Merge pull request #91 from mach3-software/feature_BagOfTricks

Tidy

.github/workflows/CDImage.yml

@@ -20,15 +20,12 @@ jobs:
           - os: Ubuntu22.04
             file: Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile
             tag_latest: ubuntu22.04latest
-            tag_release: ubuntu22.04v1.1.0
           - os: Alma9
             file: Doc/MaCh3DockerFiles/Alma9/Dockerfile
             tag_latest: alma9latest
-            tag_release: alma9v1.1.0
           - os: Fedora32
             file: Doc/MaCh3DockerFiles/Fedora32/Dockerfile
             tag_latest: fedora32latest
-            tag_release: fedora32v1.1.0
 
     name: Image CD ${{ matrix.os }}
 
@@ -43,14 +40,15 @@ jobs:
       run: |
         if [ "${{ github.event_name }}" == 'release' ]; then
           docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_release }} --build-arg MACH3_VERSION=develop
+          docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}v${{ github.event.release.tag_name }} --build-arg MACH3_VERSION=develop
         else
           docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }} --build-arg MACH3_VERSION=develop
         fi
 
     - name: Push Docker image
       run: |
         if [ "${{ github.event_name }}" == 'release' ]; then
-          docker push ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_release }}
+          docker push ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}v${{ github.event.release.tag_name }}
         else
           docker push ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }}
         fi

Diagnostics/DiagMCMC.cpp

@@ -2,26 +2,10 @@
 
 #include "manager/manager.h"
 
-
-void DiagMCMC(std::string inputFile, std::string config);
-
-int main(int argc, char *argv[]) {
-  SetMaCh3LoggerFormat();
-  if (argc != 3)
-  {
-    MACH3LOG_ERROR("How to use: DiagMCMC MCMC_Output.root config");
-    throw MaCh3Exception(__FILE__ , __LINE__ );
-  }
-  MACH3LOG_INFO("Producing single fit output");
-  std::string filename = argv[1];
-  std::string config = argv[2];
-  DiagMCMC(filename, config);
-
-  return 0;
-}
-
-
-void DiagMCMC(std::string inputFile, std::string config)
+/// @brief Main function  creating MCMCProcessor and calling MCMC Diagnostic
+/// @param inputFile MCMC Chain
+/// @param config Config file with settings
+void DiagMCMC(const std::string& inputFile, const std::string& config)
 {
   MACH3LOG_INFO("File for study: {}", inputFile);
 
@@ -47,4 +31,17 @@ void DiagMCMC(std::string inputFile, std::string config)
   delete Processor;
 }
 
+int main(int argc, char *argv[]) {
+  SetMaCh3LoggerFormat();
+  if (argc != 3)
+  {
+    MACH3LOG_ERROR("How to use: DiagMCMC MCMC_Output.root config");
+    throw MaCh3Exception(__FILE__ , __LINE__ );
+  }
+  MACH3LOG_INFO("Producing single fit output");
+  std::string filename = argv[1];
+  std::string config = argv[2];
+  DiagMCMC(filename, config);
 
+  return 0;
+}

Diagnostics/ProcessMCMC.cpp

@@ -2,15 +2,19 @@
 #include "mcmc/MCMCProcessor.h"
 #include "manager/manager.h"
 
-inline void ProcessMCMC(std::string inputFile);
+/// @brief Main function processing MCMC and Producing plots
+inline void ProcessMCMC(const std::string& inputFile);
+/// @brief Function producing comparison of posterior and more betwen a few MCMC chains
 inline void MultipleProcessMCMC();
 inline void CalcBayesFactor(MCMCProcessor* Processor);
 inline void CalcSavageDickey(MCMCProcessor* Processor);
 inline void CalcBipolarPlot(MCMCProcessor* Processor);
 inline void GetTrianglePlot(MCMCProcessor* Processor);
-inline void DiagnoseCovarianceMatrix(MCMCProcessor* Processor, std::string inputFile);
+inline void DiagnoseCovarianceMatrix(MCMCProcessor* Processor, const std::string& inputFile);
 inline void ReweightPrior(MCMCProcessor* Processor);
-inline TH2D* TMatrixIntoTH2D(TMatrixDSym* Matrix, std::string title);
+/// @brief KS: Convert TMatrix to TH2D, mostly useful for making fancy plots
+inline TH2D* TMatrixIntoTH2D(TMatrixDSym* Matrix, const std::string& title);
+/// @brief KS: Perform KS test to check if two posteriors for the same parameter came from the same distribution
 inline void KolmogorovSmirnovTest(MCMCProcessor** Processor, TCanvas* Posterior, TString canvasname);
 
