Merge branch 'HDFGroup:develop' into develop-doxy-doc

.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

CMakeFilters.cmake

@@ -173,20 +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)

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)

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)

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

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")

release_docs/INSTALL_CMake.txt

@@ -285,20 +285,26 @@ IV. Further considerations
       web site. The HDF5 2."X"."Y" product requires a minimum CMake version 3.18.
       If you are using VS2022, the CMake minimum version is 3.21.
 
-   2. If you plan to use Zlib or Szip:
+   2. If you plan to use Zlib or Szip (aka libaec):
       A. Download the binary packages and install them in a central location.
          For example on Windows, create a folder extlibs and install the
          packages there. Add the following CMake options:
             -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib
             -DZLIB_INCLUDE_DIR:PATH=some_location/include
             -DZLIB_USE_EXTERNAL:BOOL=OFF
-            -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib
+            -DSZIP_LIBRARY:FILEPATH=some_location/lib/libszaec.lib
             -DSZIP_INCLUDE_DIR:PATH=some_location/include
+            -Dlibaec_LIBRARY:FILEPATH=some_location/lib/libaec.lib
+            -Dlibaec_INCLUDE_DIR:PATH=some_location/include
             -DSZIP_USE_EXTERNAL:BOOL=OFF
          where "some_location" is the full path to the extlibs folder.
-         Also the appropriate environment variable must be set;
+         Also if the appropriate environment variable is set, the above options are not required;
             set(ENV{ZLIB_ROOT} "some_location")
             set(ENV{SZIP_ROOT} "some_location")
+            set(ENV{libaec_ROOT} "some_location")
+
+        Note that if there is a problem finding the libraries, try adding the
+        CMake variable CMAKE_FIND_DEBUG_MODE:BOOL=ON to the command line.
 
       B. Use source packages from an GIT server by adding the following CMake
          options:
@@ -307,6 +313,8 @@ IV. Further considerations
             ZLIB_GIT_BRANCH="some_branch"
             SZIP_GIT_URL:STRING="https://some_location/szip"
             SZIP_GIT_BRANCH="some_branch"
+            LIBAEC_GIT_URL:STRING="https://some_location/libaec"
+            LIBAEC_GIT_BRANCH="some_branch"
          where "some_location" is the URL to the GIT repository and "some_branch" is
          a branch in the repository, usually the default. Also set
          CMAKE_BUILD_TYPE to the configuration type.
@@ -423,7 +431,7 @@ Notes: CMake and HDF5
    2. CMake support for HDF5 development should be usable on any
       system where CMake is supported. Please send us any comments on
       how CMake support can be improved on any system. Visit the
-      KitWare site for more information about CMake.
+      Kitware site for more information about CMake.
 
    3. Build and test results can be submitted to our CDash server:
       The CDash server for community submissions of hdf5 is at
@@ -443,7 +451,7 @@ Notes: CMake and HDF5
 
 Notes: CMake in General
 
-   1. More information about using CMake can be found at the KitWare site at
+   1. More information about using CMake can be found at the Kitware site at
          www.cmake.org.
 
    2. CMake uses the command line; however, the visual CMake tool is
@@ -505,6 +513,8 @@ These five steps are described in detail below.
         <options> is:
             * SZIP_INCLUDE_DIR:PATH=<path to szip includes directory>
             * SZIP_LIBRARY:FILEPATH=<path to szip/library file>
+            * libaec_INCLUDE_DIR:PATH=<path to libaec includes directory>
+            * libaec_LIBRARY:FILEPATH=<path to libaec/library file>
             * ZLIB_INCLUDE_DIR:PATH=<path to zlib includes directory>
             * ZLIB_LIBRARY:FILEPATH=<path to zlib/library file>
             * <HDF5OPTION>:BOOL=[ON | OFF]
@@ -729,6 +739,8 @@ These five steps are described in detail below.
                ZLIB_GIT_BRANCH="${git_branch}"
                SZIP_GIT_URL:STRING="https://${git_url}/szip"
                SZIP_GIT_BRANCH="${git_branch}"
+               LIBAEC_GIT_URL:STRING="https://${git_url}/libaec"
+               LIBAEC_GIT_BRANCH="${git_branch}"
                PLUGIN_GIT_URL:STRING="https://${git_url}/plugin"
                PLUGIN_GIT_BRANCH="${git_branch}"
            ${git_url} should be changed to your location and ${git_branch} is
@@ -787,7 +799,7 @@ These five steps are described in detail below.
       The HDF Group for daily testing. It should be altered/ignored for the user's
       installation and needs.
 
-   7. More information about using CMake can be found at the KitWare site,
+   7. More information about using CMake can be found at the Kitware site,
          www.cmake.org.
 
    8. Nullsoft Scriptable Install System

release_docs/RELEASE.txt

@@ -548,6 +548,23 @@ Bug Fixes since HDF5-2.0.0 release
 
     Configuration
     -------------
+    - Use pre-installed libaec compression library
+
+      The CMake logic for finding the libaec compression library has been
+      modified for a system-installed version of the library. Two options
+      must be set;
+          HDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO
+          <LIB_PKG_NAME>_USE_EXTERNAL:BOOL=OFF
+      where <LIB_PKG_NAME> is one of ZLIB, ZLIBNG, SZIP, PLUGIN.
+      Note that HDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO disables building all plugins
+      and external libraries in-line with the HDF5 library.
+
+      In addition, the <LIB_PKG_NAME>_ROOT environment variables must be set,
+      where <LIB_PKG_NAME> is one of ZLIB, ZLIBNG, SZIP, libaec, PLUGIN.
+      Note that libaec is the expected name for using the libaec library in place of original szip.
+
+      See INSTALL_CMake.txt for more detailed information.
+
     - Changed the zlib/szip compression find message to FATAL ERROR
 
       The message was changed to indicate that zlib/szip compression was requested and

release_docs/USING_HDF5_CMake.txt

@@ -7,7 +7,7 @@ Notes: This short instruction is written for users who want to quickly
        these instructions for their own applications. For more information,
        see the "Minimum C Project Files for CMake" section.
 
-       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