VFD SWMR: sync with develop (#725)

[vchoi-hdfgroup]

• Brings CMake updates from develop

• Brings reduction in pedantic casts from develop

• Purges UFAIL from the library (Purges UFAIL from the library HDFGroup/hdf5#637)

• Committing clang-format changes

• Purges UFAIL from the library

• H5HL_insert change requested in PR

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Removes gratuitous (double)x.yF casts (Removes gratuitous (double)x.yF casts HDFGroup/hdf5#632)

• Committing clang-format changes

• Removes gratuitous (double)x.yF casts

• Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Committing clang-format changes

• Cleans up a const warning left over from previous constification (Cleans up a const warning left over from previous constification HDFGroup/hdf5#633)

• Committing clang-format changes

• Adds consts to a few global variables

• Cleans up a const warning left over from previous constification

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Formatted source

• Bring over some VOL registration changes

• VOL cleanup

• H5VL_request_status_t substitutions

• H5F.c cleanup

• Minor API tweaks from develop

• Moves H5G package init/teardown to H5Gint.c

• H5G cleanup

• H5M cleanup

• H5SM cleanup

• H5T cleanup

• H5R cleanup

• H5Lpublic.h cleanup

• H5L cleanup

• H5O cleanup

• H5A, H5CS, and H5AC cleanup

• Moved H5A init/teardown code to H5Aint.c

• Moves H5D I/O functions to H5D.c

• H5D cleanup

• Misc minor cleanup

• H5P close cleanup

• H5Tpublic.h cleanup

• Fixes err_compat test

• H5PLpublic.h cleanup

• Updates H5Ppublic.h

• H5Fpublic.h updates

• H5A.c cleanup

• Brings over H5Aexists and related changes

• Brings CMake shell testing changes from develop

• Close callback changes

• H5R and H5Tcommit normalization

• err_compat test works now

• H5O tweaks

• Updates VOL registration code

• Brings over H5VL_create_object

• H5Tconv.c reformatting

• H5T.c tweaks

• Brings datatype and reference updates from develop

• Brings VOL plugin loading changes from develop

• Brings event sets from develop

• Brings async functions over

• Tools changes

• Brings over many tools changes from develop

• Brings VOL flags from develop

• Fixes h5dump double/float tests

• Updates h5repack tests

• Brings h5diff test changes from develop

• Last h5dump changes

• Brings test changes from develop

• Committing clang-format changes

• Tidied h5_testing()

• Brings chunk iteration code + misc from develop

• Updates vds test

• Enables external link parallel test

• Brings updated property lists from develop

• H5G changes from develop

• H5MF cleanup

• Brings vfd_swmr test back into CMake

• Updates threadsafe test

• Updates plist test

• Brings recent changes from develop

• Require a C++11 compiler to build the C++ wrappers (Require a C++11 compiler to build the C++ wrappers HDFGroup/hdf5#693)

• Committing clang-format changes

• Requires a C++11 compiler to build the C++ wrappers

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes HDFGroup/hdf5#699)

• Removes pre-C99 build and header cruft (Removes pre-C99 build and header cruft HDFGroup/hdf5#700)

• Assumes ANSI C headers exist

• Assumes stdbool.h, stdint.h, and inttypes.h are present

• Assumes the C++ compiler can handle stdint.h

• Removes all work-arounds for missing functionality, especially stdbool.h

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Updates release documents

• Brings parallel changes from develop

• Adds a VFD/parallel check program for the VFD SWMR shell test

• Updates MANIFEST

• Disable building VFD SWMR acceptance tests on CMake

• Removes err.h from genall5.c

• Partial cleanup of H5Cpkg.h

• Fixes printf specifiers in H5Cdbg.c

• Java and fortran cmake changes (Java and fortran cmake changes HDFGroup/hdf5#694)

• OESS-98 convert plugin option to FetchContent, add tests

• Fixes for pkcfg files because of plugin option

• OESS-98 fix tools test for plugins

• Keep doxygen comments under 100 chars long - format hint

• Whitespace

• HDFFV-11144 - Reclassify CMake messages

• HDFFV-11099/11100 added help text

• Reworked switch statement to compare string instead

• Fix typo

• Update CDash mode

• Correct name of threadsafe

• Correct option name

• Undo accidental commit

• Note LLVM 10 to 11 format default changes

• Update format plugin

• Undo clang-format version 11 changes

• One more correction

• Update supported platforms

• Revert whitespace changes

• Correct whitespace

• Changes from PR#3

• HDFFV-11213 added option to control gcc10 warnings diagnostics

• HDFFV-11212 Use the new references correctly in JNI utility and tests

• format source

• Fix typo

• Add new test file

• HDFFV-11212 - update test and remove unused arg

• Minor non-space formatting changes

• Use H5I_INVALID_ID instead of "-1"

• source formatting

• add missing testfile, update jni function

• Undo commit of debug code

• remove mislocated file

• Fix h5repack test for handling of fapls and id close

• Update h5diff test files usage text

• HDFFV-11212 add new ref tests for JNI export dataset

• src format update

• Remove blank line typo

• src format typo

• long double requires %Lg

• Another long double foramt specifer S.B. %Lg

• issue with t128bit test

• Windows issue with h5dump and type.

• Fix review issues

• refactor function nesting and fix error checks

• format fixes

• Remove untested functions and javadoc quiet comments

• Restore TRY block.