 int nFiles;
@@ -59,7 +63,7 @@ int main(int argc, char *argv[])
   return 0;
 }
 
-void ProcessMCMC(std::string inputFile)
+void ProcessMCMC(const std::string& inputFile)
 {
   MACH3LOG_INFO("File for study: {} with config  {}", inputFile, config);
   // Make the processor)
@@ -391,8 +395,8 @@ void GetTrianglePlot(MCMCProcessor* Processor) {
   }
 }
 
-//KS: You validate stability of posterior covariance matrix, you set burn calc cov matrix increase burn calc again and compare. By performing such operation several hundred times we can check when matrix becomes stable
-void DiagnoseCovarianceMatrix(MCMCProcessor* Processor, std::string inputFile)
+/// @brief KS: You validate stability of posterior covariance matrix, you set burn calc cov matrix increase burn calc again and compare. By performing such operation several hundred times we can check when matrix becomes stable
+void DiagnoseCovarianceMatrix(MCMCProcessor* Processor, const std::string& inputFile)
 {
   //Turn of plots from Processor
   Processor->SetPrintToPDF(false);
@@ -584,7 +588,7 @@ void ReweightPrior(MCMCProcessor* Processor)
 }
 
 //KS: Convert TMatrix to TH2D, mostly useful for making fancy plots
-TH2D* TMatrixIntoTH2D(TMatrixDSym* Matrix, std::string title)       
+TH2D* TMatrixIntoTH2D(TMatrixDSym* Matrix, const std::string& title)
 {
   TH2D* hMatrix = new TH2D(title.c_str(), title.c_str(), Matrix->GetNrows(), 0.0, Matrix->GetNrows(), Matrix->GetNcols(), 0.0, Matrix->GetNcols());
   for(int i = 0; i < Matrix->GetNrows(); i++)

Diagnostics/RHat.cpp

@@ -30,8 +30,8 @@
 #include "manager/manager.h"
 
 
-//KS: This exe is meant to calculate R hat estimator. For a well converged this distribution should be centred at one. 
-//Based on Gelman et. al. arXiv:1903.08008v5
+/// KS: This exe is meant to calculate R hat estimator. For a well converged this distribution should be centred at one.
+/// Based on Gelman et. al. arXiv:1903.08008v5
 
 // *******************
 int Ntoys;

Doc/Doxyfile

@@ -115,7 +115,7 @@ ABBREVIATE_BRIEF       =
 # description.
 # The default value is: NO.
 
-ALWAYS_DETAILED_SEC    = NO
+ALWAYS_DETAILED_SEC    = YES
 
 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
 # inherited members of a class in the documentation of that class as if those
@@ -189,6 +189,14 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
+# By default Python docstrings are displayed as preformatted text and doxygen's
+# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
+# doxygen's special commands can be used and the contents of the docstring
+# documentation blocks is shown as doxygen documentation.
+# The default value is: YES.
+
+PYTHON_DOCSTRING       = YES
+
 # If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
 # documentation from any documented member that it re-implements.
 # The default value is: YES.
@@ -1897,7 +1905,7 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
@@ -2044,7 +2052,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # set to NO
 # The default value is: NO.
 
-HAVE_DOT               = NO
+HAVE_DOT               = YES
 
 # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
 # to run in parallel. When set to 0 doxygen will base this on the number of

cmake/Templates/Doxyfile.in

@@ -115,7 +115,7 @@ ABBREVIATE_BRIEF       =
 # description.
 # The default value is: NO.
 
-ALWAYS_DETAILED_SEC    = NO
+ALWAYS_DETAILED_SEC    = YES
 
 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
 # inherited members of a class in the documentation of that class as if those
@@ -189,6 +189,14 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
+# By default Python docstrings are displayed as preformatted text and doxygen's
+# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
+# doxygen's special commands can be used and the contents of the docstring
+# documentation blocks is shown as doxygen documentation.
+# The default value is: YES.
+
+PYTHON_DOCSTRING       = YES
+
 # If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
 # documentation from any documented member that it re-implements.
 # The default value is: YES.
@@ -1897,7 +1905,7 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
@@ -2044,7 +2052,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # set to NO
 # The default value is: NO.
 
