Merge pull request #341 from sys-bio/develop

Merge into master for 1.4.8 rel

CMakeLists.txt

@@ -6,7 +6,7 @@ project(rr)
 
 set(ROADRUNNER_VERSION_MAJOR 1)
 set(ROADRUNNER_VERSION_MINOR 4)
-set(ROADRUNNER_VERSION_PATCH 2)
+set(ROADRUNNER_VERSION_PATCH 8)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 
@@ -91,6 +91,9 @@ 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" )
+if(BUILD_PYTHON)
+  set(PYTHON_PACKAGE_DEST_DIR ${PYTHON_SITE_DIR}/roadrunner)
+endif()
 
 # should we build the swig Java wrapper?
 option (BUILD_JAVA_INTERFACE "build the SWIG generated Java wrapper" OFF)
@@ -133,6 +136,7 @@ OPTION (INSTALL_STATIC_LIB      "Install RoadRunner CXX static lib"
 OPTION (RR_BUILD_SHARED_CORE    "Build RoadRunner Core Shared library"           ON)
 OPTION (BUILD_TESTS             "Build the SBML C API test suite"                OFF)
 OPTION (INSTALL_SBML_MODELS     "Install SBML Models"                            ON )
+OPTION (WITH_CONDA_BUILDER      "Include files required to build the conda package" OFF)
 
 #Setup so that roadrunner is always built as a dll and linked statically with 'as much as possible'
 set(BUILD_SHARED_LIBS            ON)
@@ -201,8 +205,36 @@ else()
     find_package(LibXml2 REQUIRED)
 	message(STATUS "found libxml2, include dir: ${LIBXML2_INCLUDE_DIR}")
 	include_directories(${LIBXML2_INCLUDE_DIR})
-endif(WIN32)
+endif()
+
+find_library(LIBSBML_LIBRARY sbml libsbml HINTS ${THIRD_PARTY_INSTALL_FOLDER}/lib)
+find_library(LIBSBML_STATIC_LIBRARY sbml-static libsbml-static HINTS ${THIRD_PARTY_INSTALL_FOLDER}/lib)
+find_path(LIBSBML_INCLUDE_DIR sbml/SBMLTypes.h HINTS ${THIRD_PARTY_INSTALL_FOLDER}/include)
+
+# find libSBML deps
+
+if(WIN32)
+  find_library(ICONV_LIBRARY iconv libiconv HINTS ${THIRD_PARTY_INSTALL_FOLDER}/lib)
+  if(NOT ICONV_LIBRARY)
+    message(SEND_ERROR "Could not find libiconv, required for libSBML linking")
+  endif()
+endif()
+message(STATUS "ZLIB SDK dir: ${CMAKE_OSX_SYSROOT}/usr/lib")
+find_library(ZLIB_LIBRARY NAMES z libz libz.dylib zdll HINTS ${THIRD_PARTY_INSTALL_FOLDER}/lib ${CMAKE_OSX_SYSROOT}/usr/lib)
+message(STATUS "Find ZLIB results: ${ZLIB_LIBRARY}")
+if(NOT ZLIB_LIBRARY)
+  message(SEND_ERROR "Could not find zlib, required for libSBML linking")
+endif()
+find_library(BZ2_LIBRARY bz2 libbz2 HINTS ${THIRD_PARTY_INSTALL_FOLDER}/lib)
+if(NOT BZ2_LIBRARY)
+  message(SEND_ERROR "Could not find libbz2, required for libSBML linking")
+endif()
 
+if(WIN32)
+  set(LIBSBML_EXTRA_LIBS "${ICONV_LIBRARY};${ZLIB_LIBRARY};${BZ2_LIBRARY}" CACHE STRING "libSBML extra libraries")
+else()
+  set(LIBSBML_EXTRA_LIBS "${ZLIB_LIBRARY};${BZ2_LIBRARY}" CACHE STRING "libSBML extra libraries")
+endif()
 
 if (${BUILD_LLVM})
     link_directories(
@@ -284,6 +316,44 @@ else()
     message(STATUS "not building legacy C backend")
 endif(BUILD_LEGACY_C)
 
