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* VFD SWMR: Merges from develop (#1670)Dana Robinson2022-04-214-3/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up SWMR test scripts (both legacy and VFD) * Brings over format source changes for Java * Normalization of HL, Fortran, C++, Java w/ develop * Removes the STATIC flavor of FUNC_ENTER macros (#1622) * Removes the STATIC flavor of FUNC_ENTER macros * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes unused definitions from module headers (#1624) * Misc stuff from develop (includes some parallel things) * Brings over SWMR test quiet mode changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD SWMR: Normalization with develop (#1506)Dana Robinson2022-03-232-135/+422
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brought over plugin and test script changes * Removes remaining register keywords (#1481) * Fixed warnings in the aux process code * Minor fixes from develop * Minor changes from develop, fixed format warnings * Formatted source * Added HD prefix to timespec_get * Cleanup in new files * Removes the MANIFEST file and unused release files (#1497) * Removes the MANIFEST file and unused release files * Updated tar command * checkposix corrections * More checkposix fixes * Ripped out unused instrumentation functionality * Brought over cache tagging changes from develop * Changes to tagged metadata expulsion iteration * Fixed typo * Brought over H5O__free() changes from develop * Brings (unused) parallel page buffer test in line with develop * Moved the functionality in supervise.subr to test_vfd_swmr.sh * Tools VFD parameter updates * Committing clang-format changes * H5F VFD SWMR refactoring * Committing clang-format changes * Misc changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD SWMR: normalization with develop (#1472)Dana Robinson2022-03-0610-1430/+2005
| | | Much normalization with develop. Still needs tools changes wrt VFD plugins.
* VFD SWMR: Normalization with develop (#1270)Dana Robinson2021-12-081-646/+701
| | | Brings many October-November changes from develop
* VFD SWMR: Normalization with develop (#1078)Dana Robinson2021-10-065-16/+160
| | | Brings many changes from develop, particularly VOL changes for async
* VFD SWMR: Sync with develop (#811)Dana Robinson2021-06-301-3/+21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Normalization with develop * Removes checks and work-arounds for strtoll and strtoull (#769) * Removes checks for (v)snprintf, which are C99 (#772) * Update missing release note info. (#776) * Replaces the H5_OVERRIDE macro with override (#773) The macro is no longer necessary now that we require C++11. * Cleans up some POSIX header bits in H5private.h (#783) * Removes outdated checks for ways inline might be defined (#781) These are obsolete now that we require C99. * Removes checks for system(), which is C89/90 (#782) * Removes C++ dependency on H5private.h (#774) * Removes C++ dependency on H5private.h Most C API calls have been removed, aside from a few uses of free, where we just dropped the 'HD'. A couple of H5_ATTR_UNUSED macros were also replaced with (void) statements. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Further simplifies Autotools type size checks (#789) Also fixes an issue where clock_gettime and difftime are not detected due to earlier simplifications of this code. * Release Note (#784) * Normalization of CMake H5pubconf.h with Autotools (#791) Mostly just moving things around and changing the comments to keep the delta small. The only symbol change is that for curl/curl.h which I changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol is not used in the library and is just an artifact of the checks. * Fix tools test (#794) * Removes ancient Autotools cruft (#790) * Reorganization of C and POSIX headers in H5public.h & H5private.h (#793) * Reorganization of C and POSIX headers in H5public.h & H5private.h Consolidated and removed duplicates * It turns out Windows has sys/types.h Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removes checks for signal and set/longjmp, which are C89 (#798) Also removes checks for setjmp.h and stddef.h * Assume frexpl/f and fabsl/f, which are C99 (#799) * Assume the library has C99 types in C++ type code (#806) * Assume the library has C99 types in C++ type code * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes obsolete equivalents of C99's __func__ (#800) * Cleans up POSIX/C bits in H5private.h (#804) * Cleans up POSIX/C bits in H5private.h * Assume difftime exists (C89) * Reorg AC_CHECK_HEADERS so headers are in alphabetical order * Split off networking-related AC_CHECK_HEADERS * Remove unused UNAME_CYGWIN from configure.ac * Remove checks for unused sys/timeb.h * Tidying pass over H5private.h HD prefix macros * Tidy H5win32defs.h * Add HD prefix to various scanf calls * Committing clang-format changes * Fixes to the alarm(2) code used in the tests to make Windows happy Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Brings the tools getopt(3) replacement into the main library (#803) * Moves get_option from the tools library to the C library * Adds H5 prefix to get_option call and variables * Renames the H5_get_option long options struct and enum * Removes type guesses when C99 types are missing (#807) * Assume C99 types exist in H5detect.c (#808) * Fixes parallel issues from recent C99 changes * Adds MPE FUNC --> __func__ changes missed in earlier PRs * Fix typo * Fixes parallel issues from recent C99 changes (#809) * Fixes parallel issues from recent C99 changes * Adds MPE FUNC --> __func__ changes missed in earlier PRs * Even more missed FUNC --> __func__ macros * Removes remaining H5_TIME_WITH_SYS_TIME cruft (#810) Mostly from CMake Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* VFD SWMR: Normalization with develop (#765)Dana Robinson2021-06-171-2/+31
