Merge pull request #350 from ariadne-cps/working

Internal release 1.9.3

Author: Luca Geretti

.travis.yml

@@ -1,130 +1,95 @@
 language: cpp
 
 sudo: enabled
-dist: trusty
+dist: bionic
 
 branches:
   only:
   - master
   - working
-  - working-ci
+  - ci
 
 matrix:
   include:
 
-    - name: macOS 10.13 + AppleClang 10 + Python 3
+    - name: macOS 10.14 + AppleClang 10 + Python 3
       os: osx
-      osx_image: xcode10
-      env: COMPILER=clang++ PYTHON=3 
+      osx_image: xcode11
+      env: COMPILER=clang++ PYTHON=3
 
-    - name: macOS 10.13 + GCC 8 + Python 2 [NoCairo, NoGTK]
-      os: osx
-      osx_image: xcode10
-      env: COMPILER=g++-8 PYTHON=2 DISABLE_CAIRO=ON DISABLE_GTK=ON
-      
-#    - name: macOS 10.13 + AppleClang 10 + Python 3 [Debug, NoGTK]
+#    - name: macOS 10.14 + GCC 8 + Python 2 [NoCairo]
 #      os: osx
-#      osx_image: xcode10
-#      env: COMPILER=clang++ PYTHON=3 DEBUG=ON DISABLE_GTK=ON
+#      osx_image: xcode11
+#      env: COMPILER=g++-8 PYTHON=2 DISABLE_CAIRO=ON
 
-#    - name: macOS 10.13 + GCC 8 + Python 2 [Debug]
-#      os: osx
-#      osx_image: xcode10
-#      env: COMPILER=g++-8 PYTHON=2 DEBUG=ON
-      
-    - name: Fedora 29 + Clang 7 + Python 3 [NoGTK]
+    - name: Ubuntu 18.04 + Clang 6 + Python 3
       os: linux
-      services:
-        - docker
-      env: DOCKER=fedora:29 COMPILER=clang++ PYTHON=3 DISABLE_GTK=ON
-      
-#    - name: openSUSE Tumbleweed + GCC 8 + Python 3 [Debug]
-#      os: linux
-#      services:
-#        - docker
-#      env: DOCKER=opensuse/tumbleweed COMPILER=c++ PYTHON=3 DEBUG=ON
-      
-#    - name: Ubuntu 18.10 + GCC 8 + Python 3
-#      os: linux
-#      services:
-#        - docker
-#      env: DOCKER=ubuntu:cosmic COMPILER=g++-8 PYTHON=3   
-      
-#    - name: Ubuntu 18.04 + Clang 6 + Python 3 [Debug]
-#      os: linux
-#      services:
-#        - docker      
-#      env: DOCKER=ubuntu:bionic COMPILER=clang++-6.0 PYTHON=3 DEBUG=ON
-      
+      env: COMPILER=clang++-6.0 PYTHON=3
+
     - name: Ubuntu 18.04 + GCC 8 + Python 2
       os: linux
-      services:
-        - docker
-      env: DOCKER=ubuntu:bionic COMPILER=g++-8 PYTHON=2    
+      env: COMPILER=g++-8 PYTHON=2
 
-    - name: Ubuntu 18.04 + GCC 7 + Python 3 [Debug, Coverage]
+    - name: Ubuntu 18.04 + GCC 7 + Python 3 [Coverage]
       os: linux
-      services:
-        - docker
-      env: DOCKER=ubuntu:bionic COMPILER=g++-7 PYTHON=3 DEBUG=ON COVERAGE=ON
+      env: COMPILER=g++ PYTHON=3 COVERAGE=ON
 