+message(STATUS "
+-------------------------------------------------------------------------------
+libRoadRunner Configuration Summary
+-------------------------------------------------------------------------------
+
+    For up-to-date news and releases visit libroadrunner.org
+
+    Configured on host $ENV{COMPUTERNAME} ${HOSTNAME}
+      host OS                   ${CMAKE_SYSTEM_NAME}
+      host architecture         ${CMAKE_SYSTEM_PROCESSOR}
+
+    General flags:
+      CC                        ${CMAKE_C_COMPILER}
+      CXX                       ${CMAKE_CXX_COMPILER}
+      CPPFLAGS                  ${BUILD_DEFINITIONS}
+      CFLAGS                    ${CMAKE_C_FLAGS}
+      CXXFLAGS                  ${CMAKE_CXX_FLAGS}
+      LDFLAGS                   ${CMAKE_EXE_LINKER_FLAGS}
+
+    Installation prefix:        ${CMAKE_INSTALL_PREFIX}
+
+    Options:
+      With LLVM?                ${BUILD_LLVM}
+      With legacy C? (DEP)      ${BUILD_LEGACY_C}
+      Enable Python interface?  ${BUILD_PYTHON}
+      Enable Java interface?    ${BUILD_JAVA_INTERFACE}
+      Enable test suite?        ${BUILD_TESTS}
+
+    Dependencies (packages marked with *** are required):
+    "
+)
+
+message( "  *** libSBML")
+message( "       libSBML libs               ${LIBSBML_LIBRARY}")
+message( "       libSBML static libs        ${LIBSBML_STATIC_LIBRARY}")
+message( "       libSBML includes           ${LIBSBML_INCLUDE_DIR}")
+
+message( "" )
 
 # We alway have to build the roadrunner core, everything depends on this
 add_subdirectory(source)
@@ -314,6 +384,8 @@ if(BUILD_TESTS AND BUILD_TEST_TOOLS)
 
     file(GLOB PYTHON_TEST_DATA "${CMAKE_CURRENT_SOURCE_DIR}/testing/*.rrtest")
 
+    file(GLOB TEST_DATA_XML "${CMAKE_CURRENT_SOURCE_DIR}/testing/*.xml")
+
     foreach( f ${TEST_FILES} )
         if(NOT IS_DIRECTORY ${f})
             get_filename_component( FILE_NAME ${f} NAME )
@@ -329,6 +401,13 @@ if(BUILD_TESTS AND BUILD_TEST_TOOLS)
         endif()
     endforeach()
 
+    foreach( f ${TEST_DATA_XML} )
+        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()
@@ -383,3 +462,7 @@ if(WIN32)
         FILES win32_bin_README.txt DESTINATION bin/ RENAME README.txt
     )
 endif(WIN32)
+
+if(WITH_CONDA_BUILDER)
+  install(FILES assets/roadrunner-64x64-red.png DESTINATION assets)
+endif()

README.md

@@ -2,9 +2,9 @@
 [![GitHub version](https://badge.fury.io/gh/sys-bio%2Froadrunner.svg)](http://badge.fury.io/gh/sys-bio%2Froadrunner)
 [![Build Status](https://travis-ci.org/sys-bio/roadrunner.svg?branch=develop)](https://travis-ci.org/sys-bio/roadrunner)
 
-Copyright 2013-2015
+Copyright 2013-2016
 
-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>
+E. T. Somogyi <sup>1</sup>, J. K. Medley <sup>3</sup>, M. T. Karlsson <sup>2</sup>, M. Swat <sup>1</sup>, M. Galdzicki <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

apps/rr/CMakeLists.txt

@@ -36,7 +36,7 @@ rr-libstruct-static
 lapack
 blas
 f2c
-sbml-static.a
+${LIBSBML_STATIC_LIBRARY}
 xml2
 sundials_nvecserial.a
 sundials_cvode.a

packaging/deb/libroadrunner/debian/changelog

@@ -1,3 +1,9 @@
+libroadrunner (1.4.2) unstable; urgency=low
+
+  * Bufix release
+
+   -- Kyle Medley <[email protected]>  Fri, 29 Jan 2016 12:00:00 -0700
+
 libroadrunner (1.4.1) unstable; urgency=low
 
