Numpy2 implementation and updates on testing

.github/workflows/testing_OSX.yml

@@ -13,14 +13,15 @@ jobs:
             cc: "clang"
             fc: "gfortran-14"
             swig_builtin: "On" #uses swig 4.0.2
-            py: "/usr/bin/python3"
     steps:
      - name: Checkout repository 
        uses: actions/checkout@v4 
      - name: Preinstall 
        run: | 
-         brew install hdf5 fftw cfitsio muparser libomp swig python3
+         brew reinstall python@3.13 llvm@15
+         brew install hdf5 fftw cfitsio muparser libomp swig 
          pip install numpy==1.26.4 cmake
+         pip show numpy # cross-check numpy version for Python_Numpy_INCLUDE_DIR
      - name: Set up the build
        env:
          CXX: ${{ matrix.config.cxx }}
@@ -30,7 +31,35 @@ jobs:
        run: |
         mkdir build
         cd build
-        cmake .. -DENABLE_PYTHON=True  -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
+
+        # define paths for LLVM, Python, and OpenMP
+        export LLVM_DIR=$(brew --prefix llvm@15)
+        export PYTHON_VERSION=3.13
+        export LLVM_VERSION=15.0.7
+        export OMP_VERSION=$(brew list --versions libomp | awk '{print $2}')
+        export OMP_DIR=$(brew --prefix libomp)
+        export PYTHON_DIR=/Library/Frameworks/Python.framework/Versions/3.13/
+
+        # print paths for debugging
+        echo "Using LLVM_DIR: $LLVM_DIR"
+        echo "Using OMP_DIR: $OMP_DIR"
+        echo "python version: $(python --version) from $(which python)"
+        echo "Using Python_DIR: $PYTHON_DIR"
+
+        cmake .. \
+          -DCMAKE_INSTALL_PREFIX=/Users/runner/work/CRPropa3/CRPropa3/build \
+          -DPython_EXECUTABLE=$PYTHON_DIR/bin/python$PYTHON_VERSION \
+          -DPython_LIBRARY=$PYTHON_DIR/lib/libpython$PYTHON_VERSION.dylib \
+          -DPython_INCLUDE_PATH=$PYTHON_DIR/include/python$PYTHON_VERSION \
+          -DCMAKE_C_COMPILER=$LLVM_DIR/bin/clang \
+          -DCMAKE_CXX_COMPILER=$LLVM_DIR/bin/clang++ \
+          -DOpenMP_CXX_FLAGS="-fopenmp -I${OMP_DIR}/include" \
+          -DOpenMP_C_FLAGS="-fopenmp =libomp -I$OMP_DIR/include" \
+          -DOpenMP_libomp_LIBRARY=$OMP_DIR/$OMP_VERSION/lib/libomp.dylib \
+          -DOpenMP_C_LIB_NAMES=libomp.dylib \
+          -DOpenMP_CXX_LIB_NAMES=libomp.dylib \
+          -DNO_TCMALLOC=TRUE \
+          -DPython_NumPy_INCLUDE_DIR=/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/numpy/core/include
      - name: Build CRPropa
        run: |
          cd build

.github/workflows/testing_ubuntu22.yml

@@ -21,7 +21,10 @@ jobs:
       - name: Preinstall
         run: |
           sudo apt-get update
-          sudo apt-get install libmuparser-dev python3 python3-numpy python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          sudo apt-get install libmuparser-dev python3 python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          pip install --upgrade pip
+          pip install numpy 
+          pip show numpy
       - name: Set up the build
         env:
           CXX: ${{ matrix.config.cxx }}

.github/workflows/testing_ubuntu24.yml

@@ -0,0 +1,93 @@
+name: crpropa-testing_ubuntu24
+on: [push, pull_request]
+
+jobs:
+  x64:
+    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@v4
+      - name: Preinstall
+        run: |
+          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
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" 
+      - name: Build CRPropa
+        run: |
+          cd build
+          make
+      - name: Run tests
+        run: |
+          cd build
+          make test
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: "test-report_${{matrix.config.os}}"
+          path: build/Testing/Temporary/LastTest.log
+  arm:
+    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@v4
+      - name: Preinstall
+        run: |
+          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
+          pip show numpy
+      - name: Set up the build
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" 
+      - name: Build CRPropa
+        run: |
+          cd build
+          make
+      - name: Run tests
+        run: |
+          cd build
+          make test 
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: "test-report_${{matrix.config.os}}"
+          path: build/Testing/Temporary/LastTest.log

CMakeLists.txt

@@ -157,7 +157,7 @@ list(APPEND CRPROPA_EXTRA_LIBRARIES sophia gfortran)
 list(APPEND CRPROPA_EXTRA_INCLUDES libs/sophia)
 
 # Galactic magnetic lenses
-option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" ON)
+option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" OFF)
 option(INSTALL_EIGEN "Install provided EIGEN headers" OFF)
 SET(EIGEN_PATH  "" CACHE STRING "Use EIGEN from this path instead of the version shipped with CRPropa")
 SET(WITH_GALACTIC_LENSES FALSE)
@@ -467,23 +467,29 @@ if(ENABLE_PYTHON AND Python_FOUND)
     message(STATUS "  development libraries: NOT found!")
   endif(Python_Development_FOUND)
 