 before_install:
   - |
-    if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then 
-      if [[ "$PYTHON" == "3" ]]; then PYTHON_LIB='python'; else PYTHON_LIB=python@2; CMAKE_MACOS_PYTHON2_EXTRA_FLAGS="-DPYTHON_LIBRARY=$(python-config --prefix)/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=$(python-config --prefix)/include/python2.7"; fi 
+    if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      NPROC="sysctl -n hw.ncpu"
+      if [[ "$PYTHON" == "3" ]]; then PYTHON_LIB='python'; else PYTHON_LIB=python@2; CMAKE_PYTHON2_EXTRA_FLAGS="-DPYTHON_LIBRARY=$(python-config --prefix)/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=$(python-config --prefix)/include/python2.7"; fi
       brew cask uninstall --force oclint
-      if [[ -z "$DISABLE_GTK" ]]; then GTK_PKG=gtk; else GTK_PKG=""; fi
       if [[ -z "$DISABLE_CAIRO" ]]; then CAIRO_PKG=cairo; else CAIRO_PKG=""; fi
-      brew install gcc@8 $PYTHON_LIB mpfr gmp $GTK_PKG $CAIRO_PKG
+      brew install gcc@8 $PYTHON_LIB mpfr gmp $CAIRO_PKG
+      export PKG_CONFIG_PATH=/usr/local/opt/libffi/lib/pkgconfig
       sudo easy_install pip
       sudo pip$PYTHON install --upgrade pip
       sudo pip$PYTHON install coverage pytest
     fi
   - |
     if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-      if [[ "$PYTHON" == "3" ]]; then PYTHON_LIB='python3'; else PYTHON_LIB=python; fi 
-      docker pull $DOCKER
-      CONTAINER_ID=$(docker run --detach --tty --volume="$PWD":/ariadne --workdir=/ariadne $DOCKER "/bin/bash")
-      SH_PREFIX="docker exec --tty $CONTAINER_ID"
-    fi
-  - |
-    if [[ "$DOCKER" =~ ubuntu ]]; then 
-      $SH_PREFIX apt update
-      if [[ -z "$DISABLE_GTK" ]]; then GTK_PKG=libgtk2.0-dev; else GTK_PKG=""; fi
-      if [[ -z "$DISABLE_CAIRO" ]]; then CAIRO_PKG=libcairo2-dev; else CAIRO_PKG=""; fi     
-      PKG_INSTALL_STRING="apt install -y cmake pkg-config $COMPILER $PYTHON_LIB-pip lib$PYTHON_LIB-dev $GTK_PKG $CAIRO_PKG libmpfr-dev"
-    fi
-  - |
-    if [[ "$DOCKER" =~ opensuse|fedora ]]; then
-      if [[ "$COMPILER" == "c++" ]]; then COMPILER_PKG=gcc-c++; else COMPILER_PKG="clang gcc-c++"; fi
-      if [[ -z "$DISABLE_GTK" ]]; then GTK_PKG=gtk2-devel; else GTK_PKG=""; fi
-      if [[ -z "$DISABLE_CAIRO" ]]; then CAIRO_PKG=cairo-devel; else CAIRO_PKG=""; fi
+      NPROC=nproc
+      if [[ "$PYTHON" == "3" ]]; then PYTHON_LIB='python3'; else PYTHON_LIB=python; CMAKE_PYTHON2_EXTRA_FLAGS="-DPYTHON_LIBRARY=$(python-config --configdir)/libpython2.7.so -DPYTHON_INCLUDE_DIR=$(python-config --prefix)/include/python2.7"; fi
+      if [[ -z "$DISABLE_CAIRO" ]]; then CAIRO_PKG=libcairo2-dev; else CAIRO_PKG=""; fi
+      sudo apt update
+      sudo apt install -y cmake pkg-config lcov $COMPILER $PYTHON_LIB-pip lib$PYTHON_LIB-dev $CAIRO_PKG libmpfr-dev
+      sudo pip$PYTHON install coverage pytest
     fi
-  - if [[ "$DOCKER" =~ fedora ]]; then PKG_INSTALL_STRING="dnf install -y make cmake pkg-config $COMPILER_PKG $PYTHON_LIB-devel $GTK_PKG $CAIRO_PKG mpfr-devel"; fi  
-  - if [[ "$DOCKER" =~ opensuse ]]; then PKG_INSTALL_STRING="zypper install -y cmake pkg-config $COMPILER_PKG $PYTHON_LIB-devel python$PYTHON-pip $GTK_PKG $CAIRO_PKG mpfr-devel"; fi  
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then $SH_PREFIX sh -c "$PKG_INSTALL_STRING"; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then PIP_INSTALL_STRING="pip$PYTHON install coverage pytest"; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then $SH_PREFIX sh -c "$PIP_INSTALL_STRING"; fi
 
