Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5 into hdf…

…5_1_10

.github/workflows/main.yml

@@ -36,7 +36,7 @@ jobs:
             os: ubuntu-latest
             build_type: "Release"
             cpp: ON
-            fortran: OFF
+            fortran: ON
             java: ON
             ts: OFF
             hl: ON

.github/workflows/pr-check.yml

@@ -31,7 +31,7 @@ jobs:
             os: ubuntu-latest
             build_type: "Release"
             cpp: ON
-            fortran: OFF
+            fortran: ON
             java: ON
             ts: OFF
             hl: ON

MANIFEST

@@ -206,13 +206,74 @@
 
 ./doxygen/aliases
 ./doxygen/Doxyfile.in
+./doxygen/dox/About.dox
+./doxygen/dox/Cookbook.dox
+./doxygen/dox/DDLBNF110.dox
+./doxygen/dox/FileFormatSpec.dox
+./doxygen/dox/GettingStarted.dox
+./doxygen/dox/H5AC_cache_config_t.dox
+./doxygen/dox/H5Acreate.dox
+./doxygen/dox/H5Aiterate.dox
+./doxygen/dox/H5Fget_info.dox
+./doxygen/dox/H5Lget_info_by_idx.dox
+./doxygen/dox/H5Lget_info.dox
+./doxygen/dox/H5Literate_by_name.dox
+./doxygen/dox/H5Literate.dox
+./doxygen/dox/H5Lvisit_by_name.dox
+./doxygen/dox/H5Lvisit.dox
+./doxygen/dox/H5Oget_info_by_idx.dox
+./doxygen/dox/H5Oget_info_by_name.dox
+./doxygen/dox/H5Oget_info.dox
+./doxygen/dox/H5Ovisit_by_name.dox
+./doxygen/dox/H5Ovisit.dox
+./doxygen/dox/H5Sencode.dox
+./doxygen/dox/MetadataCachingInHDF5.dox
+./doxygen/dox/OtherSpecs.dox
+./doxygen/dox/Overview.dox
+./doxygen/dox/ReferenceManual.dox
+./doxygen/dox/Specifications.dox
+./doxygen/dox/TechnicalNotes.dox
 ./doxygen/dox/api-compat-macros.dox
-./doxygen/dox/mainpage.dox
+./doxygen/dox/maybe_metadata_reads.dox
 ./doxygen/dox/rm-template.dox
+./doxygen/examples/FF-IH_FileGroup.gif
+./doxygen/examples/FF-IH_FileObject.gif
+./doxygen/examples/FileFormatSpecChunkDiagram.jpg
+./doxygen/examples/H5Pset_metadata_read_attempts.c
+./doxygen/examples/H5Pset_object_flush_cb.c
+./doxygen/examples/H5.format.1.0.html
+./doxygen/examples/H5.format.1.1.html
+./doxygen/examples/H5.format.2.0.html
+./doxygen/examples/H5.format.html
+./doxygen/examples/H5A_examples.c
+./doxygen/examples/H5D_examples.c
 ./doxygen/examples/H5Fclose.c
 ./doxygen/examples/H5Fcreate.c
+./doxygen/examples/H5F_examples.c
+./doxygen/examples/H5Pget_metadata_read_attempts.1.c
+./doxygen/examples/H5Pget_metadata_read_attempts.2.c
+./doxygen/examples/H5Pget_metadata_read_attempts.3.c
+./doxygen/examples/H5Pget_object_flush_cb.c
+./doxygen/examples/ImageSpec.html
+./doxygen/examples/PaletteExample1.gif
+./doxygen/examples/Palettes.fm.anc.gif
+./doxygen/examples/TableSpec.html
+./doxygen/examples/ThreadSafeLibrary.html
+./doxygen/examples/VFL.html
 ./doxygen/examples/hello_hdf5.c
+./doxygen/hdf5_footer.html
+./doxygen/hdf5_header.html
+./doxygen/hdf5_navtree_hacks.js
+./doxygen/hdf5doxy.css
+./doxygen/hdf5doxy_layout.xml
+./doxygen/img/FF-IH_FileGroup.gif
+./doxygen/img/FF-IH_FileObject.gif
+./doxygen/img/FileFormatSpecChunkDiagram.jpg
 ./doxygen/img/HDFG-logo.png
+./doxygen/img/PaletteExample1.gif
+./doxygen/img/Palettes.fm.anc.gif
+./doxygen/img/ftv2node.png
+./doxygen/img/ftv2pnode.png
 