-
+  
   #  use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB
   set(Python_INSTALL_PACKAGE_DIR "${Python_SITELIB}" CACHE PATH "folder in which the python package is installed")
   message(STATUS "  package install directory: ${Python_INSTALL_PACKAGE_DIR}")
-
-
+
   # look for NumPy
   if(Python_NumPy_FOUND)
-    set(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
-    list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
-    include_directories(${Python_NumPy_INCLUDE_DIRS})
-    message(STATUS "NumPy: Found!")
-    message(STATUS "  headers: ${Python_NumPy_INCLUDE_DIRS} (version ${Python_NumPy_VERSION})")
+  set(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
+  list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
+  include_directories(${Python_NumPy_INCLUDE_DIRS})
+  message(STATUS "NumPy: Found!")
+  message(STATUS "  headers: ${Python_NumPy_INCLUDE_DIRS} (version ${Python_NumPy_VERSION})")
   elseif(Python_NumPy_FOUND)
-    message(STATUS "NumPy: NOT found!")
-    message(STATUS "  CRPropa might work just fine with Python, but features like Galactic lenses will not be available.")
+  message(STATUS "NumPy: NOT found!")
+  message(STATUS "  CRPropa might work just fine with Python, but features like Galactic lenses will not be available.")
   endif(Python_NumPy_FOUND)
+
+  # deactivate lenses if NumPy version is >= 2.0
+  if(Python_NumPy_VERSION VERSION_GREATER_EQUAL 2.0 AND WITH_GALACTIC_LENSES)
+    set(WITH_GALACTIC_LENSES FALSE CACHE BOOL "" FORCE)
+    set(ENABLE_GALACTICMAGNETICLENS OFF CACHE BOOL "" FORCE)
+    message(WARNING "NumPy version >= 2.0 detected, disabling Galactic lenses support")
+  endif()
 
   if(SWIG_VERSION VERSION_GREATER 4.0)
     # Use swig 4 builtin doxygen instead of external program

doc/pages/example_notebooks/targeting/Targeting.ipynb

@@ -91,43 +91,46 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import healpy as hp\n",
     "import matplotlib.pylab as plt\n",
+    "import crpropa as crp\n",
     "\n",
-    "crdata = np.genfromtxt('TargetedEmission.txt')\n",
-    "Id = crdata[:,3]\n",
-    "E = crdata[:,4] * EeV\n",
-    "px = crdata[:,8]\n",
-    "py = crdata[:,9]\n",
-    "pz = crdata[:,10]\n",
-    "w = crdata[:,29]\n",
-    "lons = np.arctan2(-1. * py, -1. *px)\n",
-    "lats = np.pi / 2 - np.arccos( -pz / np.sqrt(px*px + py*py+ pz*pz) )\n",
+    "# If CRPropa was compiled without the GalacticMagneticLens the ParticleMapsContainer does not exist\n",
+    "if hasattr(crp, 'ParticleMapsContainer'):\n",
+    "    crdata = np.genfromtxt('TargetedEmission.txt')\n",
+    "    Id = crdata[:,3]\n",
+    "    E = crdata[:,4] * EeV\n",
+    "    px = crdata[:,8]\n",
+    "    py = crdata[:,9]\n",
+    "    pz = crdata[:,10]\n",
+    "    w = crdata[:,29]\n",
+    "    lons = np.arctan2(-1. * py, -1. *px)\n",
+    "    lats = np.pi / 2 - np.arccos( -pz / np.sqrt(px*px + py*py+ pz*pz) )\n",
     "\n",
-    "M = ParticleMapsContainer()\n",
-    "for i in range(len(E)):\n",
-    "    M.addParticle(int(Id[i]), E[i], lons[i], lats[i], w[i])\n",
+    "    M = ParticleMapsContainer()\n",
+    "    for i in range(len(E)):\n",
+    "        M.addParticle(int(Id[i]), E[i], lons[i], lats[i], w[i])\n",
     "\n",
-    "###################################################################\n",
-    "# WARNING\n",
-    "# The calls M.getEnergies()/getParticleIds()/getMap() all segfault.\n",
-    "################################################################### \n",
+    "    ###################################################################\n",
+    "    # WARNING\n",
+    "    # The calls M.getEnergies()/getParticleIds()/getMap() all segfault.\n",
+    "    ################################################################### \n",
     "\n",
-    "#stack all maps\n",
-    "#crMap = np.zeros(49152)\n",
-    "#for pid in M.getParticleIds():\n",
-    "    #energies = M.getEnergies(int(pid))\n",
-    "    #for i, energy in enumerate(energies):\n",
-    "        #continue\n",
-    "        #crMap += M.getMap(int(pid), energy * eV )\n",
-    "#\n",
-    "##plot maps using healpy\n",
-    "#hp.mollview(map=crMap, title='Targeted emission')\n",
-    "#plt.show()"
+    "    #stack all maps\n",
+    "    #crMap = np.zeros(49152)\n",
+    "    #for pid in M.getParticleIds():\n",
+    "        #energies = M.getEnergies(int(pid))\n",
+    "        #for i, energy in enumerate(energies):\n",
+    "            #continue\n",
+    "            #crMap += M.getMap(int(pid), energy * eV )\n",
+    "    #\n",
+    "    ##plot maps using healpy\n",
+    "    #hp.mollview(map=crMap, title='Targeted emission')\n",
+    "    #plt.show()"
    ]
   },
   {