 script:
-  - CMAKE_ARGS="-DCMAKE_CXX_COMPILER=$COMPILER -DPYBIND11_PYTHON_VERSION=$PYTHON $CMAKE_MACOS_PYTHON2_EXTRA_FLAGS"
-  - if [[ -n "$COVERAGE" ]]; then CMAKE_ARGS="$CMAKE_ARGS -DCOVERAGE=ON"; fi
-  - if [[ -n "$DEBUG" ]]; then CMAKE_BUILD_TYPE="Debug"; else CMAKE_BUILD_TYPE="Release"; fi
+  - echo "Running on $($NPROC) threads ..."
+  - CMAKE_ARGS="-DCMAKE_CXX_COMPILER=$COMPILER -DPYBIND11_PYTHON_VERSION=$PYTHON $CMAKE_PYTHON2_EXTRA_FLAGS"
+  - if [[ -n "$COVERAGE" ]]; then CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_BUILD_TYPE=Debug -DCOVERAGE=ON"; else CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_BUILD_TYPE=Release"; fi
   - if [[ "$TRAVIS_BRANCH" == master ]]; then CMAKE_ARGS="$CMAKE_ARGS -DWERROR=ON"; fi
-  - CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_BUILD_TYPE=$CMAKE_BUILD_TYPE"
-  - $SH_PREFIX cmake . $CMAKE_ARGS
-  - if [[ -n "$COVERAGE" ]]; then $SH_PREFIX make tests; else $SH_PREFIX make; fi
-  - $SH_PREFIX ctest -L "primary"
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX make install; fi
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cp -Rf tutorials ~/tutorials'; fi  
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cd ~/tutorials/hybrid_evolution && cmake . '$CMAKE_ARGS; fi
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cd ~/tutorials/hybrid_evolution && make'; fi  
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cd ~/tutorials/hybrid_evolution && ./hybrid_evolution_tutorial -v 0 > /dev/null'; fi
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cd ~/tutorials/rigorous_numerics && cmake . '$CMAKE_ARGS; fi
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cd ~/tutorials/rigorous_numerics && make'; fi  
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'cd ~/tutorials/rigorous_numerics && ./rigorous_numerics_tutorial > /dev/null'; fi
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'mkdir ~/tutorials/python && cp -Rf python/tutorials/* ~/tutorials/python'; fi    
-  - if [[ -z "$COVERAGE" ]]; then $SH_PREFIX sh -c 'export LD_LIBRARY_PATH=/usr/local/lib && cd ~/tutorials/python && python'$PYTHON' tutorial.py > /dev/null'; fi  
+  - cmake . $CMAKE_ARGS
+  - if [[ -n "$COVERAGE" ]]; then make tests -j $($NPROC); else make -j $($NPROC); fi
+  - ctest -L "primary" -j $($NPROC)
+  - |
+    if [[ -z "$COVERAGE" ]]; then
+      sudo make install
+      cp -Rf tutorials ~/tutorials
+      cd ~/tutorials/hybrid_evolution
+      cmake . $CMAKE_ARGS
+      make -j $($NPROC)
+      ./hybrid_evolution_tutorial -v 0 > /dev/null
+      cd ~/tutorials/rigorous_numerics
+      cmake . $CMAKE_ARGS
+      make -j $($NPROC)
+      ./rigorous_numerics_tutorial > /dev/null
+      mkdir ~/tutorials/python
+      cd $TRAVIS_BUILD_DIR
+      cp -Rf python/tutorials/* ~/tutorials/python
+      export LD_LIBRARY_PATH=/usr/local/lib
+      cd ~/tutorials/python
+      python$PYTHON tutorial.py > /dev/null
+    fi
   
