Merge pull request #182 from mach3-software/feature_Tidy

Tidy

CONTRIBUTING.md → .github/CONTRIBUTING.md

@@ -46,6 +46,14 @@ Logger by default will print whole float. Normally to show only several signific
 ```cpp
 MACH3LOG_INFO("Here is full LLH but I only show 2 significant figures {:.2f}", LLH);
 ```
+If you want to mimic std::setw<<10
+```cpp
+MACH3LOG_INFO("Some break {:<10}", blarb);
+```
+Laslty if you want combine precision and std::setw like format
+```cpp
+MACH3LOG_INFO("Some break {:<10.2f}", blarb);
+```
 
 ## Config Syntax
 MaCh3 currently uses yaml as config handler. To help unify syntax over the code there are several YamlHelper function available [here](https://github.com/mach3-software/MaCh3/blob/develop/manager/YamlHelper.h). Most important is `GetFromManager`. For code below which checks if config entry exist and if doesn't set some default value

CMakeLists.txt

@@ -41,7 +41,7 @@ find_program(CMAKE_C_COMPILER NAMES $ENV{CC} gcc PATHS ENV PATH NO_DEFAULT_PATH)
 find_program(CMAKE_CXX_COMPILER NAMES $ENV{CXX} g++ PATHS ENV PATH NO_DEFAULT_PATH)
 
 LIST(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Modules)
-#KS: Store some handy cmake functions
+#KS: Load cmake function like DefineEnabledRequiredSwitch allowing to write more compact cmake
 include(${CMAKE_CURRENT_LIST_DIR}/cmake/Modules/MaCh3Utils.cmake)
 
 ################################## Dependencies ################################
@@ -65,7 +65,6 @@ if(ROOT_CXX_STANDARD LESS 14 AND ROOT_VERSION VERSION_LESS 6.32.00)
 endif()
 
 ############################  Setting Flags  ####################################
-# Check the where to install
 cmessage(STATUS "CMAKE_INSTALL_PREFIX: \"${CMAKE_INSTALL_PREFIX}\"")
 
 # add cmake script files

Diagnostics/RHat.cpp

@@ -161,18 +161,16 @@ int main(int argc, char *argv[]) {
 // Load chain and prepare toys
 void PrepareChains() {
 // *******************
-
-  TRandom3 *rnd = new TRandom3(0);
+  auto rnd = std::make_unique<TRandom3>(0);
 
   MACH3LOG_INFO("Generating {}", Ntoys);
 
   TStopwatch clock;
   clock.Start();
 
-  int *BurnIn = new int[Nchains]();
-  int *nEntries = new int[Nchains]();
-  int *nBranches = new int[Nchains]();
-
+  std::vector<int> BurnIn(Nchains);
+  std::vector<int> nEntries(Nchains);
+  std::vector<int> nBranches(Nchains);
   std::vector<int> step(Nchains);
 
   Draws = new double**[Nchains]();
@@ -325,7 +323,7 @@ void PrepareChains() {
   for(int j = 0; j < nDraw; j++)
   {
     MedianArr[j] = 0.;
-    double* TempDraws = new double[Ntoys*Nchains]();
+    std::vector<double> TempDraws(Ntoys * Nchains);
     for(int m = 0; m < Nchains; m++)
     {
       for(int i = 0; i < Ntoys; i++)
@@ -334,8 +332,7 @@ void PrepareChains() {
         TempDraws[im] = Draws[m][i][j];
       }
     }
-    MedianArr[j] = CalcMedian(TempDraws, Ntoys*Nchains);
-    delete[] TempDraws;
+    MedianArr[j] = CalcMedian(TempDraws.data(), Ntoys*Nchains);
   }
 
   #ifdef MULTITHREAD
@@ -351,12 +348,6 @@ void PrepareChains() {
       }
     }
   }
-  delete rnd;
-
-  delete[] BurnIn;
-  delete[] nEntries;
-  delete[] nBranches;
-
   clock.Stop();
   MACH3LOG_INFO("Finished calculating Toys, it took {:.2f}s to finish", clock.RealTime());
 }

cmake/Modules/NuOscillatorSetup.cmake

@@ -53,7 +53,7 @@ get_target_property(compile_options MaCh3CompilerOptions INTERFACE_COMPILE_OPTIO
 # Join the compile options list into a space-separated string
 string(REPLACE ";" " " compile_options_string "${compile_options}")
 
