Merge branch 'main' into anigamova-patch-2

.clang-tidy

@@ -0,0 +1,6 @@
+---
+Checks: -*,
+  ,modernize-use-override,
+WarningsAsErrors: '*'
+HeaderFilterRegex: ''
+...

.github/workflows/ci.yml

@@ -28,17 +28,18 @@ jobs:
     strategy:
       matrix:
         python: ["3.8"]
-        root: ["6.22"]
+        root: ["6.22"]  
         include:
           # to deprecate (11_2_X py2)
           - python: "2.7.18"
-            root: "6.22.0"
-          # python 3.9 root 6.24 (12_3_X)
-          - python: "3.9"
-            root: "6.24"
+            root: "6.22.0" 
           # python 3.10 root 6.26
           - python: "3.10"
             root: "6.26.4"
+          # python 3.10 root 6.32 (not available yet)
+          #- python: "3.10"
+          #  root: "6.32" # version 6.30.07 where the conflicting classes were removed from root is not available, so compiling with 6.32.00 where this issue is resolved
+
     runs-on: ubuntu-latest
     name: Compile (py${{ matrix.python }}, root${{ matrix.root }})
 

.github/workflows/cvmfs-ci.yml

@@ -0,0 +1,61 @@
+name: CI with CVMFS
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  test_workflow:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        IMAGE: ["cmscloud/al9-cms"]
+        CMSSW_VERSION: ["CMSSW_14_1_0_pre4"] # ROOT v6.30/07
+        SCRAM_ARCH: ["el9_amd64_gcc12"]
+        include:
+          - IMAGE: "cmscloud/cc7-cms"
+            CMSSW_VERSION: "CMSSW_11_3_4" # ROOT v6.22
+            SCRAM_ARCH: "slc7_amd64_gcc900"
+          - IMAGE: "cmscloud/al9-cms"
+            CMSSW_VERSION: "CMSSW_14_0_0_pre1" # ROOT v6.26/11
+            SCRAM_ARCH: "el9_amd64_gcc12"
+
+    name: Test with ${{ matrix.CMSSW_VERSION }}
+    steps:
+      # checkout the files of this repository
+      - uses: actions/checkout@v4
+      - uses: cvmfs-contrib/github-action-cvmfs@v4
+        with:
+          cvmfs_repositories: 'cms.cern.ch'
+      - uses: rhaschke/docker-run-action@v5
+        with:
+          image: ${{ matrix.IMAGE }}
+          shell: bash
+          options: -v /cvmfs:/cvmfs:shared -v ${{ github.workspace }}:/work/CombinedLimit -w /home/cmsusr -e CMSSW_VERSION=${{ matrix.CMSSW_VERSION }} -e SCRAM_ARCH=${{ matrix.SCRAM_ARCH }}
+          run: | 
+            ls /work/CombinedLimit
+            ls /cvmfs/cms.cern.ch | grep common
+            source /cvmfs/cms.cern.ch/cmsset_default.sh
+            scram project ${CMSSW_VERSION}
+            source /cvmfs/cms.cern.ch/cmsset_default.sh
+            cd ${CMSSW_VERSION}/src
+            cmsenv
+            mkdir -p HiggsAnalysis
+            cp -r /work/CombinedLimit HiggsAnalysis/
+            scramv1 b -j$(nproc)
+            echo ${PATH}
+            root --version
+            combine --help
+            combine HiggsAnalysis/CombinedLimit/data/tutorials/CAT23001/datacard-2-template-analysis.txt -M HybridNew --LHCmode LHC-limits --rMax 2.0 --clsAcc 0.01
+            combine HiggsAnalysis/CombinedLimit/data/tutorials/CAT23001/datacard-3-parametric-analysis.txt -M HybridNew --LHCmode LHC-significance -T 100 --mass 125
+            combine HiggsAnalysis/CombinedLimit/data/tutorials/CAT23001/datacard-3-parametric-analysis.txt -M Significance --mass 125
+            combine HiggsAnalysis/CombinedLimit/data/tutorials/CAT23001/datacard-1-counting-experiment.txt -M MarkovChainMC --tries 100
+            text2workspace.py HiggsAnalysis/CombinedLimit/data/tutorials/CAT23001/datacard-5-multi-signal.txt -P HiggsAnalysis.CombinedLimit.PhysicsModel:floatingXSHiggs --PO modes=ggH,qqH -o datacard-5-multi-signal.root --mass 125
+            combine datacard-5-multi-signal.root -M MultiDimFit --algo singles --mass 125
+            combine HiggsAnalysis/CombinedLimit/data/tutorials/CAT23001/datacard-5-multi-signal.txt -M ChannelCompatibilityCheck --mass 125
+
+
+

