Merge branch 'develop' into fix_chain_restart

mach3-software · Feb 3, 2025 · 431a39f · 431a39f
2 parents 9a3abdb + b87fbc8
commit 431a39f
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diff --git a/.github/CIscripts/RAM.sh b/.github/CIscripts/RAM.sh
@@ -16,7 +16,7 @@ source bin/setup.NuOscillator.sh
 NUM_CORES=$(nproc)
 
 # Start the executable in the background
-./bin/MCMCTutorial Inputs/FitterConfig.yaml &
+./bin/MCMCTutorial Inputs/FitterConfig.yaml General:MCMC:NSteps:100000 &
 
 # Get the PID of the process
 PID=$!

diff --git a/.github/workflows/CIBuild.yml b/.github/workflows/CIBuild.yml
@@ -34,6 +34,10 @@ jobs:
             file: Doc/MaCh3DockerFiles/Rocky9/Dockerfile
             tag: rocky9latest
             cmakeoptions: -DMaCh3_PYTHON_ENABLED=ON
+          - os: Alma9 NoMultithreading
+            file: Doc/MaCh3DockerFiles/Alma9/Dockerfile
+            tag: alma9latest
+            cmakeoptions: -DMaCh3_PYTHON_ENABLED=ON -DMaCh3_MULTITHREAD_ENABLED=OFF
 
     name: Build CI ${{ matrix.os }}
 
@@ -44,4 +48,4 @@ jobs:
       run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
 
     - name: Build the Docker image
-      run: docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag }} --build-arg MACH3_VERSION=${{ github.head_ref }} --build-arg CMAKE_OPTIONS="${{ matrix.cmakeoptions }}"
+      run: docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag }} --build-arg MACH3_VERSION="${{ github.head_ref }}" --build-arg CMAKE_OPTIONS="${{ matrix.cmakeoptions }}"
diff --git a/.github/workflows/README.md b/.github/workflows/README.md
@@ -0,0 +1,51 @@
+# Actions
+
+Summary of currently implemented bots
+
+## Benchmark
+* Performs several action like reweight and save output in nice chart
+
+## CDImage
+* Creates container after each commit to develop or after tag
+
+## CIBuild
+* Checks compilation on several resources
+
+## CIPythonValidations
+* Testin of pyMaCh3
+
+## CIValidations
+* Unit and integration test of MaCh3
+
+## CodeQL
+* Code scanning of MaCh3
+
+## Doxygen
+* Creates doxygen and spinhx documentation for MaCh3
+
+## Label
+* Label each PR based on modified files
+
+## Linter
+* Lint code base (currently C++ turned off)
+
+## MakeRelase
+* Make realse after tag is made
+
+## Meme
+* Nothing to add, cool meme for PR
+
+## Newsletter
+* Make weekly summary of
+
+## PRtittleChecker
+* Ensures each PR starts with suffix like tidy: for example
+
+## Stale
+* Tags stale PRs and issues
+
+## TagTutorial
+* Make tag of tutorial after MaCh3 is tagged to ensure both have corresponding tags
+
+## Telemetry
+* Add telemetry like RAM and CPU usage for each PR
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@ set(CMAKE_VERBOSE_MAKEFILE ON)
 # CMake version check
 cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
 
-project(MaCh3 VERSION 1.3.4 LANGUAGES CXX)
+project(MaCh3 VERSION 1.4.0 LANGUAGES CXX)
 set(MaCh3_VERSION ${PROJECT_VERSION})
 
 #LP - This option name is confusing, but I wont change it now.

diff --git a/Diagnostics/CombineMaCh3Chains.cpp b/Diagnostics/CombineMaCh3Chains.cpp
@@ -1,13 +1,11 @@
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wuseless-cast"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wold-style-cast"
-#pragma GCC diagnostic ignored "-Wconversion"
-#pragma GCC diagnostic ignored "-Wformat-nonliteral"
 // C++ includes
 #include <unistd.h>
 
+// MaCh3 includes
+#include "manager/manager.h"
+#include "samplePDF/Structs.h"
+
+_MaCh3_Safe_Include_Start_ //{
 // ROOT includes
 #include "TList.h"
 #include "TFile.h"
@@ -17,10 +15,7 @@
 #include "TFileMerger.h"
 #include "TKey.h"
 #include "TROOT.h"
-#pragma GCC diagnostic pop
-
-// MaCh3 includes
-#include "manager/manager.h"
+_MaCh3_Safe_Include_End_ //}
 
 /// @file CombineMaCh3Chains
 /// @author Ewan Miller

diff --git a/Diagnostics/DiagMCMC.cpp b/Diagnostics/DiagMCMC.cpp
@@ -9,7 +9,7 @@ void DiagMCMC(const std::string& inputFile, const std::string& config)
 {
   MACH3LOG_INFO("File for study: {}", inputFile);
 
-  YAML::Node Settings = YAML::LoadFile(config);
+  YAML::Node Settings = M3OpenConfig(config);
 