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings CMake updates from develop * Brings reduction in pedantic casts from develop * Purges UFAIL from the library (#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 (#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 (#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 (#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 (#699) * Removes pre-C99 build and header cruft (#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 (#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 #386 java folder copyright corrections * Whitespace * GH #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 #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 #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 (#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 (#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 (#702) * Committing clang-format changes * C++ warning and build fixes (#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 (#708) * Cleans up hsize_t and haddr_t size guessing (#709) * Cleans up definitions of haddr_t and hsize_t + cruft removal * Formatted source * Updates PGI C/C++ configurations (#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 (#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 (#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 (#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 * Updates CMake size_t and ssize_t checks for MacOS * Moved a little boilerplate over from develop * Fixes some warnings * Committing clang-format changes * Moves gcc warning macros from H5public.h to H5private.h (#724) * Moves gcc warning suppression macros out of H5public.h * Update RELEASE.txt * Formatted source * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ (#726) * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ Allows C++ library to be built on older versions of gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Moves H5PacketTable default ctor inside source file (#731) * Brings (most) H5Xdevelop.h headers from develop * Trivial H5F and H5O changes during normalization * Renames buf_ptr back to page_buf to better align with develop * Removed H5HGtrap.c * Brings changes from develop * Normalization (mainly cache) with develop * Fix Direct VFD Testing in CMake (#742) * Fixes C++ warnings when passing hsize_t values to printf in test code (#745) * Organize and align compiler flags (#741) * 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 #386 java folder copyright corrections * Whitespace * GH #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 #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 #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 * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#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 * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> * Committing clang-format changes * Cache code tidying * Constification of cache code * Renaming of static calls in cache * Fixes H5C mess made by git during merge * Committing clang-format changes * Fixes a printf format issue w/ parallel * Revert "Committing clang-format changes" This reverts commit 1265fe87fec6589f029cf3b1de6d586c90168654. * Turns off clang formatter in H5C while syncing with develop * Adds a lot of HD prefixes and cleans up err.h usage * Committing clang-format changes * Brings cache skip list optimization from develop * Brings recent changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD SWMR: sync with develop (#725)Dana Robinson2021-06-041-1/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings CMake updates from develop * Brings reduction in pedantic casts from develop * Purges UFAIL from the library (#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 (#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 (#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 (#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 (#699) * Removes pre-C99 build and header cruft (#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 (#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 #386 java folder copyright corrections * Whitespace * GH #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 #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 #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 (#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 (#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 (#702) * Committing clang-format changes * C++ warning and build fixes (#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 (#708) * Cleans up hsize_t and haddr_t size guessing (#709) * Cleans up definitions of haddr_t and hsize_t + cruft removal * Formatted source * Updates PGI C/C++ configurations (#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 (#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 (#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 (#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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Normalization with develop (#704)Dana Robinson2021-05-286-1000/+948
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* Update top-level COPYING file and remove COPYING files from subdirectories ↵Dana Robinson2021-05-031-13/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#561) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Update top-level COPYING file and remove COPYING files from subdirectories. * Remove subdirectory COPYING files from MANIFEST. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updates license url and history docsDana Robinson2021-03-257-1191/+7263
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* Merge branch 'aug-develop' into aug-merge-attempt/feature/vfd_swmrDavid Young2020-08-042-1/+138
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| * Merge pull request #2711 in HDFFV/hdf5 from bmr-HDFFV-11120 to developBinh-Minh Ribler2020-07-291-0/+11
| |\ | | | | | | | | | | | | | | | | | | | | | Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869) * commit '707e30c6be1954c0027374124207e46caae68cbc': Fixed typos in error messages. Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
| | * Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)Binh-Minh Ribler2020-07-221-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: When a buffer overflow occurred because a name length was corrupted and became very large, h5dump produced a segfault on one file and a memcpy parameter overlap on another file. This commit added checks that detect a read pass the end of the buffer to prevent these error conditions. Platforms tested: Linux/64 (jelly) SunOS 5.11 (emu)
