Merge branch 'develop' into feature_NoThrowParms

.github/workflows/CDImage.yml

@@ -40,7 +40,6 @@ jobs:
     - name: Build Docker image
       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

.github/workflows/CIValidations.yml

@@ -0,0 +1,51 @@
+name: Validations CI
+
+# The events that trigger the workflow
+on:
+  pull_request:
+    branches: [ develop ]
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    name: ${{ matrix.name }}
+
+    strategy:
+      fail-fast: false  # Prevents cancellation of remaining jobs if one fails
+      matrix:
+        include:
+          - name: SplineValidations
+          - name: CovarianceValidations
+          - name: FitterValidations
+    container:
+      image: ghcr.io/mach3-software/mach3:alma9latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+
+    - name: Get MaCh3 Validations
+      run: |
+        cd /opt/
+        git clone https://github.com/mach3-software/MaCh3Validations.git MaCh3Validations
+        cd MaCh3Validations
+        mkdir build
+        cd build
+        cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
+
+    - name: Build MaCh3 Validations
+      run: |
+        cd /opt/MaCh3Validations/build
+        make install # Build the project
+
+    - name: Validations
+      run: |
+        source /opt/MaCh3Validations/build/bin/setup.MaCh3.sh
+        source /opt/MaCh3Validations/build/bin/setup.MaCh3Validations.sh
+        cd /opt/MaCh3Validations/build
+        Apps/${{ matrix.name }}

CMakeLists.txt

@@ -188,6 +188,7 @@ LIST(APPEND ALL_FEATURES
   DEBUG
   MULTITHREAD
   GPU
+  PYTHON
   LOW_MEMORY_STRUCTS
   Oscillator
   Fitter
@@ -232,8 +233,6 @@ if( MaCh3_PYTHON_ENABLED )
 endif()
 
 
-
-
 #This is to export the target properties of MaCh3
 #Anything that links to "MaCh3" will get all of these target properties
 add_library(MaCh3 INTERFACE)
@@ -340,4 +339,4 @@ 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_SOURCE_DIR}/cmake/Templates/Doxyfile.in ${CMAKE_SOURCE_DIR}/Doc/Doxyfile @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/Templates/Doxyfile.in ${CMAKE_CURRENT_SOURCE_DIR}/Doc/Doxyfile @ONLY)

Doc/MaCh3DockerFiles/Alma9/Dockerfile

@@ -18,7 +18,7 @@ RUN git checkout ${MACH3_VERSION}
 
 RUN mkdir -p ${MACH3_INSTALL_DIR}
 WORKDIR ${MACH3_INSTALL_DIR}
-RUN cmake ${MACH3_WORK_DIR}
+RUN cmake -DMaCh3_PYTHON_ENABLED=ON ${MACH3_WORK_DIR}
 RUN make VERBOSE=1 && make install
 
 # KS: Need to set them here, otherwise container using this container will not be able to find MaCh3

Doc/MaCh3DockerFiles/Fedora32/Dockerfile

@@ -18,7 +18,7 @@ RUN git checkout ${MACH3_VERSION}
 
 RUN mkdir -p ${MACH3_INSTALL_DIR}
 WORKDIR ${MACH3_INSTALL_DIR}
-RUN cmake ${MACH3_WORK_DIR}
+RUN cmake -DMaCh3_PYTHON_ENABLED=ON ${MACH3_WORK_DIR}
 RUN make VERBOSE=1
 RUN make install
 

Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile

@@ -24,7 +24,7 @@ RUN git checkout ${MACH3_VERSION}
 
 RUN mkdir -p ${MACH3_INSTALL_DIR}
 WORKDIR ${MACH3_INSTALL_DIR}
-RUN cmake ${MACH3_WORK_DIR}
+RUN cmake -DMaCh3_PYTHON_ENABLED=ON ${MACH3_WORK_DIR}
 RUN make VERBOSE=1
 RUN make install
 

README.md

@@ -4,7 +4,7 @@ The Markov Chain 3 flavour is a framework born in 2013 as a Bayesian MCMC fitter
 The framework has also evolved to allow non MCMC modules to interrogate the likelihoods implemented.
 
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://github.com/mach3-software/MaCh3/blob/develop/LICENSE.txt)
-[![Release - v1.0.0](https://img.shields.io/badge/Release-v1.0.0-2ea44f)](https://github.com/mach3-software/MaCh3/releases)
+[![Release - v1.1.0](https://img.shields.io/badge/Release-v1.1.0-2ea44f)](https://github.com/mach3-software/MaCh3/releases)
 [![Container Image](https://img.shields.io/badge/Container-Image-brightgreen)](https://github.com/mach3-software/MaCh3/pkgs/container/mach3)
 [![Code - Documented](https://img.shields.io/badge/Code-Documented-2ea44f)](https://github.com/mach3-software/MaCh3/wiki)
 [![Code - Doxygen](https://img.shields.io/badge/Code-Doxygen-2ea44f)](https://mach3-software.github.io/MaCh3/index.html)
@@ -15,7 +15,7 @@ Example of plots made using MaCh3 apparent in scientific publications, for more
 <img src="Doc/Plots/Jarlskog.png" alt="MaCh3" align="center" width="200"/>
 
 ## Cite
-When citing MaCh3, please use [on Zenodo](https://zenodo.org/records/10949376) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10949376.svg)](https://doi.org/10.5281/zenodo.10949376).
+When citing MaCh3, please use [on Zenodo](https://zenodo.org/records/7608367) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13642670.svg)](https://doi.org/10.5281/zenodo.13642670).
 