 after_success:
-  - if [[ -n "$COVERAGE" ]]; then bash <(curl -s https://codecov.io/bash); fi
+  - |
+    if [[ -n "$COVERAGE" ]]; then
+      lcov --directory . --capture --output-file coverage.info
+      lcov --remove coverage.info '/usr/*' --output-file coverage.info
+      lcov --list coverage.info
+      bash <(curl -s https://codecov.io/bash) -f coverage.info || echo "Codecov did not collect coverage reports"
+    fi

CMakeLists.txt

@@ -1,4 +1,5 @@
 cmake_minimum_required(VERSION 3.9)
+message(STATUS "CMake version ${CMAKE_VERSION}")
 
 project(Ariadne VERSION 1.9)
 
@@ -17,6 +18,9 @@ set(CMAKE_MACOSX_RPATH 1)
 set(BUILD_SHARED_LIBS ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_CXX_STANDARD 17)
+
+set(PYBIND_SUBMODULE_COMMIT 435dbdd)
+
 foreach(WARN ${COMPILER_WARN})
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -W${WARN}")       
 endforeach()
@@ -33,7 +37,17 @@ if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O1")
 endif()
 
-set(COVERAGE_COMPILER_FLAGS -O0 --coverage -fprofile-arcs -ftest-coverage)
+option(COVERAGE "Enable coverage reporting" OFF)
+add_library(coverage_config INTERFACE)
+if(COVERAGE)
+    message(STATUS "Enabled coverage reporting")
+    target_compile_options(coverage_config INTERFACE -O0 -g --coverage)
+    if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+        target_link_options(coverage_config INTERFACE --coverage)
+    else()
+        target_link_libraries(coverage_config INTERFACE --coverage)
+    endif()
+endif()
 
 enable_testing()
 include(CTest)
@@ -94,19 +108,16 @@ else()
     message(WARNING "Unable to find Cairo. You will not be able to use graphics.")
 endif()
 
-find_package(GTK2)
-if(GTK2_FOUND)
-    set(HAVE_GTK2_H ON)
-    include_directories(SYSTEM ${GTK2_INCLUDE_DIRS})
-else()
-    message(WARNING "Unable to find GTK2. You will not be able to use graphics windows.")
-endif()
-
-
 configure_file(${PROJECT_SOURCE_DIR}/cmake/config.hpp.cmake ${PROJECT_SOURCE_DIR}/source/config.hpp)
 
 include_directories(${PROJECT_SOURCE_DIR}/source)
 
