Remove warninig related to system call on newer gcc, and furhter imrp…

…ove doxy docuemtniaton

covariance/covarianceBase.h

@@ -65,11 +65,14 @@ class covarianceBase {
   /// @brief Set matrix name
   void setName(const char *name) { matrixName = name; }
   /// @brief change parameter name
+  /// @param i Parameter index
   void setParName(int i, char *name) { _fNames.at(i) = std::string(name); }
   void setSingleParameter(const int parNo, const double parVal);
   /// @brief Set all the covariance matrix parameters to a user-defined value
+  /// @param i Parameter index
   void setPar(const int i, const double val);
   /// @brief Set current parameter value
+  /// @param i Parameter index
   void setParCurrProp(const int i, const double val);
   /// @brief Set proposed parameter value
   void setParProp(const int i, const double val) {
@@ -78,15 +81,20 @@ class covarianceBase {
   }
   void setParameters(std::vector<double> pars = std::vector<double>());
   /// @brief Set if parameter should have flat prior or not
+  /// @param i Parameter index
   void setFlatPrior(const int i, const bool eL);
 
   /// @brief set branches for output file
   void SetBranches(TTree &tree, bool SaveProposal = false);
   /// @brief Set global step scale for covariance object
+  /// @param scale Value of global step scale
   void setStepScale(const double scale);
   /// @brief DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constructors)
+  /// @param ParameterIndex Parameter Index
+  /// @param StepScale Value of individual step scale
   void setIndivStepScale(const int ParameterIndex, const double StepScale){ _fIndivStepScale.at(ParameterIndex) = StepScale; }
   /// @brief DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constructors)
+  /// @param stepscale Vector of individual step scale, should have same
   void setIndivStepScale(std::vector<double> stepscale);
   /// @brief KS: In case someone really want to change this
   inline void setPrintLength(const unsigned int PriLen) { PrintLength = PriLen; }
@@ -113,8 +121,9 @@ class covarianceBase {
   /// @brief Return CalcLikelihood if some params were thrown out of boundary return _LARGE_LOGL_
   virtual double GetLikelihood();
 
-  // Getters
+  /// @brief Return covariance matrix
   TMatrixDSym *getCovMatrix() { return covMatrix; }
+  /// @brief Return inverted covariance matrix
   TMatrixDSym *getInvCovMatrix() { return invCovMatrix; }
   /// @brief Get if param has flat prior or not
   /// @param i Parameter index
@@ -138,6 +147,7 @@ class covarianceBase {
   std::string getInputFile() const { return inputFile; }
 
   /// @brief Get diagonal error for ith parameter
+  /// @param i Parameter index
   inline double getDiagonalError(const int i) { return std::sqrt((*covMatrix)(i,i)); }
 
   // Adaptive Step Tuning Stuff
@@ -195,14 +205,24 @@ class covarianceBase {
 
   virtual double getNominal(const int i) { return getParInit(i); }
   inline double GetGenerated(const int i) { return _fGenerated[i];}
+  /// @brief Get upper parameter bound in which it is physically valid
+  /// @param i Parameter index
   inline double GetUpperBound(const int i){ return _fUpBound[i];}
+  /// @brief Get lower parameter bound in which it is physically valid
+  /// @param i Parameter index
   inline double GetLowerBound(const int i){ return _fLowBound[i]; }
-  inline double GetIndivStepScale(int ParameterIndex){return _fIndivStepScale.at(ParameterIndex); }
+  /// @brief Get individual step scale for selected parameter
+  /// @param ParameterIndex Parameter index
+  inline double GetIndivStepScale(const int ParameterIndex){return _fIndivStepScale.at(ParameterIndex); }
+  /// @brief Get current parameter value using PCA
+  /// @param i Parameter index
   inline double getParProp_PCA(const int i) {
     if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
     return fParProp_PCA(i);
   }
 
+  /// @brief Get current parameter value using PCA
+  /// @param i Parameter index
   inline double getParCurr_PCA(const int i) {
     if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
     return fParCurr_PCA(i);
@@ -268,8 +288,9 @@ class covarianceBase {
     else return _fNumPar;
   }
 
-  // Printers
+  /// @brief Print nominal value for every parameter
   void printNominal();
+  /// @brief Print nominal, current and proposed value for each parameter
   void printNominalCurrProp();
   void printPars();
   /// @brief Print step scale for each parameter
@@ -283,11 +304,14 @@ class covarianceBase {
   /// @brief fix parameters at prior values
   void toggleFixAllParameters();
   /// @brief fix parameter at prior values
+  /// @param i Parameter index
   void toggleFixParameter(const int i);
   /// @brief Fix parameter at prior values
+  /// @param name Name of parameter you want to fix
   void toggleFixParameter(const std::string& name);
 
