Merge branch 'master' into update_ug

76f7acf7 · Nate Stanley · 4fd6934b · c3847685 · 76f7acf7 · 76f7acf7
Commit 76f7acf7 authored Jan 27, 2016 by Nate Stanley
20 changed files
--- a/docs-source/api-python/app.rst.jinja2
+++ b/docs-source/api-python/app.rst.jinja2
--- a/docs-source/api-python/conf.py
+++ b/docs-source/api-python/conf.py
--- a/docs-source/api-python/index.rst
+++ b/docs-source/api-python/index.rst
--- a/docs-source/api-python/library.rst.jinja2
+++ b/docs-source/api-python/library.rst.jinja2
--- a/docs-source/api-python/process-docstring.py
+++ b/docs-source/api-python/process-docstring.py
--- a/docs-source/api-python/render.py
+++ b/docs-source/api-python/render.py
--- a/docs-source/developerguide/conf.py
+++ b/docs-source/developerguide/conf.py
@@ -92,7 +92,7 @@ pygments_style = 'sphinx'

 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'agogo'
+html_theme = 'alabaster'

 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

--- a/docs-source/usersguide/application.rst
+++ b/docs-source/usersguide/application.rst
--- a/docs-source/usersguide/conf.py
+++ b/docs-source/usersguide/conf.py
@@ -92,7 +92,7 @@ pygments_style = 'sphinx'

 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'agogo'
+html_theme = 'alabaster'

 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

--- a/docs-source/usersguide/library.rst
+++ b/docs-source/usersguide/library.rst
--- a/docs-source/usersguide/references.bib
+++ b/docs-source/usersguide/references.bib
--- a/examples/benchmark.py
+++ b/examples/benchmark.py
--- a/olla/include/openmm/Kernel.h
+++ b/olla/include/openmm/Kernel.h
--- a/olla/include/openmm/Platform.h
+++ b/olla/include/openmm/Platform.h
--- a/openmmapi/include/openmm/CustomHbondForce.h
+++ b/openmmapi/include/openmm/CustomHbondForce.h
--- a/openmmapi/include/openmm/TabulatedFunction.h
+++ b/openmmapi/include/openmm/TabulatedFunction.h
--- a/openmmapi/src/Context.cpp
+++ b/openmmapi/src/Context.cpp
--- a/openmmapi/src/ContextImpl.cpp
+++ b/openmmapi/src/ContextImpl.cpp
--- a/platforms/cpu/tests/TestCpuCheckpoints.cpp
+++ b/platforms/cpu/tests/TestCpuCheckpoints.cpp
--- a/platforms/cuda/include/CudaPlatform.h
+++ b/platforms/cuda/include/CudaPlatform.h