Merge pull request #266 from sys-bio/develop

Travis was pretty much useless, it never built this PR. Merging anyway.

.gitattributes

@@ -12,6 +12,9 @@
 *.h      text
 *.hpp    text
 
+# Python
+*.py     text
+
 # Object Pascal
 *.pas    text
 

.gitignore

@@ -6,6 +6,14 @@
 *.orig
 *.kate-swp
 
+**/.swp
+
+# Merge backups (kdiff3?)
+*.BACKUP*
+*.BASE*
+*.LOCAL*
+*.REMOTE*
+
 # libsbml auto-generated files
 third_party/libSBML-5.9.0-Source/src/bindings/swig/libsbml-packages.h
 third_party/libSBML-5.9.0-Source/src/bindings/swig/libsbml-packages.i
@@ -20,3 +28,8 @@ third_party/libSBML-5.9.0-Source/src/bindings/python/local-downcast-plugins.cpp
 third_party/libSBML-5.9.0-Source/src/bindings/python/local-downcast.cpp
 third_party/libSBML-5.9.0-Source/src/bindings/python/local-packages.i
 wrappers/C/Testing/alexTestOutput.xml
+
+# no idea
+.swm
+.swn
+.swo

.travis.yml

@@ -1,74 +1,53 @@
-#sudo: false
+sudo: required
+dist: trusty
 
 language: cpp
 
+notifications:
+  email:
+      - [email protected]
+
 compiler: gcc
 
 branches:
   only:
     - develop
-    - travis
-
-#addons:
-  #apt:
-    #sources:
-    #- llvm-toolchain-precise-3.5
-
-#addons:
-  #apt:
-    #packages:
-    #- cmake
-    #- llvm-3.4
+    - master
 
 
 before_install:
-  # https://github.com/travis-ci/travis-ci/issues/1379
-  - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+  # print the distro information
+  - lsb_release -a
+
+  # cache refresh required to install packages
   - sudo apt-get update -qq
-  - if [ "$CXX" = "g++" ]; then sudo apt-get install -qq g++-4.8; fi
-  - if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
-  - mkdir ~/install
 
-  # setup CMake 3.2.1
-  - mkdir ~/install/cmake-3.2.1
-  - cd ~/install/cmake-3.2.1
-  - wget http://www.cmake.org/files/v3.2/cmake-3.2.1-Linux-x86_64.tar.Z
-  - tar xf cmake-3.2.1-Linux-x86_64.tar.Z --strip-components=1
+  # install dependencies
+  - sudo apt-get -y install cmake swig python-dev python-numpy llvm-3.5-dev
 
-  ## get LLVM 3.5.1 sources
-  #- mkdir -p ~/src/rr-deps/llvm-3.5.1
-  #- cd ~/src/rr-deps/llvm-3.5.1
-  #- wget http://llvm.org/releases/3.5.1/llvm-3.5.1.src.tar.xz
-  #- tar xf llvm-3.5.1.src.tar.xz
-  ## build LLVM 3.5.1
-  #- mkdir -p ~/build/llvm-3.5.1
-  #- cd ~/build/llvm-3.5.1
-  #- ~/install/cmake-3.2.1/bin/cmake --version
-  #- ~/install/cmake-3.2.1/bin/cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/install/llvm-3.5.1 ~/src/rr-deps/llvm-3.5.1/llvm-3.5.1.src
-  #- make -j2 && make install
+  - mkdir ~/install
 
-  # download LLVM 3.5.1 binaries
-  - cd ~/install
-  - wget http://sourceforge.net/projects/roadrunner-deps/files/ubuntu-12.04.5/llvm-3.5.1.tar.xz
-  - tar xf llvm-3.5.1.tar.xz
+  # install roadrunner dependencies via apt:
+  - sudo sh -c 'echo "\n\ndeb http://cdn.rawgit.com/sys-bio/roadrunner-debs/master ./ \n\n" >> /etc/apt/sources.list'
+  - sudo cat /etc/apt/sources.list
+  - sudo apt-get update -qq
+  - sudo apt-get -y --force-yes install libroadrunner-deps-dev
 