-HAVE_DOT               = NO
+HAVE_DOT               = YES
 
 # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
 # to run in parallel. When set to 0 doxygen will base this on the number of

covariance/covarianceOsc.cpp

@@ -16,7 +16,6 @@ covarianceOsc::covarianceOsc(const char* name, const char *file)
 
   TVectorD* osc_baseline = (TVectorD*)infile->Get("osc_baseline");
   TVectorD* osc_density = (TVectorD*)infile->Get("osc_density");
-  double fScale = 1.0;
 
   //KS: Save all necessary information from covariance
   for(int io = 0; io < _fNumPar; io++)
@@ -27,7 +26,7 @@ covarianceOsc::covarianceOsc(const char* name, const char *file)
     _fCurrVal[io] = _fPropVal[io] = _fPreFitValue[io];
     _fError[io] = (*osc_sigma)(io);
 
-    _fIndivStepScale[io] = fScale * (*osc_stepscale)(io);
+    _fIndivStepScale[io] = (*osc_stepscale)(io);
 
     //KS: Set flat prior
     //HW: Might as well set it for everything in case default behaviour changes
@@ -243,13 +242,13 @@ void covarianceOsc::CheckOrderOfParams()  {
 
   std::vector<int> wrongParam;
   bool wrongMatrix = false;
-  if(strcmp( _fNames[0].c_str(),"sin2th_12") != 0 ){wrongParam.push_back(0); wrongMatrix = true;};
-  if(strcmp( _fNames[1].c_str(),"sin2th_23") != 0 ){wrongParam.push_back(1); wrongMatrix = true;};
-  if(strcmp( _fNames[2].c_str(),"sin2th_13") != 0 ){wrongParam.push_back(2); wrongMatrix = true;};
-  if(strcmp( _fNames[3].c_str(),"delm2_12")  != 0 ){wrongParam.push_back(3); wrongMatrix = true;};
-  if(strcmp( _fNames[4].c_str(),"delm2_23")  != 0 ){wrongParam.push_back(4); wrongMatrix = true;};
-  if(strcmp( _fNames[5].c_str(),"delta_cp")  != 0 ){wrongParam.push_back(5); wrongMatrix = true;};
-  if(PerformBetaStudy && strcmp( _fNames[6].c_str(),"beta")  != 0 ){wrongParam.push_back(6); wrongMatrix = true;};
+  if(_fNames[0] != "sin2th_12"){wrongParam.push_back(0); wrongMatrix = true;};
+  if(_fNames[1] != "sin2th_23"){wrongParam.push_back(1); wrongMatrix = true;};
+  if(_fNames[2] != "sin2th_13"){wrongParam.push_back(2); wrongMatrix = true;};
+  if(_fNames[3] != "delm2_12"){wrongParam.push_back(3); wrongMatrix = true;};
+  if(_fNames[4] != "delm2_23"){wrongParam.push_back(4); wrongMatrix = true;};
+  if(_fNames[5] != "delta_cp"){wrongParam.push_back(5); wrongMatrix = true;};
+  if(PerformBetaStudy && _fNames[6] != "beta"){wrongParam.push_back(6); wrongMatrix = true;};
 
   if(wrongMatrix)
   {

covariance/covarianceOsc.h

@@ -67,4 +67,3 @@ class covarianceOsc : public covarianceBase
     /// Enum for special treatment of beta.
     int kBeta;
 };
-

manager/MaCh3Exception.h

@@ -21,8 +21,9 @@ class MaCh3Exception : public std::exception {
     std::string fileName = (lastSlashPos != std::string::npos) ? File.substr(lastSlashPos + 1) : File;
 
     errorMessage = ((Message.empty()) ? "Terminating MaCh3" : Message);
-
-    MACH3LOG_ERROR("Find me here:  {}::{}", fileName, Line);
+    // KS: Set logger format where we only have have "information type", line would be confusing
+    spdlog::set_pattern("[%^%l%$] %v");
+    MACH3LOG_ERROR("Find me here: {}::{}", fileName, Line);
   }
 
