Merge pull request CRPropa#466 from rafaelab/installPy

Fix problems with Python, improve installation, and improve tests

.github/workflows/test_examples.yml

@@ -8,20 +8,20 @@ jobs:
       fail-fast: false
       matrix:
         config:
-         - name: "ubuntu-20"
-           os: ubuntu-20.04
-           cxx: "g++-9"
-           cc: "gcc-9"
-           fc: "gfortran-9"
-           swig_builtin: "Off" #uses swig 4.0.1
-           py: "/usr/bin/python3" #python 3.8
+         - name: "ubuntu-22"
+           os: ubuntu-22.04
+           cxx: "g++-11"
+           cc: "gcc-11"
+           fc: "gfortran-11"
+           swig_builtin: "On" #uses swig 4.0.2
+           py: "/usr/bin/python3" #python 3.10
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
       - name: Preinstall
         run: |
           sudo apt-get update
-          sudo apt-get install libmuparser-dev python3-dev python-dev python3-numpy python-numpy python3-setuptools python-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          sudo apt-get install libmuparser-dev python3 python3-dev python3-numpy python3-setuptools python-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
           pip3 install -r doc/pages/example_notebooks/requirements.txt # load requrements for notebooks
           pip3 install --upgrade Pygments
           pip3 install --upgrade numpy
@@ -33,14 +33,14 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local -DENABLE_PYTHON=True -DPYTHON_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=Off -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
+          cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local -DENABLE_PYTHON=True -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=Off -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
       - name: Build CRPropa
         run: |
           cd build
           make install -j
       - name: convert notebooks to python 
         env: 
-          PYTHONPATH: "/home/runner/.local/lib/python3.8/site-packages/"
+          PYTHONPATH: "/home/runner/.local"
           runfolder: "/home/runner/notebook_run"
         run: |
           mkdir "$runfolder"
@@ -58,7 +58,7 @@ jobs:
           done
       - name: run all python scripts
         env: 
-          PYTHONPATH: "$/home/runner/.local/lib/python3.8/site-packages/"
+          PYTHONPATH: "/home/runner/.local"
           runfolder: "/home/runner/notebook_run"
         run: | 
           cp doc/pages/example_notebooks/galactic_lensing/crpropa_output.txt "$runfolder"/

.github/workflows/testing_OSX.yaml → .github/workflows/testing_OSX.yml

@@ -7,19 +7,19 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - name: "macos-11"
-            os: macos-11
+          - name: "macos-14"
+            os: macos-14 
             cxx: "clang++"
             cc: "clang"
             fc: "gfortran-11"
             swig_builtin: "On" #uses swig 4.0.2
-            py: "/usr/bin/python"
+            py: "/usr/bin/python3"
     steps:
      - name: Checkout repository 
        uses: actions/checkout@v3 
      - name: Preinstall 
        run: | 
-         brew install hdf5 fftw cfitsio muparser libomp
+         brew install hdf5 fftw cfitsio muparser libomp numpy swig
      - name: Set up the build
        env:
          CXX: ${{ matrix.config.cxx }}
@@ -29,7 +29,7 @@ jobs:
        run: |
         mkdir build
         cd build
-        cmake .. -DENABLE_PYTHON=True -DPYTHON_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=avx
+        cmake .. -DENABLE_PYTHON=True  -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
      - name: Build CRPropa
        run: |
          cd build

.github/workflows/testing.yml → .github/workflows/testing_ubuntu20.yml

@@ -1,4 +1,4 @@
-name: crpropa-testing
+name: crpropa-testing_ubuntu20
 on: [push, pull_request]
 
 jobs:
@@ -30,7 +30,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DENABLE_PYTHON=True -DPYTHON_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
       - name: Build CRPropa
         run: |
           cd build

.github/workflows/testing_ubuntu22.yml

@@ -30,7 +30,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DENABLE_PYTHON=True -DPYTHON_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
       - name: Build CRPropa
         run: |
           cd build

