Merge/update CMake, presets,java and tools (#3393)

.gitattributes

@@ -191,19 +191,18 @@ java/examples/testfiles/examples.intro.H5_CreateGroup.txt -text
 java/examples/testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt -text
 java/examples/testfiles/examples.intro.H5_CreateGroupDataset.txt -text
 java/examples/testfiles/examples.intro.H5_ReadWrite.txt -text
-java/lib/ext/slf4j-nop-1.7.33.jar -text svneol=unset#application/zip
-java/lib/ext/slf4j-simple-1.7.33.jar -text svneol=unset#application/zip
+java/lib/ext/slf4j-nop-2.0.6.jar -text svneol=unset#application/zip
+java/lib/ext/slf4j-simple-2.0.6.jar -text svneol=unset#application/zip
 java/lib/hamcrest-core.jar -text svneol=unset#application/java-archive
 java/lib/junit.jar -text svneol=unset#application/java-archive
 java/lib/simplelogger.properties -text
-java/lib/slf4j-api-1.7.33.jar -text svneol=unset#application/zip
+java/lib/slf4j-api-2.0.6.jar -text svneol=unset#application/zip
 java/src/CMakeLists.txt -text
 java/src/Makefile.am -text
 java/src/hdf/CMakeLists.txt -text
 java/src/hdf/hdf5lib/CMakeLists.txt -text
 java/src/hdf/hdf5lib/H5.java -text
 java/src/hdf/hdf5lib/HDF5Constants.java -text
-java/src/hdf/hdf5lib/HDF5GroupInfo.java -text
 java/src/hdf/hdf5lib/HDFArray.java -text
 java/src/hdf/hdf5lib/HDFNativeData.java -text
 java/src/hdf/hdf5lib/callbacks/Callbacks.java -text

CMakeFilters.cmake

@@ -164,11 +164,11 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
       if (NOT SZIP_FOUND)
         find_package (SZIP) # Legacy find
       endif ()
-      if (SZIP_FOUND)
-        set (SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR})
-        set (SZIP_INCLUDE_DIRS ${SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR})
-        set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
-      endif ()
+    endif ()
+    if (SZIP_FOUND)
+      set (SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR})
+      set (SZIP_INCLUDE_DIRS ${SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR})
+      set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
     endif ()
   else ()
     if (BUILD_SZIP_WITH_FETCHCONTENT)
@@ -200,8 +200,6 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
         set (SZIP_PACKAGE_NAME ${SZIP_PACKAGE_NAME})
       endif ()
       set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY})
-    else ()
-      message (FATAL_ERROR "SZIP is Required for SZIP support in HDF5")
     endif ()
   endif ()
   if (SZIP_FOUND)

