` module features datasets generated using the `Amber <http://www.ambermd.org/>`_ molecular dynamics engine. 
+They can be accessed using the following accessor functions:
+
+.. currentmodule:: alchemtest.amber
+
+.. autosummary::
+
+   load_simplesolvated
+
+
+.. _amber_simplesolvated:
+
+.. include:: ../src/alchemtest/amber/simplesolvated/descr.rst
+
+.. autofunction:: alchemtest.amber.load_simplesolvated

docs/index.rst

@@ -31,3 +31,4 @@ Datasets are released under an `open license`_ that conforms to the `Open Defini
     :caption: Datasets
 
     gmx
+    amber

src/alchemtest/amber/__init__.py

@@ -0,0 +1,5 @@
+"""Amber molecular dynamics simulation datasets.
+
+"""
+
+from .access import load_simplesolvated

src/alchemtest/amber/access.py

@@ -0,0 +1,31 @@
+"""Accessors for Amber TI datasets.
+
+"""
+
+from os.path import dirname
+from os.path import join
+from glob import glob
+from sklearn.datasets.base import Bunch
+
+def load_simplesolvated():
+    """Load the Amber solvated dataset.
+
+
+    Returns
+    -------
+    data : Bunch
+        Dictionary-like object, the interesting attributes are:
+        - 'data' : the data files by alchemical leg
+        - 'DESCR': the full description of the dataset
+
+    """
+
+    module_path = dirname(__file__)
+    data = {'charge': glob(join(module_path, 'simplesolvated/charge/*/ti-*.out')),
+            'vdw': glob(join(module_path, 'simplesolvated/vdw/*/ti-*.out'))}
+
+    with open(join(module_path, 'simplesolvated', 'descr.rst')) as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)