Gambit light sync

.github/workflows/ci_linux.yml

@@ -1,4 +1,4 @@
-name: Gambit-light Linux CI on Wino
+name: Gambit-light Linux CI
 
 on:
   push:

Backends/include/gambit/Backends/backend_macros.hpp

@@ -284,7 +284,9 @@ namespace Gambit
             << "which is supposed to contain the factory for class " << std::endl               \
             << fixns(STRINGIFY(BARENAME) STRINGIFY(CONVERT_VARIADIC_ARG(ARGS)))<<", "<<std::endl\
             << "is missing or catastrophically broken." << std::endl                            \
-            << "Fix or find that backend yo -- or don't use the type." << std::endl;            \
+            << "If running gambit with the -b flag, this backend is required to " << std::endl  \
+            << "run this yaml file or check what other backends are also required." << std::endl\
+            << "Otherwise, fix or find that backend -- or don't use the type." << std::endl;    \
         backend_error().raise(LOCAL_INFO BOOST_PP_COMMA() err.str());                           \
         return NULL;                                                                            \
       }                                                                                         \

Core/include/gambit/Core/depresolver.hpp

@@ -77,6 +77,7 @@ namespace Gambit
     {
       VertexID vertex;
       str purpose;
+      bool critical;
     };
 
     /// Information in resolution queue
@@ -88,6 +89,7 @@ namespace Gambit
       VertexID toVertex;
       int dependency_type;
       bool printme;
+      bool critical;
       const Observable* obslike;
     };
 
@@ -163,6 +165,10 @@ namespace Gambit
         /// Non-null only if the functor corresponds to an ObsLike entry in the ini file.
         const str& getPurpose(VertexID);
 
+        /// Returns whether a given functor is critical
+        /// True only if the functor corresponds to a critical ObsLike entry in the ini file.
+        bool getCritical(VertexID);
+
         /// Tell functor that it invalidated the current point in model space (due to a large or NaN contribution to lnL)
         void invalidatePointAt(VertexID, bool);
 

Core/include/gambit/Core/observable.hpp

@@ -65,6 +65,9 @@ namespace Gambit
       /// Instruction to printer as to whether to write result to disk.
       bool printme;
 
+      /// Allowed to invalidate a point.
+      bool critical;
+
       /// Whether or not to log matches to the observable with functors.
       bool log_matches;
 
@@ -100,6 +103,7 @@ namespace Gambit
         functionChain(),
         subcaps(),
         printme(true),
+        critical(false),
         log_matches(true),
         include_all(false)
       {}

Core/src/depresolver.cpp

@@ -256,12 +256,13 @@ namespace Gambit
       for (const Observable& obslike : obslikes)
       {
         // Format output
-        logger() << LogTags::dependency_resolver << endl << obslike.capability << " (" << obslike.type << ") [" << obslike.purpose << "]";
+        logger() << LogTags::dependency_resolver << endl << obslike.capability << " (" << obslike.type << ") [" << obslike.purpose << "] critical:" << obslike.critical << "";
         QueueEntry target;
         target.quantity.first = obslike.capability;
         target.quantity.second = obslike.type;
         target.obslike = &obslike;
         target.printme = obslike.printme;
+        target.critical = obslike.critical;
         resolutionQueue.push(target);
       }
       logger() << EOM;
@@ -333,11 +334,11 @@ namespace Gambit
       makeFunctorsModelCompatible();
 
       graph_traits<MasterGraphType>::vertex_iterator vi, vi_end;
-      const str formatString = "%-20s %-32s %-32s %-32s %-15s %-7i %-5i %-5i\n";
+      const str formatString = "%-20s %-32s %-32s %-32s %-15s %-5i %-7i %-5i %-5i\n";
       logger() << LogTags::dependency_resolver << endl << "Vertices registered in masterGraph" << endl;
       logger() << "----------------------------------" << endl;
       logger() << boost::format(formatString)%
-       "MODULE"% "FUNCTION"% "CAPABILITY"% "TYPE"% "PURPOSE"% "STATUS"% "#DEPs"% "#BE_REQs";
+       "MODULE"% "FUNCTION"% "CAPABILITY"% "TYPE"% "PURPOSE"% "CRITICAL"% "STATUS"% "#DEPs"% "#BE_REQs";
       for (std::tie(vi, vi_end) = vertices(masterGraph); vi != vi_end; ++vi)
       {
         logger() << boost::format(formatString)%
@@ -346,6 +347,7 @@ namespace Gambit
          (*masterGraph[*vi]).capability()%
          (*masterGraph[*vi]).type()%
          (*masterGraph[*vi]).purpose()%
+         (*masterGraph[*vi]).critical()%
          (*masterGraph[*vi]).status()%
          (*masterGraph[*vi]).dependencies().size()%
          (*masterGraph[*vi]).backendreqs().size();
@@ -707,6 +709,17 @@ namespace Gambit
       return none;
     }
 
+    /// Return whether a given functor is critical.
+    bool DependencyResolver::getCritical(VertexID v)
+    {
+      for (const OutputVertex& ov : outputVertices)
+      {
+        if (ov.vertex == v) return ov.critical;
+      }
+      /// critical can safely be false if the functor does not correspond to an ObsLike entry in the ini file.
+      return false;
+    }
+
     /// Tell functor that it invalidated the current point in model space (due to a large or NaN contribution to lnL)
     void DependencyResolver::invalidatePointAt(VertexID vertex, bool isnan)
     {
@@ -1569,7 +1582,8 @@ namespace Gambit
           else // if output vertex
           {
             outVertex.vertex = fromVertex;
-            outVertex.purpose = entry.obslike->purpose;;
+            outVertex.purpose = entry.obslike->purpose;
+            outVertex.critical = entry.obslike->critical;
             outputVertices.push_back(outVertex);
             // Don't need subcaps during dry-run
             if (not boundCore->show_runorder)

Core/src/likelihood_container.cpp

@@ -91,11 +91,11 @@ namespace Gambit
     // Set the ScanID
     set_scanID();
 
-    // Find subset of vertices that match requested purpose
+    // Find subset of vertices that match requested purpose, or are critical observables
     auto all_vertices = dependencyResolver.getObsLikeOrder();
     for (auto it = all_vertices.begin(); it != all_vertices.end(); ++it)
     {
-      if (dependencyResolver.getPurpose(*it) == purpose)
+      if (dependencyResolver.getPurpose(*it) == purpose || dependencyResolver.getCritical(*it) == true)
       {
         return_types[*it] = dependencyResolver.checkTypeMatch(*it, purpose, allowed_types_for_purpose);
         target_vertices.push_back(std::move(*it));
@@ -279,6 +279,11 @@ namespace Gambit
               lnlike += *jt;
             }
           }
+          else if (dependencyResolver.getCritical(*it) == true)
+          {
+            // Don't throw an error if the target vertex is a critical obslike,
+            // but don't add it to the total LogLike
+          }
           else core_error().raise(LOCAL_INFO, "Unexpected target functor type.");
 
           // Print debug info

Core/src/yaml_parser.cpp

@@ -212,6 +212,7 @@ namespace YAML
       const std::string key = entry.first.as<std::string>(); 
       if      (key == "purpose")          rhs.purpose        = entry.second.as<std::string>();
       else if (key == "capability")       rhs.capability     = entry.second.as<std::string>();
+      else if (key == "critical")         rhs.critical       = entry.second.as<bool>();
       else if (key == "type")             rhs.type           = entry.second.as<std::string>();
       else if (key == "function")         rhs.function       = entry.second.as<std::string>();
       else if (key == "module")           rhs.module         = entry.second.as<std::string>();

Elements/include/gambit/Elements/functors.hpp

@@ -165,6 +165,8 @@ namespace Gambit
       virtual void setInUse(bool){};
       /// Setter for purpose (relevant only for next-to-output functors)
       void setPurpose(str);
+      /// Setter for critical (relevant only for next-to-output functors)
+      void setCritical(bool);
       /// Setter for vertex ID (used in printer system)
       void setVertexID(int);
       /// Set ID for timing 'vertex' (used in printer system)
@@ -197,6 +199,8 @@ namespace Gambit
       sspair quantity() const;
       /// Getter for purpose (relevant for output nodes, aka helper structures for the dep. resolution)
       str purpose() const;
+      /// Getter for critical (relevant for output nodes, aka helper structures for the dep. resolution)
+      bool critical() const;
       /// Getter for the citation key
       str citationKey() const;
       /// Getter for vertex ID
@@ -410,6 +414,8 @@ namespace Gambit
       str myOrigin;
       /// Purpose of the function (relevant for output and next-to-output functors)
       str myPurpose;
+      /// critical flag of the function (relevant for output and next-to-output functors)
+      bool myCritical;
       /// Citation key: BibTex key of the reference.
       str myCitationKey;
       /// Bound model functor claw, for checking relationships between models
@@ -600,7 +606,7 @@ namespace Gambit
       virtual std::set<sspair> model_conditional_backend_reqs_exact (str model);
 
       /// Add and activate unconditional dependencies.
-      void setDependency(str, str, void(*)(functor*, module_functor_common*), str purpose= "");
+      void setDependency(str, str, void(*)(functor*, module_functor_common*), str purpose= "", bool critical=false);
 
       /// Add conditional dependency-type pairs in advance of later conditions.
       void setConditionalDependency(str, str);

Elements/src/functors.cpp

@@ -104,6 +104,9 @@ namespace Gambit
     /// Setter for purpose (relevant only for next-to-output functors)
     void functor::setPurpose(str purpose) { myPurpose = purpose; }
 
+    /// Setter for critical flag (relevant only for next-to-output functors)
+    void functor::setCritical(bool critical) { myCritical = critical; }
+
     /// Setter for vertex ID (used in printer system)
     void functor::setVertexID(int ID) { myVertexID = ID; }
 
@@ -145,6 +148,8 @@ namespace Gambit
     sspair functor::quantity() const { return std::make_pair(myCapability, myType); }
     /// Getter for purpose (relevant for output nodes, aka helper structures for the dep. resolution)
     str functor::purpose()     const { return myPurpose; }
+    /// Getter for critical (relevant for output nodes, aka helper structures for the dep. resolution)
+    bool functor::critical()   const { return myCritical; }
     /// Getter for citation key
     str functor::citationKey() const { return myCitationKey; }
     /// Getter for vertex ID
@@ -1166,12 +1171,13 @@ namespace Gambit
     }
 
     /// Add and activate unconditional dependencies.
-    void module_functor_common::setDependency(str dep, str dep_type, void(*resolver)(functor*, module_functor_common*), str purpose)
+    void module_functor_common::setDependency(str dep, str dep_type, void(*resolver)(functor*, module_functor_common*), str purpose, bool critical)
     {
       sspair key (dep, Utils::fix_type(dep_type));
       myDependencies.insert(key);
       dependency_map[key] = resolver;
       this->myPurpose = purpose; // only relevant for output nodes
+      this->myCritical = critical; // only relevant for output nodes
     }
 
     /// Add conditional dependency-type pairs in advance of later conditions.
@@ -1529,6 +1535,8 @@ namespace Gambit
         if (dependency_map.find(key) != dependency_map.end()) (*dependency_map[key])(dep_functor,this);
         // propagate purpose from next to next-to-output nodes
         dep_functor->setPurpose(this->myPurpose);
+        // propagate critical from next to next-to-output nodes
+        dep_functor->setCritical(this->myCritical);
         // propagate this functor's dependees and subcaps on to the resolving functor
         dep_functor->notifyOfDependee(this);
         // save the pointer to the resolving functor to allow this functor to notify it of future dependees

