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/.travis.yml
+++ b/.travis.yml
@@ -9,14 +9,19 @@ addons:
      - python-scipy
      - libfftw3-dev
+env:
+  global:
+    - CCACHE=$HOME/ccache/lib/ccache/bin
 matrix:
  include:
    - sudo: required
      env: ==CPU_OPENCL==
           OPENCL=true
           CUDA=false
-           CC=gcc
+           CC=$CCACHE/gcc
-           CXX=g++
+           CXX=$CCACHE/g++
           CMAKE_FLAGS="
           -OPENMM_BUILD_OPENCL_LIB=ON
           -DOPENMM_BUILD_OPENCL_TESTS=ON
@@ -32,10 +37,13 @@ matrix:
      addons: {apt: {packages: []}}
    - sudo: required
+      dist: trusty
      env: ==CUDA_COMPILE==
           CUDA=true
           OPENCL=false
-           CUDA_VERSION="7.0-28"
+           CUDA_VERSION="7.5-18"
+           CC=$CCACHE/gcc
+           CXX=$CCACHE/g++
           CMAKE_FLAGS="
             -DOPENMM_BUILD_CUDA_TESTS=OFF
             -DOPENMM_BUILD_OPENCL_TESTS=OFF
@@ -44,7 +52,12 @@ matrix:
             -DOPENMM_BUILD_SERIALIZATION_TESTS=OFF
             -DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF
             -DOPENMM_BUILD_EXAMPLES=OFF
-             -DOPENCL_LIBRARY=/usr/local/cuda-7.0/lib64/libOpenCL.so"
+             -DOPENCL_LIBRARY=/usr/local/cuda-7.5/lib64/libOpenCL.so
+             -DCUDA_CUDART_LIBRARY=/usr/local/cuda-7.5/lib64/libcudart.so
+             -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-7.5/bin/nvcc
+             -DCUDA_SDK_ROOT_DIR=/usr/local/cuda-7.5/
+             -DCUDA_TOOLKIT_INCLUDE=/usr/local/cuda-7.5/include
+             -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/"
      addons: {apt: {packages: []}}
    - language: objective-c
@@ -62,35 +75,39 @@ matrix:
      env: ==STATIC_LIB==
           OPENCL=false
           CUDA=false
-           CC=clang
+           CC=$CCACHE/clang
-           CXX=clang++
+           CXX=$CCACHE/clang++
           CMAKE_FLAGS="-DOPENMM_BUILD_STATIC_LIB=ON"
    - sudo: false
      python: 2.7_with_system_site_packages
-      env: ==PYTNON_2==
+      env: ==PYTHON_2==
           OPENCL=false
           CUDA=false
-           CC=clang
+           CC=$CCACHE/clang
-           CXX=clang++
+           CXX=$CCACHE/clang++
           DOCS_DEPLOY=true
-           CMAKE_FLAGS=""
+           CMAKE_FLAGS="-DOPENMM_GENERATE_API_DOCS=ON"
    - sudo: false
      python: 3.4
      env: ==PYTHON_3==
           OPENCL=false
           CUDA=false
-           CC=gcc
+           CC=$CCACHE/gcc
-           CXX=g++
+           CXX=$CCACHE/g++
           CMAKE_FLAGS=""
 before_install:
+  - START_TIME=$(date +%s)
+  - wget https://anaconda.org/omnia/ccache/3.2.4/download/${TRAVIS_OS_NAME}-64/ccache-3.2.4-0.tar.bz2
+  - mkdir -p $HOME/ccache && tar xf ccache-3.2.4-0.tar.bz2 -C $HOME/ccache
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
      brew install doxygen swig fftw;
      sudo easy_install pytest;
    fi
  - if [[ "$OPENCL" == "true" ]]; then
+      sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu $(lsb_release -sc) main universe restricted multiverse";
      sudo apt-get -yq update > /dev/null 2>&1 ;
      sudo apt-get install -qq fglrx=2:8.960-0ubuntu1 opencl-headers;
    fi
@@ -107,8 +124,8 @@ before_install:
    fi
  - if [[ "$CUDA" == "true" ]]; then
-      wget "http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1204/x86_64/cuda-repo-ubuntu1204_${CUDA_VERSION}_amd64.deb";
+      wget "http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1404/x86_64/cuda-repo-ubuntu1404_${CUDA_VERSION}_amd64.deb";
-      sudo dpkg -i cuda-repo-ubuntu1204_${CUDA_VERSION}_amd64.deb;
+      sudo dpkg -i cuda-repo-ubuntu1404_${CUDA_VERSION}_amd64.deb;
      sudo apt-get update -qq;
      export CUDA_APT=${CUDA_VERSION%-*};
      export CUDA_APT=${CUDA_APT/./-};
@@ -120,7 +137,6 @@ before_install:
    fi
 script:
-  - CTEST_STOP_TIME=$(python -c "from datetime import datetime, timedelta; import sys; sys.stdout.write((datetime.now() + timedelta(minutes=25)).strftime('%H:%M:%S'))")
  - cmake . $CMAKE_FLAGS -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM
  - make -j2 install
  - if [[ "$OPENCL" == "true" ]]; then ./TestOpenCLDeviceQuery; fi
@@ -131,20 +147,19 @@ script:
          make PythonInstall;
      fi;
      python -m simtk.testInstallation;
-      (cd python/tests && py.test -v *);
+      (cd python/tests && py.test -v);
    fi
-  - # run all of the tests, making sure failures at this stage don't cause travis failures
+  # Run the tests, and rerun any failing tests.