-#KS this may look hacky however CPM isn't build for passing stuff like this. If CMAKE_CUDA_ARCHITECTURES is passed CPM it will be string not list. Thus we convert it to list
+#KS: This may seem hacky, but when CMAKE_CUDA_ARCHITECTURES is passed, it's treated as a string rather than a list. Since CMake uses semi-colon-delimited strings to represent lists, we convert it to a proper list to handle CUDA architectures correctly.
 set(CMAKE_CUDA_ARCHITECTURES_STRING ${CMAKE_CUDA_ARCHITECTURES})
 string(REPLACE " " ";" CMAKE_CUDA_ARCHITECTURES "${CMAKE_CUDA_ARCHITECTURES}")
 

covariance/covarianceBase.cpp

@@ -48,9 +48,9 @@ covarianceBase::~covarianceBase(){
   delete[] randParams;
   delete[] corr_throw;
 
-  if (covMatrix != NULL) delete covMatrix;
-  if (invCovMatrix != NULL) delete invCovMatrix;
-  if (throwMatrix_CholDecomp != NULL) delete throwMatrix_CholDecomp;
+  if (covMatrix != nullptr) delete covMatrix;
+  if (invCovMatrix != nullptr) delete invCovMatrix;
+  if (throwMatrix_CholDecomp != nullptr) delete throwMatrix_CholDecomp;
 
   for(int i = 0; i < _fNumPar; i++)
   {
@@ -63,7 +63,7 @@ covarianceBase::~covarianceBase(){
   const int nThreads = MaCh3Utils::GetNThreads();
   for (int iThread = 0;iThread < nThreads; iThread++)  delete random_number[iThread];
   delete[] random_number;
-  if (throwMatrix != NULL) delete throwMatrix;
+  if (throwMatrix != nullptr) delete throwMatrix;
 }
 
 // ********************************************
@@ -118,7 +118,7 @@ void covarianceBase::init(const char *name, const char *file) {
 
   // Should put in a 
   TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name));
-  if (CovMat == NULL) {
+  if (CovMat == nullptr) {
     MACH3LOG_ERROR("Could not find covariance matrix name {} in file {}", name, file);
     MACH3LOG_ERROR("Are you really sure {} exists in the file?", name);
     throw MaCh3Exception(__FILE__ , __LINE__ );
@@ -349,7 +349,7 @@ void covarianceBase::init(TMatrixDSym* covMat) {
 // Set the covariance matrix for this class
 void covarianceBase::setCovMatrix(TMatrixDSym *cov) {
 // ********************************************
-  if (cov == NULL) {
+  if (cov == nullptr) {
     MACH3LOG_ERROR("Could not find covariance matrix you provided to setCovMatrix");
     throw MaCh3Exception(__FILE__ , __LINE__ );
   }
@@ -1149,7 +1149,7 @@ void covarianceBase::resetIndivStepScale() {
 // HW: Code for throwing from separate throw matrix, needs to be set after init to ensure pos-def
 void covarianceBase::setThrowMatrix(TMatrixDSym *cov){
 // ********************************************
-   if (cov == NULL) {
+   if (cov == nullptr) {
     MACH3LOG_ERROR("Could not find covariance matrix you provided to setThrowMatrix");
     throw MaCh3Exception(__FILE__ , __LINE__ );
   }
@@ -1192,9 +1192,9 @@ void covarianceBase::setThrowMatrix(TMatrixDSym *cov){
 void covarianceBase::updateThrowMatrix(TMatrixDSym *cov){
 // ********************************************
   delete throwMatrix;
-  throwMatrix = NULL;
+  throwMatrix = nullptr;
   delete throwMatrix_CholDecomp;
-  throwMatrix_CholDecomp = NULL;
+  throwMatrix_CholDecomp = nullptr;
   setThrowMatrix(cov);
 }
 

mcmc/FitterBase.cpp

@@ -93,10 +93,9 @@ FitterBase::~FitterBase() {
   clock = nullptr;
   if(stepClock != nullptr) delete stepClock;
   stepClock = nullptr;
-  MACH3LOG_INFO("Closing MaCh3 Fitter Engine");
+  MACH3LOG_DEBUG("Closing MaCh3 Fitter Engine");
 }
 
-
 // *******************
 // Prepare the output tree
 void FitterBase::SaveSettings() {
@@ -1134,8 +1133,8 @@ void FitterBase::RunSigmaVar() {
       TH1D ***sigmaArray_y_norm = new TH1D**[numVar]();
 
       // Set up for single mode
-      TH1D ****sigmaArray_mode_x = NULL;
-      TH1D ****sigmaArray_mode_y = NULL;
+      TH1D ****sigmaArray_mode_x = nullptr;
+      TH1D ****sigmaArray_mode_y = nullptr;
       if (DoByMode)
       {
         sigmaArray_mode_x = new TH1D***[numVar]();