Merge pull request #198 from mach3-software/feature_randomFixes

Random Fixes

.github/workflows/Doxygen.yml

@@ -48,19 +48,20 @@ jobs:
       - run: sudo apt-get install -y perl
 
       # Runs a single command using the runners shell
-      - name: Doxygen Action
-        uses: mattnotmitt/[email protected]
+      - uses: DenverCoder1/[email protected]
         with:
-          doxyfile-path: './Doxyfile'
-          working-directory: ./Doc
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          folder: Doc/html
+          branch: gh-pages
+          config_file: Doc/Doxyfile
 
       - name: Upload Doxygen Artifact
         uses: actions/upload-artifact@v4
         with:
           retention-days: 1
           name: DoxygenHTML
           path: Doc/html
-          
+
   Sphinx:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
@@ -120,7 +121,7 @@ jobs:
           name: DocumentationHTML
           path: to-upload
 
-          
+
   Deploy:
     runs-on: ubuntu-latest
     needs: [Doxygen, Sphinx]

.gitignore

@@ -2,16 +2,10 @@
 *.o
 *.sif
 
-#ignore some stuff in libconfig
-*.lo
-*.la
-*.Plo
-lib/*
-
 build*/
 install/
-Doc/latex/
-Doc/html/
+Doc/html
+Doc/latex
 
 # Ignore emacs/vim stuff
 *#* 

.mailmap

@@ -6,6 +6,7 @@ Edward Atkin <[email protected]> EdAtkin <[email protected]
 
 # Daniel Barrow
 Daniel Barrow <[email protected]> dbarrow257 <[email protected]>
+Daniel Barrow <[email protected]> dbarrow257 <[email protected]>
 
 # Kamil Skwarczynski
 Kamil Skwarczynski <[email protected]> Kamil <[email protected]>

CMakeLists.txt

@@ -245,6 +245,7 @@ install(EXPORT MaCh3-targets
         NAMESPACE MaCh3::
         DESTINATION ${CMAKE_INSTALL_PREFIX}/
 )
+install(DIRECTORY cmake DESTINATION ${CMAKE_BINARY_DIR})
 
 #KS: Options to print dependency graph
 DefineEnabledRequiredSwitch(MaCh3_DependancyGraph FALSE)
@@ -331,4 +332,4 @@ if(NOT TARGET uninstall)
 endif()
 
 # KS: Configure the Doxygen input file, this is to ensure whenever we update MaCh3 version Doxyfile will have same version.
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/Templates/Doxyfile.in ${CMAKE_CURRENT_SOURCE_DIR}/Doc/Doxyfile @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/Templates/Doxyfile.in ${CMAKE_CURRENT_SOURCE_DIR}/Doc/Doxyfile @ONLY)

Diagnostics/GetPenaltyTerm.cpp

@@ -110,7 +110,7 @@ void ReadXSecFile(const std::string& inputFile)
     }
   }
   #ifdef MULTITHREAD
-  #pragma omp parallel for
+  #pragma omp parallel for collapse(2)
   #endif
   for (int i = 0; i < size; i++)
   {
@@ -126,7 +126,7 @@ void ReadXSecFile(const std::string& inputFile)
 
 void GetPenaltyTerm(const std::string& inputFile, const std::string& configFile)
 {
-  TCanvas* canvas = new TCanvas("canvas", "canvas", 0, 0, 1024, 1024);
+  auto canvas = std::make_unique<TCanvas>("canvas", "canvas", 0, 0, 1024, 1024);
   canvas->SetGrid();
   canvas->SetTickx();
   canvas->SetTicky();
@@ -173,7 +173,7 @@ void GetPenaltyTerm(const std::string& inputFile, const std::string& configFile)
   // Set all the branches to off
   Chain->SetBranchStatus("*", false);
 
-  double* fParProp = new double[RelevantBranches];
+  std::vector<double> fParProp(RelevantBranches);
   // Turn on the branches which we want for parameters
   for (int i = 0; i < RelevantBranches; ++i) 
   {
@@ -250,14 +250,13 @@ void GetPenaltyTerm(const std::string& inputFile, const std::string& configFile)
   }
 
   int AllEvents = int(Chain->GetEntries());
-  TH1D **hLogL = new TH1D *[NSets];
-  for(int i = 0; i < NSets; i++)
-  {
+  std::vector<std::unique_ptr<TH1D>> hLogL(NSets);
+  for (int i = 0; i < NSets; i++) {
     std::string NameTemp = "LogL_" + SetsNames[i];
-    hLogL[i] = new TH1D(NameTemp.c_str(), NameTemp.c_str(), AllEvents, 0 , AllEvents);
+    hLogL[i] = std::make_unique<TH1D>(NameTemp.c_str(), NameTemp.c_str(), AllEvents, 0, AllEvents);
     hLogL[i]->SetLineColor(kBlue);
   }
-  double* logL = new double[NSets]();
+  std::vector<double> logL(NSets, 0.0);
   for(int n = 0; n < AllEvents; ++n)
   {
     if(n%10000 == 0) MaCh3Utils::PrintProgressBar(n, AllEvents);
@@ -337,7 +336,6 @@ void GetPenaltyTerm(const std::string& inputFile, const std::string& configFile)
     }
   }//End loop over steps
 
