More granular options parsing for Environment

src/core/inc/Environment.h

@@ -170,10 +170,27 @@ class BaseEnvironment {
   //! @name Constructor/Destructor methods
   //@{
   //! Default constructor.
-  BaseEnvironment(const char* passedOptionsInputFileName, EnvOptionsValues* alternativeOptionsValues);
+  /*!
+   * initialOptionsValues apply first, followed by any overrides
+   * present in passedOptionsInputFileName.  Historically the behavior was:
+   *   IF      alternative options passed in, use them exclusively
+   *   ELSE IF input file, parse and set options from it
+   *   ELSE    use default options
+   * so the input file was ignored when options object was passed in.
+   */
+  BaseEnvironment(const char* passedOptionsInputFileName, EnvOptionsValues* initialOptionsValues);
 
+  //! Alternate constructor.
+  /*!
+   * initialOptionsValues apply first, followed by any overrides
+   * present in passedOptionsInputFileName.  Historically the behavior was:
+   *   IF      alternative options passed in, use them exclusively
+   *   ELSE IF input file, parse and set options from it
+   *   ELSE    use default options
+   * so the input file was ignored when options object was passed in.
+   */
   BaseEnvironment(const std::string & passedOptionsInputFileName,
-                  EnvOptionsValues* alternativeOptionsValues);
+                  EnvOptionsValues* initialOptionsValues);
 
   //! Destructor
   /*! It deallocates memory and does other cleanup for the class object and its class members when
@@ -456,7 +473,7 @@ class EmptyEnvironment : public BaseEnvironment {
   //! @name Constructor/Destructor methods
   //@{
   //! Default constructor. Does nothing.
-  /*! It initialized BaseEnvironment with no input file and a NULL pointer for the alternativeOptionsValues.*/
+  /*! It initializes BaseEnvironment with no input file and default options */
   EmptyEnvironment();
 
   //! Destructor
@@ -484,26 +501,58 @@ class FullEnvironment : public BaseEnvironment {
    * Initializes the full communicator, reads the options, deals with multiple
    * sub-environments, e.g. dealing with sub/self/inter0-communicators, handles
    * path for output files.
+   *
+   * initialOptionsValues apply first, followed by any overrides
+   * present in passedOptionsInputFileName.  Historically the behavior was:
+   *   IF      alternative options passed in, use them exclusively
+   *   ELSE IF input file, parse and set options from it
+   *   ELSE    use default options
+   * so the input file was ignored when options object was passed in.
    */
 #ifdef QUESO_HAS_MPI
-  FullEnvironment(RawType_MPI_Comm inputComm, const char* passedOptionsInputFileName, const char* prefix, EnvOptionsValues* alternativeOptionsValues);
+  FullEnvironment(RawType_MPI_Comm inputComm, const char* passedOptionsInputFileName, const char* prefix, EnvOptionsValues* initialOptionsValues);
 
+  //! Parallel constructor.
+  /*!
+   * initialOptionsValues apply first, followed by any overrides
+   * present in passedOptionsInputFileName.  Historically the behavior was:
+   *   IF      alternative options passed in, use them exclusively
+   *   ELSE IF input file, parse and set options from it
+   *   ELSE    use default options
+   * so the input file was ignored when options object was passed in.
+   */
   FullEnvironment(RawType_MPI_Comm inputComm,
                   const std::string& passedOptionsInputFileName,
                   const std::string& prefix,
-                  EnvOptionsValues* alternativeOptionsValues);
+                  EnvOptionsValues* initialOptionsValues);
 #endif
 
   //! Serial constructor.
   /*!
    * No communicator is passed. Output path handling is exactly as in the
    * parallel ctor.
+   *
+   * initialOptionsValues apply first, followed by any overrides
+   * present in passedOptionsInputFileName.  Historically the behavior was:
+   *   IF      alternative options passed in, use them exclusively
+   *   ELSE IF input file, parse and set options from it
+   *   ELSE    use default options
+   * so the input file was ignored when options object was passed in.
    */
-  FullEnvironment(const char* passedOptionsInputFileName, const char* prefix, EnvOptionsValues* alternativeOptionsValues);
+  FullEnvironment(const char* passedOptionsInputFileName, const char* prefix, EnvOptionsValues* initialOptionsValues);
 