 ./examples/Attributes.txt
 ./examples/Makefile.am
@@ -548,6 +609,7 @@
 ./src/H5err.txt
 ./src/H5detect.c
 ./src/H5make_libsettings.c
+./src/H5module.h
 ./src/H5mpi.c
 ./src/H5overflow.txt
 ./src/H5private.h

bin/checkposix

@@ -44,7 +44,7 @@ foreach $arg (@ARGV) {
     #
     # If a user specifies one file, process it no matter what so people
     # can inspect files we normally skip (like H5system.c).
-    if($#ARGV gt 0 and $filename =~ /H5FDmulti|H5FDstdio|H5VLpassthru|H5system|H5detect|H5make_libsettings/) {
+    if($#ARGV gt 0 and $filename =~ /H5FDmulti|H5FDstdio|H5system|H5detect|H5make_libsettings/) {
         print "$filename is exempt from using Standard library macro wrappers\n";
         next;
     }
@@ -84,7 +84,7 @@ foreach $arg (@ARGV) {
         # Now find all function calls on this line which don't start with 'H'
         while (($name)=/\b([a-z_A-GI-Z]\w*)\s*\(/) {
             $_ = $';
-              
+
             # Ignore C statements that look sort of like function
             # calls.
             next if $name =~ /^(if|for|offsetof|return|sizeof|switch|while|void)$/;
@@ -141,7 +141,7 @@ foreach $arg (@ARGV) {
             }
 
             # TESTING (not comprehensive - just noise reduction)
-            
+
             # Test macros and functions (testhdf5.h)
             next if $name =~ /^(AddTest|TestErrPrintf|TestSummary|TestCleanup|TestShutdown)$/;
             next if $name =~ /^(CHECK|CHECK_PTR|CHECK_PTR_NULL|CHECK_PTR_EQ|CHECK_I)$/;

c++/src/CMakeLists.txt

@@ -199,11 +199,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}"
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT cpplibraries
 )

config/clang-warnings/error-general

@@ -26,9 +26,6 @@
 #
 -Wunused-variable
 #
-#     H5VLpassthru.c
-#       -Werror=unused-parameter
-#
 -Wunused-parameter
 #
 #

config/clang-warnings/noerror-general

@@ -26,9 +26,6 @@
 #
 -Wunused-variable
 #
-#     H5VLpassthru.c
-#       -Werror=unused-parameter
-#
 -Wunused-parameter
 #
 #

config/cmake/HDFCompilerFlags.cmake

@@ -134,7 +134,7 @@ if (NOT MSVC AND NOT MINGW)
       # gcc automatically inlines based on the optimization level
       # this is just a failsafe
       list (APPEND H5_CFLAGS "-finline-functions")
-    elseif (CMAKE_C_COMPILER_ID STREQUAL "Clang")
+    elseif (CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
       ADD_H5_FLAGS (HDF5_CMAKE_C_FLAGS "${HDF5_SOURCE_DIR}/config/clang-warnings/general")
       if (HDF5_ENABLE_WARNINGS_AS_ERRORS)
         ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/clang-warnings/error-general")
@@ -160,13 +160,13 @@ if (NOT MSVC AND NOT MINGW)
       list (APPEND H5_CFLAGS "-Winline -Wreorder -Wport -Wstrict-aliasing")
     elseif (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND CMAKE_C_COMPILER_VERSION VERSION_GREATER_EQUAL 4.8)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/developer-general")
-    elseif (CMAKE_C_COMPILER_ID STREQUAL "Clang")
+    elseif (CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/clang-warnings/developer-general")
     endif ()
   else ()
     if (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND CMAKE_C_COMPILER_VERSION VERSION_GREATER_EQUAL 4.8)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/no-developer-general")
-    elseif (CMAKE_C_COMPILER_ID STREQUAL "Clang")
+    elseif (CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/clang-warnings/no-developer-general")
     endif ()
   endif ()