-  # roadrunner third party:
-  - mkdir -p ~/build/roadrunner-tp
-  - cd ~/build/roadrunner-tp
-  - ~/install/cmake-3.2.1/bin/cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/install/roadrunner-tp $TRAVIS_BUILD_DIR/third_party
-  - make -j2
+  - echo "TRAVIS_BUILD_DIR $TRAVIS_BUILD_DIR"
+  # build roadrunner:
+  - mkdir -p ~/build/roadrunner
 
 install:
-  - cd ~/build/roadrunner-tp
+  - cd ~/build/roadrunner
+  - cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/install/roadrunner -DTHIRD_PARTY_INSTALL_FOLDER=/usr -DLLVM_CONFIG_EXECUTABLE=/usr/lib/llvm-3.5/bin/llvm-config -DBUILD_PYTHON=ON -DPYTHON_EXECUTABLE=/usr/bin/python -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython2.7.so python2.7 -DBUILD_TESTS=ON -DBUILD_TEST_TOOLS=ON -DUSE_TR1_CXX_NS=ON -DBUILD_JAVA_INTERFACE=OFF "$TRAVIS_BUILD_DIR"
+  - make -j2
   - make install
 
-before_script:
-  - echo "TRAVIS_BUILD_DIR $TRAVIS_BUILD_DIR"
-  # roadrunner:
-  - mkdir -p ~/build/roadrunner
-  - cd ~/build/roadrunner
-  - ~/install/cmake-3.2.1/bin/cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/install/roadrunner -DTHIRD_PARTY_INSTALL_FOLDER=~/install/roadrunner-tp -DLLVM_CONFIG_EXECUTABLE=~/install/llvm-3.5.1/bin/llvm-config -DBUILD_PYTHON=OFF -DBUILD_TESTS=OFF -DUSE_TR1_CXX_NS=ON -DBUILD_JAVA_INTERFACE=OFF -DBUILD_TEST_TOOLS=OFF "$TRAVIS_BUILD_DIR"
+before_script: true
 
 script:
   - cd ~/build/roadrunner
-  - make -j2 && make install
+  - make -j2 && make install
+  - ctest -VV
+  # display results of compiled tests
+  - cat autotest/compiled-test-suite/results.xml

AUTHORS.txt

@@ -26,5 +26,17 @@ The C# backend was ported to C++ by
 The Plugin Framework was designed and developed by
 
     Totte Karlsson
+
+with Tellurium integration and further enhancements by
 
-For more information visit libroadRunner.org
+    Kiri Choi
+
+The continuous integration (CI) system and Java API were developed by
+
+    J Kyle Medley
+
+Redesign of the integrator interface was done by
+
+    Wilbert Copeland
+
+For more information visit libroadrunner.org

CMakeLists.txt

@@ -1,6 +1,19 @@
 cmake_minimum_required(VERSION 2.8)
 project(rr)
 
+# libRoadRunner semantic versioning (http://semver.org/) - used to generate
+# source files expose library version information
+
+set(ROADRUNNER_VERSION_MAJOR 1)
+set(ROADRUNNER_VERSION_MINOR 4)
+set(ROADRUNNER_VERSION_PATCH 2)
+
+set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
+
+set(CMAKE_MACOSX_RPATH 1)
+
+# ** Configuration Options *****************************************************
+
 # These will be the defaults ...
 if(WIN32)
     SET(RR_BUILDS_ROOT      "c:/builds")
@@ -31,6 +44,8 @@ endif(WIN32)
 # add cmake files to find things, prepend with our path
 SET(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/ ${CMAKE_MODULE_PATH})
 
+# TODO: add some logic to automatically set based on compiler version
+set(RR_USE_CXX11 FALSE CACHE BOOL "Set to TRUE to enable C++11 features")
 
 set(LLVM_INSTALL_PREFIX CACHE PATH "If LLVM was built using CMake, this is the location where it was installed")
 