CMakeInstallation.cmake

@@ -138,7 +138,7 @@ install (
 option (HDF5_PACK_EXAMPLES  "Package the HDF5 Library Examples Compressed File" OFF)
 if (HDF5_PACK_EXAMPLES)
   configure_file (
-      ${HDF_RESOURCES_DIR}/HDF5_Examples.cmake.in
+      ${HDF_RESOURCES_DIR}/examples/HDF5_Examples.cmake.in
       ${HDF5_BINARY_DIR}/HDF5_Examples.cmake @ONLY
   )
   install (
@@ -150,23 +150,27 @@ if (HDF5_PACK_EXAMPLES)
   option (EXAMPLES_USE_RELEASE_NAME "Use the released examples artifact name" OFF)
   option (EXAMPLES_DOWNLOAD "Download to use released examples files" OFF)
   if (EXAMPLES_DOWNLOAD)
-    if (NOT EXAMPLES_USE_LOCALCONTENT)
-      set (EXAMPLES_URL ${EXAMPLES_TGZ_ORIGPATH}/${EXAMPLES_TGZ_ORIGNAME})
+    if (EXAMPLES_USE_RELEASE_NAME)
+      set (EXAMPLES_NAME ${EXAMPLES_TGZ_ORIGNAME})
     else ()
-      set (EXAMPLES_URL ${TGZPATH}/${EXAMPLES_TGZ_ORIGNAME})
+      set (EXAMPLES_NAME ${HDF5_EXAMPLES_COMPRESSED})
     endif ()
-    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-      message (VERBOSE "Examples file is ${EXAMPLES_URL}")
+    if (NOT EXAMPLES_USE_LOCALCONTENT)
+      set (EXAMPLES_URL ${EXAMPLES_TGZ_ORIGPATH}/${EXAMPLES_NAME})
+      file (DOWNLOAD ${EXAMPLES_URL} ${HDF5_BINARY_DIR}/${HDF5_EXAMPLES_COMPRESSED} STATUS EX_DL)
+      message (STATUS "Examples file is ${EXAMPLES_URL} STATUS=${EX_DL}")
+    else ()
+      set (EXAMPLES_URL ${TGZPATH}/${EXAMPLES_NAME})
+      file (COPY_FILE ${EXAMPLES_URL} ${HDF5_BINARY_DIR}/${HDF5_EXAMPLES_COMPRESSED} RESULT EX_DL)
+      message (STATUS "Examples file is ${EXAMPLES_URL} RESULT=${EX_DL}")
     endif ()
-    file (DOWNLOAD ${EXAMPLES_URL} ${HDF5_BINARY_DIR}/${HDF5_EXAMPLES_COMPRESSED})
     if (EXISTS "${HDF5_BINARY_DIR}/${HDF5_EXAMPLES_COMPRESSED}")
       execute_process(
           COMMAND ${CMAKE_COMMAND} -E tar xzf ${HDF5_EXAMPLES_COMPRESSED}
           WORKING_DIRECTORY ${HDF5_BINARY_DIR}
           COMMAND_ECHO STDOUT
       )
     endif ()
-    set (EXAMPLES_USE_RELEASE_NAME ON CACHE BOOL "" FORCE)
   else ()
     if (EXISTS "${HDF5_EXAMPLES_COMPRESSED_DIR}/${HDF5_EXAMPLES_COMPRESSED}")
       execute_process(
@@ -176,20 +180,18 @@ if (HDF5_PACK_EXAMPLES)
       )
     endif ()
   endif ()
-  if (EXAMPLES_USE_RELEASE_NAME)
-    get_filename_component (EX_LAST_EXT ${HDF5_EXAMPLES_COMPRESSED} LAST_EXT)
-    if (${EX_LAST_EXT} STREQUAL ".zip")
-      get_filename_component (EX_DIR_NAME ${HDF5_EXAMPLES_COMPRESSED} NAME_WLE)
-    else ()
-      get_filename_component (EX_DIR_NAME ${HDF5_EXAMPLES_COMPRESSED} NAME_WLE)
-      get_filename_component (EX_DIR_NAME ${EX_DIR_NAME} NAME_WLE)
-    endif ()
-    execute_process(
-        COMMAND ${CMAKE_COMMAND} -E rename ${EX_DIR_NAME} HDF5Examples
-        WORKING_DIRECTORY ${HDF5_BINARY_DIR}
-        COMMAND_ECHO STDOUT
-    )
+  get_filename_component (EX_LAST_EXT ${HDF5_EXAMPLES_COMPRESSED} LAST_EXT)
+  if (${EX_LAST_EXT} STREQUAL ".zip")
+    get_filename_component (EX_DIR_NAME ${HDF5_EXAMPLES_COMPRESSED} NAME_WLE)
+  else ()
+    get_filename_component (EX_DIR_NAME ${HDF5_EXAMPLES_COMPRESSED} NAME_WLE)
+    get_filename_component (EX_DIR_NAME ${EX_DIR_NAME} NAME_WLE)
   endif ()
+  execute_process(
+      COMMAND ${CMAKE_COMMAND} -E rename ${EX_DIR_NAME} HDF5Examples
+      WORKING_DIRECTORY ${HDF5_BINARY_DIR}
+      COMMAND_ECHO STDOUT
+  )
   install (
     DIRECTORY ${HDF5_BINARY_DIR}/HDF5Examples
     DESTINATION ${HDF5_INSTALL_DATA_DIR}
@@ -204,13 +206,13 @@ if (HDF5_PACK_EXAMPLES)
   )
   install (
       FILES
-          ${HDF_RESOURCES_DIR}/CTestScript.cmake
+          ${HDF_RESOURCES_DIR}/examples/CTestScript.cmake
       DESTINATION ${HDF5_INSTALL_DATA_DIR}
       COMPONENT hdfdocuments
   )
   install (
       FILES
-          ${HDF_RESOURCES_DIR}/HDF5_Examples_options.cmake
+          ${HDF_RESOURCES_DIR}/examples/HDF5_Examples_options.cmake
       DESTINATION ${HDF5_INSTALL_DATA_DIR}
       COMPONENT hdfdocuments
   )