config/cmake/libh5cc.in

@@ -29,4 +29,4 @@ printf 'dir is %s\n' "$dir"
 
 export PKG_CONFIG_PATH=$dir/lib/pkgconfig
 
-@_PKG_CONFIG_COMPILER@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@-@_PKG_CONFIG_VERSION@` $@
+@_PKG_CONFIG_COMPILER@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@` $@

config/gnu-warnings/error-general

@@ -3,7 +3,6 @@
 # circumstances, so ask the compiler to treat them as errors:
 #
 -Werror=bad-function-cast
--Werror=declaration-after-statement
 -Werror=implicit-function-declaration
 -Werror=missing-declarations
 -Werror=missing-prototypes
@@ -30,9 +29,6 @@
 #
 -Wunused-variable
 #
-#     H5VLpassthru.c
-#       -Werror=unused-parameter
-#
 -Wunused-parameter
 #
 #

config/gnu-warnings/noerror-general

@@ -3,7 +3,6 @@
 # circumstances, so ask the compiler to treat them as errors:
 #
 -Wbad-function-cast
--Wdeclaration-after-statement
 -Wimplicit-function-declaration
 -Wmissing-declarations
 -Wmissing-prototypes
@@ -30,9 +29,6 @@
 #
 -Wunused-variable
 #
-#     H5VLpassthru.c
-#       -Werror=unused-parameter
-#
 -Wunused-parameter
 #
 #

configure.ac

@@ -1089,18 +1089,37 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   AC_SUBST([DOXYGEN_OPTIMIZE_OUTPUT_FOR_C])
   AC_SUBST([DOXYGEN_MACRO_EXPANSION])
   AC_SUBST([DOXYGEN_OUTPUT_DIRECTORY])
-
+  AC_SUBST([DOXYGEN_EXAMPLES_DIRECTORY])
+  AC_SUBST([DOXYGEN_LAYOUT_FILE])
+  AC_SUBST([DOXYGEN_HTML_HEADER])
+  AC_SUBST([DOXYGEN_HTML_FOOTER])
+  AC_SUBST([DOXYGEN_HTML_EXTRA_STYLESHEET])
+  AC_SUBST([DOXYGEN_HTML_EXTRA_FILES])
+  AC_SUBST([DOXYGEN_SERVER_BASED_SEARCH])
+  AC_SUBST([DOXYGEN_EXTERNAL_SEARCH])
+  AC_SUBST([DOXYGEN_SEARCHENGINE_URL])
+
+# SRCDIR Environment variables used inside doxygen macro for the source location:
   DOXYGEN_PACKAGE=${PACKAGE_NAME}
   DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
   DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
   DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
-  DOXYGEN_PROJECT_BRIEF="C-API Reference"
+  DOXYGEN_PROJECT_BRIEF=
   DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox'
   DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
   DOXYGEN_MACRO_EXPANSION=YES
   DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs
-
-  DX_INIT_DOXYGEN([HDF5], [../doxygen/Doxyfile], [hdf5lib_docs])
+  DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples $(SRCDIR)/src $(SRCDIR)/examples $(SRCDIR)/test'
+  DOXYGEN_LAYOUT_FILE='$(SRCDIR)/doxygen/hdf5doxy_layout.xml'
+  DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
+  DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
+  DOXYGEN_HTML_EXTRA_STYLESHEET='$(SRCDIR)/doxygen/hdf5doxy.css'
+  DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png'
+  DOXYGEN_SERVER_BASED_SEARCH=NO
+  DOXYGEN_EXTERNAL_SEARCH=NO
+  DOXYGEN_SEARCHENGINE_URL=
+
+  DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])
 
 else
   AC_MSG_RESULT([no])