Actually try something which will not break everything

CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
 
 #KS: Enable language, necessary when using CUDA
 enable_language(CXX)
-set(MaCh3_VERSION 1.1.8)
+set(MaCh3_VERSION 1.2.0)
 
 # Try to find CUDA
 find_package(CUDAToolkit QUIET)

Doc/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MaCh3"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.1.8
+PROJECT_NUMBER         = 1.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

manager/YamlHelper.h

@@ -164,13 +164,10 @@ inline TMacro YAMLtoTMacro(const YAML::Node& yaml_node, const std::string& name)
   // Convert the YAML node to a string representation
   std::string macro_string = YAMLtoSTRING(yaml_node);
 
-  std::cout<<macro_string<<std::endl;
   // Create a TMacro object with the collected lines
   TMacro macro(name.c_str(), name.c_str());
   macro.AddLine(macro_string.c_str());
 
-  macro.Print();
-
   return macro;
 }
 

mcmc/FitterBase.cpp

@@ -313,9 +313,7 @@ void FitterBase::addSystObj(covarianceBase * const cov) {
 // Similar to systematic really, but handles the oscillation weights
 void FitterBase::addOscHandler(covarianceOsc * const oscf) {
 // *************************
-
   osc = oscf;
-
   if (save_nominal) {
     CovFolder->cd();
     std::vector<double> vec = oscf->getNominalArray();
@@ -339,15 +337,13 @@ void FitterBase::addOscHandler(covarianceOsc * const oscf) {
     TMacro ConfigSave = YAMLtoTMacro(Config, (std::string("Config_") + oscf->getName()));
     ConfigSave.Write();
   }
-
   return;
 }
 
 // *******************
 // Process the MCMC output to get postfit etc
 void FitterBase::ProcessMCMC() {
 // *******************
-
   if (fitMan == NULL) return;
 
   // Process the MCMC
@@ -383,7 +379,6 @@ void FitterBase::ProcessMCMC() {
       MACH3LOG_INFO("Opening output again to update with means..");
       outputFile = new TFile(fitMan->raw()["General"]["Output"]["Filename"].as<std::string>().c_str(), "UPDATE");
     }
-
     Central->Write("PDF_Means");
     Errors->Write("PDF_Errors");
     Central_Gauss->Write("Gauss_Means");

mcmc/MCMCProcessor.cpp

@@ -36,7 +36,7 @@ MCMCProcessor::MCMCProcessor(const std::string &InputFile) :
   AccProbValues = nullptr;
   AccProbBatchedAverages = nullptr;
 
-  //KS: Warning this only work when you project from Chain, will nor work when you try SetBranchAddress etc. Turn it on only if you know how to use it
+  //KS: WARNING this only work when you project from Chain, will nor work when you try SetBranchAddress etc. Turn it on only if you know how to use it
   PlotJarlskog = false;
 
   //KS:Hardcoded should be a way to get it via config or something
@@ -2485,13 +2485,6 @@ void MCMCProcessor::FindInputFiles() {
   bool InputNotFound = false;
   //CW: Get the xsec Covariance matrix
   CovPos[kXSecPar] = GetFromManager<std::vector<std::string>>(Settings["General"]["Systematics"]["XsecCovFile"], {"none"});
-  // If someone used factory approach have this option here
-  if(CovPos[kXSecPar].back() == "none") {
-    // Check if xsec_cov exists first before accessing CovFile
-    if(Settings["General"]["Systematics"]["xsec_cov"]) {
-      CovPos[kXSecPar] = GetFromManager<std::vector<std::string>>(Settings["General"]["Systematics"]["xsec_cov"]["CovFile"], {"none"});
-    }
-  }
   if(CovPos[kXSecPar].back() == "none")
   {
     MACH3LOG_WARN("Couldn't find XsecCov branch in output");

mcmc/MaCh3Factory.cpp

@@ -35,28 +35,29 @@ std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan, std::vector<samp
 }
 
