Merge pull request #110 from rseng/update/analysis-2024-02-28

Update from update/analysis-2024-02-28

_repos/github/CRPropa/CRPropa3/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 +444,43 @@ 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: ${Python_SITELIB}")
+  if(Python_Development_FOUND)
+    message(STATUS "  development libraries: Found!")
+  elseif(Python_Development_FOUND)
+    message(STATUS "  development libraries: NOT found!")
+  endif(Python_Development_FOUND)
+
+
+  #  use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB 
+  set(Python_INSTALL_PACKAGE_DIR "${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})")
+  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 +498,22 @@ 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 +525,15 @@ 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 +544,6 @@ 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 +648,23 @@ 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)

_repos/github/Griffan/VerifyBamID/CMakeLists.txt

@@ -66,6 +66,22 @@ enable_testing()
 add_test(NAME myTest1
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
         COMMAND VerifyBamID --DisableSanityCheck --BamFile resource/test/test.bam --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2)
-#add_test( NAME myTest2
+add_test(NAME myTest2
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND sh -c "diff resource/test/expected/result.Ancestry result.Ancestry && rm result.Ancestry result.selfSM")
+add_test(NAME myTest3
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND VerifyBamID --DisableSanityCheck --PileupFile resource/test/expected/result.Pileup --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2)
+add_test(NAME myTest4
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND sh -c "diff resource/test/expected/result.Ancestry result.Ancestry && rm result.Ancestry result.selfSM")
+add_test(NAME myTest5
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND VerifyBamID --DisableSanityCheck --PileupFile resource/test/test.LongRead.pileup --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2)
+add_test(NAME myTest6
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND sh -c "diff resource/test/expected/test.LongRead.pileup.Ancestry result.Ancestry && rm result.Ancestry result.selfSM")
+
+#add_test( NAME myTestPlot
 #          WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
 #          COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey)

_repos/github/MeasureTransport/MParT/CMakeLists.txt

@@ -88,7 +88,7 @@ if(NOT Kokkos_FOUND)
         FetchContent_Declare(
             kokkos
             GIT_REPOSITORY https://github.com/kokkos/kokkos
-            GIT_TAG 4.2.00
+            GIT_TAG 3.7.00
             GIT_SHALLOW TRUE
         )
         FetchContent_MakeAvailable(kokkos)

_repos/github/PDB-REDO/libcifpp/CMakeLists.txt

@@ -27,7 +27,7 @@ cmake_minimum_required(VERSION 3.16)
 # set the project name
 project(
 	libcifpp
-	VERSION 6.1.0
+	VERSION 7.0.0
 	LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -546,55 +546,7 @@ if(NOT PROJECT_IS_TOP_LEVEL)
 endif()
 
 if(BUILD_TESTING)
-	# We're using the older version 2 of Catch2
-	FetchContent_Declare(
-		Catch2
-		GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-		GIT_TAG v2.13.9)
-
-	FetchContent_MakeAvailable(Catch2)
-
-	list(
-		APPEND
-		CIFPP_tests
-		unit-v2
-		unit-3d
-		format
-		model
-		rename-compound
-		sugar
-		spinner
-		validate-pdbx)
-
-	foreach(CIFPP_TEST IN LISTS CIFPP_tests)
-		set(CIFPP_TEST "${CIFPP_TEST}-test")
-		set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")
-
-		add_executable(
-			${CIFPP_TEST} ${CIFPP_TEST_SOURCE}
-			"${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
-
-		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
-			Catch2::Catch2)
-		target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
-
-		if(MSVC)
-			# Specify unwind semantics so that MSVC knowns how to handle exceptions
-			target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
-		endif()
-
-		add_custom_target(
-			"run-${CIFPP_TEST}"
-			DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
-
-		add_custom_command(
-			OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
-			COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
-			${CMAKE_CURRENT_SOURCE_DIR}/test)
-
-		add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
-			${CMAKE_CURRENT_SOURCE_DIR}/test)
-	endforeach()
+	add_subdirectory(test)
 endif()
 
 # Optionally install the update scripts for CCD and dictionary files

_repos/github/fogellab/multiWGCNA/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: multiWGCNA
 Type: Package
 Title: multiWGCNA
-Version: 1.1.3
+Version: 1.1.4
 Authors@R: c(
     person("Dario", "Tommasini", email="[email protected]",
       role = c("aut","cre"),

_repos/github/gnudatalanguage/gdl/CMakeLists.txt

@@ -13,6 +13,19 @@ if (NOT EXISTS "${CMAKE_SOURCE_DIR}/src/whereami/.git" )
   message(FATAL_ERROR "The src/whereami git submodule is not initialised.\n Please run `git submodule update --init`")
 endif()
 
+# create version string based on git metadata (based on https://github.com/nocnokneo/cmake-git-versioning-example)
+# in case version.hpp does not exist (it is shipped in GDL tarballs but not stored in the repo)
+if (NOT EXISTS "${CMAKE_SOURCE_DIR}/src/version.hpp")
+  find_package(Git REQUIRED)
+  add_custom_target(version
+    ${CMAKE_COMMAND} -D SRC=${CMAKE_SOURCE_DIR}/src/version.hpp.in
+                     -D DST=${CMAKE_BINARY_DIR}/version.hpp
+                     -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
+                     -P ${CMAKE_SOURCE_DIR}/CMakeModules/GenerateVersionHeader.cmake
+    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  )
+endif()
+
 # Set some policies to fix warnings in newer versions of cmake
 # Since VERSION_GREATER_EQUAL is available only since 3.7, we use 
 # VERSION_GREATER combined with VERSION_EQUAL to achieve what we want
@@ -33,8 +46,6 @@ set(CMAKE_C_STANDARD 99)
 # advice by Orion, mandatory for FC 28
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-# X.X.X git becomes release X.X.X+1
-set(VERSION "1.0.4 git")
 enable_testing()
 
 # cf issue 511, managing MultiArch on Debian ...
@@ -1031,6 +1042,10 @@ endif(EXPAT)
 
 add_subdirectory(src)
 
+if (TARGET version)
+  add_dependencies(gdl version)
+endif()
+
 if(NOT PYTHON_MODULE)
     add_subdirectory(testsuite)
 endif(NOT PYTHON_MODULE)

_repos/github/lanl/spiner/CMakeLists.txt

@@ -56,7 +56,7 @@ option(SPINER_BUILD_TESTS "Compile Tests" OFF)
 cmake_dependent_option(SPINER_TEST_USE_KOKKOS "Use kokkos offloading for tests"
                        ON "SPINER_BUILD_TESTS" OFF)
 cmake_dependent_option(
-  SPINER_TEST_USE_KOKKOS_CUDA "Use kokkos cuda offloading for tests" ON
+  SPINER_TEST_USE_KOKKOS_CUDA "Use kokkos cuda offloading for tests (affects submodule-build only)" ON
   "SPINER_TEST_USE_KOKKOS" ON)
 
 # CTest