CMakeLists.txt

@@ -1,15 +1,9 @@
-if(APPLE)
-  # rpath specific patches
-  cmake_minimum_required(VERSION 2.8.12)
-else(APPLE)
-  # require > 2.8.8 for FILE DOWNLOAD fixes
-  # allow < 2.8.12 for debian backports
-  cmake_minimum_required(VERSION 2.8.11)
-endif(APPLE)
+cmake_minimum_required(VERSION 3.14)
 
 project(CRPropa Fortran C CXX)
 set(CRPROPA_RELEASE_VERSION 3.2.1+)  # Update for new release
 
+set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
 set(CRPROPA_EXTRA_SOURCES)
@@ -18,17 +12,6 @@ set(CRPROPA_EXTRA_LIBRARIES)
 set(CRPROPA_SWIG_DEFINES)
 set(CRPROPA_SWIG_INPUTS)
 
-macro(USE_CXX11)
-  if(CMAKE_VERSION VERSION_LESS "3.1")
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=gnu++11")
-    endif()
-  else()
-    set(CMAKE_CXX_STANDARD 11)
-  endif()
-endmacro(USE_CXX11)
-USE_CXX11()
-
 if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE)
   set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Wl,--as-needed")
   set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Wl,--as-needed")
@@ -110,6 +93,15 @@ if(ENABLE_TESTING)
   if(APPLE)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DGTEST_USE_OWN_TR1_TUPLE=1")
   endif(APPLE)
+
+  # temporary workaround for newer clang versions due to its handling of unwinding
+  #   see: https://github.com/google/googletest/issues/3062
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 15)
+      add_definitions(-DCRPROPA_TESTS_SKIP_EXCEPTIONS)
+    endif (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 15)
+  endif(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+
 endif(ENABLE_TESTING)
 
 #
@@ -164,12 +156,13 @@ add_subdirectory(libs/sophia)
 list(APPEND CRPROPA_EXTRA_LIBRARIES sophia gfortran)
 list(APPEND CRPROPA_EXTRA_INCLUDES libs/sophia)
 
-# GlacticMagneticLenses
-option(ENABLE_GALACTICMAGETICLENS "Galactic Magnetic Lens" ON)
+# Galactic magnetic lenses
+option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" ON)
 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)
-if(ENABLE_GALACTICMAGETICLENS)
+
+if(ENABLE_GALACTICMAGNETICLENS)
   SET(WITH_GALACTIC_LENSES TRUE)
 
   if(EIGEN_PATH)
@@ -196,7 +189,7 @@ if(ENABLE_GALACTICMAGETICLENS)
   list(APPEND CRPROPA_EXTRA_SOURCES src/magneticLens/ModelMatrix.cpp)
   list(APPEND CRPROPA_EXTRA_SOURCES src/magneticLens/Pixelization.cpp)
   list(APPEND CRPROPA_EXTRA_SOURCES src/magneticLens/ParticleMapsContainer.cpp)
-endif(ENABLE_GALACTICMAGETICLENS)
+endif(ENABLE_GALACTICMAGNETICLENS)
 
 # OpenMP (optional for shared memory multiprocessing)
 option(ENABLE_OPENMP "OpenMP for multithreading" ON)
@@ -451,14 +444,45 @@ endif(BUILD_DOC)
 # Python
 # ----------------------------------------------------------------------------
 option(ENABLE_PYTHON "Create python library via SWIG" ON)
-find_package(PythonInterp)
-find_package(PythonLibs)
 
-if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
+find_package(Python 3.0 REQUIRED COMPONENTS Interpreter Development NumPy)
 
