Merge remote-tracking branch 'origin/develop' into aug23_mar3

Conflicts:
	core/src/ParaGridIO.cpp
	core/src/include/ModelComponent.hpp

core/src/DevGridIO.cpp

@@ -141,11 +141,11 @@ void dumpModelData(const ModelState& state, netCDF::NcGroup& dataGroup)
         const std::string& name = entry.first;
         if (entry.second.getType() == ModelArray::Type::H) {
             netCDF::NcVar var(dataGroup.addVar(name, netCDF::ncDouble, dims2));
-            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value);
             var.putVar(entry.second.getData());
         } else if (entry.second.getType() == ModelArray::Type::Z) {
             netCDF::NcVar var(dataGroup.addVar(name, netCDF::ncDouble, dims3));
-            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value);
             var.putVar(entry.second.getData());
         }
     }

core/src/MissingData.cpp

@@ -9,31 +9,7 @@
 
 namespace Nextsim {
 
-template <>
-const std::map<int, std::string> Configured<MissingData>::keyMap = {
-    { MissingData::MISSINGVALUE_KEY, "model.missing_value" },
-};
-static const double missingDefault = -0x1p300;
-double MissingData::m_value = missingDefault;
-void MissingData::configure()
-{
-    m_value
-        = Configured::getConfiguration(keyMap.at(MissingData::MISSINGVALUE_KEY), missingDefault);
-}
+const double MissingData::defaultValue = -0x1p300;
+double MissingData::value = MissingData::defaultValue;
 
-ConfigMap MissingData::getConfig()
-{
-    return {
-        { keyMap.at(MISSINGVALUE_KEY), m_value },
-    };
-}
-
-MissingData::HelpMap& MissingData::getHelpText(HelpMap& map, bool getAll)
-{
-    map["MissingData"] = {
-        { keyMap.at(MISSINGVALUE_KEY), ConfigType::NUMERIC, { "-∞", "∞" }, "-2³⁰⁰", "",
-            "Missing data indicator used for input and output." },
-    };
-    return map;
-}
 } /* namespace Nextsim */

core/src/Model.cpp

@@ -31,6 +31,7 @@ const std::map<int, std::string> Configured<Model>::keyMap = {
     { Model::STOPTIME_KEY, "model.stop" },
     { Model::RUNLENGTH_KEY, "model.run_length" },
     { Model::TIMESTEP_KEY, "model.time_step" },
+    { Model::MISSINGVALUE_KEY, "model.missing_value" },
 };
 
 Model::Model()
@@ -68,8 +69,8 @@ void Model::configure()
     TimePoint timeNow = iterator.parseAndSet(startTimeStr, stopTimeStr, durationStr, stepStr);
     m_etadata.setTime(timeNow);
 
-    MissingData mdi;
-    mdi.configure();
+    MissingData::value
+        = Configured::getConfiguration(keyMap.at(MISSINGVALUE_KEY), MissingData::defaultValue);
 
     initialFileName = Configured::getConfiguration(keyMap.at(RESTARTFILE_KEY), std::string());
 
@@ -91,9 +92,8 @@ ConfigMap Model::getConfig() const
         { keyMap.at(STOPTIME_KEY), stopTimeStr },
         { keyMap.at(RUNLENGTH_KEY), durationStr },
         { keyMap.at(TIMESTEP_KEY), stepStr },
+        { keyMap.at(MISSINGVALUE_KEY), MissingData::value },
     };
-    // MissingData has a static getState
-    cMap.merge(MissingData::getConfig());
 
     return cMap;
 }
@@ -114,6 +114,8 @@ Model::HelpMap& Model::getHelpText(HelpMap& map, bool getAll)
             "Model physics timestep, formatted a ISO8601 duration (P prefix). " },
         { keyMap.at(RESTARTFILE_KEY), ConfigType::STRING, {}, "", "",
             "The file path to the restart file to use for the run." },
+        { keyMap.at(MISSINGVALUE_KEY), ConfigType::NUMERIC, { "-∞", "∞" }, "-2³⁰⁰", "",
+            "Missing data indicator used for input and output." },
     };
 
     return map;
@@ -122,7 +124,6 @@ Model::HelpMap& Model::getHelpText(HelpMap& map, bool getAll)
 Model::HelpMap& Model::getHelpRecursive(HelpMap& map, bool getAll)
 {
     getHelpText(map, getAll);
-    MissingData::getHelpRecursive(map, getAll);
     PrognosticData::getHelpRecursive(map, getAll);
     Module::getHelpRecursive<IDiagnosticOutput>(map, getAll);
     return map;

core/src/ModelComponent.cpp

@@ -7,6 +7,8 @@
 
 #include "include/ModelComponent.hpp"
 