 // ********************************************
-covarianceXsec* MaCh3CovarianceFactory(manager *fitMan, const std::string& name) {
+covarianceXsec* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix) {
 // ********************************************
-  MACH3LOG_INFO("Initialising {} matrix", name);
-
   // config for our matrix
-  YAML::Node Settings = fitMan->raw()["General"]["Systematics"][name];
+  YAML::Node Settings = FitManager->raw()["General"]["Systematics"];
+  auto CovMatrixName = Settings[std::string(PreFix) + "CovName"].as<std::string>();
+  MACH3LOG_INFO("Initialising {} matrix", CovMatrixName);
+
   // yaml files initialising out matrix
-  auto CovMatrixFile = Settings["CovFile"].as<std::vector<std::string>>();
+  auto CovMatrixFile = Settings[std::string(PreFix) + "CovFile"].as<std::vector<std::string>>();
 
   // PCA threshold, -1 means no pca
-  auto PCAThreshold = GetFromManager<double>(Settings["PCAThreshold"], -1);
+  auto PCAThreshold = GetFromManager<double>(Settings[std::string(PreFix) + "PCAThreshold"], -1);
   // do we pca whole matrix or only submatrix
-  auto PCAParamRegion = GetFromManager<std::vector<double>>(Settings["PCAParams"], {-999, -999});
+  auto PCAParamRegion = GetFromManager<std::vector<double>>(Settings[std::string(PreFix) + "PCAParams"], {-999, -999});
 
-  // create our glorious matrix
+  /// @todo this massive hack with "xsec_cov" is because we have const char * ... will have to fix it later...
   covarianceXsec* xsec = new covarianceXsec(CovMatrixFile, "xsec_cov", PCAThreshold, PCAParamRegion[0], PCAParamRegion[1]);
 
   // Fill the parameter values with their nominal values
   // should _ALWAYS_ be done before overriding with fix or flat
   xsec->setParameters();
 
-  auto FixParams = GetFromManager<std::vector<std::string>>(Settings["FixParams"], {});
+  auto FixParams = GetFromManager<std::vector<std::string>>(Settings[std::string(PreFix) + "FixParams"], {});
 
   // Fixed xsec parameters loop
   if (FixParams.size() == 1 && FixParams.at(0) == "All") {
@@ -69,14 +70,13 @@ covarianceXsec* MaCh3CovarianceFactory(manager *fitMan, const std::string& name)
     }
   }
   //Global step scale for matrix
-  auto StepScale = Settings["StepScale"].as<double>();
+  auto StepScale = Settings[std::string(PreFix) + "StepScale"].as<double>();
 
-  MACH3LOG_INFO("With Step Scale {:.4f}", StepScale);
   xsec->setStepScale(StepScale);
 
-  // TODO
   // Adaptive MCMC stuff
-  //xsec->initialiseAdaption(FitManager->raw());
+  if(FitManager->raw()["AdaptionOptions"])
+    xsec->initialiseAdaption(FitManager->raw());
 
   MACH3LOG_INFO("Factory successful");
 

mcmc/MaCh3Factory.h

@@ -28,24 +28,28 @@ std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan, std::vector<samp
 /// @brief Factory function for creating a covariance matrix for systematic handling.
 ///
 /// @param fitMan Pointer to the manager class that holds the configuration settings.
-/// @param name Name of the systematic matrix to initialize. This corresponds to a key in the YAML configuration.
+/// @param name Prefix, for example Xsec, then code will look for XsecCovFile
 /// @return Pointer to the initialized covarianceXsec matrix object.
 ///
 /// @note Example YAML configuration:
 /// @code
+///MaCh3CovarianceFactory(, Xsec)
+///
 /// General:
 ///   Systematics:
-///     xsec_cov:
-///       CovFile: ["inputs/blarb1.yaml",
-///                 "inputs/blarb2.yaml"]
-///       FixParams: ["Param_0",
-///                   "Param_1"]
-///       PCAThreshold: -1
-///       #PCAThreshold: 0.00001
+///       XsecCovName: "xsec_cov"
+///       XsecCovFile: ["inputs/blarb1.yaml",
+///                     "inputs/blarb2.yaml"]
+///       XsecFix: ["Param_0",
+///                 "Param_1"]
+///       XsecPCAThreshold: -1
+///       #XsecPCAThreshold: 0.00001
 ///
-///       PCAParams: [-999, -999]
-///       StepScale: 0.0075
+///       XsecPCAParams: [-999, -999]
+///       XsecStepScale: 0.0075
 /// @endcode
 ///
 /// @todo add adaptive stuff
-covarianceXsec* MaCh3CovarianceFactory(manager *fitMan, const std::string& name);
+covarianceXsec* MaCh3CovarianceFactory(manager *fitMan, const std::string& PreFix);
+
+