Merge pull request #208 from SwissTPH/c++11

Update to C++11

CMakeLists.txt

@@ -18,13 +18,12 @@ set (CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
 
 # -----  Compile options  -----
 
-# C++11 would be nice, but we have to compile for relatively old platforms
 if (NOT MSVC)
   # Enable builds on Raspberry pi (although without optimizations)
   if (${CMAKE_SYSTEM_PROCESSOR} MATCHES "^arm")
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++98")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
   else (${CMAKE_SYSTEM_PROCESSOR} MATCHES "^arm")
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++98 -msse2 -mfpmath=sse")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -msse2 -mfpmath=sse")
   endif (${CMAKE_SYSTEM_PROCESSOR} MATCHES "^arm")
 endif (NOT MSVC)
 

doc/coding practices.markdown

@@ -65,14 +65,12 @@ Memory management
 There are two forms of memory management in C++:
 
 *   do-it-yourself C-style with pointers
-*   managed containers: vector, auto_ptr, etc.
+*   managed containers: vector, unique_ptr, etc.
 
 I've tended towards the latter. Usually it's possible to arrange data into a
 hierarchical structure, and in this case these containers will do most of the
 work.
 
-There is however one caveat to watch out for: auto_ptr doesn't have the usual
-copy semantics, and so cannot be used in lists (std::vector, std::map, etc.)!
-There are several ways of getting around this: boost::shared_ptr, storing
-pointers in lists rather than the objects themselves (boost::ptr_container is
-useful for this, since at some point the objects also need to be deleted).
+TODO: boost::shared_ptr has been used in the past to get around the limitations
+of `std::auto_ptr`; now that we are using a later C++ standard we can migrate
+away from some of these BOOST facilities.

model/Clinical/CMDecisionTree.cpp

@@ -414,6 +414,7 @@ class CMDTDeploy : public CMDecisionTree, interventions::HumanIntervention {
 // ———  static functions  ———
 
 // Memory management: lists all decisions and frees memory at program exit
+// TODO: use C++11 move semantics
 ptr_vector<CMDecisionTree> decision_library;
 
 // Saves a decision to decision_library, making it const.

model/Clinical/ClinicalModel.cpp

@@ -56,7 +56,7 @@ void ClinicalModel::init( const Parameters& parameters, const scnXml::Scenario&
         if( scenario.getHealthSystem().getImmediateOutcomes().present() ){
             opt_imm_outcomes = true;
 
-            if( util::CommandLine::DEPRECATION_WARNINGS ){
+            if( util::CommandLine::option(util::CommandLine::DEPRECATION_WARNINGS) ){
                 cerr << "Deprecation warning: healthSystem: use of ImmediateOutcomes can be replaced by the more flexible DecisionTree5Day (optional)" << endl;
             }
         }

model/Clinical/ESCaseManagement.h

@@ -26,12 +26,6 @@
 #include "WithinHost/WHInterface.h"
 #include "schema/pharmacology.h"
 
-#include <cassert>
-#include <list>
-#include <limits>
-#include <boost/ptr_container/ptr_unordered_map.hpp>
-#include <boost/ptr_container/ptr_vector.hpp>
-
 namespace OM { namespace Clinical {
 using WithinHost::WHInterface;
 

model/Host/Human.cpp

@@ -123,10 +123,8 @@ bool Human::update(bool doUpdate) {
                 // report removal due to expiry
                 mon::reportEventMHI( mon::MHR_SUB_POP_REM_TOO_OLD, *this, 1 );
                 m_cohortSet = mon::updateCohortSet( m_cohortSet, expIt->first, false );
-                // erase element, but continue iteration (note: this is simpler in C++11)
-                map<ComponentId,SimTime>::iterator toErase = expIt;
-                ++expIt;
-                m_subPopExp.erase( toErase );
+                // erase element, but continue iteration
+                expIt = m_subPopExp.erase( expIt );
             }else{
                 ++expIt;
             }

model/PkPd/Drug/LSTMDrugType.cpp

@@ -42,7 +42,7 @@ using WithinHost::Genotypes;
 // -----  Static variables and functions  -----
 