   /// @brief Returns the error message associated with this exception.

manager/Monitor.cpp

@@ -60,7 +60,7 @@ std::string GetMaCh3Version() {
   // Check if the file is opened successfully
   if (!versionFile.is_open()) {
     MACH3LOG_ERROR("Error: Couldn't open version.h {}", file);
-    throw;
+    throw MaCh3Exception(__FILE__, __LINE__);
   }
 
   std::string line;
@@ -100,7 +100,7 @@ void GetOSInfo() {
 
 // ************************
 //KS: Simple function retrieving CPU info
-void GetCPUInfo(){
+void GetCPUInfo() {
 // ************************
 
   //KS: Use -m 1 to limit to only one grep because in one computing node there is a lot of CPU which are the same
@@ -162,7 +162,7 @@ std::string TerminalToString(const char* cmd) {
   std::string result;
   std::unique_ptr<FILE, decltype(&pclose)> pipe(popen(cmd, "r"), pclose);
   if (!pipe) {
-    throw std::runtime_error("popen() failed!");
+    throw MaCh3Exception(__FILE__, __LINE__, "popen() failed!");
   }
   while (fgets(buffer.data(), buffer.size(), pipe.get()) != nullptr) {
     result += buffer.data();
@@ -259,9 +259,8 @@ int getValue(std::string Type){ //Note: this value is in KB!
   }
   else
   {
-    std::cerr << "Not supported getValue: " << Type << std::endl;
-    std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
-    throw;
+    MACH3LOG_ERROR("Not supported getValue: {}", Type);
+    throw MaCh3Exception(__FILE__, __LINE__);
   }
 
   return result;
@@ -293,6 +292,4 @@ void PrintConfig(const YAML::Node& node){
   }
 }
 
-
-
 }

mcmc/FitterBase.cpp

@@ -24,7 +24,7 @@ FitterBase::FitterBase(manager * const man) : fitMan(man) {
   stepClock = new TStopwatch;
   #ifdef DEBUG
   // Fit summary and debug info
-  debug = fitMan->raw()["General"]["Debug"].as<bool>();
+  debug = GetFromManager<bool>(fitMan->raw()["General"]["Debug"], false);
   #endif
 
   std::string outfile = fitMan->raw()["General"]["OutputFile"].as<std::string>();
@@ -73,7 +73,7 @@ FitterBase::FitterBase(manager * const man) : fitMan(man) {
   syst_llh = nullptr;
 
   TotalNSamples = 0;
-  fTestLikelihood = GetFromManager<bool>(fitMan->raw()["General"]["Fitter"]["FitTestLikelihood"], false);;
+  fTestLikelihood = GetFromManager<bool>(fitMan->raw()["General"]["Fitter"]["FitTestLikelihood"], false);
 }
 
 // *************************
@@ -113,12 +113,12 @@ void FitterBase::SaveSettings() {
   if (std::getenv("MaCh3_ROOT") == NULL) {
     MACH3LOG_ERROR("Need MaCh3_ROOT environment variable");
     MACH3LOG_ERROR("Please remember about source bin/setup.MaCh3.sh");
-    throw;
+    throw MaCh3Exception(__FILE__ , __LINE__ );
   }
 
   if (std::getenv("MACH3") == NULL) {
     MACH3LOG_ERROR("Need MACH3 environment variable");
-    throw;
+    throw MaCh3Exception(__FILE__ , __LINE__ );
   }
 
   std::string header_path = std::string(std::getenv("MACH3"));
@@ -176,8 +176,7 @@ void FitterBase::PrepareOutput() {
     // Check that we have added samples
     if (!samples.size()) {
       MACH3LOG_CRITICAL("No samples Found! If this is what you want find me here");
-      MACH3LOG_CRITICAL("{}:{}", __FILE__, __LINE__);
-      throw;
+      throw MaCh3Exception(__FILE__ , __LINE__ );
     }
 
     // Prepare the output trees

mcmc/LikelihoodFit.cpp

@@ -6,7 +6,7 @@ LikelihoodFit::LikelihoodFit(manager *man) : FitterBase(man) {
 // *******************
     NPars = 0;
     NParsPCA = 0;
-    fMirroring = true;
+    fMirroring = GetFromManager<bool>(fitMan->raw()["General"]["Fitter"]["Mirroring"], false);
 }