-  - ctest -j2 --output-on-failure --schedule-random --stop-time $CTEST_STOP_TIME || true
+  - python devtools/run-ctest.py --start-time $START_TIME
-  - # get a list of all of the failed tests into this stupid ctest format
-  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then
-      ctest -I FailedTests.log;
-    fi
  - if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
-      pip install sphinx numpydoc;
+      pip install sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen;
-      make DoxygenApiDocs PythonApiDocs;
+      make sphinxhtml;
+      make C++ApiDocs PythonApiDocs;
      mkdir -p api-docs;
+      mv sphinx-docs/userguide/html api-docs/userguide;
+      mv sphinx-docs/developerguide/html api-docs/developerguide;
      mv api-python api-docs;
      mv api-c++ api-docs;
    fi
@@ -163,3 +178,7 @@ deploy:
    on:
      branch: master
      condition: '! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true"'
+cache:
+  directories:
+    - $HOME/.ccache
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -536,6 +536,8 @@ IF(OPENMM_BUILD_PYTHON_WRAPPERS)
 ENDIF(OPENMM_BUILD_PYTHON_WRAPPERS)
 #
 # Allow automated build and dashboard.
 #

--- a/README.md
+++ b/README.md
@@ -3,23 +3,22 @@
 Introduction
 ------------
-[OpenMM](https://simtk.org/home/openmm) is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
+[OpenMM](http://openmm.org) is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
 provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.  
 Getting Help
 ------------
-Need Help? Check out the [documentation](https://simtk.org/docman/?group_id=161) and [discussion forums](https://simtk.org/forums/viewforum.php?f=161).
+Need Help? Check out the [documentation](http://docs.openmm.org/) and [discussion forums](https://simtk.org/forums/viewforum.php?f=161).
-[C++ API Reference](https://simtk.org/api_docs/openmm/api6_0/c++/)
+[C++ API Reference](http://docs.openmm.org/6.3.0/api-c++/namespaceOpenMM.html)
-[Python API Reference](https://simtk.org/api_docs/openmm/api6_0/python/)
+[Python API Reference](http://docs.openmm.org/6.3.0/api-python/annotated.html)
 Badges
 ------
-* Travis CI `linux` integration tests: [![Build Status](https://travis-ci.org/pandegroup/openmm.png?branch=master)](https://travis-ci.org/pandegroup/openmm)
+* Travis CI `linux` and `osx` integration tests:
-* Jenkins `openmm-dev` conda `osx` build: [![Jenkins `openmm-dev` conda `osx` build](https://jenkins.choderalab.org/job/conda-openmm-dev-osx-2/badge/icon)](https://jenkins.choderalab.org/job/conda-openmm-dev-osx-2/) [[console log]](https://jenkins.choderalab.org/job/conda-openmm-dev-osx-2/lastBuild/consoleFull)
+  * GitHub master [![Build Status](https://travis-ci.org/pandegroup/openmm.png?branch=master)](https://travis-ci.org/pandegroup/openmm)
-* Jenkins `openmm-dev` conda `linux` build: [![Jenkins `openmm-dev` conda `linux` build](https://jenkins.choderalab.org/job/conda-openmm-dev-linux-vagrant-2/badge/icon)](https://jenkins.choderalab.org/job/conda-openmm-dev-linux-vagrant-2/) [[console log]](https://jenkins.choderalab.org/job/conda-openmm-dev-linux-vagrant-2/lastBuild/consoleFull)
+  * `openmm-dev` recipe [![Build Status](https://travis-ci.org/omnia-md/conda-dev-recipes.svg?branch=master)](https://travis-ci.org/omnia-md/conda-dev-recipes)
-* Binstar `openmm` conda release: ![Binstar `openmm` conda release](https://binstar.org/omnia/openmm/badges/version.svg)
+* Anaconda Cloud `openmm` conda release: [![Binstar `openmm` conda release](https://anaconda.org/omnia/openmm/badges/version.svg)](https://anaconda.org/omnia/openmm)
-* Binstar `openmm-dev` conda package: ![Binstar `openmm-dev` conda package](https://binstar.org/omnia/openmm-dev/badges/version.svg)
+* Anaconda Cloud `openmm-dev` conda package: [![Binstar `openmm-dev` conda package](https://anaconda.org/omnia/openmm-dev/badges/version.svg)](https://anaconda.org/omnia/openmm-dev)
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -5,11 +5,16 @@ install:
 # Setup shell for VS2010, x64, release mode
  - >
    "%ProgramFiles%\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 /release
 # Set path to python, git-bash tools.
  - "set PATH=C:\\Python34-x64;C:\\Python34-x64\\Scripts;%PATH%"
  - "set PATH=C:\\Program Files (x86)\\Git\\bin;%PATH%"
-  - pip install nose
+  - pip install pytest
+# Use cclash for compiler caching (experimental)
+  - ps: wget https://github.com/inorton/cclash/releases/download/0.3.14/cclash-0.3.14.zip -OutFile cclash-0.3.14.zip
+  - ps: 7z x cclash-0.3.14.zip
+  - "set PATH=%APPVEYOR_BUILD_FOLDER%\\cclash-0.3.14;%PATH%"
+  - "set CCLASH_DIR=C:\\ProgramData\\cclash"
 # Download FFTW3 for PME plugin
  - C:\MinGW\msys\1.0\bin\wget -q ftp://ftp.fftw.org/pub/fftw/fftw-3.3.4-dll64.zip
@@ -22,26 +27,43 @@ install:
 # Download and install some OpenMM build dependencies (doxygen, swig)
  - choco install -y doxygen.portable swig > null
-# Set CMake options
+# Download OpenCL Headers and build the ICD loader
-  - ps: $env:CMAKE_FLAGS='-DOPENMM_BUILD_PME_PLUGIN=ON -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib -DFFTW_INCLUDES=C:/fftw -DCMAKE_BUILD_TYPE=Release -DOPENMM_BUILD_EXAMPLES=OFF -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG"'
+  - ps: $opencl_registry = "https://www.khronos.org/registry/cl"
+  - ps: mkdir C:/opencl > $null
+  - ps: cd C:/opencl
+  - ps: wget $opencl_registry/specs/opencl-icd-1.2.11.0.tgz -OutFile opencl-icd-1.2.11.0.tgz
+  - ps: 7z x opencl-icd-1.2.11.0.tgz > $null
+  - ps: 7z x opencl-icd-1.2.11.0.tar > $null
+  - ps: mv .\icd\* .
+  - ps: mkdir inc/CL > $null
+  - ps: wget $opencl_registry/api/1.2/ | select -ExpandProperty links | where {$_.href -like "*.h*"} | select -ExpandProperty outerText | foreach{ wget $opencl_registry/api/1.2/$_ -OutFile inc/CL/$_ }
+  - ps: mkdir lib > $null
+  - ps: cd lib
+  - cmake -G "NMake Makefiles" ..
+  - nmake
+  - cd %APPVEYOR_BUILD_FOLDER%
+build_script:
+  - ps: $env:CMAKE_FLAGS =
+      "-DOPENMM_BUILD_PME_PLUGIN=ON
+       -DOPENCL_INCLUDE_DIR=C:/opencl/inc
+       -DOPENCL_LIBRARY=C:/opencl/lib/OpenCL.lib
+       -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib
+       -DFFTW_INCLUDES=C:/fftw
+       -DOPENMM_BUILD_EXAMPLES=OFF
+       -DOPENMM_BUILD_OPENCL_TESTS=OFF
+       -DCMAKE_BUILD_TYPE=Release
+       -LA"
  - mkdir build
  - cd build
-  - cmake -G "NMake Makefiles" %CMAKE_FLAGS% -LA ..
+  - cmake -G "NMake Makefiles" %CMAKE_FLAGS% -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG" ..
