Merge remote-tracking branch 'origin/update_h5fl' into ts_h5i

qkoziol · Jan 13, 2025 · dd06492 · dd06492
2 parents 43afbb4 + 146da28
commit dd06492
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diff --git a/.github/workflows/cve.yml b/.github/workflows/cve.yml
@@ -30,14 +30,11 @@ jobs:
     steps:
       - uses: actions/[email protected]
 
-      - name: Install Autotools Dependencies (Linux)
-        run: |
-          sudo apt update
-          sudo apt install automake autoconf libtool libtool-bin
       - name: Install HDF5
         run: |
-          ./autogen.sh
-          ./configure --prefix=/usr/local --disable-tests
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DBUILD_TESTING:BOOL=OFF $GITHUB_WORKSPACE
           make
           sudo make install
       - name: Checkout CVE test repository

diff --git a/.github/workflows/netcdf.yml b/.github/workflows/netcdf.yml
@@ -52,6 +52,7 @@ jobs:
             -DHDF5_BUILD_DOC:BOOL=OFF \
             -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON \
             -DZLIB_USE_LOCALCONTENT:BOOL=OFF \
+            -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON \
             -DH5_NO_DEPRECATED_SYMBOLS:BOOL=OFF \
             -DBUILD_TESTING:BOOL=OFF \
             -DCMAKE_INSTALL_PREFIX:PATH=/usr/local \

diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake
@@ -85,6 +85,7 @@ endif ()
 if(NOT DEFINED ZLIBNG_PACKAGE_NAME)
   set(ZLIBNG_PACKAGE_NAME "zlib-ng")
 endif ()
+option (HDF5_ENABLE_ZLIB_SUPPORT "Enable Zlib Filters" OFF)
 if (HDF5_ENABLE_ZLIB_SUPPORT)
   if (NOT H5_ZLIB_HEADER)
     if (NOT ZLIB_USE_EXTERNAL)
@@ -160,6 +161,7 @@ set(H5_SZIP_FOUND FALSE)
 if(NOT DEFINED LIBAEC_PACKAGE_NAME)
   set(LIBAEC_PACKAGE_NAME "libaec")
 endif ()
+option (HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF)
 if (HDF5_ENABLE_SZIP_SUPPORT)
   option (HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" ON)
   if (NOT SZIP_USE_EXTERNAL)
@@ -171,20 +173,26 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
     set(libaec_USE_STATIC_LIBS ${HDF5_USE_LIBAEC_STATIC})
     set(SZIP_FOUND FALSE)
     # Search pure Config mode, there is not a FindSZIP module available
-    find_package (SZIP NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} OPTIONAL_COMPONENTS ${LIBAEC_SEARCH_TYPE})
-    set(H5_SZIP_FOUND ${SZIP_FOUND})
+    find_package (${LIBAEC_PACKAGE_NAME} NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} OPTIONAL_COMPONENTS ${LIBAEC_SEARCH_TYPE})
+    set(H5_SZIP_FOUND ${${LIBAEC_PACKAGE_NAME}_FOUND})
     if (H5_SZIP_FOUND)
       set (H5_SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR})
       set (H5_SZIP_INCLUDE_DIRS ${H5_SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR})
-      set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
+      if(LIBAEC_PACKAGE_NAME STREQUAL "libaec")
+        set (LINK_COMP_LIBS ${LINK_COMP_LIBS} libaec::sz libaec::aec)
+      else ()
+        set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
+      endif ()
     endif ()
+    message (VERBOSE "H5_SZIP_FOUND=${SZIP_FOUND} and LINK_COMP_LIBS=${LINK_COMP_LIBS}")
   else ()
     if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
       EXTERNAL_SZIP_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT} ${HDF5_ENABLE_SZIP_ENCODING})
       message (VERBOSE "Filter SZIP is built using library AEC")
       set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${H5_SZIP_STATIC_LIBRARY})
     endif ()
   endif ()
+  message (VERBOSE "LINK_COMP_LIBS=${LINK_COMP_LIBS}")
   if (H5_SZIP_FOUND)
     set (H5_HAVE_FILTER_SZIP 1)
     set (H5_HAVE_SZLIB_H 1)

diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
@@ -465,11 +465,12 @@ The HDF5 data model, file format, API, library, and tools are open and distribut
         endif ()
       endif ()
       if (H5_SZIP_FOUND AND SZIP_USE_EXTERNAL)
+        set (SZIP_PROJNAME "${LIBAEC_PACKAGE_NAME}")
         if (WIN32)
-          set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${H5_SZIP_INCLUDE_DIR_GEN};SZIP;ALL;/")
+          set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${H5_SZIP_INCLUDE_DIR_GEN};${SZIP_PROJNAME};ALL;/")
         else ()
-          set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${H5_SZIP_INCLUDE_DIR_GEN};SZIP;libraries;/")
-          set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${H5_SZIP_INCLUDE_DIR_GEN};SZIP;configinstall;/")
+          set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${H5_SZIP_INCLUDE_DIR_GEN};${SZIP_PROJNAME};libraries;/")
+          set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${H5_SZIP_INCLUDE_DIR_GEN};${SZIP_PROJNAME};configinstall;/")
         endif ()
       endif ()
       if (PLUGIN_FOUND AND PLUGIN_USE_EXTERNAL)

diff --git a/CMakeTests.cmake b/CMakeTests.cmake
@@ -26,7 +26,7 @@
   option (HDF5_DISABLE_TESTS_REGEX "Regex pattern to set execution of specific tests to DISABLED" "")
   mark_as_advanced (HDF5_DISABLE_TESTS_REGEX)
 
-  option (HDF5_TEST_API "Execute HDF5 API tests" OFF)
+  option (HDF5_TEST_API "Execute HDF5 API tests" ON)
   mark_as_advanced (HDF5_TEST_API)
   if (HDF5_TEST_API)
     option (HDF5_TEST_API_INSTALL "Install HDF5 API tests" OFF)

diff --git a/HDF5Examples/Using_CMake.txt b/HDF5Examples/Using_CMake.txt
@@ -5,7 +5,7 @@
 Notes: This short instruction is written for users who want to quickly build
        HDF5 Examples using the HDF5 binary package using the CMake tools.
 
-       More information about using CMake can be found at the KitWare
+       More information about using CMake can be found at the Kitware
        site, www.cmake.org.
 
        CMake uses the command line; however, the visual CMake tool is

diff --git a/c++/test/dsets.cpp b/c++/test/dsets.cpp
@@ -1451,7 +1451,7 @@ test_read_string(H5File &file)
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_dset(const void *params)
+test_dset(void *params)
 {
     hid_t fapl_id;
     fapl_id     = h5_fileaccess(); // in h5test.c, returns a file access template

diff --git a/c++/test/h5cpputil.h b/c++/test/h5cpputil.h
@@ -138,20 +138,20 @@ verify_val(Type1 x, Type2 value, float epsilon, const char *msg, int line, const
 #ifdef __cplusplus
 extern "C" {
 #endif
-void test_array(const void *params);
-void test_attr(const void *params);
-void test_compound(const void *params);
-void test_dsproplist(const void *params);
-void test_file(const void *params);
-void test_filters(const void *params);
-void test_links(const void *params);
-void test_h5s(const void *params);
-void test_iterate(const void *params);
-void test_object(const void *params);
-void test_reference(const void *params);
-void test_types(const void *params);
-void test_vlstrings(const void *params);
-void test_dset(const void *params);
+void test_array(void *params);
+void test_attr(void *params);
+void test_compound(void *params);
+void test_dsproplist(void *params);
+void test_file(void *params);
+void test_filters(void *params);
+void test_links(void *params);
+void test_h5s(void *params);
+void test_iterate(void *params);
+void test_object(void *params);
+void test_reference(void *params);
+void test_types(void *params);
+void test_vlstrings(void *params);
+void test_dset(void *params);
 