-  delete[] logL;
   // Directory for posteriors
   std::string OutputName = inputFile + "_PenaltyTerm" +".root";
   TFile* OutputFile = new TFile(OutputName.c_str(), "recreate");
@@ -359,13 +357,9 @@ void GetPenaltyTerm(const std::string& inputFile, const std::string& configFile)
     hLogL[i]->Write();
 
     canvas->Print(Form("%s_PenaltyTerm.pdf",inputFile.c_str()), "pdf");
-    delete hLogL[i];
   }
   canvas->Print(Form("%s_PenaltyTerm.pdf]",inputFile.c_str()), "pdf");
-  delete[] hLogL;
-  delete[] fParProp;
   delete Chain;
-  delete canvas;
 
   for (int i = 0; i < size; i++)
   {

Diagnostics/RHat.cpp

@@ -36,18 +36,18 @@ int Nchains;
 
 int nDraw;
 
-std::vector<TString> BranchNames;  
-std::vector<std::string> MCMCFile;  
+std::vector<TString> BranchNames;
+std::vector<std::string> MCMCFile;
 std::vector<bool> ValidPar;
 
 double ***Draws;
 
 double** Mean;
 double** StandardDeviation;
-    
+
 double* MeanGlobal;
 double* StandardDeviationGlobal;
-    
+
 double* BetweenChainVariance;
 double* MarginalPosteriorVariance;
 double* RHat;
@@ -58,10 +58,10 @@ double* MedianArr;
 
 double** MeanFolded;
 double** StandardDeviationFolded;
-    
+
 double* MeanGlobalFolded;
 double* StandardDeviationGlobalFolded;
-    
+
 double* BetweenChainVarianceFolded;
 double* MarginalPosteriorVarianceFolded;
 double* RHatFolded;
@@ -81,7 +81,7 @@ void CapVariable(double var, double cap);
 
 // *******************
 int main(int argc, char *argv[]) {
-// *******************    
+// *******************
 
   SetMaCh3LoggerFormat();
   MaCh3Utils::MaCh3Welcome();
@@ -420,7 +420,7 @@ void InitialiseArrays() {
 
 // *******************
 void RunDiagnostic() {
-// *******************    
+// *******************
   CalcRhat();
   //In case in future we expand this
 }
@@ -430,17 +430,17 @@ void RunDiagnostic() {
 // Probably most of it could be moved cleverly to MCMC Processor, keep it separate for now
 void CalcRhat() {
 // *******************
-    
+
   TStopwatch clock;
   clock.Start();
 
-//KS: Start parallel region
-// If we would like to do this for thousands of chains we might consider using GPU for this
+  //KS: Start parallel region
+  // If we would like to do this for thousands of chains we might consider using GPU for this
   #ifdef MULTITHREAD
   #pragma omp parallel
   {
   #endif
-    
+
     #ifdef MULTITHREAD
     #pragma omp for collapse(2)
     #endif
@@ -479,7 +479,7 @@ void CalcRhat() {
     #ifdef MULTITHREAD
     #pragma omp for collapse(2)
     #endif
-      //Calculate the standard deviation for each parameter within each considered chain
+    //Calculate the standard deviation for each parameter within each considered chain
     for (int m = 0; m < Nchains; ++m)
     {
       for (int j = 0; j < nDraw; ++j)
@@ -579,8 +579,8 @@ void CalcRhat() {
 
 // *******************
 void SaveResults() {
-// *******************    
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
+// *******************
+  #pragma GCC diagnostic ignored "-Wfloat-conversion"
 
   std::string NameTemp = "";
   //KS: If we run over many many chains there is danger that name will be so absurdly long we run over system limit and job will be killed :(
@@ -591,7 +591,7 @@ void SaveResults() {
       std::string temp = MCMCFile[i];
 
       while (temp.find(".root") != std::string::npos) {
-          temp = temp.substr(0, temp.find(".root"));
+        temp = temp.substr(0, temp.find(".root"));
       }
 
       NameTemp = NameTemp + temp + "_";
@@ -674,13 +674,13 @@ void SaveResults() {
   RhatFoldedLogPlot->Write();
 
   //KS: Now we make fancy canvases, consider some function to have less copy pasting
-  TCanvas *TempCanvas = new TCanvas("Canvas", "Canvas", 1024, 1024);
+  auto TempCanvas = std::make_unique<TCanvas>("Canvas", "Canvas", 1024, 1024);
   gStyle->SetOptStat(0);
   TempCanvas->SetGridx();
   TempCanvas->SetGridy();
 
   // Random line to write useful information to TLegend
-  TLine *TempLine = new TLine(0 , 0, 0, 0);
+  auto TempLine = std::make_unique<TLine>(0, 0, 0, 0);
   TempLine->SetLineColor(kBlack);
 
