Merge branch 'hotfix-0.57.1'

CHANGES

@@ -3,6 +3,11 @@ QUESO: Quantification of Uncertainty for Estimation,
 Simulation, and Optimization.
 -----------------------------------------------------
 
+Version 0.57.1 (Jun 23, 2017)
+  * Fix bug in GPMSA getpot parse
+  * GCC 4.4 compatibility fixes
+  * Fix boost macro bug in build system
+
 Version 0.57.0 (Apr 22, 2017)
   * Add methods to calculate normalized GP parameters
   * GCC-4.4.7 compatibility fixes

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.57.0], [[email protected]])
+AC_INIT([queso], [0.57.1], [[email protected]])
 PACKAGE_DESCRIPTION="The parallel C++ statistical library QUESO: Quantification of uncertainty for estimation, simulation and optimization"
 AC_SUBST([PACKAGE_DESCRIPTION])
 PACKAGE_URL="https://github.com/libqueso/queso"
@@ -97,8 +97,12 @@ AC_ARG_ENABLE([boost-program-options],
               AS_HELP_STRING([--disable-boost-program-options], [Disables use
                               of boost program options for parsing the QUESO
                               input file.  GetPot will be used instead.]),
-              [enable_program_options="no"],
-              [enable_program_options="yes"])
+              [case "${enableval}" in
+               yes) enable_program_options=yes ;;
+               no)  enable_program_options=no ;;
+               *)   AC_MSG_ERROR(bad value ${enableval} for --disable-boost-program-options) ;;
+              esac],
+              [enable_program_options=yes])
 
 #-------------------
 # Compilers and MPI
@@ -195,8 +199,7 @@ AS_IF([test "x$enable_program_options" != "xno"],
 
 AS_IF([test "x$enable_program_options" = "xno"],
       [
-       QUESO_CPPFLAGS="$QUESO_CPPFLAGS -DDISABLE_BOOST_PROGRAM_OPTIONS"
-       AC_SUBST(QUESO_CPPFLAGS)
+       AC_DEFINE(DISABLE_BOOST_PROGRAM_OPTIONS, 1, [Flag determining whether boost program options is disabled])
       ])
 
 BOOST_FIND_HEADER([boost/scoped_ptr.hpp])

src/basic/inc/ScalarFunction.h

@@ -158,7 +158,7 @@ class BaseScalarFunction {
   const VectorSet<V, M> & m_domainSet;
 
 private:
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   //! Input parser
   ScopedPtr<BoostInputOptionsParser>::Type m_parser;
 #endif

src/basic/src/ScalarFunction.C

@@ -22,13 +22,14 @@
 //
 //-----------------------------------------------------------------------el-
 
+#include <queso/config_queso.h>
 #include <queso/ScalarFunction.h>
 #include <queso/VectorSet.h>
 #include <queso/VectorSpace.h>
 #include <queso/GslVector.h>
 #include <queso/GslMatrix.h>
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #include <queso/BoostInputOptionsParser.h>
 #else
 #include <queso/getpot.h>
@@ -47,15 +48,15 @@ BaseScalarFunction<V, M>::BaseScalarFunction(const char * prefix,
   : m_env(domainSet.env()),
     m_prefix((std::string)(prefix) + "func_"),
     m_domainSet(domainSet),
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
     m_parser(new BoostInputOptionsParser(m_env.optionsInputFileName())),
 #endif
     m_fdStepSize(1, std::atof(QUESO_BASESCALARFN_FD_STEPSIZE_ODV))
 {
   unsigned int dim = m_domainSet.vectorSpace().dimLocal();
 
   // Snarf fd step size from input file.
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   m_parser->registerOption<std::string>(m_prefix + "fdStepSize",
                                         QUESO_BASESCALARFN_FD_STEPSIZE_ODV,
                                         "step size for finite difference");

src/basic/src/SequenceStatisticalOptions.C

@@ -25,9 +25,9 @@
 #include <queso/Defines.h>
 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #include <boost/program_options.hpp>
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 #include <queso/SequenceStatisticalOptions.h>
 #include <queso/Miscellaneous.h>

src/core/inc/BoostInputOptionsParser.h

@@ -21,7 +21,8 @@
 // Boston, MA  02110-1301  USA
 //
 //-----------------------------------------------------------------------el-
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#include <queso/config_queso.h>
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 #ifndef UQ_BOOST_INPUT_OPTIONS_H
 #define UQ_BOOST_INPUT_OPTIONS_H
@@ -106,4 +107,4 @@ class BoostInputOptionsParser : public BaseInputOptionsParser
 