   * Refactored solver API

packaging/deb/libroadrunner/debian/control

@@ -28,7 +28,7 @@ Description: Simulation library for SBML
 Package: libroadrunner
 Section: libs
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libroadrunner-deps (= ${binary:Version})
+Depends: ${shlibs:Depends}, ${misc:Depends}, libroadrunner-deps (>= 2.0.2)
 Description: Simulation library for SBML
  libRoadRunner is a ODE/stochastic simulation and
  modeling environment for SBML

source/CMakeLists.txt

@@ -248,17 +248,19 @@ if(RR_BUILD_SHARED_CORE)
     if(UNIX)
         target_link_libraries (${target}
             pthread
-            sbml-static
+            ${LIBSBML_STATIC_LIBRARY}
             dl
             f2c${staticLibExt}
             )
+        target_link_libraries(${target} ${LIBSBML_EXTRA_LIBS})
     else()
         target_link_libraries (${target}
             libf2c
-            libsbml
-        ws2_32
-        iphlpapi
+            ${LIBSBML_LIBRARY}
+            ws2_32
+            iphlpapi
             )
+        target_link_libraries(${target} ${LIBSBML_EXTRA_LIBS})
     endif(UNIX)
 
 
@@ -276,6 +278,7 @@ if(RR_BUILD_SHARED_CORE)
             LIBRARY DESTINATION lib COMPONENT rr_core
             ARCHIVE DESTINATION lib COMPONENT rr_core
             )
+        install(TARGETS roadrunner DESTINATION ${PYTHON_PACKAGE_DEST_DIR})
     endif()
 
 
@@ -329,22 +332,24 @@ target_link_libraries (${target}-static
 
 if(WIN32)
     target_link_libraries (${target}-static
-        libsbml-static
+        ${LIBSBML_STATIC_LIBRARY}
         libf2c
-    ws2_32
-    iphlpapi
+        ws2_32
+        iphlpapi
         )
+    target_link_libraries(${target}-static ${LIBSBML_EXTRA_LIBS})
 endif(WIN32)
 
 
 if(UNIX)
     target_link_libraries (${target}-static
-        sbml-static
+        ${LIBSBML_STATIC_LIBRARY}
         f2c
         xml2
         dl
         pthread
         )
+    target_link_libraries(${target}-static ${LIBSBML_EXTRA_LIBS})
 endif(UNIX)
 
 #Libxml we can't build right now

source/CVODEIntegrator.cpp

@@ -321,7 +321,7 @@ namespace rr
             }
             else if (key == "absolute_tolerance" || key == "relative_tolerance")
             {
-                CVodeSetMaxNumSteps(mCVODE_Memory, getValueAsInt("maximum_num_steps"));
+                CVodeSetMaxNumSteps(mCVODE_Memory, getValueAsInt("maximum_num_steps")); // FIXME: is this intentional?
                 setCVODETolerances();
             }
         }
@@ -1043,5 +1043,3 @@ namespace rr
 	}
 
 }
-
-

source/GillespieIntegrator.cpp

@@ -194,7 +194,7 @@ namespace rr
 
         // Set default integrator settings.
         addSetting("seed",              defaultSeed(), "Seed", "Set the seed into the random engine. (ulong)", "(ulong) Set the seed into the random engine.");
-        addSetting("variable_step_size",false, "Variable Step Size", "Perform a variable time step simulation. (bool)", "(bool) Enabling this setting will allow the integrator to adapt the size of each time step. This will result in a non-uniform time column.");
+        addSetting("variable_step_size",true, "Variable Step Size", "Perform a variable time step simulation. (bool)", "(bool) Enabling this setting will allow the integrator to adapt the size of each time step. This will result in a non-uniform time column.");
         addSetting("initial_time_step", 0.0,   "Initial Time Step", "Specifies the initial time step size. (double)", "(double) Specifies the initial time step size.");
         addSetting("minimum_time_step", 0.0,   "Minimum Time Step", "Specifies the minimum absolute value of step size allowed. (double)", "(double) The minimum absolute value of step size allowed.");
         addSetting("maximum_time_step", 0.0,   "Maximum Time Step", "Specifies the maximum absolute value of step size allowed. (double)", "(double) The maximum absolute value of step size allowed.");
@@ -205,14 +205,20 @@ namespace rr
 	{
 		double tf = 0;
 		bool singleStep;
+		bool varStep = getValue("variable_step_size").convert<bool>();
+		double minTimeStep = getValue("minimum_time_step").convert<double>();
 
 		assert(hstep > 0 && "hstep must be > 0");
 