 // The list of drugTypes drugs. Not checkpointed.
-//TODO: do we need to store by pointer?
+// TODO: use C++11 move semantics
 typedef boost::ptr_vector<LSTMDrugType> DrugTypesT;
 DrugTypesT drugTypes;
 map<string,size_t> drugTypeNames;
@@ -189,7 +189,7 @@ LSTMDrugType::LSTMDrugType (size_t index, const scnXml::PKPDDrug& drugData) :
         const scnXml::Conversion& conv = pk.getConversion().get();
         try{
             metabolite = findDrug(conv.getMetabolite());
-        }catch( util::xml_scenario_error e ){
+        }catch( util::xml_scenario_error& e ){
             throw util::xml_scenario_error( "PK: metabolite drug not found; metabolite must be defined *before* parent drug!" );
         }
         conversion_rate.setParams( conv.getRate() );

model/PkPd/Drug/LSTMDrugType.h

@@ -175,6 +175,7 @@ class LSTMDrugType {
     // TODO: at the moment we're storing all PK & PD data regardless of which
     // model is used. Evaluate whether this is sensible or not.
 
+    // TODO: use C++11 move semantics
     /* PD parameters (may vary based on infection genotype). */
     boost::ptr_vector<LSTMDrugPD> PD;
 
@@ -203,4 +204,4 @@ class LSTMDrugType {
 };
 
 } }
-#endif
+#endif

model/PkPd/LSTMModel.h

@@ -155,6 +155,7 @@ class LSTMModel {
     void checkpoint (istream& stream);
     void checkpoint (ostream& stream);
 
+    // TODO: use C++11 move semantics
     typedef ptr_vector<LSTMDrug> DrugVec;
     /// Drugs with non-zero blood concentrations:
     DrugVec m_drugs;
@@ -166,4 +167,4 @@ class LSTMModel {
 };
 
 } }
-#endif
+#endif

model/Population.h

@@ -75,6 +75,7 @@ class Population
 
     /// Type of population list. Store pointers to humans only to avoid copy
     /// operations which (AFAIAA) are otherwise required in C++98.
+    // TODO: use C++11 move semantics
     typedef boost::ptr_list<Host::Human> HumanPop;
     /// Iterator type of population
     typedef HumanPop::iterator Iter;

model/Simulator.cpp

@@ -53,8 +53,8 @@ bool Simulator::startedFromCheckpoint;  // static
 
 const char* CHECKPOINT = "checkpoint";
 
-std::auto_ptr<Population> sim::p_humanPop;
-std::auto_ptr<TransmissionModel> sim::p_transmission;
+std::unique_ptr<Population> sim::p_humanPop;
+std::unique_ptr<TransmissionModel> sim::p_transmission;
 
 enum Phase {
     STARTING_PHASE = 0,
@@ -111,9 +111,9 @@ Simulator::Simulator( util::Checksum ck, const scnXml::Scenario& scenario ) :
     // genotypes (both from Human, from Population::init()) and
     // Monitoring::AgeGroup (from Surveys.init()):
     // Note: PerHost dependency can be postponed; it is only used to set adultAge
-    sim::p_humanPop = auto_ptr<Population>(
+    sim::p_humanPop = unique_ptr<Population>(
             new Population( scenario.getDemography().getPopSize() ));
-    sim::p_transmission = auto_ptr<TransmissionModel>(
+    sim::p_transmission = unique_ptr<TransmissionModel>(
             TransmissionModel::createTransmissionModel(scenario.getEntomology(), sim::humanPop().size()) );
 