Logs/src/logging.cpp

@@ -194,7 +194,7 @@ namespace Gambit
        //std::cout<<"Sorting tags..."<<std::endl;
        for(std::set<int>::iterator tag = mail.tags.begin(); tag != mail.tags.end(); ++tag)
        {
-         // Debugging crap... to be deleted.
+         // Debugging stuff... to be deleted.
          // std::cout<<"Sorting tag "<<tag2str()[*tag]<<std::endl;
          // std::cout<<"empty?"<<components().empty()<<std::endl;
          // for(std::set<int>::iterator tag2 = components().begin(); tag2 != components().end(); ++tag2)

Printers/include/gambit/Printers/printers/hdf5printer/hdf5tools.hpp

@@ -6,7 +6,7 @@
 ///  HDF5 databases.
 ///
 ///  Currently I am using the C++ bindings for
-///  HDF5, however they are a bit crap and it may
+///  HDF5, however they not great and it may
 ///  be better to just write our own.
 ///
 ///  *********************************************

Printers/src/printers/hdf5printer/hdf5tools.cpp

@@ -6,7 +6,7 @@
 ///  HDF5 databases.
 ///
 ///  Currently I am using the C++ bindings for
-///  HDF5, however they are a bit crap and it may
+///  HDF5, however they not great and it may
 ///  be better to just write our own.
 ///
 ///  *********************************************

ScannerBit/include/gambit/ScannerBit/plugin_interface.hpp

@@ -176,7 +176,7 @@ namespace Gambit
                 template <typename... args>
                 auto operator()(args&... params) -> typename find_variadic_type <void (args...), T...>::ret_type
                 {
-                    static_assert(find_variadic_type <void (args...), T...>::value, "\n\033[00;31;1mPlugin Interface:  Entered argument types do not match any of the plugin mains' argument types.\033[00m\n");
+                    static_assert(find_variadic_type <void (args...), T...>::value, "\n\u001B[00;31;1mPlugin Interface:  Entered argument types do not match any of the plugin mains' argument types.\u001B[00m\n");
                     return Plugin_Main_Interface_Base<typename find_variadic_type <void (args...), T...>::func_type>::operator()(params...);
                 }
             };

ScannerBit/include/gambit/ScannerBit/scanners/diver_1.0.5/diver.hpp

@@ -0,0 +1,50 @@
+//  GAMBIT: Global and Modular BSM Inference Tool
+//  *********************************************
+///  \file
+///
+///  ScannerBit interface to Diver 1.0.5
+///
+///  Header file
+///
+///  *********************************************
+///
+///  Authors (add name and date if you modify):
+///
+///  \author Pat Scott
+///          (p.scott@imperial.ac.uk)
+///  \date 2019 Dec
+///
+///  *********************************************
+
+#ifndef __diver_hpp__
+#define __diver_hpp__
+
+#include "gambit/ScannerBit/scanner_plugin.hpp"
+
+// C++ prototype of the main run_de function for Diver.
+extern "C" void cdiver(double (*)(double[], const int, int&, bool&, const bool, void*&), int, const double[], const double[],
+		       const char[], int, int, const int[], bool, const int, const int, int, int, const double[], double,
+		       double, bool, bool, int, bool, bool, double, int, bool, bool, double(*)(const double[], const int, void*&),
+		       double, double, int, bool, bool, int, bool, int, double, int, void*&, int);
+
+namespace Gambit
+{
+
+  namespace Diver_1_0_5
+  {
+
+    /// Structure for passing likelihood and printer data through Diver to the objective function.
+    struct diverScanData
+    {
+      Scanner::like_ptr likelihood_function;
+      Scanner::printer_interface* printer;
+    };
+
+    /// Function to be minimised by Diver
+    double objective(double params[], const int param_dim, int &fcall, bool &quit, const bool validvector, void*& context);
+
+  }
+
+}
+
+#endif // #defined __diver_hpp__