CMakeLists.txt

@@ -222,6 +222,7 @@ set (HDF_CONFIG_DIR          ${HDF5_SOURCE_DIR}/config)
 set (HDF_RESOURCES_DIR       ${HDF5_SOURCE_DIR}/config/cmake)
 set (HDF5_SRC_DIR            ${HDF5_SOURCE_DIR}/src)
 set (HDF5_TEST_SRC_DIR       ${HDF5_SOURCE_DIR}/test)
+set (HDF5_TEST_PAR_DIR       ${HDF5_SOURCE_DIR}/testpar)
 set (HDF5_CPP_SRC_DIR        ${HDF5_SOURCE_DIR}/c++)
 set (HDF5_CPP_TST_DIR        ${HDF5_SOURCE_DIR}/c++/test)
 set (HDF5_HL_SRC_DIR         ${HDF5_SOURCE_DIR}/hl)
@@ -236,9 +237,9 @@ set (HDF5_JAVA_JNI_SRC_DIR         ${HDF5_SOURCE_DIR}/java/src/jni)
 set (HDF5_JAVA_HDF5_SRC_DIR        ${HDF5_SOURCE_DIR}/java/src/hdf)
 set (HDF5_JAVA_TEST_SRC_DIR        ${HDF5_SOURCE_DIR}/java/test)
 set (HDF5_JAVA_LIB_DIR             ${HDF5_SOURCE_DIR}/java/lib)
-set (HDF5_JAVA_LOGGING_JAR         ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-1.7.33.jar)
-set (HDF5_JAVA_LOGGING_NOP_JAR     ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7.33.jar)
-set (HDF5_JAVA_LOGGING_SIMPLE_JAR  ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.33.jar)
+set (HDF5_JAVA_LOGGING_JAR         ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-2.0.6.jar)
+set (HDF5_JAVA_LOGGING_NOP_JAR     ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-2.0.6.jar)
+set (HDF5_JAVA_LOGGING_SIMPLE_JAR  ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-2.0.6.jar)
 set (HDF5_DOXYGEN_DIR              ${HDF5_SOURCE_DIR}/doxygen)
 
 set (HDF5_SRC_INCLUDE_DIRS ${HDF5_SRC_DIR})
@@ -573,15 +574,6 @@ if (HDF5_ENABLE_COVERAGE)
   endif ()
 endif ()
 
-#-----------------------------------------------------------------------------
-# Option to indicate using dmalloc
-#-----------------------------------------------------------------------------
-# option (HDF5_ENABLE_USING_DMALLOC "Indicate that dmalloc is used" OFF)
-# if (HDF5_ENABLE_USING_DMALLOC)
-#   find_package (DMALLOC)
-#   set (H5_HAVE_DMALLOC DMALLOC_FOUND)
-# endif ()
-
 #-----------------------------------------------------------------------------
 # Option to indicate using a memory checker
 #-----------------------------------------------------------------------------
@@ -661,6 +653,13 @@ if (${HDF_CFG_NAME} MATCHES "Debug" OR ${HDF_CFG_NAME} MATCHES "Developer")
   mark_as_advanced (HDF5_ENABLE_INSTRUMENT)
 endif ()
 
+#-----------------------------------------------------------------------------
+# Add some definitions for Developer Builds
+#-----------------------------------------------------------------------------
+if (${HDF_CFG_NAME} MATCHES "Developer")
+  include (${HDF_RESOURCES_DIR}/HDF5DeveloperBuild.cmake)
+endif ()
+
 #-----------------------------------------------------------------------------
 # Option to embed library info into executables
 #-----------------------------------------------------------------------------
@@ -989,11 +988,11 @@ if (BUILD_TESTING)
   mark_as_advanced (HDF5_TEST_JAVA)
 
   if (NOT HDF5_EXTERNALLY_CONFIGURED)
-    if (EXISTS "${HDF5_SOURCE_DIR}/test" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/test")
+    if (EXISTS "${HDF5_TEST_SRC_DIR}" AND IS_DIRECTORY "${HDF5_TEST_SRC_DIR}")
       add_subdirectory (test)
     endif ()
     if (H5_HAVE_PARALLEL)
-      if (EXISTS "${HDF5_SOURCE_DIR}/testpar" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/testpar")
+      if (EXISTS "${HDF5_TEST_PAR_DIR}" AND IS_DIRECTORY "${HDF5_TEST_PAR_DIR}")
         add_subdirectory (testpar)
       endif ()
     endif ()