+find_package(Kirk)
+
+if(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+  add_definitions(-Wno-non-template-friend)
+endif()
+
 add_subdirectory(source)
 add_subdirectory(tests)
 add_subdirectory(examples)
@@ -120,9 +131,21 @@ if(PYTHONLIBS_FOUND)
         message(STATUS "pybind11 dependency not available.")
         find_package(Git)
         if(GIT_FOUND)
-            message(STATUS "Downloading it...")
-            execute_process(COMMAND git submodule update --init --recursive OUTPUT_QUIET ERROR_QUIET)
-            message(STATUS "Downloaded pybind11 dependency successfully.")
+            message(STATUS "Downloading pybind11 repository...")
+            if (NOT EXISTS ${PROJECT_SOURCE_DIR}/.git)
+                execute_process(COMMAND git init WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} OUTPUT_QUIET ERROR_QUIET)
+                execute_process(COMMAND rm -Rf ${PROJECT_SOURCE_DIR}/external/pybind11 OUTPUT_QUIET ERROR_QUIET)
+                execute_process(COMMAND git submodule add -f https://github.com/pybind/pybind11 external/pybind11 WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} OUTPUT_QUIET ERROR_QUIET)
+                execute_process(COMMAND git checkout ${PYBIND_SUBMODULE_COMMIT} WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/pybind11 OUTPUT_QUIET ERROR_QUIET)
+                execute_process(COMMAND git submodule update --init --recursive WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/pybind11 OUTPUT_QUIET ERROR_QUIET)
+            else()
+                execute_process(COMMAND git submodule update --init --recursive WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} OUTPUT_QUIET ERROR_QUIET)
+            endif()
+            if(NOT EXISTS ${PROJECT_SOURCE_DIR}/external/pybind11/CMakeLists.txt)
+                message(ERROR "pybind11 download failure.")
+            else()
+                message(STATUS "Downloaded pybind11 dependency successfully.")
+            endif()
         else()
             message(ERROR "Git not found, pybind11 dependency could not be downloaded.")
         endif()
@@ -162,12 +185,6 @@ add_library(ariadne SHARED
     $<TARGET_OBJECTS:ariadne-hybrid>
 )
 
-if(COVERAGE)
-    target_link_libraries(ariadne gcov)
-    target_link_libraries(ariadne-kernel gcov)
-    target_link_libraries(ariadne-core gcov)
-endif()
-
 target_link_libraries(ariadne dl)
 target_link_libraries(ariadne-kernel dl)
 target_link_libraries(ariadne-core dl)
@@ -176,6 +193,12 @@ target_link_libraries(ariadne ${GMP_LIBRARIES} ${MPFR_LIBRARIES})
 target_link_libraries(ariadne-kernel ${GMP_LIBRARIES} ${MPFR_LIBRARIES})
 target_link_libraries(ariadne-core ${GMP_LIBRARIES} ${MPFR_LIBRARIES})
 
+if(COVERAGE)
+    target_link_libraries(ariadne coverage_config)
+    target_link_libraries(ariadne-kernel coverage_config)
+    target_link_libraries(ariadne-core coverage_config)
+endif()
+
 if(GMPXX_FOUND)
     target_link_libraries(ariadne ${GMPXX_LIBRARIES})
     target_link_libraries(ariadne-kernel ${GMP_LIBRARIES} ${MPFR_LIBRARIES})
@@ -187,10 +210,5 @@ if(CAIRO_FOUND)
     target_link_libraries(ariadne-kernel ${CAIRO_LIBRARIES})
 endif()
 
-if(GTK2_FOUND)
-    target_link_libraries(ariadne ${GTK2_LIBRARIES})
-    target_link_libraries(ariadne-kernel ${GTK2_LIBRARIES})
-endif()
-
 install(TARGETS ariadne DESTINATION lib)
 install(DIRECTORY source/ DESTINATION include/ariadne FILES_MATCHING PATTERN "*.hpp")

README.md

@@ -7,7 +7,7 @@
 Ariadne is a tool for reachability analysis and model checking of hybrid systems. Additionally, it is a framework for rigorous computation featuring arithmetic, linear algebra, calculus, geometry, algebraic and differential equations, and optimization solvers.
 
 * This repository contains the main development fork of the tool. For a more stable version with a less sophisticated user interface, see the *release-1.0* repository.
-* The latest internal release is [v1.9.2](https://github.com/ariadne-cps/ariadne/releases/tag/v1.9.2). However, the code in the master branch should always be usable.
+* For the latest internal release, see the [releases](https://github.com/ariadne-cps/ariadne/releases) page. However, the code in the master branch should always be usable.
 