.github/workflows/docs.yml

@@ -18,11 +18,8 @@ jobs:
         python-version: 3.8
     - name: Build documentation
       run: |
-        python3 -m pip install mkdocs pymdown-extensions mkdocs-cinder
-        mkdocs build --verbose --clean
-    - name: Deploy documentation
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./site
-
+        python3 -m pip install mkdocs pymdown-extensions mkdocs-material mike
+        git fetch origin gh-pages --depth=1
+        git config user.name ci-bot
+        git config user.email ci-bot@example.com
+        mike deploy --push v9.2.X latest 

BuildFile.xml

@@ -9,6 +9,7 @@
 <lib name="Smatrix"/>
 <use   name="boost_program_options"/>
 <use   name="boost_filesystem"/>
+<flags CXXFLAGS="-DBOOST_BIND_GLOBAL_PLACEHOLDERS -Wno-free-nonheap-object"/>
 <export>
    <lib name="1"/>
 </export>

CMakeLists.txt

@@ -0,0 +1,138 @@
+cmake_minimum_required( VERSION 3.11 FATAL_ERROR )
+set(CMAKE_CXX_STANDARD 17)
+project(CMSCombine VERSION 0.0.1)
+
+option( MODIFY_ROOTMAP "Modify generated Rootmap to take out classes already bundled in StatAnalysis" FALSE )
+
+# Can build with CMake after e.g. setting up StatAnalysis release like this:
+# export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
+# source $ATLAS_LOCAL_ROOT_BASE/user/atlasLocalSetup.sh; asetup StatAnalysis,0.3.2
+# mkdir build; cd build
+# cmake path/to/source # change this path to where-ever you cloned Combine repo to
+# make -j4
+
+list(APPEND CMAKE_PREFIX_PATH $ENV{ROOTSYS})
+find_package( ROOT REQUIRED COMPONENTS Core MathMore RooFitCore RooFit RooStats Minuit HistFactory RooFitHS3)
+find_package(Eigen3 REQUIRED)
+find_package(Vdt)
+find_package(LCG QUIET) # only used for FindBoost in StatAnalysis
+find_package( Boost REQUIRED COMPONENTS program_options filesystem )
+
+message(STATUS "Using ROOT From: ${ROOT_INCLUDE_DIRS}")
+include(${ROOT_USE_FILE})
+
+include_directories(${ROOT_INCLUDE_DIRS})
+include_directories(BEFORE ${CMAKE_CURRENT_SOURCE_DIR})
+add_definitions(${ROOT_CXX_FLAGS})
+
+set(LIBNAME CMSCombine)
+
+file(GLOB HEADERS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} interface/*.h*)
+file(GLOB SOURCES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} src/*.c*)
+
+# includes require "HiggsAnalysis/CombinedLimit" prefix in many places
+# so create a symlink in the build dir
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/HiggsAnalysis)
+execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_BINARY_DIR}/HiggsAnalysis/CombinedLimit" )
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+ROOT_GENERATE_DICTIONARY(G__${LIBNAME} HiggsAnalysis/CombinedLimit/src/classes.h LINKDEF src/classes_def.xml
+        MODULE ${LIBNAME}
+        OPTIONS --deep)
+add_library(${LIBNAME} SHARED ${SOURCES} G__${LIBNAME}.cxx)
+set_target_properties(${LIBNAME} PROPERTIES PUBLIC_HEADER "${HEADERS}")
+target_link_libraries (${LIBNAME} Eigen3::Eigen ${ROOT_LIBRARIES} ${Boost_LIBRARIES} VDT::VDT)
+
+add_executable(combine bin/combine.cpp)
+target_link_libraries(combine PUBLIC ${LIBNAME})
+
+
+# Create empty __init__.py file in the build directory that will be installed
+# in the Python library directories.
+set(empty_init_py "${CMAKE_CURRENT_BINARY_DIR}/__init__.py")
+
+if(MODIFY_ROOTMAP)
+        # edit the generated rootmap in-situ before installation
+
+        # Define the path to the generated file
+        set(GENERATED_FILE_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib${LIBNAME}.rootmap")
+
+        # Define the custom command to search and replace in-place
+        add_custom_command(
+          OUTPUT "${GENERATED_FILE_PATH}.bak"  # Declare the generated file as output
+          DEPENDS "${GENERATED_FILE_PATH}"  # Ensure it depends on the original generated file
+          COMMAND sed -i.bak -e "/class RooParamKeysPdf/d"
+                            -e "/class RooStarMomentMorph/d"