CMakePresets.json

@@ -14,28 +14,35 @@
       }
     },
     {
-      "name": "ci-StdCompression",
+      "name": "ci-CompressionVars",
       "hidden": true,
-      "inherits": "ci-base-tgz",
       "cacheVariables": {
         "BUILD_ZLIB_WITH_FETCHCONTENT": "ON",
         "ZLIB_PACKAGE_NAME": {"type": "STRING", "value": "zlib"},
         "ZLIB_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/madler/zlib/releases/download/v1.2.13"},
         "ZLIB_TGZ_ORIGNAME": {"type": "STRING", "value": "zlib-1.2.13.tar.gz"},
-        "ZLIB_USE_LOCALCONTENT": "OFF",
         "BUILD_SZIP_WITH_FETCHCONTENT": "ON",
         "LIBAEC_PACKAGE_NAME": {"type": "STRING", "value": "libaec"},
         "LIBAEC_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/MathisRosenhauer/libaec/releases/download/v1.0.6"},
-        "LIBAEC_TGZ_ORIGNAME": {"type": "STRING", "value": "libaec-1.0.6.tar.gz"},
-        "LIBAEC_USE_LOCALCONTENT": "OFF"
+        "LIBAEC_TGZ_ORIGNAME": {"type": "STRING", "value": "libaec-1.0.6.tar.gz"}
+      }
+    },
+    {
+      "name": "ci-StdCompression",
+      "hidden": true,
+      "inherits": ["ci-base-tgz", "ci-CompressionVars"],
+      "cacheVariables": {
+        "HDF5_PACKAGE_EXTLIBS": "ON",
+        "ZLIB_USE_LOCALCONTENT": "OFF",
+        "LIBAEC_USE_LOCALCONTENT": "OFF",
+        "HDF5_ENABLE_SZIP_SUPPORT": "ON"
       }
     },
     {
       "name": "ci-base-plugins",
       "hidden": true,
-      "inherits": "ci-base-tgz",
       "cacheVariables": {
-        "PLUGIN_TGZ_NAME": {"type": "STRING", "value": "hdf5_plugins-1.14.0.tar.gz"},
+        "PLUGIN_TGZ_NAME": {"type": "STRING", "value": "hdf5_plugins.tar.gz"},
         "PLUGIN_PACKAGE_NAME": {"type": "STRING", "value": "pl"},
         "BSHUF_TGZ_NAME": {"type": "STRING", "value": "bitshuffle.tar.gz"},
         "BSHUF_PACKAGE_NAME": {"type": "STRING", "value": "bshuf"},
@@ -63,32 +70,49 @@
       }
     },
     {
-      "name": "ci-StdPlugins",
+      "name": "ci-PluginsVars",
       "hidden": true,
-      "inherits": ["ci-base-plugins", "ci-base-tgz"],
       "cacheVariables": {
         "HDF5_ENABLE_PLUGIN_SUPPORT": "ON",
         "PLUGIN_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/HDFGroup/hdf5_plugins/archive/refs/tags"},
-        "PLUGIN_TGZ_ORIGNAME": {"type": "STRING", "value": "hdf5_plugins-1.14.0.tar.gz"}
+        "PLUGIN_TGZ_ORIGNAME": {"type": "STRING", "value": "hdf5_plugins-master.tar.gz"}
       }
     },
-     {
-      "name": "ci-StdExamples",
+    {
+      "name": "ci-StdPlugins",
       "hidden": true,
-      "inherits": "ci-base",
+      "inherits": ["ci-base-plugins", "ci-PluginsVars", "ci-base-tgz"],
       "cacheVariables": {
-        "HDF5_PACK_EXAMPLES": "ON",
-        "HDF5_EXAMPLES_COMPRESSED": {"type": "STRING", "value": "hdf5-examples-2.0.3.tar.gz"},
+          "H5PL_VERS_MAJOR": "1",
+          "H5PL_VERS_MINOR": "12",
+          "H5PL_VERS_RELEASE": "3"
+      }
+    },
+    {
+      "name": "ci-ExamplesVars",
+      "hidden": true,
+      "cacheVariables": {
+        "HDF5_EXAMPLES_COMPRESSED": {"type": "STRING", "value": "hdf5-examples-2.0.4.tar.gz"},
         "HDF5_EXAMPLES_COMPRESSED_DIR": {"type": "STRING", "value": "${sourceParentDir}/temp"},
         "EXAMPLES_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/HDFGroup/hdf5-examples/archive/refs/tags/"},
-        "EXAMPLES_TGZ_ORIGNAME": {"type": "STRING", "value": "2.0.3.tar.gz"},
+        "EXAMPLES_TGZ_ORIGNAME": {"type": "STRING", "value": "2.0.4.tar.gz"}
+      }
+    },
+    {
+      "name": "ci-StdExamples",
+      "hidden": true,
+      "inherits": ["ci-base", "ci-ExamplesVars", "ci-base-tgz"],
+      "cacheVariables": {
+        "EXAMPLES_USE_RELEASE_NAME": "ON",
+        "EXAMPLES_USE_LOCALCONTENT": "OFF",
+        "HDF5_PACK_EXAMPLES": "ON",
         "EXAMPLES_DOWNLOAD": "ON"
       }
     },
-   {
+    {
       "name": "ci-StdShar",
       "hidden": true,
-      "inherits": "ci-StdCompression",
+      "inherits": ["ci-StdCompression", "ci-StdExamples"],
       "cacheVariables": {
         "HDF_PACKAGE_NAMESPACE": {"type": "STRING", "value": "hdf5::"},
         "HDF5_INSTALL_MOD_FORTRAN": "NO",
@@ -105,8 +129,7 @@
         "ci-x64-Release-MSVC",
         "ci-CPP",
         "ci-Java",
-        "ci-StdShar",
-        "ci-StdExamples"
+        "ci-StdShar"
       ]
     },
     {
@@ -117,8 +140,7 @@
         "ci-CPP",
         "ci-Fortran",
         "ci-Java",
-        "ci-StdShar",
-        "ci-StdExamples"
+        "ci-StdShar"
       ]
     },
     {
@@ -129,8 +151,7 @@
         "ci-CPP",
         "ci-Fortran",
         "ci-Java",
-        "ci-StdShar",
-        "ci-StdExamples"
+        "ci-StdShar"
       ]
     },
     {
@@ -141,8 +162,7 @@
         "ci-CPP",
         "ci-Fortran",
         "ci-Java",
-        "ci-StdShar",
-        "ci-StdExamples"
+        "ci-StdShar"
       ]
     }
   ],