   // Make the processor
   auto Processor = std::make_unique<MCMCProcessor>(inputFile);

diff --git a/Diagnostics/GetPenaltyTerm.cpp b/Diagnostics/GetPenaltyTerm.cpp
@@ -1,10 +1,8 @@
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wuseless-cast"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wold-style-cast"
-#pragma GCC diagnostic ignored "-Wconversion"
-#pragma GCC diagnostic ignored "-Wformat-nonliteral"
+// MaCh3 includes
+#include "manager/manager.h"
+#include "samplePDF/Structs.h"
+
+_MaCh3_Safe_Include_Start_ //{
 // ROOT includes
 #include "TFile.h"
 #include "TBranch.h"
@@ -22,14 +20,7 @@
 #include "TColor.h"
 #include "TObjString.h"
 #include "TROOT.h"
-#pragma GCC diagnostic pop
-
-#ifdef MULTITHREAD
-#include "omp.h"
-#endif
-
-#include "manager/manager.h"
-
+_MaCh3_Safe_Include_End_ //}
 
 /// @file GetPenaltyTerm.cpp
 /// @brief KS: This file contains the implementation of the function to extract specific penalty terms from systematic chains.
@@ -85,7 +76,7 @@ void ReadXSecFile(const std::string& inputFile)
   XSecFile["Systematics"] = YAML::Node(YAML::NodeType::Sequence);
   for(unsigned int i = 0; i < XsecCovPos.size(); i++)
   {
-    YAML::Node YAMLDocTemp = YAML::LoadFile(XsecCovPos[i]);
+    YAML::Node YAMLDocTemp = M3OpenConfig(XsecCovPos[i]);
     for (const auto& item : YAMLDocTemp["Systematics"]) {
       XSecFile["Systematics"].push_back(item);
     }

diff --git a/Diagnostics/ProcessMCMC.cpp b/Diagnostics/ProcessMCMC.cpp
@@ -74,7 +74,7 @@ void ProcessMCMC(const std::string& inputFile)
   // Make the processor)
   auto Processor = std::make_unique<MCMCProcessor>(inputFile);
 
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   const bool PlotCorr = GetFromManager<bool>(Settings["PlotCorr"], false);
@@ -152,7 +152,7 @@ void ProcessMCMC(const std::string& inputFile)
 
 void MultipleProcessMCMC()
 {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   constexpr Color_t PosteriorColor[] = {kBlue-1, kRed, kGreen+2};
@@ -318,7 +318,7 @@ void MultipleProcessMCMC()
 // KS: Calculate Bayes factor for a given hypothesis, most informative are those related to osc params. However, it make relative easy interpretation for switch dials
 void CalcBayesFactor(const std::unique_ptr<MCMCProcessor>& Processor)
 {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   std::vector<std::string> ParNames;
@@ -338,7 +338,7 @@ void CalcBayesFactor(const std::unique_ptr<MCMCProcessor>& Processor)
 
 void CalcSavageDickey(const std::unique_ptr<MCMCProcessor>& Processor)
 {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   std::vector<std::string> ParNames;
@@ -356,7 +356,7 @@ void CalcSavageDickey(const std::unique_ptr<MCMCProcessor>& Processor)
 
 void CalcParameterEvolution(const std::unique_ptr<MCMCProcessor>& Processor)
 {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   std::vector<std::string> ParNames;
@@ -371,7 +371,7 @@ void CalcParameterEvolution(const std::unique_ptr<MCMCProcessor>& Processor)
 
 void CalcBipolarPlot(const std::unique_ptr<MCMCProcessor>& Processor)
 {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   std::vector<std::string> ParNames;
@@ -383,7 +383,7 @@ void CalcBipolarPlot(const std::unique_ptr<MCMCProcessor>& Processor)
 }
 
 void GetTrianglePlot(const std::unique_ptr<MCMCProcessor>& Processor) {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   for (const auto& dg : Settings["TrianglePlot"])
@@ -433,7 +433,7 @@ void DiagnoseCovarianceMatrix(const std::unique_ptr<MCMCProcessor>& Processor, c
   Canvas->Print(Form("Correlation_%s.pdf[", OutName.c_str()), "pdf");
   Canvas->Print(Form("Covariance_%s.pdf[", OutName.c_str()), "pdf");
 