+                            -e "/class RooStats::HistFactory::RooBSpline/d"
+                            -e "/class RooStats::HistFactory::RooBSplineBases/d" 
+                            -e "/class ResponseFunction/d"
+                            -e "/class RooTwoSidedCBShape/d"
+                            "${GENERATED_FILE_PATH}"
+          COMMENT "Removing conflicting classes from generated rootmap"
+        )
+
+        # Define a custom target that depends on the custom command output
+        add_custom_target(
+                ModifyRootmapFile  # Name of the custom target
+                DEPENDS "${GENERATED_FILE_PATH}.bak"  # Ensure the custom command is executed
+        )
+
+        # Add the custom target as a dependency to another target to ensure it's built
+        add_dependencies(combine ModifyRootmapFile)
+endif()
+
+#####################
+# Installation part #
+#####################
+
+
+# Install the dictionaries.
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/lib${LIBNAME}_rdict.pcm
+        ${CMAKE_CURRENT_BINARY_DIR}/lib${LIBNAME}.rootmap
+        DESTINATION lib)
+
+# Install the libraries and header files.
+install(TARGETS ${LIBNAME}
+        LIBRARY DESTINATION lib
+        PUBLIC_HEADER DESTINATION include/HiggsAnalysis/CombinedLimit/interface
+        )
+# dictionary requires classes.h to be in include path exactly as it was specified
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/HiggsAnalysis/CombinedLimit/src/classes.h
+        DESTINATION include/HiggsAnalysis/CombinedLimit/src)
+
+# Install the "combine" executable in the bin directory.
+install(TARGETS combine DESTINATION bin)
+
+# Install the scripts like "text2workspace" to the bin directory.
+install(DIRECTORY scripts/ DESTINATION bin)
+
+# This block is commented out for now, while using the less sophisticated location below
+# Check if the Python library installation directory is outside the install
+# prefix. If it is, we error out because CMake should not install files outside
+# the prefix. In the future, one can imagine to let the user choose where the
+# Python libraries get installed in the prefix with a CMake configuration flag.
+#find_package(Python COMPONENTS Interpreter Development) # To get the Python library install directory into Python_SITELIB
+#cmake_path(IS_PREFIX CMAKE_INSTALL_PREFIX "${Python_SITELIB}" sitelib_in_prefix)
+#if(NOT ${sitelib_in_prefix})
+#    message( FATAL_ERROR "Your Python library installation directory ${Python_SITELIB} "
+#            "is outside the install prefix ${CMAKE_INSTALL_PREFIX}! "
+#            "This is not supported for now. Consider changing the install prefix "
+#            "with the -DCMAKE_INSTALL_PREFIX:PATH=<path> cmake configuration option.")
+#endif()
+#
+## The the Python library installation directory relative to the install prefix.
+#file(RELATIVE_PATH Python_SITELIB_IN_PREFIX ${CMAKE_INSTALL_PREFIX} ${Python_SITELIB})
+
+set(Python_SITELIB_IN_PREFIX "python")
+
+
+message (STATUS "Using Python install location:" ${Python_SITELIB_IN_PREFIX})
+# The python package will be installed in such a way that the original
+# CMSSW-style directory structure is kept, for maximal compatibility.
+install(DIRECTORY python/ DESTINATION ${Python_SITELIB_IN_PREFIX}/HiggsAnalysis/CombinedLimit)
+
+# Create empty __init__.py files in the Python package subdirectories such that
+# the Python imports work.
+file(TOUCH ${empty_init_py})
+INSTALL(FILES ${empty_init_py} DESTINATION ${Python_SITELIB_IN_PREFIX}/HiggsAnalysis)
+INSTALL(FILES ${empty_init_py} DESTINATION ${Python_SITELIB_IN_PREFIX}/HiggsAnalysis/CombinedLimit)

README.md

@@ -4,6 +4,10 @@ HiggsAnalysis-CombinedLimit
 ### Official documentation
 
 All documentation, including installation instructions, is hosted at
-http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/
+http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/latest
 