     // Depends on transmission model (for species indexes):

model/Transmission/Anopheles/AnophelesModel.cpp

@@ -249,7 +249,7 @@ void AnophelesModel::initVectorTrap(const scnXml::Description1& desc, size_t ins
     TrapParams params;
     params.relAvail = desc.getRelativeAvailability().getValue();
     params.availDecay= DecayFunction::makeObject(desc.getDecayOfAvailability(), "decayOfAvailability");
-    trapParams.push_back(params);
+    trapParams.push_back(move(params));
 }
 
 void AnophelesModel::deployVectorPopInterv (size_t instance){

model/Transmission/Anopheles/AnophelesModel.h

@@ -31,7 +31,6 @@
 
 #include <vector>
 #include <limits>
-#include <boost/shared_ptr.hpp>
 
 namespace OM {
 namespace Transmission {
@@ -82,6 +81,38 @@ class AnophelesModel
             nhh_sigma_dff(numeric_limits<double>::signaling_NaN())
     {}
 
+    AnophelesModel (AnophelesModel&& o):
+            humanBase(move(o.humanBase)),
+            mosqSeekingDuration(move(o.mosqSeekingDuration)),
+            mosqSeekingDeathRate(move(o.mosqSeekingDeathRate)),
+            probMosqSurvivalOvipositing(move(o.probMosqSurvivalOvipositing)),
+            nhh_avail(move(o.nhh_avail)),
+            nhh_sigma_df(move(o.nhh_sigma_df)),
+            nhh_sigma_dff(move(o.nhh_sigma_dff)),
+            trapParams(move(o.trapParams)),
+            transmission(move(o.transmission)),
+            seekingDeathRateIntervs(move(o.seekingDeathRateIntervs)),
+            probDeathOvipositingIntervs(move(o.probDeathOvipositingIntervs)),
+            baitedTraps(move(o.baitedTraps)),
+            partialEIR(move(o.partialEIR))
+    {}
+
+    void operator= (AnophelesModel&& o) {
+        humanBase = move(o.humanBase);
+        mosqSeekingDuration = move(o.mosqSeekingDuration);
+        mosqSeekingDeathRate = move(o.mosqSeekingDeathRate);
+        probMosqSurvivalOvipositing = move(o.probMosqSurvivalOvipositing);
+        nhh_avail = move(o.nhh_avail);
+        nhh_sigma_df = move(o.nhh_sigma_df);
+        nhh_sigma_dff = move(o.nhh_sigma_dff);
+        trapParams = move(o.trapParams);
+        transmission = move(o.transmission);
+        seekingDeathRateIntervs = move(o.seekingDeathRateIntervs);
+        probDeathOvipositingIntervs = move(o.probDeathOvipositingIntervs);
+        baitedTraps = move(o.baitedTraps);
+        partialEIR = move(o.partialEIR);
+    }
+
     /** Called to initialise variables instead of a constructor. At this point,
      * the size of the human population is known but that population has not
      * yet been constructed. Called whether data is loaded from a check-point
@@ -300,11 +331,13 @@ class AnophelesModel
     //@}
 
     struct TrapParams {
+        TrapParams(): relAvail(numeric_limits<double>::signaling_NaN()) {}
+        TrapParams(TrapParams&& o): relAvail(o.relAvail), availDecay(move(o.availDecay)) {}
+
         // Initial availability of a trap relative to an adult
         double relAvail;
         // Decay of availability
-        // note: can't use "auto_ptr" inside a vector, otherwise that would suffice
-        boost::shared_ptr<util::DecayFunction> availDecay;
+        unique_ptr<util::DecayFunction> availDecay;
     };
     // Parameters for trap interventions. Doesn't need checkpointing.
     vector<TrapParams> trapParams;

model/Transmission/Anopheles/FixedEmergence.cpp

@@ -58,7 +58,7 @@ void FixedEmergence::init2( double tsP_A, double tsP_df, double tsP_dff, double
     transmission.initState ( tsP_A, tsP_df, tsP_dff, initNvFromSv, initOvFromSv, forcedS_v );
 
     // Crude estimate of mosqEmergeRate: (1 - P_A(t) - P_df(t)) / (T * ρ_S) * S_T(t)
-    mosqEmergeRate = forcedS_v;
+    mosqEmergeRate = move(forcedS_v);
     vectors::scale (mosqEmergeRate, initNv0FromSv);
 