| * | Merge pull request #2714 in HDFFV/hdf5 from ↵Dana Robinson2020-07-281-0/+15
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:h5s_set_extent_none to develop * commit 'e4603ff8a171e82de6373ba6eddcf59d5eeab5aa': Updated the Java tests to deal with H5Sset_extent_none changes Fixed additional typos in tselect.c comments. Fixes typo in tselect.c Updates H5Sset_extent_none() to set H5S_NULL
| | * | Updates H5Sset_extent_none() to set H5S_NULLDana Robinson2020-07-281-0/+15
| | |/ | | | | | | | | | | | | | | | | | | | | | The API call used to set the internal H5S_NO_CLASS value which produced errors when such a dataspace was passed to many other API calls. Fixes HDFFV-11027
| * | Add release notes for toolsAllen Byrne2020-07-201-2/+38
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| * Fix for jira issue HDFFV-11080:vchoi2020-07-141-0/+14
| | | | | | | | | | (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
| * HDFFV-11116 Add option for install location of Fortran MOD filesAllen Byrne2020-07-092-3/+36
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| * Lib files needed are now copied to a subdirectory in the java/testLarry Knox2020-07-021-0/+8
| | | | | | | | | | | | directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
| * - added comment to explain a klugeBinh-Minh Ribler2020-06-291-1/+9
| | | | | | | | - added the associated entry to release notes
| * Added note for HDFFV-10591.Binh-Minh Ribler2020-06-191-0/+12
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| * OESS-65 fix packaging config filesAllen Byrne2020-05-081-0/+1
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| * Remove old szip lineAllen Byrne2020-04-231-1/+0
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| * OESS-65 add option to use AEC library in place of SZipAllen Byrne2020-04-223-0/+20
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| * Trim trailing whitespaceQuincey Koziol2020-04-204-3068/+3068
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| * Merge branch 'develop' of ↵Jacob Smith2020-04-071-0/+39
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a
| | * Move intel warnings to subfolder, update autotools filesAllen Byrne2020-04-061-1/+3
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| | * Corrected noteAllen Byrne2020-04-061-3/+3
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| | * Update release note for CMake warningsAllen Byrne2020-04-031-0/+2
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| | * TRILAB-192 add comparable clang flagsAllen Byrne2020-03-271-0/+2
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| | * TRILAB-24 use CHECK_STRUCT_HAS_MEMBERAllen Byrne2020-03-241-0/+7
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| | * TRILAB-192 add release noteAllen Byrne2020-03-241-0/+15
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| | * Fixed the RELEASE.txt note for HDFFV-11057Dana Robinson2020-03-181-9/+8
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| | * Fix shutdown errors when using the HDF5_VOL_CONNECTOR environmentDana Robinson2020-03-181-0/+12
| | | | | | | | | | | | | | | variable to set a dynamically loaded plugin as the default VOL connector. Fixes HDFFV-11057
| * | Add Splitter VFD to library.Jacob Smith2020-03-131-0/+14
| |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | * "Simultaneous and equivalent" Read-Write and Write-Only channels for file I/O. * Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for now, preventing issues with multi-file drivers. Add Mirror VFD to library. * Write-only operations over a network. * Uses TCP/IP sockets. * Server and auxiliary server-shutdown programs provided in a new directory, `utils/mirror_vfd`. * Automated testing via loopback ("remote" of localhost).
| * Update examples and fix old version references.Allen Byrne2020-02-268-209/+213
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| * Update Windows platformsAllen Byrne2020-02-241-5/+1
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| * HDFFV-11036 add release noteAllen Byrne2020-02-241-1/+8
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| * TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-212-1/+8
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| * Merge developJordan Henderson2020-02-214-37/+237
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| | * Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size ↵M. Scot Breitenfeld2020-02-181-0/+3
| | | | | | | | | | | | | | | | | | inh5fget_file_image_f. HDFFV-11029
| | * Update sanitizer note.Allen Byrne2020-02-111-3/+12
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| | * HDFFV-11014, fix the h5repack issue that misses a few attributes during the ↵Muqun Yang2020-02-071-0/+10
| | | | | | | | | | | | repacking. The flag that checks the object reference attribute is not updated properly. The fix is trivial. Just need to move the flag update line into the inner loop. Tested at Jelly. Also update the release.txt.
| | * Add RELEASE.txt note for token refactoring changesJordan Henderson2020-02-051-0/+44
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| | * HDFFV-11012 - add release noteAllen Byrne2020-02-051-0/+7
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| | * HDFFV-10996 add release noteAllen Byrne2020-02-041-0/+6
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| | * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-01-241-7/+4
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '590aaff33046df99a4d88ba59e4b461e060b36e4': Optimized the floating point comparisons a little bit. Fix for failing h5diff tests involving floating-point compares. Removed H5_DEC_ENUM Revert "Revert "Moved -Wunsuffixed-float-constants to the developer warnings."" Revert "Moved -Wunsuffixed-float-constants to the developer warnings." Moved -Wunsuffixed-float-constants to the developer warnings. Fixed a bug in testpar/t_cache.c concerning checking expected vs. actual cache entry reads and writes.
| | | * Revert "Revert "Moved -Wunsuffixed-float-constants to the developer warnings.""Dana Robinson2020-01-231-7/+4
| | | | | | | | | | | | | | | | This reverts commit 6486e06545bf637d46e18a787395542f4fca143a.
| | * | Note for common warnings filesAllen Byrne2020-01-171-0/+9
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