+  //! Serial constructor.
+  /*!
+   * initialOptionsValues apply first, followed by any overrides
+   * present in passedOptionsInputFileName.  Historically the behavior was:
+   *   IF      alternative options passed in, use them exclusively
+   *   ELSE IF input file, parse and set options from it
+   *   ELSE    use default options
+   * so the input file was ignored when options object was passed in.
+   */
   FullEnvironment(const std::string& passedOptionsInputFileName,
                   const std::string& prefix,
-                  EnvOptionsValues* alternativeOptionsValues);
+                  EnvOptionsValues* initialOptionsValues);
 
   //! Destructor
  ~FullEnvironment();
@@ -526,7 +575,7 @@ class FullEnvironment : public BaseEnvironment {
   void        construct(const char *prefix);
 
   //! Checks the options input file and reads the options.
-  void        readOptionsInputFile();
+  void        readOptionsInputFile(const std::string& prefix);
   //void        queso_terminate_handler();
 
 };

src/core/inc/EnvironmentOptions.h

@@ -94,6 +94,15 @@ class EnvOptionsValues
   //! Copy constructor
   EnvOptionsValues(const EnvOptionsValues& src);
 
+  //! Set parameter option names to begin with prefix
+  void set_prefix(const std::string& prefix);
+
+  //! Set default values for parameter options
+  void set_defaults();
+
+  //! Given prefix, read the input file for parameters named "prefix"+*
+  void parse(const BaseEnvironment& env, const std::string& prefix);
+
   //! Destructor
   virtual ~EnvOptionsValues();
   //@}

src/core/inc/InfiniteDimensionalMCMCSamplerOptions.h

@@ -47,9 +47,21 @@ namespace QUESO {
 class InfiniteDimensionalMCMCSamplerOptions
 {
 public:
+  //! Constructor
+  InfiniteDimensionalMCMCSamplerOptions();
+
   //! Given prefix, read the input file for parameters named prefix_*
   InfiniteDimensionalMCMCSamplerOptions(const BaseEnvironment& env, const char* prefix);
 
+  //! Set default values for parameter options
+  void set_defaults();
+
+  //! Set parameter option names to begin with prefix
+  void set_prefix(const std::string& prefix);
+
+  //! Given prefix, read the input file for parameters named "prefix"+*
+  void parse(const BaseEnvironment& env, const std::string& prefix);
+
   //! Destructor
   virtual ~InfiniteDimensionalMCMCSamplerOptions();
 
@@ -86,10 +98,10 @@ class InfiniteDimensionalMCMCSamplerOptions
 
 private:
 #ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
-  BoostInputOptionsParser * m_parser;
+  ScopedPtr<BoostInputOptionsParser>::Type m_parser;
 #endif  // QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
 
-  const BaseEnvironment& m_env;
+  const BaseEnvironment* m_env;
 
   std::string m_option_help;
   std::string m_option_dataOutputDirName;

src/core/inc/OptimizerOptions.h

@@ -71,6 +71,15 @@ class OptimizerOptions
   //! Copy constructor
   OptimizerOptions(const OptimizerOptions & rhs);
 
+  //! Set default values for parameter options
+  void set_defaults();
+
+  //! Set parameter option names to begin with prefix
+  void set_prefix(const std::string& prefix);
+
+  //! Given prefix, read the input file for parameters named "prefix"+*
+  void parse(const BaseEnvironment& env, const std::string& prefix);
+
   //! Destructor
   virtual ~OptimizerOptions();
   //@}
@@ -135,7 +144,9 @@ class OptimizerOptions
 private:
   const BaseEnvironment * m_env;
 
-  BoostInputOptionsParser * m_parser;
+#ifndef QUESO_DISABLE_BOOST_PROGRAM_OPTIONS
+  ScopedPtr<BoostInputOptionsParser>::Type m_parser;
+#endif
 
   // The input options as strings so we can parse the input file later
   std::string m_option_help;