Replacement of Class Referenced with std::shared_ptr

.github/workflows/testing_plugin-template.yml

@@ -39,7 +39,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install libmuparser-dev python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
           pip install numpy
-      - name: Set up the build
+      - name: Configure Plugin
         env:
           CXX: ${{ matrix.config.cxx }}
           CC: ${{ matrix.config.cc }}
@@ -48,8 +48,8 @@ jobs:
           cd plugin-template
           mkdir build
           cd build
-          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" -DUSE_OWN_CRPROPA=ON 
-      - name: Build CRPropa
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" -DUSE_OWN_CRPROPA=On 
+      - name: Build Plugin
         run: |
           cd plugin-template/build
           make
@@ -63,6 +63,75 @@ jobs:
         with:
           name: "test-report_${{matrix.config.os}}"
           path: plugin-template/build/Testing/Temporary/LastTest.log
+  x64-old-crpropa:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "ubuntu-24"
+            os: ubuntu-24.04
+            cxx: "g++-14"
+            cc: "gcc-14"
+            fc: "gfortran-14"
+            swig_builtin: "On" 
+            py: "/usr/bin/python3" 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          ref: "3.3"
+          repository: "CRPropa/CRPropa3"
+      - name: Preinstall
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmuparser-dev python3-venv python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          python -m venv $GITHUB_WORKSPACE/venv
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install numpy
+      - name: Install CRPropa
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          mkdir build
+          cd build
+          cmake .. -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
+          make -j
+          make install
+      - name: Configure Plugin
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/venv/lib
+          cd plugin-template
+          mkdir build
+          cd build
+          cmake .. -DCRPropa_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" -DUSE_OWN_CRPROPA=Off
+      - name: Build Plugin
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/venv/lib
+          cd plugin-template/build
+          make
+      - name: Run tests
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/venv/lib
+          cd plugin-template/build
+          ctest --output-on-failure --repeat until-pass:3
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: "test-report_${{matrix.config.os}}-old-crpropa"
+          path: plugin-template/build/Testing/Temporary/LastTest.log
   arm:
     runs-on: ${{ matrix.config.os }}
     strategy:
@@ -85,7 +154,7 @@ jobs:
           sudo apt-get install libmuparser-dev python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
           pip install numpy
           pip show numpy
-      - name: Set up the build
+      - name: Configure Plugin
         env:
           CXX: ${{ matrix.config.cxx }}
           CC: ${{ matrix.config.cc }}
@@ -94,8 +163,8 @@ jobs:
           cd plugin-template
           mkdir build
           cd build
-          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" -DUSE_OWN_CRPROPA=ON 
-      - name: Build CRPropa
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" -DUSE_OWN_CRPROPA=On 
+      - name: Build Plugin
         run: |
           cd plugin-template/build
           make
@@ -109,7 +178,76 @@ jobs:
         with:
           name: "test-report_${{matrix.config.os}}"
           path: plugin-template/build/Testing/Temporary/LastTest.log
-
+  arm-old-crpropa:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "ubuntu-24"
+            os: ubuntu-24.04-arm
+            cxx: "g++-14"
+            cc: "gcc-14"
+            fc: "gfortran-14"
+            swig_builtin: "On" 
+            py: "/usr/bin/python3" 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          ref: "3.3"
+          repository: "CRPropa/CRPropa3"
+      - name: Preinstall
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmuparser-dev python3-venv python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          python -m venv $GITHUB_WORKSPACE/venv
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install numpy
+          pip show numpy
+      - name: Install CRPropa
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          mkdir build
+          cd build
+          cmake .. -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
+          make -j
+          make install
+      - name: Configure Plugin
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/venv/lib
+          cd plugin-template
+          mkdir build
+          cd build
+          cmake .. -DCRPropa_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" -DUSE_OWN_CRPROPA=Off 
+      - name: Build Plugin
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/venv/lib
+          cd plugin-template/build
+          make
+      - name: Run tests
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/venv/lib
+          cd plugin-template/build
+          ctest --output-on-failure --repeat until-pass:3
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: "test-report_${{matrix.config.os}}-old-crpropa"
+          path: plugin-template/build/Testing/Temporary/LastTest.log
   mac:
     runs-on: ${{ matrix.config.os }}
     strategy:
@@ -130,11 +268,11 @@ jobs:
         run: | 
           brew install hdf5 fftw cfitsio muparser libomp swig 
           python3 -m venv venv
-          source venv/bin/activate
+          source $GITHUB_WORKSPACE/venv/bin/activate
           python -m pip install --upgrade pip
           pip install numpy cmake
           pip show numpy # cross-check numpy version for Python_NumPy_INCLUDE_DIR
-      - name: Set up the build
+      - name: Configure Plugin
         env:
           CXX: ${{ matrix.config.cxx }}
           CC: ${{ matrix.config.cc }}
@@ -152,9 +290,9 @@ jobs:
             -DENABLE_TESTING=On \
             -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \
             -DPython_INSTALL_PACKAGE_DIR=$GITHUB_WORKSPACE/venv/lib/python3.14/site-packages \
-            -DUSE_OWN_CRPROPA=ON
+            -DUSE_OWN_CRPROPA=On
 