-# Run the build
  - cmake --build . --target install
  - cmake --build . --target PythonInstall
-build: false
 test_script:
-  - ctest || exit 0
+  - python %APPVEYOR_BUILD_FOLDER%\devtools\run-ctest.py
-  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-  - ps: >
-     If (Test-Path "Testing\\Temporary\\LastTestsFailed.log") {
-         cat Testing\\Temporary\\LastTestsFailed.log
-         cat FailedTests.log
-         ctest -I FailedTests.log
-     }
  - cd python\tests
-  - nosetests -vv --processes=-1 --process-timeout=200
+  - py.test -v
-  - cd %APPVEYOR_BUILD_FOLDER%
+cache:
+- C:\ProgramData\cclash -> appveyor.yml
--- a/cmake_modules/ApiDoxygen.cmake
+++ b/cmake_modules/ApiDoxygen.cmake
-find_package(Doxygen)
-set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
-IF(DOXYGEN_FOUND)
-    SET(DOXY_CONFIG "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
-    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in 
-          ${DOXY_CONFIG}
-          @ONLY )
-    ADD_CUSTOM_COMMAND(
-        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/html/index.html"
-        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-        COMMENT "Generating API documentation using Doxygen"
-        SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in") 
-    ADD_CUSTOM_TARGET(DoxygenApiDocs 
-        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-        COMMENT "Generating API documentation using Doxygen"
-        SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in") 
-    FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/html/")
-    IF(OPENMM_GENERATE_API_DOCS)
-        INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/html/"
-                DESTINATION "docs/api/")
-    ENDIF(OPENMM_GENERATE_API_DOCS)
-ELSE(DOXYGEN_FOUND)
-ENDIF(DOXYGEN_FOUND)
--- a/devtools/forcefield-scripts/processTinkerForceField.py
+++ b/devtools/forcefield-scripts/processTinkerForceField.py
--- a/devtools/forcefield-scripts/residuesFinal.xml
+++ b/devtools/forcefield-scripts/residuesFinal.xml
--- a/devtools/run-ctest.py
+++ b/devtools/run-ctest.py
+"""
+Run test suite through CTest, with some options set for the CI environment.
+- Runs with a per-test and overall timeout which can be governed by the
+  avialable time on the CI system.
+- Reruns tests which fail (does not rerun tests which merely timeout).
+"""
+from __future__ import print_function
+import sys
+import os.path
+import shutil
+import time
+from glob import glob
+from os.path import join, exists
+from subprocess import call
+from argparse import ArgumentParser
+from datetime import datetime, timedelta
+from xml.etree import ElementTree
+def main():
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--start-time",
+        help="Time at which the overall CI job started (unix timestamp)",
+        type=int,
+        default=int(time.time()))
+    parser.add_argument(
+        "--job-duration",
+        help="Overall time budget for the CI job (minutes). Default=30",
+        default=30.,
+        type=float)
+    parser.add_argument(
+        "--run-percent",
+        help="Allocate this percent test execution time executing the main "
+        "test suite. The remaining fraction will be used for re-running "
+        "failing tests. Default=90",
+        type=float,
+        default=90.)
+    parser.add_argument(
+        '--timeout',
+        help="Timeout for individual tests (seconds). Default=180",
+        type=str,
+        default='180')
+    args = parser.parse_args()
+    status = execute_tests(args)
+    if status != 0:
+        status = execute_failed_tests(args)
+    return status
+def execute_tests(options):
+    start_time = datetime.fromtimestamp(options.start_time)
+    stop_time = start_time + timedelta(minutes=options.job_duration)
+    # timedelta for the amount of time from now until the CI job runs out
+    remaining = stop_time - datetime.now()
+    # tell CTest only to use some fraction of the remaining time for this
+    # invocation
+    stop_time = start_time + timedelta(
+        seconds=(options.run_percent / 100.0) * remaining.seconds)
+    if os.path.isdir('Testing'):
+        shutil.rmtree('Testing')
+    return call(['ctest',
+                 '--output-on-failure',
+                 '--schedule-random',
+                 '-T', 'Test',
+                 '--timeout', options.timeout,
+                 '--stop-time', stop_time.strftime('%H:%M:%S')])
+def execute_failed_tests(options):
+    matches = glob('Testing/*/Test.xml')
+    assert len(matches) == 1
+    root = ElementTree.parse(matches[0])
+    tests = root.findall('.//Testing/Test')
+    def failed_without_timeout(test_node):
+        if test_node.get('Status') == 'failed':
+            return test_node.find(
+                'Results/NamedMeasurement[@name="Exit Code"]/Value').text != 'Timeout'
+    failed_tests = [t.find('Name').text
+                    for t in tests if failed_without_timeout(t)]
+    print('*'*30)
+    print('Rerunning failing tests...')