-		if (getValue("variable_step_size").convert<bool>())
+		if (varStep)
 		{
-			if (getValue("minimum_time_step").convert<double>() > 0.0)
+			if (minTimeStep > 0.0)
 			{
-				tf = t + getValue("minimum_time_step").convert<double>();
+				if (minTimeStep > hstep) // no step bigger than hstep
+				{
+					minTimeStep = hstep;
+				}
+				tf = t + minTimeStep;
 				singleStep = false;
 			}
 			else
@@ -273,6 +279,10 @@ namespace rr
 				// no reaction occurs
 				return std::numeric_limits<double>::infinity();
 			}
+			if (t + tau > tf)        // if time exhausted, don't allow reaction to proceed
+			{
+				return tf;
+			}
 
 			t = t + tau;
 

source/Integrator.cpp

@@ -48,6 +48,7 @@ namespace rr
     {
         std::stringstream ss;
         ss << "< roadrunner.Integrator() >\n";
+        ss << "  name: " << getName() << "\n";
         ss << "  settings:\n";
         ss << getSettingsRepr();
         return ss.str();
@@ -57,7 +58,7 @@ namespace rr
     std::string Integrator::toRepr() const
     {
         std::stringstream ss;
-        ss << "< roadrunner.Integrator() " << settingsPyDictRepr() << " >\n";
+        ss << "< roadrunner.Integrator() \"" << getName() << "\" " << settingsPyDictRepr() << " >\n";
         return ss.str();
     }
 

source/NLEQSolver.cpp

@@ -80,7 +80,7 @@ std::string NLEQSolver::getNLEQHint() {
 	return "Steady-state nonlinear systems of equations solver";
 }
 
-double NLEQSolver::solve(const vector<double>& yin)
+double NLEQSolver::solve()
 {
     Log(Logger::LOG_DEBUG) << "NLEQSolver::solve";
 
@@ -90,7 +90,7 @@ double NLEQSolver::solve(const vector<double>& yin)
 //     nleq->relativeTolerance = getValue("relative_tolerance");
 //     nleq->minDamping = getValue("minimum_damping");
 
-    double result = nleq->solve(yin);
+    double result = nleq->solve();
     delete nleq;
     return result;
 }

source/NLEQSolver.h

@@ -88,7 +88,7 @@ class RR_DECLSPEC NLEQSolver : public SteadyStateSolver
         static std::string getNLEQHint();
 
         // ** Solver routines
-        double solve(const vector<double>& yin);
+        double solve();
 
     private:
         ExecutableModel *model; // Model generated from the SBML. Static so we can access it from standalone function

source/SBMLValidator.cpp

@@ -109,8 +109,29 @@ static bool isStoichDefined(const SpeciesReference* s) {
 bool isStoichDefined(const std::string sbml) {
     SBMLDocument *doc = NULL;
 
-    if(sbml.substr(0,5) != "<?xml")
-      throw std::runtime_error("SBML document must begin with an XML declaration");
+    bool sbml_decl_okay = false;
+
+    // check for <?xml
+    size_t pos = sbml.find("<");
+    if (pos != std::string::npos) {
+      pos = sbml.find("?", pos+1);
+      if (pos != std::string::npos) {
+        pos = sbml.find("xml", pos+1);
+        if (pos != std::string::npos)
+          sbml_decl_okay = true;
+      }
+    }
+
+    // check for <sbml
+    pos = sbml.find("<");
+    if (pos != std::string::npos) {
+      pos = sbml.find("sbml", pos+1);
+      if (pos != std::string::npos)
+        sbml_decl_okay = true;
+    }
+
+    if (!sbml_decl_okay)
+      throw std::runtime_error("SBML document must begin with an XML declaration or an SBML declaration");
 
     try {
         doc =  readSBMLFromString (sbml.c_str());

source/Solver.cpp

@@ -207,6 +207,7 @@ namespace rr
     {
         std::stringstream ss;
         ss << "< roadrunner.Solver() >\n";
+        ss << "  name: " << getName() << "\n";
         ss << "  settings:\n";
         ss << getSettingsRepr();
         return ss.str();
@@ -215,7 +216,7 @@ namespace rr
     std::string Solver::toRepr() const
     {
         std::stringstream ss;
-        ss << "< roadrunner.Solver() " << settingsPyDictRepr() << " >\n";
+        ss << "< roadrunner.Solver() \"" << getName() << "\" " << settingsPyDictRepr() << " >\n";
         return ss.str();
     }
 }