• Change string append errors to memory exception

• revert to H5_JNI_FATAL_ERROR - support functions need work

• Add assertion error for h5util functions

• remove duplicate function

• format fix

• Revert HD function error handling

• Update copyright comments

• GH Remove outdated line in copyright header from java test files (and other files found to be initially created since 2006). HDFGroup/hdf5#386 java folder copyright corrections

• Whitespace

• GH Fix crash in H5TS_win32_thread_exit HDFGroup/hdf5#359 implement and fix tools 1.6 API usage

• remove excessive comments

• Flip inits to correct ifdef section

• rework ifdef to be simpler

• format issue

• Reformat ifdef inits

• remove static attribute

• format compliance

• Update names

• Revert because logic relies on float not being int

• Changes noticed from creating merge of 1 12 merges from develop HDFGroup/hdf5#412

• Double underscore change

• Correct compiler version variable used

• Remove header guard underscores

• Whitespace cleanup

• Split format source and commit changes on repo push

• remove pre-split setting

• Change windows TS to use older VS.

• correct window os name

• HDFFV-11212 JNI export util and Javadoc

• Suggested review changes

• Another change found

• Committing clang-format changes

• HDFFV-11113 long double in tools

• HDFFV-11113 add note

• Disable long double tests for now

• HDFFV-11228 remove arbitrary CMake warning groups.

• Make each flag a string

• Some Javadoc warning fixes

• Updated javadoc fixes

• WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

• Committing clang-format changes

• HDFFV-11229 Add release note

• HDFFV-11229 windows testfile needed

• fix typo

• Remove non supported message text

• HDFFV-11229 - change ldouble test to check both native and general

• HDFFV-11229 add second file compare

• HDFFV-11229 fix reference file

• HDFFV-11229 autotools check two refs

• HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

• Committing clang-format changes

• Update release note

• Update attribute type of ref file

• Change source of ninja for macs

• try port instead of brew

• Recommended is to use brew.

• Undo non long double changes

• remove unneeded file

• Fix perl and doxygen CMake code

• Add "option" command for clang options

• Rework CMake add_custom to use the BYPRODUCTS argument

• Add stamp files to BYPRODUCTS

• Only one copy of file exists

• Fix custom cmmand depends targets

• Fix fortran custom command DEPENDS

• Add LD_LIBRARY_PATH to tests

• Add custom target for DEPENDS

• Add h5detect conditionaly to generated target DEPENDS

• Correct DEPENDS targets

• Parallel builds need the mpi compiler for pkgconfig scripts.

• install only if MPI build

• Fortran target depends

• Remove incorrect source attribute

• doxygen adjustments

• doxygen build updates

• Correct version

• Correct function version - function has been merged to 1.12

• Correct version string for map functions

• Cleanup warnings for tools debug builds

• TRILAB-227 - fix indexing for h5diff selections

• Correct location of pos to index function call

• TRILAB-227 Enable test

• Quote subset args

• Use MATCHES because of AppleClang

• if blocks needed for build modes

• Update list of DT platforms

• VS2019 correctly displays float values

• revert VS2019 change

• Issue pkg-config: files without version HDFGroup/hdf5#669 remove version from pkgcfg filename

• remove version from h5cc script

• Java reference functions updated

enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging

• Correct BYPRODUCTS argument

• Correct more genereated files BYPRODUCTS

• BYPRODUCTS must have unique locations

• Fix typo

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Removes alternative function enter/leave macro scheme (Removes alternative function enter/leave macro scheme HDFGroup/hdf5#678)

• Committing clang-format changes

• Converted BEGIN_FUNC, etc. macros to FUNC_ENTER

• Rips out the BEGIN_FUNC, etc. macros

• Removes 'end if', etc. comments from H5HL package

• Committing clang-format changes

• Fixes an H5EA iterate issue

• Fixes an issue in the H5FA iterator code

• Further cleanup in bin/trace after macro removal

• Iterator changes in H5EA and H5FA

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Split H5L.c internal code to H5Lint.c (Split H5L.c internal code to H5Lint.c HDFGroup/hdf5#691)

• Committing clang-format changes

• Splits internal parts of H5L.c to H5Lint.c

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Clean up type size checks in configure.ac (Clean up type size checks in configure.ac HDFGroup/hdf5#702)

• Committing clang-format changes

• C++ warning and build fixes (C++ warning and build fixes HDFGroup/hdf5#707)

• Committing clang-format changes

• C++ build and warning updates

• Fixes all warnings on C++ (with gcc 9.3)

• Updates CMake and Autotools C++ builds

• Undo warning clobber

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Removes some DEC Alpha cruft from H5detect and H5private.h (Removes some DEC Alpha cruft from H5detect and H5private.h HDFGroup/hdf5#708)

• Cleans up hsize_t and haddr_t size guessing (Cleans up hsize_t and haddr_t size guessing HDFGroup/hdf5#709)

• Cleans up definitions of haddr_t and hsize_t + cruft removal

• Formatted source

• Updates PGI C/C++ configurations (Updates PGI C/C++ configurations HDFGroup/hdf5#715)

• Updates PGI C/C++ configurations

Tweaks some settings and configures pgc++ to use C++11

• Updated copyright information

• Adds an Intel C++ configuration file (Adds an Intel C++ configuration file HDFGroup/hdf5#716)

• Adds an Intel C++ configuration file

• Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

• Updates bin/trace script to correctly wrap H5TRACE macros near clang-format column limit (Updates bin/trace script to correctly wrap H5TRACE macros near clang-format column limit HDFGroup/hdf5#719)

• Removes clang-format comments from H5O.c call

• Fixes bin/trace to correctly wrap lines near the clang-format limit

• Removed unused variable from bin/trace

• Fixes issue with ccmake that prevents building Fortran (Fixes issue with ccmake that prevents building Fortran HDFGroup/hdf5#723)

ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations

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