 #endif  // UQ_BOOST_INPUT_OPTIONS_H
 
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS

src/core/inc/Environment.h

@@ -38,15 +38,15 @@
 #include <fstream>
 
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 // Forward declarations
 namespace boost {
   namespace program_options {
     class options_description;
     class variables_map;
     }
 }
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 namespace QUESO {
 
@@ -340,25 +340,25 @@ class BaseEnvironment {
   void    setOptionsInputFileAccessState(bool newState) const; // Yes, 'const'
 
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #ifdef UQ_USES_COMMAND_LINE_OPTIONS
   const boost::program_options::options_description& allOptionsDesc () const;
 #endif
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   //! Access function to private attribute m_allOptionsMap. It is an instance of boost::program_options::variables_map(), which
   //! allows concrete variables to map which store variables in real map.
   boost::program_options::variables_map&      allOptionsMap () const;
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   //! This method scans the input file provided by the user to QUESO.
   /*! It checks if no input file is passed and updates the private attribute m_allOptionsDesc, which
    * keeps all the options.*/
   void    scanInputFileForMyOptions(const boost::program_options::options_description& optionsDesc) const;
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
   //! Access function to private attribute m_displayVerbosity. It manages how much information will be
   //! release during the use of the QUESO library.
@@ -446,10 +446,10 @@ class BaseEnvironment {
 
   std::string m_optionsInputFileName;
   mutable bool m_optionsInputFileAccessState; // Yes, 'mutable'
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   ScopedPtr<boost::program_options::options_description>::Type m_allOptionsDesc;
   ScopedPtr<boost::program_options::variables_map>::Type m_allOptionsMap;
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   ScopedPtr<GetPot>::Type m_input;
 
   unsigned int m_subId;

src/core/inc/EnvironmentOptions.h

@@ -29,9 +29,10 @@
 #include <set>
 #include <vector>
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#include <queso/config_queso.h>
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #include <queso/BoostInputOptionsParser.h>
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 #include <queso/ScopedPtr.h>
 
@@ -55,14 +56,14 @@
 #define UQ_ENV_NUM_DEBUG_PARAMS_ODV         0
 #define UQ_ENV_DEBUG_PARAM_ODV              0.
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 // Forward declarations
 namespace boost {
   namespace program_options {
     class options_description;
     }
 }
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 namespace QUESO {
 
@@ -172,9 +173,9 @@ class EnvOptionsValues
 private:
   const BaseEnvironment * m_env;
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   ScopedPtr<BoostInputOptionsParser>::Type m_parser;
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
   //! Input file option name for flagging helpful printing output
   std::string m_option_help;
@@ -262,13 +263,13 @@ class EnvironmentOptions
   EnvOptionsValues  m_ov;
 
 private:
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   //! Define my environment options as the default options
   void   defineMyOptions  (boost::program_options::options_description& optionsDesc) const;
 
   //! Gets the option values of the environment.
   void   getMyOptionValues(boost::program_options::options_description& optionsDesc);
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
   //! Environment.
   const BaseEnvironment& m_env;
@@ -280,9 +281,9 @@ class EnvironmentOptions
   /*! Uses boost::program_options::options_description. A set of option descriptions.
    * This provides convenient interface for adding new option method, and facilities
    * to search for options by name.*/
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   ScopedPtr<boost::program_options::options_description>::Type m_optionsDesc;
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
   std::string              m_option_help;
 

src/core/inc/InfiniteDimensionalMCMCSamplerOptions.h

@@ -26,11 +26,11 @@
 
 #include <queso/Environment.h>
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #include <queso/BoostInputOptionsParser.h>
 #else
 #include <queso/getpot.h>
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 namespace QUESO {
 