 The source code of this documentation can be found in the `docs/` folder in this repository.
+
+### Publication 
+
+The `Combine` tool publication can be found [here](https://arxiv.org/abs/2404.06614). Please consider citing this reference if you use the `Combine` tool. 

bin/combine.cpp

@@ -32,7 +32,7 @@
 using namespace std;
 
 // Update whenever we have a new Tag
-std::string combineTagString = "v9.1.0";
+std::string combineTagString = "v9.2.1";
 // 
 
 int main(int argc, char **argv) {
@@ -90,11 +90,11 @@ int main(int argc, char **argv) {
   combiner.statOptions().add_options()
     ("toys,t", po::value<int>(&runToys)->default_value(0), "Number of Toy MC extractions")
     ("seed,s", po::value<int>(&seed)->default_value(123456), "Toy MC random seed")
-    ("hintMethod,H",  po::value<string>(&whichHintMethod)->default_value(""), "Run first this method to provide a hint on the result")
+    ("hintMethod,H",  po::value<string>(&whichHintMethod)->default_value(""), "First run this method to provide a hint on the result")
     ;
   combiner.ioOptions().add_options()
     ("name,n",     po::value<string>(&name)->default_value("Test"), "Name of the job, affects the name of the output tree")
-    ("mass,m",     po::value<float>(&iMass)->default_value(120.), "Higgs mass to store in the output tree")
+    ("mass,m",     po::value<float>(&iMass)->default_value(120.), "Mass to store in the output tree")
     ("dataset,D",  po::value<string>(&dataset)->default_value("data_obs"), "Name of the dataset for observed limit - use this to replace dataset in workspace for example with a toy dataset. Format as file:workspace:object or file:object")
     ("dataMapName",  po::value<string>(&dataMapName)->default_value("data_obs"), "Name of the dataset for observed limit pattern in the datacard")
     ("toysFile",   po::value<string>(&toysFile)->default_value(""), "Read toy mc or other intermediate results from this file")
@@ -186,15 +186,15 @@ int main(int argc, char **argv) {
   }
 
   if (seed == -1) {
-    if (verbose > 0) std::cout << ">>> Using OpenSSL to get a really random seed " << std::endl;
+    if (verbose > 0) std::cout << ">>> Using OpenSSL to get a truly random seed " << std::endl;
     FILE *rpipe = popen("openssl rand 8", "r");
     if (rpipe == 0) { std::cout << "Error when running 'openssl rand 8'" << std::endl; return 2101; }
     if (fread(&seed, sizeof(int), 1, rpipe) != 1) {
         std::cout << "Error when reading from 'openssl rand 8'" << std::endl; return 2102; 
     }
-    std::cout << ">>> Used OpenSSL to get a really random seed " << seed << std::endl;
+    std::cout << ">>> Used OpenSSL to get a truly random seed " << seed << std::endl;
   } else {
-    std::cout << ">>> random number generator seed is " << seed << std::endl;
+    std::cout << ">>> Random number generator seed is " << seed << std::endl;
   }
   RooRandom::randomGenerator()->SetSeed(seed); 
 
@@ -232,7 +232,7 @@ int main(int argc, char **argv) {
     combiner.applyOptions(vm);
     CascadeMinimizer::applyOptions(vm);
   } catch (std::exception &ex) {
-    cerr << "Error when configuring the combiner:\n\t" << ex.what() << std::endl;
+    cerr << "Error when configuring combine:\n\t" << ex.what() << std::endl;
     return 2001;
   }
 
@@ -243,7 +243,7 @@ int main(int argc, char **argv) {
       cerr << "Error when configuring the algorithm " << whichMethod << ":\n\t" << ex.what() << std::endl;
       return 2002;
   }
-  cout << ">>> method used is " << whichMethod << endl;
+  cout << ">>> Method used is " << whichMethod << endl;
 
   if (!whichHintMethod.empty()) {
       map<string, LimitAlgo *>::const_iterator it_hint = methods.find(whichHintMethod);
@@ -255,7 +255,7 @@ int main(int argc, char **argv) {
       } 
       hintAlgo = it_hint->second;
       hintAlgo->applyDefaultOptions();
-      cout << ">>> method used to hint where the upper limit is " << whichHintMethod << endl;
+      cout << ">>> Method used to hint where the upper limit is " << whichHintMethod << endl;
   }
 
   TString fileName = "higgsCombine" + name + "."+whichMethod+"."+massName+toyName+"root";