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   const int entries = int(Processor->GetnSteps());
@@ -579,7 +579,7 @@ void DiagnoseCovarianceMatrix(const std::unique_ptr<MCMCProcessor>& Processor, c
 
 void ReweightPrior(const std::unique_ptr<MCMCProcessor>& Processor)
 {
-  YAML::Node card_yaml = YAML::LoadFile(config.c_str());
+  YAML::Node card_yaml = M3OpenConfig(config.c_str());
   YAML::Node Settings = card_yaml["ProcessMCMC"];
 
   const auto& Prior = Settings["PriorReweighting"];

diff --git a/Diagnostics/RHat.cpp b/Diagnostics/RHat.cpp
@@ -1,10 +1,8 @@
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wuseless-cast"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wold-style-cast"
-#pragma GCC diagnostic ignored "-Wconversion"
-#pragma GCC diagnostic ignored "-Wformat-nonliteral"
+// MaCh3 includes
+#include "manager/manager.h"
+#include "samplePDF/Structs.h"
+
+_MaCh3_Safe_Include_Start_ //{
 // ROOT includes
 #include "TObjArray.h"
 #include "TChain.h"
@@ -20,14 +18,7 @@
 #include "TColor.h"
 #include "TStyle.h"
 #include "TROOT.h"
-#pragma GCC diagnostic pop
-
-#ifdef MULTITHREAD
-#include "omp.h"
-#endif
-
-// MaCh3 includes
-#include "manager/manager.h"
+_MaCh3_Safe_Include_End_ //}
 
 /// @file RHat.cpp
 /// @brief This executable calculates the \f$ \hat{R} \f$ estimator for Markov Chain Monte Carlo (MCMC) convergence.

diff --git a/Diagnostics/RHat_HighMem.cpp b/Diagnostics/RHat_HighMem.cpp
@@ -1,10 +1,8 @@
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wuseless-cast"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wfloat-conversion"
-#pragma GCC diagnostic ignored "-Wold-style-cast"
-#pragma GCC diagnostic ignored "-Wconversion"
-#pragma GCC diagnostic ignored "-Wformat-nonliteral"
+// MaCh3 includes
+#include "manager/manager.h"
+#include "samplePDF/Structs.h"
+
+_MaCh3_Safe_Include_Start_ //{
 // ROOT includes
 #include "TObjArray.h"
 #include "TChain.h"
@@ -20,14 +18,7 @@
 #include "TColor.h"
 #include "TStyle.h"
 #include "TROOT.h"
-#pragma GCC diagnostic pop
-
-#ifdef MULTITHREAD
-#include "omp.h"
-#endif
-
-// MaCh3 includes
-#include "manager/manager.h"
+_MaCh3_Safe_Include_End_ //}
 
 /// @file RHat.cpp
 /// @brief This executable calculates the \f$ \hat{R} \f$ estimator for Markov Chain Monte Carlo (MCMC) convergence.

diff --git a/Doc/Doxyfile b/Doc/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "MaCh3"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.3.4
+PROJECT_NUMBER         = 1.4.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

diff --git a/Doc/MaCh3DockerFiles/Rocky9/Dockerfile b/Doc/MaCh3DockerFiles/Rocky9/Dockerfile
@@ -5,6 +5,8 @@ FROM kamilskwarczynski/nukamil:latest AS mach3_build
 # Add a label for the author
 LABEL maintainer="The MaCh3 Collaboration"
 LABEL website="https://mach3-software.github.io/MaCh3/"
+LABEL compiler="GNU 11.4.1"
+LABEL root_version="v6.30.04"
 LABEL org.opencontainers.image.description="Official MaCh3 container"
 
 # Declare the build argument

diff --git a/README.md b/README.md
@@ -128,7 +128,6 @@ The following fitting algorithms are available:
 | MINUIT2    | [Ref](https://cds.cern.ch/record/2296388/)     | Yes      |
 | PSO        | [Ref](https://doi.org/10.1162/EVCO_r_00180)    | No       |
 
-
 ## Debug
 Several debugging options are available which are heavy for RAM and performance and, therefore not used by default. To enable it:
 ```bash
@@ -160,6 +159,7 @@ Based on several test here are recommended version:
 | Fedora32    | ✅     |
 | CentOS7     | ❔     |
 | Windows     | ❌     |
+| MacOS       | ❌     |
 
 ✅ - Part of CI/CD <br>
 ❔ - Not part of CI/CD but used by some users/developers so it might work <br>

diff --git a/cmake/Templates/setup.MaCh3.sh.in b/cmake/Templates/setup.MaCh3.sh.in
@@ -59,13 +59,19 @@ function add_to_PYTHONPATH () {
     d=$(cd -- "$d" && { pwd -P || pwd; }) 2>/dev/null  # canonicalize symbolic links
     if [ -z "$d" ]; then continue; fi  # skip nonexistent directory
 
-    case ":$PYTHONPATH:" in
-      *":$d:"*) :;;
-      *) export PYTHONPATH=$d:$PYTHONPATH;;
-    esac
+    if [ "$d" == "/usr/bin" ] || [ "$d" == "/usr/bin64" ] || [ "$d" == "/usr/local/bin" ] || [ "$d" == "/usr/local/bin64" ]; then
+      case ":$PYTHONPATH:" in
+        *":$d:"*) :;;
+        *) export PYTHONPATH=$PYTHONPATH:$d;;
+      esac
+    else
+      case ":$PYTHONPATH:" in
+        *":$d:"*) :;;
+        *) export PYTHONPATH=$d:$PYTHONPATH;;
+      esac
+    fi
   done
 }
-
 fi