 /* Prototypes for the cleanup routines */
 void cleanup_array(void *params);

diff --git a/c++/test/tarray.cpp b/c++/test/tarray.cpp
@@ -477,7 +477,7 @@ test_array_info()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_array(const void *params)
+test_array(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tattr.cpp b/c++/test/tattr.cpp
@@ -1956,7 +1956,7 @@ test_attr_corder_create_basic(FileCreatPropList &fcpl, FileAccPropList &fapl)
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_attr(const void *params)
+test_attr(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tcompound.cpp b/c++/test/tcompound.cpp
@@ -729,7 +729,7 @@ test_compound_set_size()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_compound(const void *params)
+test_compound(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tdspl.cpp b/c++/test/tdspl.cpp
@@ -114,7 +114,7 @@ test_transfplist()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_dsproplist(const void *params)
+test_dsproplist(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tfile.cpp b/c++/test/tfile.cpp
@@ -968,7 +968,7 @@ test_file_info()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_file(const void *params)
+test_file(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tfilter.cpp b/c++/test/tfilter.cpp
@@ -227,7 +227,7 @@ test_szip_filter(H5File &file1)
  */
 const H5std_string FILE1("tfilters.h5");
 extern "C" void
-test_filters(const void *params)
+test_filters(void *params)
 {
     (void)params;
 

diff --git a/c++/test/th5s.cpp b/c++/test/th5s.cpp
@@ -471,7 +471,7 @@ test_h5s_compound_scalar_read()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_h5s(const void *params)
+test_h5s(void *params)
 {
     (void)params;
 

diff --git a/c++/test/titerate.cpp b/c++/test/titerate.cpp
@@ -440,7 +440,7 @@ test_HDFFV_9920()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_iterate(const void *params)
+test_iterate(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tlinks.cpp b/c++/test/tlinks.cpp
@@ -709,7 +709,7 @@ test_visit(hid_t fapl_id, hbool_t new_format)
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_links(const void *params)
+test_links(void *params)
 {
     hid_t    fapl_id, fapl2_id; /* File access property lists */
     unsigned new_format;        /* Whether to use the new format or not */

diff --git a/c++/test/tobject.cpp b/c++/test/tobject.cpp
@@ -712,7 +712,7 @@ test_intermediate_groups()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_object(const void *params)
+test_object(void *params)
 {
     (void)params;
 

diff --git a/c++/test/trefer.cpp b/c++/test/trefer.cpp
@@ -827,7 +827,7 @@ test_reference_region_1D()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_reference(const void *params)
+test_reference(void *params)
 {
     (void)params;
 

diff --git a/c++/test/ttypes.cpp b/c++/test/ttypes.cpp
@@ -1093,7 +1093,7 @@ test_operators()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_types(const void *params)
+test_types(void *params)
 {
     (void)params;
 

diff --git a/c++/test/tvlstr.cpp b/c++/test/tvlstr.cpp
@@ -934,7 +934,7 @@ test_vl_rewrite()
  *-------------------------------------------------------------------------
  */
 extern "C" void
-test_vlstrings(const void *params)
+test_vlstrings(void *params)
 {
     (void)params;
 

diff --git a/config/cmake/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake
@@ -65,6 +65,8 @@ set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRIN
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include")
 #set(ENV{SZIP_ROOT} "some_location")
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include")
+#set(ENV{libaec_ROOT} "some_location")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -Dlibaec_LIBRARY:FILEPATH=some_location/lib/libaec.lib -Dlibaec_INCLUDE_DIR:PATH=some_location/include")
 
 ### disable using ext zlib
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF")

diff --git a/doxygen/dox/FileFormatSpec.dox b/doxygen/dox/FileFormatSpec.dox
@@ -1,23 +1,7 @@
-/** \page FMT3 HDF5 File Format Specification Version 3.0
+\ref FMT3
 
-\htmlinclude H5.format.html
+\ref FMT2
 
-*/
+\ref FMT11
 
-/** \page FMT2 HDF5 File Format Specification Version 2.0
-
-\htmlinclude H5.format.2.0.html
-
-*/
-
-/** \page FMT11 HDF5 File Format Specification Version 1.1
-
-\htmlinclude H5.format.1.1.html
-
-*/
-
-/** \page FMT1 HDF5 File Format Specification Version 1.0
-
-\htmlinclude H5.format.1.0.html
-
-*/
+\ref FMT1