Merge branch 'master' of bitbucket.org:glavaux/cosmotool

CMakeLists.txt

@@ -13,14 +13,20 @@ set(NumPy_FIND_REQUIRED TRUE)
 include(${CMAKE_SOURCE_DIR}/FindPyLibs.cmake)
 include(${CMAKE_SOURCE_DIR}/FindNumPy.cmake)
 
-get_git_head_revision(HEAD GIT_VER)
-
 option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
 option(BUILD_STATIC_LIBS "Build static libraries." ON)
 option(ENABLE_SHARP "Enable SHARP support." ON)
 option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
 option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
 option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
+option(USE_GIT_VERSION "Use GIT version to pad version number" OFF)
+option(YORICK_SUPPORT "Add for pleasant yorick support" ON)
+option(BUILD_PYTHON "Build the python modules" ON)
+IF(USE_GIT_VERSION)
+  get_git_head_revision(HEAD GIT_VER)
+  SET(EXTRA_VERSION "-${GIT_VER}")
+ENDIF(USE_GIT_VERSION)
+
 
 #IF(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
 #  SET(CosmoTool_local CosmoTool_static)
@@ -32,13 +38,15 @@ MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
 
 include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
 
-IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
+IF(YORICK_SUPPORT)
+  IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
     SET(FOUND_NETCDF4 1)
     FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1")
-ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
+  ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
     SET(FOUND_NETCDF3 1)
     FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
-ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
+  ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
+ENDIF(YORICK_SUPPORT)
 
 find_program(CYTHON cython)
 
@@ -48,7 +56,7 @@ endif(HDF5_ROOTDIR)
 find_package(HDF5 COMPONENTS CXX HL)
 
 
-set(NETCDF_FIND_REQUIRED TRUE)
+set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT})
 set(GSL_FIND_REQUIRED TRUE)
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
@@ -60,14 +68,16 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "0")
-SET(CPACK_PACKAGE_VERSION_PATCH "0-${GIT_VER}")
+SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${GalaxExplorer_VERSION_MAJOR}.${GalaxExplorer_VERSION_MINOR}")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
 SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
 SET(CPACK_SOURCE_IGNORE_FILES 
 "/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile")
 
 add_subdirectory(src)
 add_subdirectory(sample)
-add_subdirectory(python)
+if(BUILD_PYTHON)
+  add_subdirectory(python)
+endif(BUILD_PYTHON)
 
 include(CPack)

sample/CMakeLists.txt

@@ -1,7 +1,9 @@
 SET(tolink ${GSL_LIBRARIES} ${CosmoTool_local} ${CosmoTool_LIBS})
 include_directories(${CMAKE_SOURCE_DIR}/src)
-include_directories(${FFTW3_INCLUDE_DIRS}
+include_directories(${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${GSL_INCLUDE_PATH})
-${EIGEN3_INCLUDE_DIRS} ${NETCDF_INCLUDE_PATH} ${GSL_INCLUDE_PATH})
+if(YORICK_SUPPORT)
+  include_directories(${NETCDF_INCLUDE_PATH})
+endif(YORICK_SUPPORT)
 include_directories(${CMAKE_SOURCE_DIR}/sample)
 
 IF(SHARP_INCLUDE_PATH)
@@ -63,8 +65,10 @@ if (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND)
   IF (FFTW3_LIBRARY_FULL)
     SET(FFTW3_LIB ${FFTW3_LIB} ${FFTW3_LIBRARY_FULL})
   ENDIF (FFTW3_LIBRARY_FULL)
+  IF(YORICK_SUPPORT)
     add_executable(test_fft_calls test_fft_calls.cpp)
     target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIB})
+  ENDIF(YORICK_SUPPORT)
 endif (FFTW3_FOUND AND FFTW3F_FOUND AND  EIGEN3_FOUND)
 
 if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
@@ -81,15 +85,17 @@ target_link_libraries(test_cosmopower ${tolink})
 if (Boost_FOUND)
   include_directories(${Boost_INCLUDE_DIRS})
 
+  IF (YORICK_SUPPORT)
     add_executable(testSmooth testSmooth.cpp)
     target_link_libraries(testSmooth ${tolink})
 
     add_executable(simple3DFilter simple3DFilter.cpp)
     target_link_libraries(simple3DFilter ${tolink})
+  ENDIF (YORICK_SUPPORT)
 endif (Boost_FOUND)
 