 ### Installation ###
 
@@ -19,21 +19,27 @@ The build system is CMake. The library is tested for compilation using gcc and c
 
 #### Dependencies
 
-The only required library dependencies of Ariadne are GMP and MPFR. If you want to enable the graphical output you will require Cairo (to save into png files) and GTK2 (for window display). Finally, the Python bindings require the Python headers (either Python 2 or 3 are supported). In particular for Python, there is an internal Git submodule dependency on the header-only [pybind11](https://github.com/pybind/pybind11) library. Therefore in order to fetch the dependency, Git must be installed.
+The only required library dependencies of Ariadne are GMP and MPFR. If you want to enable the graphical output you will require Cairo in order to save into png files. Finally, the Python bindings require the Python headers (either Python 2 or 3 are supported). In particular for Python, there is an internal Git submodule dependency on the header-only [pybind11](https://github.com/pybind/pybind11) library. Therefore in order to fetch the dependency, Git must be installed.
 
 Finally, if you want to build the documentation, you need Doxygen and a working Latex distribution (including the Math packages).
 
 Specific instructions for Ubuntu and macOS follow (documentation packages are excluded).
 
 ##### Ubuntu
-Aptitude packages: `cmake git libgmp-dev libmpfr-dev libgtk2.0-dev libcairo2-dev`
+Aptitude packages: `cmake pkg-config git libgmp-dev libmpfr-dev libcairo2-dev`
 
 Additional Aptitude package required for the Python interface: `python3-dev` or `python-dev`.
 
 ##### macOS
 1. Install the Command Line Developer Tools (will also be asked when installing Homebrew) from the Apple Store
 
-2. Install Homebrew from http://brew.sh/ . Homebrew packages required: `cmake git mpfr gmp gtk cairo`
+2. Install Homebrew from http://brew.sh/ . Homebrew packages required: `cmake git mpfr gmp cairo`
+
+For Cairo support, you may need to set up a permanent variable for the path of pkgconfig by adding the following line in your `~\.bash_profile`:
+
+```
+export PKG_CONFIG_PATH=/usr/local/opt/libffi/lib/pkgconfig
+```
 
 #### Building
 

cmake/FindKirk.cmake

@@ -0,0 +1,13 @@
+find_path(KIRK_INCLUDE_DIR kirk/kirk-real-obj.h PATH_SUFFIXES kirk)
+#check_include_files(kirk/kirk-real-obj.h HAVE_KIRK_REAL_OBJ_H)
+find_library(KIRK_LIBRARY kirk)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(KIRK DEFAULT_MSG KIRK_LIBRARY KIRK_INCLUDE_DIR)
+
+#Diagnostic messages
+#message(KIRK_FOUND=${KIRK_FOUND})
+#message(KIRK_LIBRARY=${KIRK_LIBRARY})
+#message(KIRK_INCLUDE_DIR=${KIRK_INCLUDE_DIR})
+#message(HAVE_KIRK_REAL_OBJ_H=${HAVE_KIRK_REAL_OBJ_H})
+

cmake/config.hpp.cmake

@@ -14,6 +14,5 @@
 
 #cmakedefine HAVE_GMPXX_H
 #cmakedefine HAVE_CAIRO_H
-#cmakedefine HAVE_GTK2_H
 
 #endif /* ARIADNE_CONFIG_HPP */

doc/Doxyfile.in

@@ -1423,7 +1423,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1453,15 +1453,15 @@ MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_EXTENSIONS     =
+MATHJAX_EXTENSIONS     = TeX/AMSmath TeX/AMSsymbols
 
 # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
 # of code that will be used on startup of the MathJax code. See the MathJax site
 # (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
 # example see the documentation.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_CODEFILE       =
+MATHJAX_CODEFILE       = @CMAKE_CURRENT_SOURCE_DIR@/doc/macros.js
 
 # When the SEARCHENGINE tag is enabled doxygen will generate a search box for
 # the HTML output. The underlying search engine uses javascript and DHTML and