-      - name: Build CRPropa
+      - name: Build Plugin
         run: |
           cd plugin-template/build
           make
@@ -170,3 +308,86 @@ jobs:
         with:
           name: "test-report_${{matrix.config.name}}"
           path: plugin-template/build/Testing/Temporary/LastTest.log
+  mac-old-crpropa:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "macos-14"
+            os: macos-14 
+            cxx: "clang++"
+            cc: "clang"
+            fc: "gfortran-14"
+            swig_builtin: "On" #uses swig 4.0.2
+            py: "/usr/bin/python3" # python 3.14
+    steps:
+      - name: Checkout repository 
+        uses: actions/checkout@v6
+        with:
+          ref: "3.3"
+          repository: "CRPropa/CRPropa3"
+      - name: Preinstall 
+        run: | 
+          brew install hdf5 fftw cfitsio muparser libomp swig 
+          python -m venv $GITHUB_WORKSPACE/venv
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install numpy cmake
+          pip show numpy # cross-check numpy version for Python_NumPy_INCLUDE_DIR
+      - name: Install CRPropa
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+          CRPROPA_DATA_PATH: "/Users/runner/work/CRPropa3/CRPropa3/build/data"
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          mkdir build
+          cd build
+          cmake .. \
+            -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv \
+            -DENABLE_PYTHON=True \
+            -DPython_EXECUTABLE=$GITHUB_WORKSPACE/venv/bin/python \
+            -DENABLE_TESTING=On \
+            -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \
+            -DPython_INSTALL_PACKAGE_DIR=$GITHUB_WORKSPACE/venv/lib/python3.14/site-packages
+          make -j
+          make install
+      - name: Configure Plugin
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+          CRPROPA_DATA_PATH: "/Users/runner/work/CRPropa3/CRPropa3/build/data"
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          cd plugin-template
+          mkdir build
+          cd build
+
+          cmake .. \
+            -DCRPropa_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv \
+            -DENABLE_PYTHON=True \
+            -DENABLE_TESTING=On \
+            -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \
+            -DUSE_OWN_CRPROPA=Off
+
+      - name: Build Plugin
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          cd plugin-template/build
+          make
+      - name: Run tests
+        env:
+          CRPROPA_DATA_PATH: "/Users/runner/work/CRPropa3/CRPropa3/plugin-template/build/data"
+        run: |
+          source $GITHUB_WORKSPACE/venv/bin/activate
+          cd plugin-template/build
+          ctest --output-on-failure --repeat until-pass:3
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: "test-report_${{matrix.config.name}}-old-crpropa"
+          path: plugin-template/build/Testing/Temporary/LastTest.log

.gitignore

@@ -12,6 +12,7 @@ install/
 lib/
 share/
 doc/api/
+.vscode/
 
 !final_doc/
 !conda-bld/build.sh

CHANGELOG.md

@@ -1,14 +1,21 @@
 ## CRPropa vNext
 
 ### Bug fixes:
+* Double free error can no be prevented by handing over stack objects as reference to `ref_ptr<T>` instead as pointer
 
 ### New features:
 
 ### Interface changes:
+* `Module::process(Candidate* cand)` removed, now `Module::process(ref_ptr<Candidate> cand)` needs to be overriden instead
+* Stack objects now need to be handed over as reference not as pointer to `ref_ptr<T>`
 
 ### Features that are deprecated and will be removed after this release
 
 ### Removed features
+* `Referenced` class removed, `ref_ptr<T>` now reference counts over `std:shared_ptr<T>`
+* `Module::process(Candidate* cand)` removed, now `Module::process(ref_ptr<Candidate> cand)` needs to be overriden instead. This breaks most plugins, see [Plugin Readme](plugin-template/README.md#compability-with-older-crpropa-versions) for an easy fix.
+* Removed `Clock.h` (can be replaced with `std::chrono::high_resolution_clock` from `chrono.h`)
+* Removed `AssocVector.h` (can be replaced with `std::unordered_map` from `unordered_map.h`)
 
 ### New plugins and resources linked on the webpages
 

CMakeLists.txt

@@ -1,9 +1,18 @@
 cmake_minimum_required(VERSION 3.14)
 
-project(CRPropa Fortran C CXX)
+project(CRPropa VERSION 3.3.0 LANGUAGES Fortran C CXX)
 set(CRPROPA_RELEASE_VERSION 3.3.0+)  # Update for new release
 set(CRPROPA_DATAFILE_VER "2026-07-08")  # Version of data files
 
+# calculate the version tag for easy in code version check
+math(EXPR CRPROPA_VERSION_TAG "
+  ${CRPropa_VERSION_MAJOR}*1000000 + ${CRPropa_VERSION_MINOR}*1000 + ${CRPropa_VERSION_PATCH}
+")
+# if pre release version add one to CRPROPA_VERSION_TAG
+if(${CRPROPA_RELEASE_VERSION} MATCHES "[\+]$")
+  math(EXPR CRPROPA_VERSION_TAG "${CRPROPA_VERSION_TAG} + 1")
+endif()
+
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
@@ -321,7 +330,6 @@ include_directories(include ${CRPROPA_EXTRA_INCLUDES})
 add_library(crpropa SHARED
   ${CMAKE_CURRENT_SOURCE_DIR}/src/base64.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/Candidate.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/src/Clock.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/Common.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/Cosmology.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/EmissionMap.cpp
@@ -530,8 +538,13 @@ if(ENABLE_PYTHON AND Python_FOUND)
     set_target_properties(crpropa-swig PROPERTIES
       BUILD_RPATH "$<TARGET_FILE_DIR:crpropa>"
       INSTALL_RPATH "@loader_path;${CMAKE_INSTALL_FULL_LIBDIR}"
+      LINK_FLAGS "-flat_namespace -undefined suppress"
+    )
+  else()
+    set_target_properties(crpropa-swig PROPERTIES
+      BUILD_RPATH "$<TARGET_FILE_DIR:crpropa>"
+      INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}"
     )
-    set_property(TARGET crpropa-swig APPEND PROPERTY LINK_FLAGS "-flat_namespace -undefined suppress")
   endif(APPLE)