bin/README.md

@@ -0,0 +1,30 @@
+# Scripts in `bin` and their purpose
+
+Programs run via `autogen.sh` (or the equivalent in CMake) are indicated.
+
+|Program|Purpose|
+|-------|-------|
+|`buildhdf5`|Convenience script to build HDF5 using the Autotools|
+|`checkapi`|Checks if public API calls are used in internal functions|
+|`chkcopyright`|Checks if files have appropriate copyright statements|
+|`cmakehdf5`|Convenience script to build HDF5 using CMake|
+|`debug-ohdr`|Examines debug output from `H5O_open/close` to look for open objects|
+|`format_source`|Runs `clang-format` over the source files, applying our rules|
+|`genparser`|Creates the flex/bison-based parser files in the high-level library|
+|`h5cc.in`|Input file from which h5cc is created|
+|`h5redeploy.in`|Input file from which h5redeploy is created|
+|`h5vers`|Updates the library version number|
+|`make_err`|Generates the H5E header files (called in `autogen.sh`)|
+|`make_vers`|Generates H5version.h (called in `autogen.sh`)|
+|`make_overflow`|Generates H5overflow.h (called in `autogen.sh`)|
+|`output_filter`|Used in the tools test code to strip extraneous output before we diff files|
+|`restore.sh`|Removes files generated by `autogen.sh`|
+|`runbkprog`|Used by CMake to run test programs in the background|
+|`switch_maint_mode`|Switches maintainer mode on/off in `configure.ac`|
+|`trace`|Adds `TRACE` macros to HDF5 C library source files (run by `autogen.sh`)|
+|`warnhist`|Generates compiler warning statistics for gcc/clang when fed output of make|
+
+## TODO
+
+* chkcopyright is currently semi-broken as it doesn't handle the full variety of copyright headers we need. We're leaving it in place, though, in the hopes that someone will update it in the future.
+* Extending warnhist to better understand the output of additional compilers/languages would be nice.