@@ -75,10 +90,15 @@ option(BUILD_LEGACY_C "Build the legacy C code generating backend (deprecated)")
 
 # should we build the swig python wrapper?
 option (BUILD_PYTHON "build the SWIG generated python wrapper" OFF)
+set( PYTHON_SITE_DIR site-packages CACHE PATH "Path to Python site packages directory" )
 
 # should we build the swig Java wrapper?
 option (BUILD_JAVA_INTERFACE "build the SWIG generated Java wrapper" OFF)
 
+if(BUILD_TESTS OR BUILD_JAVA_INTERFACE)
+  enable_testing()
+endif()
+
 if(BUILD_LLVM AND NOT LLVM_FOUND)
     message(FATAL_ERROR "BUILD_LLVM is enabled, but no LLVM installation was found")
 endif()
@@ -90,15 +110,20 @@ mark_as_advanced(
     INSTALL_C_API
     INSTALL_C_API_PYTHON
     INSTALL_STATIC_LIB
+    RR_USE_CXX11
     )
 
 set(RR_GENERATED_HEADER_PATH ${CMAKE_CURRENT_BINARY_DIR}/source)
 set(RR_ROADRUNNER_INSTALL_PATH ${CMAKE_INSTALL_PREFIX})
 set(RR_ROADRUNNER_INSTALL_LIB_PATH ${RR_ROADRUNNER_INSTALL_PATH}/lib)
 set(RR_SOURCE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
 
-# new clang on OSX and msvc use std namespace. 
-option (USE_TR1_CXX_NS          "Use the tr1 c++ namespace for swig smart pointer" ${CMAKE_COMPILER_IS_GNUCXX})
+# new clang on OSX and msvc use std namespace.
+if(RR_USE_CXX11)
+    option (USE_TR1_CXX_NS          "Use the tr1 c++ namespace for swig smart pointer" OFF)
+else()
+    option (USE_TR1_CXX_NS          "Use the tr1 c++ namespace for swig smart pointer" ${CMAKE_COMPILER_IS_GNUCXX})
+endif()
 OPTION (INSTALL_CXX_API         "Generate C++ api"                               ON )
 OPTION (INSTALL_C_API           "Generate C API"                                 ON )
 OPTION (INSTALL_C_API_PYTHON    "Package ctypes  Python wrapper for the C API"   ON )
@@ -149,6 +174,17 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY     ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY     ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY     ${PROJECT_BINARY_DIR}/bin)
 
+#** Apply Project/Compiler Settings ********************************************
+
+# Set C++11 flags
+if(RR_USE_CXX11)
+    IF(NOT MSVC)
+        set(CMAKE_CXX_FLAGS "-std=c++11 ${CMAKE_CXX_FLAGS}")
+    else()
+        message(WARNING "RR_USE_CXX11 enabled but has no effect on Microsoft compilers")
+    endif()
+endif()
+
 include_directories(
     ${RR_ROOT}
     ${THIRD_PARTY_FOLDER}
@@ -163,7 +199,7 @@ if (WIN32)
 else()
     #UNIX
     find_package(LibXml2 REQUIRED)
-	message(STATUS "found libxml2, include dir: ${LIBXML2_INCLUDE_DIR}") 
+	message(STATUS "found libxml2, include dir: ${LIBXML2_INCLUDE_DIR}")
 	include_directories(${LIBXML2_INCLUDE_DIR})
 endif(WIN32)
 
@@ -189,11 +225,11 @@ if(${MSVC})
         -DCRT_NONSTDC_NO_DEPRECATE
         -D_CRT_SECURE_NO_WARNINGS    #MS wanting you to changes basically all standard C functions :(
         )
-        
+
     #  4251 About exporting std classes
     #  4018 Comparing unsigned/signed ints
-    #  4996 Deprecated functions   
-    add_definitions( "/wd4251 /wd4018 /wd4996 /nologo" )   
+    #  4996 Deprecated functions
+    add_definitions( "/wd4251 /wd4018 /wd4996 /nologo" )
 