+    print('*'*30)
+    start_time = datetime.fromtimestamp(options.start_time)
+    stop_time = start_time + timedelta(minutes=options.job_duration)
+    return call(['ctest',
+                 '--output-on-failure',
+                 '--schedule-random',
+                 '-R', '|'.join(failed_tests),
+                 '--timeout', options.timeout,
+                 '--stop-time', stop_time.strftime('%H:%M:%S')])
+if __name__ == '__main__':
+    sys.exit(main())
--- a/docs-source/CMakeLists.txt
+++ b/docs-source/CMakeLists.txt
@@ -3,77 +3,18 @@
 #
 find_package(Doxygen QUIET)
-mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
+set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
 IF(DOXYGEN_EXECUTABLE)
    # Generate C++ API documentation
-    SET(DOXY_CONFIG_C++ "${CMAKE_BINARY_DIR}/DoxyfileC++")
-    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in 
-          ${DOXY_CONFIG_C++}
-          @ONLY )
-    FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
-    FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h")
-    ADD_CUSTOM_COMMAND(
-        OUTPUT "${CMAKE_BINARY_DIR}/api-c++/index.html"
-        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_C++}
-        DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
-        WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
-        COMMENT "Generating C++ API documentation using Doxygen")
-    ADD_CUSTOM_TARGET(C++ApiDocs 
-        DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
-        COMMENT "Generating C++ API documentation using Doxygen"
-        SOURCES 
-            "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
-            ${OPENMM_INCLUDES}
-            ${OLLA_INCLUDES}
-    ) 
-    FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/")
-    INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/"
-            DESTINATION "docs/api-c++/")
-    INSTALL(FILES "C++ API Reference.html"
-            DESTINATION "docs/")
-    ADD_CUSTOM_TARGET(DoxygenApiDocs
-        DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
-        COMMENT "Generating C++ API documentation using Doxygen"
-        SOURCES 
-        "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
-        "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
-        ${OPENMM_INCLUDES}
-        ${OLLA_INCLUDES}
-    )
-    set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
    IF (OPENMM_GENERATE_API_DOCS)
-        SET_TARGET_PROPERTIES(DoxygenApiDocs PROPERTIES EXCLUDE_FROM_ALL FALSE)
+        ADD_SUBDIRECTORY(api-c++)
    ENDIF (OPENMM_GENERATE_API_DOCS)
    # Generate Python API documentation
+    IF (OPENMM_BUILD_PYTHON_WRAPPERS AND OPENMM_GENERATE_API_DOCS)
-    IF (OPENMM_BUILD_PYTHON_WRAPPERS)
+        ADD_SUBDIRECTORY(api-python)
-        SET(DOXY_CONFIG_PYTHON "${CMAKE_BINARY_DIR}/DoxyfilePython")
+    ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS AND OPENMM_GENERATE_API_DOCS)
-        CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in 
-            ${DOXY_CONFIG_PYTHON}
-            @ONLY )
-        ADD_CUSTOM_COMMAND(
-            OUTPUT "${CMAKE_BINARY_DIR}/api-python/index.html"
-            COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_PYTHON}
-            DEPENDS RunSwig
-            WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
-            COMMENT "Generating Python API documentation using Doxygen")
-        ADD_CUSTOM_TARGET(PythonApiDocs 
-            DEPENDS "${CMAKE_BINARY_DIR}/api-python/index.html"
-            COMMENT "Generating Python API documentation using Doxygen"
-            SOURCES 
-                "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
-                ${OPENMM_INCLUDES}
-                ${OLLA_INCLUDES}
-        ) 
-        FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-python/")
-        INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-python/"
-                DESTINATION "docs/api-python/")
-        INSTALL(FILES "Python API Reference.html"
-                DESTINATION "docs/")
-        ADD_DEPENDENCIES(DoxygenApiDocs PythonApiDocs)
-    ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS)
 ENDIF(DOXYGEN_EXECUTABLE)

--- a/docs-source/DoxyfilePython.in
+++ b/docs-source/DoxyfilePython.in
-# Doxyfile 1.5.3
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = @PROJECT_NAME@
-PROJECT_NUMBER         = 
-OUTPUT_DIRECTORY       = 
-CREATE_SUBDIRS         = NO
-OUTPUT_LANGUAGE        = English
-BRIEF_MEMBER_DESC      = YES
-REPEAT_BRIEF           = YES