 # How to Compile
 MaCh3 follows standard cmake pattern. By default you should get most optimal build setting although below we list many configurable options:
@@ -32,18 +32,20 @@ Don't forget to:
 source bin/setup.MaCh3.sh
 ```
 ## Building against MaCh3
-If you compiled MaCh3 and sourced it you can simply call
-```
-find_package(MaCh3)
-```
-and cmake will find it. Alternatively, you can use CPM, for example:
+To include MaCh3 in your cmake project you can use following syntax
 ```
 CPMFindPackage(
   NAME MaCh3
   GIT_TAG "blarb"
   GITHUB_REPOSITORY mach3-software/MaCh3
 )
 ```
+Where "blarb" is the MaCh3 version. You can find a list of releases [here](https://github.com/mach3-software/MaCh3/wiki/0.1.-History)  
+If you compiled MaCh3 and sourced it you can simply call
+```
+find_package(MaCh3)
+```
+
 Once you found MaCh3 you might want to link your library against MaCh3. You can do this as follows:
 ```
 target_link_libraries(blarb MaCh3::All)
@@ -55,7 +57,7 @@ Some functionalities rely on setting `Env{MACH3}` which should point to path exp
 
 MaCh3 can be compiled with a python interface by specifying the cmake option
 ```
-cmake ../ MaCh3_PYTHON_ENABLED=ON
+cmake ../ -DMaCh3_PYTHON_ENABLED=ON
 make && make install
 ```
 and then adding the path to the installed module to your `PYTHONPATH` environment variable:

cmake/Templates/MaCh3Config.cmake.in

@@ -10,6 +10,7 @@ set(DEBUG_LEVEL @DEBUG_LEVEL@)
 set(MaCh3_DEBUG_ENABLED @MaCh3_DEBUG_ENABLED@)
 set(MaCh3_MULTITHREAD_ENABLED @MaCh3_MULTITHREAD_ENABLED@)
 set(MaCh3_GPU_ENABLED @MaCh3_GPU_ENABLED@)
+set(MaCh3_PYTHON_ENABLED @MaCh3_PYTHON_ENABLED@)
 set(MaCh3_MINUIT2_ENABLED @MaCh3_MINUIT2_ENABLED@)
 
 get_filename_component(MaCh3_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)

covariance/covarianceBase.cpp

@@ -953,12 +953,6 @@ void covarianceBase::setParameters(const std::vector<double>& pars) {
 	  }
     }
   }
-
-  MACH3LOG_DEBUG("Set parameters to:");
-  for(size_t par_i = 0 ; par_i < pars.size() ; ++par_i){
-    MACH3LOG_DEBUG("{} : {}", par_i, _fPropVal[par_i]);
-  }
-
   // And if pca make the transfer
   if (pca) {
     TransferToPCA();

mcmc/FitterBase.cpp

@@ -175,8 +175,8 @@ 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");
-      throw MaCh3Exception(__FILE__ , __LINE__ );
+      MACH3LOG_CRITICAL("No samples Found! Is this really what you wanted?");
+      //throw MaCh3Exception(__FILE__ , __LINE__ );
     }
 
     // Prepare the output trees

mcmc/MinuitFit.cpp

@@ -37,7 +37,7 @@ void MinuitFit::runMCMC() {
   //KS: add config or something
   minuit->SetPrintLevel(2);
   minuit->SetTolerance(0.01);
-  minuit->SetMaxFunctionCalls(fitMan->raw()["General.NSteps"].as<double>());
+  minuit->SetMaxFunctionCalls(fitMan->raw()["General"]["Minuit2"]["NSteps"].as<double>());
   minuit->SetMaxIterations(10000);
 
   MACH3LOG_INFO("Preparing Minuit");

plotting/plottingUtils/CMakeLists.txt

@@ -21,9 +21,7 @@ target_link_libraries( Plotting ${ROOT_LIBRARIES} MaCh3::Manager )
 
 ## to be compiled into python module needs to be compiled as position independent library
 if( MaCh3_PYTHON_ENABLED )
-
     set_property( TARGET Plotting PROPERTY POSITION_INDEPENDENT_CODE ON )
-
 endif()
 
 install(TARGETS Plotting
@@ -32,4 +30,4 @@ install(TARGETS Plotting
     PUBLIC_HEADER DESTINATION include/plotting
 )
 
-add_library(MaCh3::Plotting ALIAS Plotting)
+add_library(MaCh3::Plotting ALIAS Plotting)

plotting/plottingUtils/inputManager.cpp

@@ -205,7 +205,7 @@ std::vector<std::string> InputManager::getTaggedValues(const std::vector<std::st
     if (valTags.size() == 0) continue;
 
     // count how many of the specified tags match the tags of the current value 
-    int tagCount = 0;
+    unsigned int tagCount = 0;
     for ( const std::string &tag: tags )
     {
       if ( std::find( valTags.begin(), valTags.end(), tag ) != valTags.end() ) 
@@ -734,4 +734,4 @@ void InputManager::fillFileData(InputFile &inputFileDef, bool printThoughts) {
   }
 }
 
-} // namespace MaCh3Plotting
+} // namespace MaCh3Plotting