   /// @brief Is parameter fixed or not
+  /// @param i Parameter index
   bool isParameterFixed(const int i) {
     if (_fError[i] < 0) { return true; }
     else                { return false; }

covariance/covarianceOsc.h

@@ -18,7 +18,7 @@ class covarianceOsc : public covarianceBase
   inline int CheckBounds() override;
   /// @brief Retrieves the proposed parameters.
   double *getPropPars();
-  /// @brief Propose MCMC step, including mass fliping
+  /// @brief Propose MCMC step, including mass flipping
   void proposeStep() override;
   /// @brief Sets whether to flip delta M23.
   void setFlipDeltaM23(bool flip){flipdelM = flip;}
@@ -28,6 +28,7 @@ class covarianceOsc : public covarianceBase
   /// @warning May become deprecated
   void useReactorPrior(bool reactor){reactorPrior = reactor;};
   /// @brief Sets extra branches for processing.
+  /// @param tree ROOT tree to which we set additional variables
   void setExtraBranches(TTree &tree);
 
   /// @brief Get baseline

manager/MaCh3Logger.h

@@ -22,9 +22,11 @@ inline void SetMaCh3LoggerFormat()
   //KS: %H for hour, %M for minute, %S for second, [%s:%#] for class and line
   //For documentation see https://github.com/gabime/spdlog/wiki/3.-Custom-formatting
   #ifdef DEBUG
-  spdlog::set_pattern("[%H:%M:%S][%s:%#][%^%l%$] %v");
+  //spdlog::set_pattern("[%H:%M:%S][%s:%#][%^%l%$] %v");
+  spdlog::set_pattern("[%s:%#][%^%l%$] %v");
   #else
-  spdlog::set_pattern("[%H:%M:%S][%s][%^%l%$] %v");
+  //spdlog::set_pattern("[%H:%M:%S][%s][%^%l%$] %v");
+  spdlog::set_pattern("[%s][%^%l%$] %v");
   #endif
 }
 

mcmc/MCMCProcessor.cpp

@@ -3399,7 +3399,9 @@ void MCMCProcessor::ReweightPrior(std::vector<std::string> Names, std::vector<do
   std::string OutputFilename = MCMCFile + "_reweighted.root";
 
   //KS: Simply create copy of file and add there new branch
-  system(("cp "+InputFile+" "+OutputFilename).c_str());
+  int ret = system(("cp " + InputFile + " " + OutputFilename).c_str());
+  if (ret != 0)
+    MACH3LOG_WARN("Error: system call to copy file failed with code {}", ret);
 
   TFile *OutputChain = new TFile(OutputFilename.c_str(), "UPDATE");
   OutputChain->cd();

splines/SplineMonolith.h

@@ -68,9 +68,16 @@ class SMonolith : public SplineBase {
     inline void Initialise();
     /// @brief CW: Function to scan through the MasterSpline of TSpline3
     /// @param MasterSpline Vector of TSpline3_red pointers which we strip back
+    /// @param NEvents Number of MC events
+    /// @param MaxPoints Maximal number of knots per splines
+    /// @param numParams Total number of parameters
+    /// @param numKnots Total number of knots, which is sum of individual knots per each spline
     inline void ScanMasterSpline(std::vector<std::vector<TSpline3_red*> > &MasterSpline, unsigned int &NEvents, int &MaxPoints, short int &numParams, int &nSplines, unsigned int &numKnots);
     /// @brief CW: Function to scan through the MasterSpline of TF1
     /// @param MasterSpline Vector of TF1_red pointers which we strip back
+    /// @param NEvents Number of MC events
+    /// @param MaxPoints Maximal number of knots per splines
+    /// @param numParams Total number of parameters
     inline void ScanMasterSpline(std::vector<std::vector<TF1_red*> > &MasterSpline, unsigned int &NEvents, int &MaxPoints, short int &numParams);
     /// @brief CW: Prepare the TSpline3_red objects for the GPU
     /// @param MasterSpline Vector of TSpline3_red pointers which we strip back
@@ -101,6 +108,9 @@ class SMonolith : public SplineBase {
     /// @param spl pointer to TSpline3_red that will be checked
     inline bool isFlat(TSpline3_red* &spl);
     /// @brief CW: Gets the polynomial coefficients for TF1
+    /// @param spl pointer to TF1_red that will be checked
+    /// @param nPoints number of knots
+    /// @param coeffs Array holding coefficients for each knot
     inline void getTF1Coeff(TF1_red* &spl, int &nPoints, float *&coeffs);
 
     /// @brief CW:Code used in step by step reweighting, Find Spline Segment for each param
@@ -117,6 +127,7 @@ class SMonolith : public SplineBase {
     /// @brief KS: Prepare spline file that can be used for fast loading
     inline void PrepareSplineFile();
     /// @brief KS: Load preprocessed spline file
+    /// @param FileName Path to ROOT file with predefined reduced Spline Monolith
     inline void LoadSplineFile(std::string FileName);
 
     /// Array of FastSplineInfo structs: keeps information on each xsec spline for fast evaluation