@@ -83,9 +83,9 @@ class InfiniteDimensionalMCMCSamplerOptions
   const BaseEnvironment& env() const;
 
 private:
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   BoostInputOptionsParser * m_parser;
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
   const BaseEnvironment& m_env;
 

src/core/src/BoostInputOptionsParser.C

@@ -22,7 +22,8 @@
 //
 //-----------------------------------------------------------------------el-
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#include <queso/config_queso.h>
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #include <boost/program_options.hpp>
 
 #include <queso/BoostInputOptionsParser.h>
@@ -176,4 +177,4 @@ template void BoostInputOptionsParser::getOption<std::vector<unsigned int, std::
 template void BoostInputOptionsParser::getOption<std::vector<double, std::allocator<double> > >(const std::string&, std::vector<double, std::allocator<double> >&) const;
 
 }  // End namespace QUESO
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS

src/core/src/Environment.C

@@ -24,9 +24,9 @@
 
 #include <queso/Environment.h>
 
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #include <boost/program_options.hpp>
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
 #include <queso/getpot.h>
 
@@ -153,10 +153,10 @@ BaseEnvironment::BaseEnvironment(
   m_fullCommSize               (1),
   m_optionsInputFileName       (""),
   m_optionsInputFileAccessState(true),
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   m_allOptionsDesc             (),
   m_allOptionsMap              (),
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   m_input                      (new GetPot),
   m_subComm                    (),
   m_subRank                    (-1),
@@ -192,10 +192,10 @@ BaseEnvironment::BaseEnvironment(
   m_fullCommSize               (1),
   m_optionsInputFileName       (passedOptionsInputFileName),
   m_optionsInputFileAccessState(true),
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   m_allOptionsDesc             (),
   m_allOptionsMap              (),
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
   m_input                      (new GetPot),
   m_subComm                    (),
   m_subRank                    (-1),
@@ -369,7 +369,7 @@ BaseEnvironment::setOptionsInputFileAccessState(bool newState) const
   return;
 }
 //-------------------------------------------------------
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 #ifdef UQ_USES_COMMAND_LINE_OPTIONS
 const boost::program_options::options_description&
 BaseEnvironment::allOptionsDesc() const
@@ -379,9 +379,9 @@ BaseEnvironment::allOptionsDesc() const
   return *m_allOptionsDesc;
 }
 #endif
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 //-------------------------------------------------------
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 boost::program_options::variables_map&
 BaseEnvironment::allOptionsMap() const
 {
@@ -390,9 +390,9 @@ BaseEnvironment::allOptionsMap() const
   queso_require_msg(m_allOptionsMap, "m_allOptionsMap variable is NULL");
   return *m_allOptionsMap;
 }
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 //-------------------------------------------------------
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 void
 BaseEnvironment::scanInputFileForMyOptions(const boost::program_options::options_description& optionsDesc) const
 {
@@ -444,7 +444,7 @@ BaseEnvironment::scanInputFileForMyOptions(const boost::program_options::options
 
   return;
 }
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 //-----------------------------------------------------
 unsigned int
 BaseEnvironment::displayVerbosity() const
@@ -1235,10 +1235,10 @@ FullEnvironment::construct (RawType_MPI_Comm inputComm,
     // If there's an input file, we grab the options from there.  Otherwise the
     // defaults are used
     if (m_optionsInputFileName != "") {
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
       m_allOptionsMap.reset(new boost::program_options::variables_map());
       m_allOptionsDesc.reset(new boost::program_options::options_description("Allowed options"));
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
       readOptionsInputFile();
 
@@ -1516,10 +1516,10 @@ FullEnvironment::construct (const char *prefix)
     // If there's an input file, we grab the options from there.  Otherwise the
     // defaults are used
     if (m_optionsInputFileName != "") {
-#ifndef DISABLE_BOOST_PROGRAM_OPTIONS
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
       m_allOptionsMap.reset(new boost::program_options::variables_map());
       m_allOptionsDesc.reset(new boost::program_options::options_description("Allowed options"));
-#endif  // DISABLE_BOOST_PROGRAM_OPTIONS
+#endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
       readOptionsInputFile();