+if(ENABLE_PYTHON AND Python_FOUND)
   find_package(SWIG 3.0 REQUIRED)
-  include(python/Python.cmake)
-  include_directories(${PYTHON_INCLUDE_PATH})
+  include_directories(${Python_INCLUDE_DIRS})
+
+  # print Python info in detail
+  message(STATUS "Python: Found!")
+  message(STATUS "  version ${Python_VERSION}")
+  message(STATUS "  executable: ${Python_EXECUTABLE}")
+  message(STATUS "  libraries: ${Python_LIBRARIES}")
+  message(STATUS "  headers: ${Python_INCLUDE_DIRS}")
+  message(STATUS "  site packages: ${Python_SITELIB}")
+  if(Python_Development_FOUND)
+    message(STATUS "  development libraries: Found!")
+  elseif(Python_Development_FOUND)
+    message(STATUS "  development libraries: NOT found!")
+  endif(Python_Development_FOUND)
+
+
+  #  use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB 
+  if(NOT DEFINED Python_INSTALL_PACKAGE_DIR)
+    set(Python_INSTALL_PACKAGE_DIR "${Python_SITELIB}")
+  endif(NOT DEFINED Python_INSTALL_PACKAGE_DIR)
+  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})")
+  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.")
+  endif(Python_NumPy_FOUND)
 
   if(SWIG_VERSION VERSION_GREATER 4.0)
     # Use swig 4 builtin doxygen instead of external program
@@ -476,39 +500,22 @@ if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
 
   if(ENABLE_SWIG_BUILTIN)
     set(BUILTIN "-builtin")
-    set(PY3 "-py3")
     if(SWIG_VERSION VERSION_LESS 4.0.2)
         message(WARNING, "The SWIG builtin option should not be used with SWIG version below 4.0.2 due to https://github.com/swig/swig/issues/1595")
     endif()
   else(ENABLE_SWIG_BUILTIN)
     set(BUILTIN "")
-    set(PY3 "")
   endif(ENABLE_SWIG_BUILTIN)
 
-  if(PYTHON_VERSION_STRING VERSION_GREATER 3.0)
-    list(APPEND CRPROPA_SWIG_DEFINES -DSWIG_PYTHON3)
-  endif(PYTHON_VERSION_STRING VERSION_GREATER 3.0)
-
-  # tries to import numpy
-  execute_process(COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/python/checkNumpy.py" OUTPUT_VARIABLE numpyIncludePath)
-  if(numpyIncludePath)
-    MESSAGE(STATUS "Found numpy headers in " ${numpyIncludePath})
-    SET(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
-    list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
-    include_directories(${numpyIncludePath})
-  else(numpyIncludePath)
-    MESSAGE(STATUS "Numpy not found.")
-  endif(numpyIncludePath)
-
   set(SWIG_INCLUDES)
   foreach(p in ${SWIG_INCLUDE_DIRECTORIES})
     list(APPEND SWIG_INCLUDES -I${p})
   endforeach()
 
   file(GLOB_RECURSE CRPROPA_SWIG_INPUTS python/*.i)
-  set_source_files_properties( ${CMAKE_CURRENT_BINARY_DIR}/crpropa_wrap.cxx PROPERTIES GENERATED true )
+  set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/crpropa_wrap.cxx PROPERTIES GENERATED true)
   add_custom_target(crpropa-swig-wrapper
-    COMMAND swig ${BUILTIN} -c++ -python ${PY3} -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_SOURCE_DIR}/libs/HepPID/include ${SWIG_INCLUDES} ${CRPROPA_SWIG_DEFINES} -dirprot -o ${CMAKE_CURRENT_BINARY_DIR}/crpropa_wrap.cxx -outdir ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR}/python/crpropa${BUILTIN}.i
+    COMMAND swig ${BUILTIN} -c++ -python -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_SOURCE_DIR}/libs/HepPID/include ${SWIG_INCLUDES} ${CRPROPA_SWIG_DEFINES} -dirprot -o ${CMAKE_CURRENT_BINARY_DIR}/crpropa_wrap.cxx -outdir ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR}/python/crpropa${BUILTIN}.i
     DEPENDS ${CRPROPA_SWIG_INPUTS} ${CRPROPA_INCLUDES} )
 
   if(BUILD_DOC AND DOXYGEN_FOUND)
@@ -520,14 +527,15 @@ if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
   # disable warnings on automatically generated interface code
   set_target_properties(crpropa-swig PROPERTIES COMPILE_FLAGS "-w")
   set_target_properties(crpropa-swig PROPERTIES OUTPUT_NAME "_crpropa")
-  target_link_libraries(crpropa-swig crpropa ${PYTHON_LIBRARIES})
+  target_link_libraries(crpropa-swig crpropa ${Python_LIBRARIES} ${Python_LIBRARY})
   add_dependencies(crpropa-swig crpropa-swig-wrapper)
 