+#include "include/MissingData.hpp"
+
 namespace Nextsim {
 
 std::unordered_map<std::string, ModelComponent*> ModelComponent::registeredModules;
@@ -101,12 +103,12 @@ ModelArray ModelComponent::mask(const ModelArray& data)
     case (ModelArray::Type::H):
     case (ModelArray::Type::U):
     case (ModelArray::Type::V): {
-        return data * oceanMask() + MissingData::value() * (1 - oceanMask());
+        return data * oceanMask() + MissingData::value * (1 - oceanMask());
         break;
     }
     case (ModelArray::Type::Z): {
         ModelArray copy = ModelArray::ZField();
-        copy = MissingData::value();
+        copy = MissingData::value;
         size_t nZ = data.dimensions()[data.nDimensions() - 1];
         for (size_t iOcean = 0; iOcean < nOcean; ++iOcean) {
             size_t i = oceanIndex[iOcean];

core/src/ParaGridIO.cpp

@@ -230,7 +230,7 @@ void ParaGridIO::dumpModelState(
             ModelArray::Type type = entry.second.getType();
             std::vector<netCDF::NcDim>& ncDims = dimMap.at(type);
             netCDF::NcVar var(dataGroup.addVar(entry.first, netCDF::ncDouble, ncDims));
-            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value);
             var.putVar(entry.second.getData());
         }
     }
@@ -359,7 +359,7 @@ void ParaGridIO::writeDiagnosticTime(
             netCDF::NcVar var((isNew) ? dataGroup.addVar(entry.first, netCDF::ncDouble, ncDims)
                                       : dataGroup.getVar(entry.first));
             if (isNew)
-                var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+                var.putAtt(mdiName, netCDF::ncDouble, MissingData::value);
 
             var.putVar(indexArrays.at(type), extentArrays.at(type), entry.second.getData());
         }

core/src/RectGridIO.cpp

@@ -108,11 +108,11 @@ void RectGridIO::dumpModelState(const ModelState& state, const ModelMetadata& me
         const std::string& name = entry.first;
         if (entry.second.getType() == ModelArray::Type::H && entry.second.trueSize() > 0) {
             netCDF::NcVar var(dataGroup.addVar(name, netCDF::ncDouble, dims2));
-            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value);
             var.putVar(entry.second.getData());
         } else if (entry.second.getType() == ModelArray::Type::Z && entry.second.trueSize() > 0) {
             netCDF::NcVar var(dataGroup.addVar(name, netCDF::ncDouble, dims3));
-            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value);
             var.putVar(entry.second.getData());
         }
     }

core/src/include/MissingData.hpp

@@ -14,18 +14,8 @@ namespace Nextsim {
 
 class MissingData : public Configured<MissingData> {
 public:
-    inline static double value() { return m_value; }
-    void configure() override;
-    enum {
-        MISSINGVALUE_KEY,
-    };
-
-    static ConfigMap getConfig();
-    static HelpMap& getHelpRecursive(HelpMap& map, bool getAll) { return getHelpText(map, getAll); }
-    static HelpMap& getHelpText(HelpMap& map, bool getAll);
-
-private:
-    static double m_value;
+    static const double defaultValue;
+    static double value;
 };
 
 } /* namespace Nextsim */

core/src/include/Model.hpp

@@ -34,6 +34,7 @@ class Model : public Configured<Model> {
         STOPTIME_KEY,
         RUNLENGTH_KEY,
         TIMESTEP_KEY,
+        MISSINGVALUE_KEY,
     };
 
     ConfigMap getConfig() const;

core/test/CMakeLists.txt

@@ -153,7 +153,6 @@ add_executable(testModelComponent
     "ModelComponent_test.cpp"
     "${CoreSrc}/ModelComponent.cpp"
     "${CoreSrc}/MissingData.cpp"
-    "${CoreSrc}/Configurator.cpp"
     "${CoreSrc}/ModelArray.cpp"
     "${CoreSrc}/${ModelArrayStructure}/ModelArrayDetails.cpp"
 )

physics/src/modules/include/FluxConfiguredAtmosphere.hpp

@@ -10,6 +10,8 @@
 
 #include "IAtmosphereBoundary.hpp"
 
+#include "include/Configured.hpp"
+
 namespace Nextsim {
 
 //! A class to provide constant atmospheric forcings that can be configured at run time.