     // All set up to drive simulation from forcedS_v
@@ -112,7 +112,7 @@ bool FixedEmergence::initIterate (MosqTransmission& transmission) {
     FSRotateAngle -= rAngle;
     vectors::expIDFT (forcedS_v, FSCoeffic, FSRotateAngle);
     // We use the stored initXxFromYy calculated from the ideal population age-structure (at init).
-    mosqEmergeRate = forcedS_v;
+    mosqEmergeRate = move(forcedS_v);
     vectors::scale (mosqEmergeRate, initNv0FromSv);
 
     const double LIMIT = 0.1;

model/Transmission/Anopheles/MosqTransmission.cpp

@@ -63,17 +63,17 @@ void MosqTransmission::initialise ( const scnXml::AnophelesParams::LifeCycleOpti
             throw util::xml_scenario_error(
                 "VECTOR_LIFE_CYCLE_MODEL: requires <lifeCycle> element with "
                 "model parameters for each anopheles species");
-        emergence = boost::shared_ptr<EmergenceModel>( new LCEmergence() );
+        emergence = unique_ptr<EmergenceModel>( new LCEmergence() );
         emergence->initLifeCycle( lcOpt.get() );
         */
     }else if (util::ModelOptions::option( util::VECTOR_SIMPLE_MPD_MODEL )){
         if (!simpleMPDOpt.present())
             throw util::xml_scenario_error(
                 "VECTOR_SIMPLE_MPD_MODEL: requires <simpleMPD> element with "
                 "model parameters for each anopheles species");
-        emergence = boost::shared_ptr<EmergenceModel>(new SimpleMPDEmergence(simpleMPDOpt.get()) );
+        emergence = unique_ptr<EmergenceModel>(new SimpleMPDEmergence(simpleMPDOpt.get()) );
     }else
-        emergence = boost::shared_ptr<EmergenceModel>( new FixedEmergence() );
+        emergence = unique_ptr<EmergenceModel>( new FixedEmergence() );
 
 
     // -----  Set model variables  -----

model/Transmission/Anopheles/MosqTransmission.h

@@ -26,7 +26,6 @@
 #include "schema/entomology.h"
 
 #include <limits>
-#include <boost/shared_ptr.hpp>
 
 class MosqLifeCycleSuite;
 
@@ -53,6 +52,42 @@ class MosqTransmission {
     //@{
     MosqTransmission();
 
+    MosqTransmission (MosqTransmission&& o):
+            emergence(move(o.emergence)),
+            mosqRestDuration(move(o.mosqRestDuration)),
+            EIPDuration(move(o.EIPDuration)),
+            N_v_length(move(o.N_v_length)),
+            minInfectedThreshold(move(o.minInfectedThreshold)),
+            P_A(move(o.P_A)),
+            P_df(move(o.P_df)),
+            P_dif(move(o.P_dif)),
+            P_dff(move(o.P_dff)),
+            N_v(move(o.N_v)),
+            S_v(move(o.S_v)),
+            fArray(move(o.fArray)),
+            ftauArray(move(o.ftauArray)),
+            uninfected_v(move(o.uninfected_v)),
+            timeStep_N_v0(move(o.timeStep_N_v0))
+    {}
+
+    void operator= (MosqTransmission&& o) {
+            emergence = move(o.emergence);
+            mosqRestDuration = move(o.mosqRestDuration);
+            EIPDuration = move(o.EIPDuration);
+            N_v_length = move(o.N_v_length);
+            minInfectedThreshold = move(o.minInfectedThreshold);
+            P_A = move(o.P_A);
+            P_df = move(o.P_df);
+            P_dif = move(o.P_dif);
+            P_dff = move(o.P_dff);
+            N_v = move(o.N_v);
+            S_v = move(o.S_v);
+            fArray = move(o.fArray);
+            ftauArray = move(o.ftauArray);
+            uninfected_v = move(o.uninfected_v);
+            timeStep_N_v0 = move(o.timeStep_N_v0);
+    }
+
     /** Initialise parameters and variables.
      * 
      * This is only a fraction of parameter initialisation; see also
@@ -153,7 +188,7 @@ class MosqTransmission {
     /** @brief Emergence model
      * 
      * Code to calculate emergence of mosquitoes from water bodies goes here. */
-    boost::shared_ptr<EmergenceModel> emergence;
+    unique_ptr<EmergenceModel> emergence;
 
