Rootless heplike

.gitignore

@@ -2,6 +2,7 @@
 *.d
 
 # Compiled Object files
+build/
 *.slo
 *.lo
 *.o
@@ -30,3 +31,6 @@
 *.exe
 *.out
 *.app
+
+# Hidden files
+.*

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 2.8.11)
+cmake_minimum_required (VERSION 2.8.12)
 project (HEPLike)
 enable_testing()
 
@@ -34,25 +34,30 @@ if(COMPILER_SUPPORTS_CXX11)
 endif()
 
 
-
 ###########################
 #
 #    Packages search
 #
 ###########################
-# looking for yaml-cpp
-find_package(Yaml-cpp)
+# Use provided version of yaml-cpp
+add_subdirectory(${PROJECT_SOURCE_DIR}/yaml-cpp EXCLUDE_FROM_ALL)
 # looking for boost
 find_package(Boost REQUIRED)
 # GSL
 find_package(GSL REQUIRED)
-# ROOT:
-find_package(ROOT REQUIRED COMPONENTS MathCore RIO Hist Tree Net)
 
-include(${ROOT_USE_FILE})
-include_directories(${CMAKE_SOURCE_DIR}/include ${ROOT_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS})
-add_definitions(${ROOT_CXX_FLAGS})
+include_directories(${CMAKE_SOURCE_DIR}/yaml-cpp/include)
+include_directories(${CMAKE_SOURCE_DIR}/include ${Boost_INCLUDE_DIRS})
+
+option(USE_ROOT "Compile with ROOT enabled" TRUE)
+if(USE_ROOT)
+  # ROOT:
+  find_package(ROOT REQUIRED COMPONENTS MathCore RIO Hist Tree Net)
 
+  include(${ROOT_USE_FILE})
+  include_directories(${ROOT_INCLUDE_DIRS})
+  add_definitions(${ROOT_CXX_FLAGS})
+endif()
 
 ###########################
 #
@@ -63,23 +68,17 @@ if(NOT DEFINED EXECUTABLE)
   set(EXECUTABLE FALSE)
 endif()
 
-if(NOT DEFINED USE_ROOT)
-  set(USE_ROOT TRUE)
-endif()
-
+# Configure the file
+set(outhdr "${CMAKE_SOURCE_DIR}/include/cmake_variables.h")
+configure_file("${CMAKE_SOURCE_DIR}/include/cmake_variables.h.in" ${outhdr})
 
 ###########################
 #
 #    Libraries
 #
 ###########################
-if(USE_ROOT)
-
-  file(GLOB HL_SOURCES ${CMAKE_SOURCE_DIR}/src/*.cc)
-else()
-  file(GLOB HL_SOURCES ${CMAKE_SOURCE_DIR}/src/HL_Stats.cc ${CMAKE_SOURCE_DIR}/src/HL_nDimGaussian.cc ${CMAKE_SOURCE_DIR}/src/HL_nDimBifurGaussian.cc ${CMAKE_SOURCE_DIR}/src/HL_Limit.cc ${CMAKE_SOURCE_DIR}/src/HL_Gaussian.cc ${CMAKE_SOURCE_DIR}/src/HL_Data.cc ${CMAKE_SOURCE_DIR}/src/HL_BifurGaussian.cc )
 
-endif()  
+file(GLOB HL_SOURCES ${CMAKE_SOURCE_DIR}/src/*.cc)
 
 add_library(HEPLike_static ${HL_SOURCES})
 add_library(HEPLike_shared SHARED ${HL_SOURCES})
@@ -94,8 +93,8 @@ target_link_libraries(HEPLike_shared PRIVATE ${ROOT_LIBRARIES} ${Boost_LIBRARIES
 #
 ###########################
 
-if(EXECUTABLE AND USE_ROOT)
-  
+if(EXECUTABLE)
+
   execute_process (
     COMMAND bash -c "ln -s ../data_toy/ data"
     )
@@ -110,15 +109,21 @@ if(EXECUTABLE AND USE_ROOT)
   add_executable(Data_Fit_example  main/Data_Fit_example.cc)
   add_executable(Test_YAML  main/Test_YAML.cc)
 
-  target_link_libraries(Br_example HEPLike_shared yaml-cpp ${ROOT_LIBRARIES} ${Boost_LIBRARIES} )
-  target_link_libraries(BrBifurGaussian_example HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES} ${GSL_LIBRARIES} )
-  target_link_libraries(Limit_example HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES} ${GSL_LIBRARIES})
-  target_link_libraries(Ndim_Gaussian HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES}  ${GSL_LIBRARIES})  
-  target_link_libraries(ProfLikelihood_example HEPLike_static yaml-cpp   ${ROOT_LIBRARIES} ${Boost_LIBRARIES}  ${GSL_LIBRARIES})  
-  target_link_libraries(Ndim_BifurGaussian_example HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES}  ${GSL_LIBRARIES})  
-  target_link_libraries(Ndim_Likelihood_example  HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES}  ${GSL_LIBRARIES})  
-  target_link_libraries(Data_Fit_example HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES}  ${GSL_LIBRARIES})  
-  target_link_libraries(Test_YAML  HEPLike_static yaml-cpp  ${ROOT_LIBRARIES} ${Boost_LIBRARIES}  ${GSL_LIBRARIES})  
+  if(USE_ROOT)
+    set(LIBRARIES ${ROOT_LIBRARIES} ${Boost_LIBRARIES} ${GSL_LIBRARIES})
+  else()
+    set(LIBARRIES ${Boost_LIBRARIES} ${GSL_LIBRARIES})
+  endif()
+
+  target_link_libraries(Br_example HEPLike_shared yaml-cpp ${LIBRARIES} )
+  target_link_libraries(BrBifurGaussian_example HEPLike_static yaml-cpp  ${LIBRARIES})
+  target_link_libraries(Limit_example HEPLike_static yaml-cpp  ${LIBRARIES})
+  target_link_libraries(Ndim_Gaussian HEPLike_static yaml-cpp  ${LIBRARIES})
+  target_link_libraries(ProfLikelihood_example HEPLike_static yaml-cpp   ${LIBRARIES})
+  target_link_libraries(Ndim_BifurGaussian_example HEPLike_static yaml-cpp  ${LIBRARIES})
+  target_link_libraries(Ndim_Likelihood_example  HEPLike_static yaml-cpp  ${LIBRARIES})
+  target_link_libraries(Data_Fit_example HEPLike_static yaml-cpp  ${LIBRARIES})
+  target_link_libraries(Test_YAML  HEPLike_static yaml-cpp  ${LIBRARIES})
 