     SET (CMAKE_CXX_FLAGS             "${CMAKE_CXX_FLAGS} /EHsc ")
     SET (CMAKE_SHARED_LINKER_FLAGS     "${CMAKE_SHARED_LINKER_FLAGS} ") #/FORCE:MULTIPLE")
@@ -269,12 +305,35 @@ endif(INSTALL_CXX_API)
 
 add_subdirectory(wrappers)
 
-if(BUILD_TEST_TOOLS)
+if(BUILD_TESTS AND BUILD_TEST_TOOLS)
     message(STATUS "building tests")
+    file (GLOB TEST_FILES "testing/*" )
+
+    file (GLOB PYTHON_TEST_FILES "wrappers/Python/roadrunner/testing/*" )
+    list( APPEND TEST_FILES ${PYTHON_TEST_FILES} )
+
+    file(GLOB PYTHON_TEST_DATA "${CMAKE_CURRENT_SOURCE_DIR}/testing/*.rrtest")
+
+    foreach( f ${TEST_FILES} )
+        if(NOT IS_DIRECTORY ${f})
+            get_filename_component( FILE_NAME ${f} NAME )
+            configure_file( ${f} testing/${FILE_NAME} COPYONLY )
+            configure_file( ${f} lib/site-packages/roadrunner/testing/${FILE_NAME} COPYONLY )
+        endif()
+    endforeach()
+
+    foreach( f ${PYTHON_TEST_DATA} )
+        if(NOT IS_DIRECTORY ${f})
+            get_filename_component( FILE_NAME ${f} NAME )
+            configure_file( ${f} lib/site-packages/roadrunner/testing/test_data/${FILE_NAME} COPYONLY )
+        endif()
+    endforeach()
+
     add_subdirectory(testing)
+    add_subdirectory(autotest)
 else()
     message(STATUS "NOT building tests")
-endif(BUILD_TEST_TOOLS)
+endif()
 
 
 #======================= INSTALL STUFF ========================================================
@@ -308,20 +367,12 @@ if(${BORLAND})
     endforeach()
 endif()
 
-if(WIN32)
-#One day these may be statically linked
-set(RUNTIMES libxml2.DLL iconv.dll zlib1.dll)
-foreach(runtime ${RUNTIMES})
-    install(    FILES     ${THIRD_PARTY_FOLDER}/dependencies/libsbml/bin/${runtime}
-        DESTINATION bin
-        COMPONENT rr_core)
-endforeach()
-endif()
+configure_file(VERSION.txt.in VERSION.txt @ONLY)
 
 install(
-    FILES     
+    FILES
     NOTICE.txt
-    VERSION.txt
+    ${CMAKE_CURRENT_BINARY_DIR}/VERSION.txt
     NEWS.txt
     DESTINATION .
 )

README.md

@@ -4,7 +4,7 @@
 
 Copyright 2013-2015
 
-E. T. Somogyi <sup>1</sup>, M. T. Karlsson <sup>2</sup>, M. Swat <sup>1</sup>, M. Galdzicki <sup>3</sup>, J. K. Medley <sup>3</sup> and H. M. Sauro <sup>3</sup>
+E. T. Somogyi <sup>1</sup>, M. T. Karlsson <sup>2</sup>, M. Swat <sup>1</sup>, M. Galdzicki <sup>3</sup>, J. K. Medley <sup>3</sup>, K. Choi <sup>3</sup>, W. Copeland <sup>3</sup> and H. M. Sauro <sup>3</sup>
 
 1. Biocomplexity Institute, Indiana University, Simon Hall MSB1, Bloomington, IN 47405
 2. Dune Scientific, 10522 Lake City Way NE, #302 Seattle WA

VERSION.txt.in

@@ -0,0 +1 @@
+@ROADRUNNER_VERSION@