-ABBREVIATE_BRIEF       = 
-ALWAYS_DETAILED_SEC    = NO
-INLINE_INHERITED_MEMB  = NO
-FULL_PATH_NAMES        = NO
-STRIP_FROM_PATH        = 
-STRIP_FROM_INC_PATH    = 
-SHORT_NAMES            = NO
-JAVADOC_AUTOBRIEF      = YES
-QT_AUTOBRIEF           = NO
-MULTILINE_CPP_IS_BRIEF = NO
-DETAILS_AT_TOP         = YES
-INHERIT_DOCS           = YES
-SEPARATE_MEMBER_PAGES  = NO
-TAB_SIZE               = 4
-ALIASES                = 
-OPTIMIZE_OUTPUT_FOR_C  = NO
-OPTIMIZE_OUTPUT_JAVA   = YES
-BUILTIN_STL_SUPPORT    = NO
-CPP_CLI_SUPPORT        = NO
-DISTRIBUTE_GROUP_DOC   = YES
-SUBGROUPING            = YES
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-EXTRACT_ALL            = YES
-EXTRACT_PRIVATE        = NO
-EXTRACT_STATIC         = NO
-EXTRACT_LOCAL_CLASSES  = YES
-EXTRACT_LOCAL_METHODS  = NO
-EXTRACT_ANON_NSPACES   = NO
-HIDE_UNDOC_MEMBERS     = NO
-HIDE_UNDOC_CLASSES     = NO
-HIDE_FRIEND_COMPOUNDS  = NO
-HIDE_IN_BODY_DOCS      = YES
-INTERNAL_DOCS          = NO
-CASE_SENSE_NAMES       = YES
-HIDE_SCOPE_NAMES       = YES
-SHOW_INCLUDE_FILES     = YES
-INLINE_INFO            = YES
-SORT_MEMBER_DOCS       = YES
-SORT_BRIEF_DOCS        = NO
-SORT_BY_SCOPE_NAME     = NO
-GENERATE_TODOLIST      = YES
-GENERATE_TESTLIST      = YES
-GENERATE_BUGLIST       = YES
-GENERATE_DEPRECATEDLIST= YES
-ENABLED_SECTIONS       = 
-MAX_INITIALIZER_LINES  = 30
-SHOW_USED_FILES        = YES
-SHOW_DIRECTORIES       = YES
-FILE_VERSION_FILTER    =
-SHOW_NAMESPACES        = NO
-SHOW_FILES             = NO
-SHOW_DIRECTORIES       = NO
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-QUIET                  = NO
-WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
-WARN_IF_DOC_ERROR      = YES
-WARN_NO_PARAMDOC       = NO
-WARN_FORMAT            = "$file:$line: $text    "
-WARN_LOGFILE           = 
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-INPUT                  = "@CMAKE_BINARY_DIR@/python/simtk/openmm" "@CMAKE_BINARY_DIR@/python/simtk/openmm/app"
-INPUT_ENCODING         = UTF-8
-FILE_PATTERNS          = 
-RECURSIVE              = NO
-EXCLUDE                = 
-EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = 
-EXCLUDE_SYMBOLS        = SerializationNode SerializationProxy SwigPyIterator
-EXAMPLE_PATH           = 
-EXAMPLE_PATTERNS       = 
-EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             = 
-INPUT_FILTER           = "@PYTHON_EXECUTABLE@ @CMAKE_BINARY_DIR@/python/filterPythonFiles.py"
-FILTER_PATTERNS        = 
-FILTER_SOURCE_FILES    = YES
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-SOURCE_BROWSER         = NO
-INLINE_SOURCES         = NO
-STRIP_CODE_COMMENTS    = YES
-REFERENCED_BY_RELATION = YES
-REFERENCES_RELATION    = YES
-REFERENCES_LINK_SOURCE = YES
-USE_HTAGS              = NO
-VERBATIM_HEADERS       = YES
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-ALPHABETICAL_INDEX     = NO
-COLS_IN_ALPHA_INDEX    = 5
-IGNORE_PREFIX          = 
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-GENERATE_HTML          = YES
-HTML_OUTPUT            = api-python
-HTML_FILE_EXTENSION    = .html
-HTML_HEADER            = 
-HTML_FOOTER            = 
-HTML_STYLESHEET        = 
-HTML_ALIGN_MEMBERS     = YES
-GENERATE_HTMLHELP      = NO
-HTML_DYNAMIC_SECTIONS  = YES
-CHM_FILE               = 
-HHC_LOCATION           = 
-GENERATE_CHI           = NO
-BINARY_TOC             = NO
-TOC_EXPAND             = NO
-DISABLE_INDEX          = NO
-ENUM_VALUES_PER_LINE   = 4
-GENERATE_TREEVIEW      = YES
-TREEVIEW_WIDTH         = 250
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-GENERATE_LATEX         = NO
-LATEX_OUTPUT           = latex
-LATEX_CMD_NAME         = latex
-MAKEINDEX_CMD_NAME     = makeindex
-COMPACT_LATEX          = NO
-PAPER_TYPE             = a4wide
-EXTRA_PACKAGES         = 
-LATEX_HEADER           = 
-PDF_HYPERLINKS         = NO
-USE_PDFLATEX           = NO
-LATEX_BATCHMODE        = NO
-LATEX_HIDE_INDICES     = NO
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-GENERATE_RTF           = NO
-RTF_OUTPUT             = rtf
-COMPACT_RTF            = NO
-RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    = 
-RTF_EXTENSIONS_FILE    = 
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-GENERATE_MAN           = NO
-MAN_OUTPUT             = man
-MAN_EXTENSION          = .3
-MAN_LINKS              = NO
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-GENERATE_XML           = NO
-XML_OUTPUT             = xml
-XML_SCHEMA             = 
-XML_DTD                = 
-XML_PROGRAMLISTING     = YES
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-GENERATE_AUTOGEN_DEF   = NO
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-GENERATE_PERLMOD       = NO
-PERLMOD_LATEX          = NO
-PERLMOD_PRETTY         = YES
-PERLMOD_MAKEVAR_PREFIX = 
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor   
-#---------------------------------------------------------------------------
-ENABLE_PREPROCESSING   = YES
-MACRO_EXPANSION        = YES
-EXPAND_ONLY_PREDEF     = YES
-SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = 
-INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = 
-EXPAND_AS_DEFINED      = 
-SKIP_FUNCTION_MACROS   = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references   
-#---------------------------------------------------------------------------
-TAGFILES               = 
-GENERATE_TAGFILE       = "api-python/@PROJECT_NAME@DoxygenTagfile"
-ALLEXTERNALS           = NO
-EXTERNAL_GROUPS        = YES
-PERL_PATH              = /usr/bin/perl
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool   
-#---------------------------------------------------------------------------
-CLASS_DIAGRAMS         = YES
-MSCGEN_PATH            = /Applications/Doxygen.app/Contents/Resources/
-HIDE_UNDOC_RELATIONS   = YES
-HAVE_DOT               = NO
-CLASS_GRAPH            = YES
-COLLABORATION_GRAPH    = YES
-GROUP_GRAPHS           = YES
-UML_LOOK               = NO
-TEMPLATE_RELATIONS     = YES
-INCLUDE_GRAPH          = YES
-INCLUDED_BY_GRAPH      = YES
-CALL_GRAPH             = NO
-CALLER_GRAPH           = NO
-GRAPHICAL_HIERARCHY    = YES
-DIRECTORY_GRAPH        = YES
-DOT_IMAGE_FORMAT       = png
-DOT_PATH               = 
-DOTFILE_DIRS           = 
-DOT_GRAPH_MAX_NODES    = 50
-MAX_DOT_GRAPH_DEPTH    = 0
-DOT_TRANSPARENT        = NO
-DOT_MULTI_TARGETS      = NO
-GENERATE_LEGEND        = YES
-DOT_CLEANUP            = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine   
-#---------------------------------------------------------------------------
-SEARCHENGINE           = YES
--- a/docs-source/api-c++/CMakeLists.txt
+++ b/docs-source/api-c++/CMakeLists.txt
+set(STAGING_OUTPUT_FILES "") # Will contain all required package files
+file(GLOB STAGING_INPUT_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
+    "*.rst"
+    "*.rst.jinja2"
+    "*.py"
+    "_static/logo.png"
+)
+set(WRAPPER_DOXYGEN_DIR "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
+file(MAKE_DIRECTORY "${WRAPPER_DOXYGEN_DIR}")
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+    ${WRAPPER_DOXYGEN_DIR}/Doxyfile
+    @ONLY
+)
+add_custom_command(
+    OUTPUT "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
+    COMMAND "${DOXYGEN_EXECUTABLE}"
+    DEPENDS "${WRAPPER_DOXYGEN_DIR}/Doxyfile"
+    WORKING_DIRECTORY "${WRAPPER_DOXYGEN_DIR}"
+    COMMENT "Parsing OpenMM header files with Doxygen..."
+)
+foreach(INIT_FILE ${STAGING_INPUT_FILES})
+    set(infile "${CMAKE_CURRENT_SOURCE_DIR}/${INIT_FILE}")
+    set(outfile "${CMAKE_CURRENT_BINARY_DIR}/${INIT_FILE}")
+    add_custom_command(
+        OUTPUT "${outfile}"
+        COMMAND "${CMAKE_COMMAND}" -E copy_if_different "${infile}" "${outfile}"
+        DEPENDS "${infile}"
+        COMMENT "CMake-copying file ${infile} to ${outfile}")
+    set(STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES} "${outfile}")
+endforeach(INIT_FILE ${STAGING_INPUT_FILES})
+add_custom_command(
+    OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/library.rst"
+    COMMAND "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/render.py"
+            "${WRAPPER_DOXYGEN_DIR}/xml/"
+    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/render.py"
+            "${CMAKE_CURRENT_BINARY_DIR}/library.rst.jinja2"
+            "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
+    )
+add_custom_command(
+    OUTPUT "${CMAKE_BINARY_DIR}/api-c++/index.html"
+    COMMAND "${PYTHON_EXECUTABLE}" -m sphinx . "${CMAKE_BINARY_DIR}/api-c++"
+    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
+    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/conf.py"
+            "${CMAKE_CURRENT_BINARY_DIR}/library.rst"
+            "${CMAKE_CURRENT_BINARY_DIR}/index.rst"
+            "${CMAKE_CURRENT_BINARY_DIR}/_static/logo.png"
+            "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
+)
+file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/api-c++/)
+add_custom_target(C++ApiDocs
+        DEPENDS ${CMAKE_BINARY_DIR}/api-c++/index.html)
+INSTALL(DIRECTORY "${CMAKE_BINARY_DIR}/api-c++/"
+        DESTINATION "docs/api-c++/")