-IF (ENABLE_OPENMP)
+IF (ENABLE_OPENMP AND YORICK_SUPPORT)
   add_executable(gadgetToDensity gadgetToDensity.cpp)
   target_link_libraries(gadgetToDensity ${tolink})
-ENDIF (ENABLE_OPENMP)
+ENDIF (ENABLE_OPENMP AND YORICK_SUPPORT)
 

src/CMakeLists.txt

@@ -15,13 +15,15 @@ SET(CosmoTool_SRCS
 IF (ENABLE_OPENMP)
 ENDIF (ENABLE_OPENMP)
 
-IF(FOUND_NETCDF3)
+IF (YORICK_SUPPORT)
+  IF(FOUND_NETCDF3)
 	SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc3.cpp)
-ELSE(FOUND_NETCDF3)
+  ELSE(FOUND_NETCDF3)
-IF(FOUND_NETCDF4)
+  IF(FOUND_NETCDF4)
 	SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc4.cpp)
-ENDIF(FOUND_NETCDF4)
+  ENDIF(FOUND_NETCDF4)
-ENDIF(FOUND_NETCDF3)
+  ENDIF(FOUND_NETCDF3)
+ENDIF(YORICK_SUPPORT)
 
 
 if (HDF5_FOUND)
@@ -59,9 +61,13 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
 	growthFactor.hpp
 )
 
-include_directories(${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
+include_directories(${Boost_INCLUDE_DIRS} ${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
 
-set(CosmoTool_LIBS  ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
+set(CosmoTool_LIBS ${GSL_LIBRARIES})
+if(YORICK_SUPPORT)
+  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
+  include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
+endif(YORICK_SUPPORT)
 if (HDF5_FOUND)
   set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES})
   include_directories(${HDF5_INCLUDE_DIRS})

src/hdf5_array.hpp

@@ -90,10 +90,31 @@ namespace CosmoTool {
   
   #undef HDF5_TYPE
 
+  // Extent generator
+  template<std::size_t r>
+  struct hdf5_extent_gen {
+    typedef typename boost::detail::multi_array::extent_gen<r> type;
+    
+    static inline type build(hsize_t *d)
+    {
+      return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
+    }
+  };
+
+  template<>
+  struct hdf5_extent_gen<0> {    
+    static inline boost::multi_array_types::extent_gen build(hsize_t *d)
+    {
+      return boost::extents;
+    }
+  };
+  
+
 //!_______________________________________________________________________________________
 //!     
 //!     write_hdf5 multi_array
 //!         
+//!     \author Guilhem Lavaux (2014-2015)
 //!     \author leo Goodstadt (04 March 2013)
 //!     
 //!_______________________________________________________________________________________
@@ -216,24 +237,11 @@ namespace CosmoTool {
   class InvalidDimensions: virtual std::exception {
   };
   
-  template<std::size_t r>
-  struct hdf5_extent_gen {
-    typedef typename boost::detail::multi_array::extent_gen<r> type;
-    
-    static inline type build(hsize_t *d)
-    {
-      return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
-    }
-  };
-
-  template<>
-  struct hdf5_extent_gen<0> {    
-    static inline boost::multi_array_types::extent_gen build(hsize_t *d)
-    {
-      return boost::extents;
-    }
-  };
   
+  // ----------------------------------------------------------------------
+  // Conditional resize support
+  // If the Array type support resize then it is called. Otherwise
+  // the dimensions are checked and lead to a failure if they are different
   
   template<typename Array> class array_has_resize {
     struct Fallback { int resize; };
@@ -283,6 +291,8 @@ namespace CosmoTool {
     hdf5_check_array(data, dims);
   }
 
+  // ----------------------------------------------------------------------
+  
   template<typename ArrayType, typename hdf5_data_type>
   void hdf5_read_array_typed(H5::CommonFG& fg, const std::string& data_set_name, 
                              ArrayType& data, 
@@ -311,8 +321,7 @@ namespace CosmoTool {
   {
       typedef typename ArrayType::element T;
       
-      get_hdf5_data_type<T> hdf_data_type;
+      hdf5_read_array_typed(fg, data_set_name, data, get_hdf5_data_type<T>::type(), auto_resize);
-      hdf5_read_array_typed(fg, data_set_name, data, hdf_data_type.type(), auto_resize);
   }