-  install(DIRECTORY "${CMAKE_SOURCE_DIR}/python/crpropa" DESTINATION "${PYTHON_SITE_PACKAGES}")
-  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/crpropa.py" DESTINATION "${PYTHON_SITE_PACKAGES}/crpropa")
-  install(TARGETS crpropa-swig LIBRARY DESTINATION "${PYTHON_SITE_PACKAGES}/crpropa")
+  install(DIRECTORY "${CMAKE_SOURCE_DIR}/python/crpropa" DESTINATION "${Python_INSTALL_PACKAGE_DIR}")
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/crpropa.py" DESTINATION "${Python_INSTALL_PACKAGE_DIR}/crpropa")
+  install(TARGETS crpropa-swig LIBRARY DESTINATION "${Python_INSTALL_PACKAGE_DIR}/crpropa")
   install(FILES ${CRPROPA_SWIG_INPUTS} DESTINATION share/crpropa/swig_interface)
-endif(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
+
+endif(ENABLE_PYTHON AND Python_FOUND)
 
 
 # ----------------------------------------------------------------------------
@@ -538,7 +546,6 @@ install(TARGETS crpropa DESTINATION lib)
 install(DIRECTORY include/ DESTINATION include FILES_MATCHING PATTERN "*.h")
 install(DIRECTORY ${CMAKE_BINARY_DIR}/include/ DESTINATION include FILES_MATCHING PATTERN "*.h")
 install(DIRECTORY ${CMAKE_BINARY_DIR}/data/ DESTINATION share/crpropa/ PATTERN ".git" EXCLUDE)
-
 install(DIRECTORY libs/kiss/include/ DESTINATION include)
 
 # ------------------------------------------------------------------
@@ -643,23 +650,23 @@ if(ENABLE_TESTING)
   endif(WITH_GALACTIC_LENSES)
 
   # python tests
-  if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
+  if(ENABLE_PYTHON AND Python_FOUND)
     CONFIGURE_FILE(test/testMagneticLensPythonInterface.py testMagneticLensPythonInterface.py COPYONLY)
     if(numpyIncludePath AND WITH_GALACTIC_LENSES)
-      add_test(testMagneticLensPythonInterface ${PYTHON_EXECUTABLE} testMagneticLensPythonInterface.py)
+      add_test(testMagneticLensPythonInterface ${Python_EXECUTABLE} testMagneticLensPythonInterface.py)
     endif(numpyIncludePath AND WITH_GALACTIC_LENSES)
 
     CONFIGURE_FILE(test/testSimulationExecution.py testSimulationExecution.py COPYONLY)
-    add_test(testSimulationExecution ${PYTHON_EXECUTABLE} testSimulationExecution.py)
+    add_test(testSimulationExecution ${Python_EXECUTABLE} testSimulationExecution.py)
 
     CONFIGURE_FILE(test/testDiffusionSDE.py testDiffusionSDE.py COPYONLY)
-    add_test(testDiffusionSDE ${PYTHON_EXECUTABLE} testDiffusionSDE.py)
+    add_test(testDiffusionSDE ${Python_EXECUTABLE} testDiffusionSDE.py)
 
     CONFIGURE_FILE(test/testMomentumDiffusion.py testMomentumDiffusion.py COPYONLY)
-    add_test(testMomentumDiffusion ${PYTHON_EXECUTABLE} testMomentumDiffusion.py)
+    add_test(testMomentumDiffusion ${Python_EXECUTABLE} testMomentumDiffusion.py)
 
     CONFIGURE_FILE(test/testPythonExtension.py testPythonExtension.py COPYONLY)
-    add_test(testPythonExtension ${PYTHON_EXECUTABLE} testPythonExtension.py)
-  endif(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
+    add_test(testPythonExtension ${Python_EXECUTABLE} testPythonExtension.py)
+  endif(ENABLE_PYTHON AND Python_FOUND)
 
 endif(ENABLE_TESTING)