   RhatPlot->GetXaxis()->SetTitle("R hat");
@@ -696,7 +696,7 @@ void SaveResults() {
   Legend->SetLineWidth(0);
   Legend->SetLineColor(0);
 
-  Legend->AddEntry(TempLine, Form("Number of throws=%.0i, Number of chains=%.1i", Ntoys, Nchains), "");
+  Legend->AddEntry(TempLine.get(), Form("Number of throws=%.0i, Number of chains=%.1i", Ntoys, Nchains), "");
   Legend->AddEntry(RhatPlot, "Rhat Gelman 2013", "l");
   Legend->AddEntry(RhatFoldedPlot, "Rhat-Folded Gelman 2021", "l");
 
@@ -721,7 +721,7 @@ void SaveResults() {
   Legend->SetLineWidth(0);
   Legend->SetLineColor(0);
 
-  Legend->AddEntry(TempLine, Form("Number of throws=%.0i, Number of chains=%.1i", Ntoys, Nchains), "");
+  Legend->AddEntry(TempLine.get(), Form("Number of throws=%.0i, Number of chains=%.1i", Ntoys, Nchains), "");
   Legend->AddEntry(RhatLogPlot, "Rhat Gelman 2013", "l");
   Legend->AddEntry(RhatFoldedLogPlot, "Rhat-Folded Gelman 2021", "l");
 
@@ -749,7 +749,7 @@ void SaveResults() {
   const double Mean2 = EffectiveSampleSizeFoldedPlot->GetMean();
   const double RMS2 = EffectiveSampleSizeFoldedPlot->GetRMS();
 
-  Legend->AddEntry(TempLine, Form("Number of throws=%.0i, Number of chains=%.1i", Ntoys, Nchains), "");
+  Legend->AddEntry(TempLine.get(), Form("Number of throws=%.0i, Number of chains=%.1i", Ntoys, Nchains), "");
   Legend->AddEntry(EffectiveSampleSizePlot, Form("S_{eff, BDA2} #mu = %.2f, #sigma = %.2f",Mean1 ,RMS1), "l");
   Legend->AddEntry(EffectiveSampleSizeFoldedPlot, Form("S_{eff, BDA2} Folded, #mu = %.2f, #sigma = %.2f",Mean2 ,RMS2), "l");
 
@@ -772,8 +772,6 @@ void SaveResults() {
   delete EffectiveSampleSizeFoldedPlot;
 
   delete Legend;
-  delete TempCanvas;
-  delete TempLine;
 
   delete RhatLogPlot;
   delete RhatFoldedLogPlot;
@@ -788,7 +786,7 @@ void SaveResults() {
 //KS: Pseudo destructor
 void DestroyArrays() {
 // *******************
-    
+
   MACH3LOG_INFO("Killing all arrays");
   delete[] MeanGlobal;
   delete[] StandardDeviationGlobal;
@@ -829,22 +827,19 @@ void DestroyArrays() {
   delete[] StandardDeviationFolded;
 }
 
-
 // *******************
 //calculate median
 double CalcMedian(double arr[], const int size) {
-// *******************   
+// *******************
   std::sort(arr, arr+size);
   if (size % 2 != 0)
     return arr[size/2];
   return (arr[(size-1)/2] + arr[size/2])/2.0;
 }
 
-
 // *******************
 //calculate median
 void CapVariable(double var, const double cap) {
-// *******************   
-
+// *******************
   if(std::isnan(var) || !std::isfinite(var)) var = cap;
 }

Doc/Doxyfile

@@ -51,14 +51,14 @@ PROJECT_BRIEF          = "Reference Guide"
 # and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
 # to the output directory.
 
-PROJECT_LOGO           = "../Doc/mach3logo_small.png"
+PROJECT_LOGO           = "Doc/mach3logo_small.png"
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       =
+OUTPUT_DIRECTORY       = Doc/
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -670,7 +670,7 @@ LAYOUT_FILE            =
 # search path. Do not use file names with spaces, bibtex cannot handle them. See
 # also \cite for info how to create references.
 
-CITE_BIB_FILES         = ../Doc/bibliography.bib
+CITE_BIB_FILES         = Doc/bibliography.bib
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
@@ -741,7 +741,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = mainpage.md ../ ../manager ../splines ../samplePDF ../OscClass ../mcmc ../Diagnostics ../plotting ../plotting/plottingUtils ../Diagnostics/Diagnostics_utils ../covariance Plots/
+INPUT                  = . Doc/mainpage.md manager splines samplePDF mcmc Diagnostics plotting plotting/plottingUtils Diagnostics/Diagnostics_utils covariance
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -891,7 +891,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = mainpage.md
+USE_MDFILE_AS_MAINPAGE = Doc/mainpage.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1080,7 +1080,7 @@ HTML_STYLESHEET        =
 # see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = ../Doc/MaCh3.css
+HTML_EXTRA_STYLESHEET  = Doc/MaCh3.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note

Doc/html/nojekyll.txt

@@ -0,0 +1 @@
+