 private:
     // -----  parameters (constant after initialisation)  -----

model/Transmission/Anopheles/SimpleMPDEmergence.cpp

@@ -140,7 +140,7 @@ bool SimpleMPDEmergence::initIterate (MosqTransmission& transmission) {
     FSRotateAngle -= rAngle;
     vectors::expIDFT (forcedS_v, FSCoeffic, FSRotateAngle);
     // We use the stored initXxFromYy calculated from the ideal population age-structure (at init).
-    mosqEmergeRate = forcedS_v;
+    mosqEmergeRate = move(forcedS_v);
     vectors::scale (mosqEmergeRate, initNv0FromSv);
 
     // Finally, update nOvipositingDelayed and invLarvalResources

model/Transmission/PerHost.cpp

@@ -144,7 +144,7 @@ void PerHost::checkpointIntervs( istream& stream ){
                 throw util::base_exception( "" );       // see catch block below
             PerHostInterventionData *v = params->makeHumanPart( stream, id );
             activeComponents.push_back( v );
-        }catch( util::base_exception e ){
+        }catch( util::base_exception& e ){
             // two causes, both boil down to index being wrong
             throw util::checkpoint_error( "bad value in checkpoint file" );
         }

model/Transmission/PerHost.h

@@ -28,7 +28,6 @@
 #include "util/DecayFunction.h"
 #include "util/checkpoint_containers.h"
 #include <boost/ptr_container/ptr_list.hpp>
-#include <boost/shared_ptr.hpp>
 
 namespace OM {
 namespace Transmission {
@@ -280,6 +279,7 @@ class PerHost
     // entoAvailability param stored in HostMosquitoInteraction.
     double _relativeAvailabilityHet;
 
+    // TODO: use C++11 move semantics
     typedef boost::ptr_list<PerHostInterventionData> ListActiveComponents;
     ListActiveComponents activeComponents;
 

model/Transmission/VectorModel.cpp

@@ -166,7 +166,7 @@ VectorModel::VectorModel (const scnXml::Entomology& entoData,
     numSpecies = anophelesList.size();
     if (numSpecies < 1)
         throw util::xml_scenario_error ("Can't use Vector model without data for at least one anopheles species!");
-    species.resize (numSpecies, AnophelesModel());
+    species.resize (numSpecies);
 
     for(size_t i = 0; i < numSpecies; ++i) {
         string name = species[i].initialise (anophelesList[i],

model/WithinHost/Diagnostic.cpp

@@ -110,6 +110,7 @@ bool Diagnostic::isPositive( double dens ) const {
 
 // ———  diagnostics (static)  ———
 
+// TODO: use C++11 move semantics
 typedef boost::ptr_map<string,Diagnostic> Diagnostic_set;
 Diagnostic_set diagnostic_set;
 const Diagnostic* diagnostics::monitoring_diagnostic = 0;

model/WithinHost/Treatments.cpp

@@ -29,6 +29,7 @@ namespace WithinHost {
 
 // ———  static  ———
 
+// TODO: use C++11 move semantics
 boost::ptr_vector<Treatments> Treatments::treatments;
 
 TreatmentId Treatments::addTreatment( const scnXml::TreatmentOption& desc ){

model/WithinHost/Treatments.h

@@ -81,6 +81,7 @@ class Treatments : public interventions::TriggeredDeployments {
 
 private:
     // static:
+    // TODO: use C++11 move semantics
     static boost::ptr_vector<Treatments> treatments;
 
     // non-static: