updates and fixes

README.rst

@@ -24,8 +24,8 @@ modification, separation, for any purpose and without a charge.
     :scale: 100%
     :target: https://alchemtest.readthedocs.io/en/latest/
 
-.. |doi| image:: https://zenodo.org/badge/XXXXX.svg
+.. |doi| image:: https://zenodo.org/badge/83470847.svg
     :alt: Zenodo DOI
     :scale: 100%
-    :target: https://zenodo.org/badge/latestdoi/XXXXX
+    :target: https://zenodo.org/badge/latestdoi/83470847
 

docs/conf.py

@@ -58,9 +58,22 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.1.0-dev'
+#version = u'0.2'
 # The full version, including alpha/beta/rc tags.
-release = u'0.1.0-dev'
+#release = u'0.2.0'
+
+# automatically get the version information (requires that
+# alchemtest is installed)
+# We always display the full release string; if something else is
+# desired, see the commented out code
+
+from alchemtest._version import get_versions
+release = get_versions()['version']
+del get_versions
+
+version = release
+#version = release.split("+")[0]  # only major.minor.patch
+#version = "."join(release.split(".")[:2])  # only major.minor
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -6,6 +6,8 @@
 alchemtest: the simple alchemistry test set
 ===========================================
 
+|doi|
+
 **alchemtest** is a collection of test datasets for alchemical free energy
 calculations.  The datasets come from a variety of software packages, primarily
 molecular dynamics engines, and are used as the test set for `alchemlyb`_.  The
@@ -23,6 +25,10 @@ suite it may contain bugs. Please raise any issues or questions in the
 `Issue Tracker`_. `Contributions of data sets`_ and code in the form
 of pull requests are very welcome.
 
+.. |doi| image:: https://zenodo.org/badge/83470847.svg
+    :alt: Zenodo DOI
+    :scale: 100%
+    :target: https://zenodo.org/badge/latestdoi/83470847
 
 .. _`alchemlyb`: https://github.com/alchemistry/alchemlyb
 .. _`open license`:

src/alchemtest/namd/access.py

@@ -21,8 +21,8 @@ def load_tyr2ala():
     """
 
     module_path = dirname(__file__)
-    data = {'forward': glob(join(module_path, 'tyr2ala/in-aqua/forward/*.fepout')),
-            'backward': glob(join(module_path, 'tyr2ala/in-aqua/backward/*.fepout'))}
+    data = {'forward': glob(join(module_path, 'tyr2ala/in-aqua/forward/*.fepout.bz2')),
+            'backward': glob(join(module_path, 'tyr2ala/in-aqua/backward/*.fepout.bz2'))}
 
     with open(join(module_path, 'tyr2ala', 'descr.rst')) as rst_file:
         fdescr = rst_file.read()

src/alchemtest/namd/tyr2ala/descr.rst

@@ -24,5 +24,6 @@ Data Set Characteristics:
     :License: `CC0 <https://creativecommons.org/publicdomain/zero/1.0/>`_
               Public Domain Dedication
 
-This dataset was generated using the `NAMD <http://www.ambermd.org/>`_
-molecular dynamics engine.
+This dataset was generated using the `NAMD
+<http://http://www.ks.uiuc.edu/Research/namd/>`_ molecular dynamics
+engine.