   add_test(HL_Test_YAML Test_YAML ../data_toy/examples/test_3dimassym.yaml)
   add_test(HL_Limit Limit_example xterm)
@@ -127,7 +132,7 @@ if(EXECUTABLE AND USE_ROOT)
   add_test(HL_Ndim_Gaussian Ndim_Gaussian)
   add_test(HL_ProfLikelihood_example ProfLikelihood_example ${CMAKE_CURRENT_BINARY_DIR})
   add_test(HL_Ndim_BifurGaussian_example Ndim_BifurGaussian_example)
-
 
-
+
+
 endif()

include/GAMBIT_Stats.h

@@ -0,0 +1,31 @@
+//   HEPLike: High Energy Physics Likelihoods
+//
+//   Module with statistic functions from GAMBIT
+//
+//////////////////////////////////////////////////
+
+/* Copyright (c) 2017-2021, The GAMBIT Collaboration
+   All rights reserved.
+
+   Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+   3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef GAMBIT_STATS_H
+#define GAMBIT_STATS_H
+
+namespace HL_Stats
+{
+  double gaussian_loglikelihood(double theory, double obs, double theoryerr, double obserr, bool profile_systematics);
+  double gaussian_upper_limit(double theory, double obs, double theoryerr, double obserr, bool profile_systematics);
+
+}
+
+#endif

include/HL_Data.h

@@ -3,6 +3,7 @@
 //   Header for baseic class
 //
 //   author: Jihyun Bhom, Marcin Chrzaszcz
+//   author: Tomas Gonzalo
 //////////////////////////////////////////////////
 #ifndef HL_DATA_H
 #define HL_DATA_H
@@ -26,54 +27,53 @@ class HL_Data
 
   HL_Data();
   HL_Data(std::string);
-
+  HL_Data(std::string,YAML::Node);
+
   std::string HFile;
   void Read();
+  std::string find_path(std::string);
   void set_debug_yaml(bool);
-  
-  
-  
+
+
+
  protected:
 
   YAML::Node config;
 
   //HL_LIke info:
   std::string HL_FileName;
   std::string HL_Name;
-  
+
   // bibligraphic data:
   std::string HL_DOI;
   std::string HL_BibCite;
   std::string HL_BibEntry;
   std::string HL_Arxiv;
   std::string HL_SubmissionYear;
   std::string HL_PublicationYear;
-    
+
   // Collaborations numbers
   std::string HL_Collaborations;
   std::string HL_Collaboration_number;
-  
+
   // addition data
   std::string HL_ExperimentalDataLumi; // 1fb for example
   std::string HL_ExperimentalDataYears;
   std::string HL_Decay;
   std::string HL_Kinematics;
-  
-  
+
+
   std::string HL_Author;
   std::string HL_Email;
   std::string HL_Type;
-
-
-
 
 
   bool initialized;
   bool HL_debug_yaml;
 
   void read_standard();
 
-  
+
 };
 
 

include/HL_ExpPoints.h

@@ -17,20 +17,15 @@
 //HEPLike headers
 #include "HL_Stats.h"
 #include "HL_Data.h"
+#include "HL_Root.h"
 
 //external:
 #include "yaml-cpp/yaml.h"
 #include "gsl/gsl_cdf.h"
 #include "gsl/gsl_sf_erf.h"
 #include "gsl/gsl_math.h"
 #include "gsl/gsl_sf_exp.h"
-#include "TFile.h"
-#include "TTree.h"
-#include "TGraph.h"
-#include "TAxis.h"
-#include "TMath.h"
-#include "TH1D.h"
-#include "TBranch.h" 
+
 
 class HL_ExpPoints: public HL_Data
 {
@@ -39,47 +34,39 @@ class HL_ExpPoints: public HL_Data
 
   explicit HL_ExpPoints() :  HL_Data() {};
   explicit HL_ExpPoints(std::string s) :  HL_Data(s) { };
-  
-  
+
+
   void Read();
   double GetChi2(vector<double> theory);
   double GetLogLikelihood(vector<double> theory);
   double GetLikelihood(vector<double> theory);
   bool InitData();
   void SetFun( double FUN( vector<double>, vector<double>));
 
-  
+
  private:
 
   TTree *HL_tree;
   double xmin;
   double xmax;
   double central_mes_val;
-  std::string ObsName;   
-  
+  std::string ObsName;
+
   std::string HL_RootFile;
   std::string HL_PATH;
   std::string HL_weight;
   vector<std::string> HL_obs;
   vector<TBranch*> HL_Branches;
   TBranch *HL_weight_branch;
-
-
-  TFile *f;
-
-  double (*fun)(vector<double>, vector<double>);
-
-  vector<vector<double>> points;
-  vector<double> weights;
-
-
 
 
+  TFile *f;
 
+  double (*fun)(vector<double>, vector<double>);
 
+  vector<vector<double>> points;
+  vector<double> weights;
 
-
-
 };