+INSTALL(FILES "${CMAKE_CURRENT_SOURCE_DIR}/../C++ API Reference.html"
+        DESTINATION "docs/")
--- a/docs-source/api-c++/Doxyfile.in
+++ b/docs-source/api-c++/Doxyfile.in
--- a/docs-source/api-c++/_static/logo.png
+++ b/docs-source/api-c++/_static/logo.png
+../../api-python/_static/logo.png
\ No newline at end of file
--- a/docs-source/api-c++/conf.py
+++ b/docs-source/api-c++/conf.py
+import sys
+import os
+extensions = ['sphinx.ext.mathjax','sphinx.ext.autosummary',
+              'sphinx.ext.autodoc', 'sphinxcontrib.lunrsearch',
+              'sphinxcontrib.autodoc_doxygen']
+autosummary_generate = True
+autodoc_member_order = 'bysource'
+source_suffix = '.rst'
+master_doc = 'index'
+project = u'OpenMM'
+copyright = u'2015, Stanford University and the Authors'
+version = '@OPENMM_MAJOR_VERSION@.@OPENMM_MINOR_VERSION@'
+release = '@OPENMM_MAJOR_VERSION@.@OPENMM_MINOR_VERSION@'
+exclude_patterns = ['_build', '_templates']
+html_static_path = ['_static']
+templates_path = ['_templates']
+pygments_style = 'sphinx'
+html_theme = "alabaster"
+html_theme_options = {
+    'description': "High performance molecular simulation on GPUs",
+    'github_button': False,
+    # 'github_user': 'pandegroup',
+    # 'github_repo': 'openmm',
+    'logo_name': False,
+    'logo': 'logo.png',
+}
+html_sidebars = {
+    '**': [
+        'about.html',
+        'searchbox.html',
+        'navigation.html',
+    ]
+}
+doxygen_xml = "doxygen/xml"
--- a/docs-source/api-c++/index.rst
+++ b/docs-source/api-c++/index.rst
+OpenMM C++ API
+=================
+The C++ API provides information about the classes and methods available in OpenMM for C++ developers. The public API is based on a small number of classes.
+.. toctree::
+   :maxdepth: 2
+   library
+:cpp:class:`System <OpenMM::System>`\ : A System specifies generic properties of the system to be
+simulated: the number of particles it contains, the mass of each one, the size
+of the periodic box, etc.  The interactions between the particles are specified
+through a set of Force objects (see below) that are added to the System.  Force
+field specific parameters, such as particle charges, are not direct properties
+of the System.  They are properties of the Force objects contained within the
+System.
+:cpp:class:`Force <OpenMM::Force>`\ : The Force objects added to a System define the behavior of the
+particles.  Force is an abstract class; subclasses implement specific behaviors.
+The Force class is actually slightly more general than its name suggests.  A
+Force can, indeed, apply forces to particles, but it can also directly modify
+particle positions and velocities in arbitrary ways.  Some thermostats and
+barostats, for example, can be implemented as Force classes.  Examples of Force
+subclasses include :cpp:class:`HarmonincBondForce <OpenMM::HarmonincBondForce>`, :cpp:class:`NonbondedForce <OpenMM::NonbondedForce>`, and :cpp:class:`MonteCarloBarostat <OpenMM::MonteCarloBarostat>`.
+:cpp:class:`Context <OpenMM::Context>`\ : This stores all of the state information for a simulation:
+particle positions and velocities, as well as arbitrary parameters defined by
+the Forces in the System.  It is possible to create multiple Contexts for a
+single System, and thus have multiple simulations of that System in progress at
+the same time.
+:cpp:class:`Integrator <OpenMM::Integrator>`\ : This implements an algorithm for advancing the simulation
+through time.  It is an abstract class; subclasses implement specific
+algorithms.  Examples of Integrator subclasses include :cpp:class:`LangevinIntegrator <OpenMM::LangevinIntegrator>`,
+:cpp:class:`VerletIntegrator <OpenMM::VerletIntegrator>`, and :cpp:class:`BrownianIntegrator <OpenMM::BrownianIntegrator>`.
+:cpp:class:`State <OpenMM::State>`\ : A State stores a snapshot of the simulation at a particular point
+in time.  It is created by calling a method on a Context. This is the only way to query the
+values of state variables, such as particle positions and velocities; Context
+does not provide methods for accessing them directly.
--- a/docs-source/api-c++/library.rst.jinja2
+++ b/docs-source/api-c++/library.rst.jinja2
--- a/docs-source/api-c++/render.py
+++ b/docs-source/api-c++/render.py
--- a/docs-source/api-python/CMakeLists.txt
+++ b/docs-source/api-python/CMakeLists.txt
--- a/docs-source/api-python/_static/logo.png
+++ b/docs-source/api-python/_static/logo.png
--- a/docs-source/api-python/_templates/class.rst
+++ b/docs-source/api-python/_templates/class.rst