* 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* Removes outdated checks for ways inline might be defined (#781)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>
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Modify h5repack to integrate with VOL connectors
Update tools library to accomodate VOL connectors
Update logic in h5tools_fopen for VOL connectors
Add command-line options to h5repack for specifying in/out VOL
connectors
Implement h5tools_set_vol_fapl
Fix library shutdown issue
Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme
Avoid H5Ocopy in h5repack when using different VOL connectors
Update h5tools_test_utils.c for ROS3 and HDFS integration
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions
Tested:
Windows, linux
Bring r18076-18096 from hdf5_1_8_coverity branch to trunk:
r18076:
Correct Coverity issue #1 by removing dead code
r18077:
Fix coverity item 142. When an error occurred while copying a linked list in
H5S_point_copy, the library would not free the partially allocated list. Added
code to free the list in this case.
r18078:
Correct Coverity issue #2 by removing impossible to reach code.
r18079:
Correct #3 by removing impossible to reach code.
r18080:
Correct Coverity issue #4 by removing impossible to reach code.
r18081:
fix coverity 26 , check (dblik->parent) before calls H5HF_man_iblock_detach().
r18082:
Fixed coverity issues 321 and 316.
321: freed sm_buf in error handling to remove resource leak.
Also set sm_buf to NULL after other instances in which
it is freed to prevent double free.
316: initialized nmembs to 0.
r18083:
Correct Coverity issue #6 by removing debugging knob from error reporting code.
r18084:
Fix coverity item 269 + others. When a error occurred in a function using the
h5tools error framework, the "past_catch" variable would not be set to true
because that statement was before the label that goto jumped to. This could
cause a failure in the cleanup section to go back to the start of the section,
freeing variables twice, etc.
Moved the label infront of past_catch=TRUE.
r18085:
fixed coverity #27, check if (heap) before use heap->obj....
r18086:
fixed coverity #28, check curr_span not null before use it at if(curr_span &&
(io_bytes_left==0 || curr_seq>=maxseq))
r18087:
Correct Coverity issue #7 by cleaning up correctly on error
r18088:
Correct Coverity #8 by removing unchanged variable checking code.
r18089:
Correct Coverity issue #9 - remove impossible to reach code.
r18090:
Correct Coverity issue #11 by removing impossible to reach code. Also clean
up some minor style issues.
r18091:
Fix coverity items 314 and 318. Changed the improper assertion of the return
value of a library function to a check, and a return(void) on failure.
r18092:
Fix coverity item 70. Changed the improper assertion of the return value of a
library function to a check, and a return(void) on failure.
r18093:
Correct Coverity issue #12 by removing dead code.
r18094:
Correct Coverity issue #16 by removing debugging code.
r18095:
Fixed coverity issue # 271.
Removed redundant checking and freeing of sm_buf1 and sm_buf2.
r18096:
Correct Coverity issue #17 by refactoring test to remove dead code.
Also, removed previous "coverity" statements in comments, we'll review
those issues again and see if we can figure them out, now that we have more
experience with Coverity.
Tested on:
Mac OS X/32 10.6.2 (amazon)
Bring Coverity changes into the trunk: (also other minor cleanups)
r17991:
Fix Coverity items 175 and 176. Fixed memory leak on error in print_enum in
H5LT.c.
r17993: (r17992 was not a Coverity change)
Close Coverity issue #206: inconsistently checking whether dt->shared was
non-NULL after H5T_alloc() returned a valid 'dt' value (which should guarantee
that dt->shared is valid).
r17994:
Fix Coverity item 149. Fixed file handle leak on error in H5FD_stdio_open.
r17995:
Fixed Coverity issues 154 to 161:
Added H5MP_close routine to error handling in the event *mp has not been
freed before error.
r17996:
Close Coverity issue #126: potentially leaking merged_spans on routine failure.
r17997:
Fix Coverity items 147 and 148. Fixed resource leaks on error in H5FDloc.c.
r17998:
Coverity issue 269-272:
Added integer result variable to functions that could return negative.
Assigned to unsigned after checking.
Added H5E_BEGIN_TRY block around H5Tclose and removed H5E_THROW in the
catch block.
Checked buffer is NULL before free. Changed HGOTO_ERROR outside of the if
block to H5E_THROW.
r17999:
Close Coverity issue #127: release temporary spans in more generic manner.
(Also add error checking to previous fix)
r18000:
Resolved Coverity issues 211 and 212 in H5T.c. Added comments to ignore
Coverity warning regarding not checking pointer for NULL, as we are using
an assert which catches the issue.
r18001:
Fix Coverity item 146. Fixed resource leak on error in H5O_layout_copy.
r18002:
Fix Coverity items 143 and 145. Fixed resource leaks on error in
H5D_compact_copy and H5D_contig_copy.
r18003:
Close Coverity issue #192: close file on error
r18004:
Fix Coverity issue #125: release temporary spans on error
r18005:
Resolved Coverity issues 5, 25, and 83 (in H5T.c):
Separated embedded functions in order to check for NULL on return of
H5I_object before passing into H5T_copy.
Check to see if new_dt is NULL within error handling before
dereferencing it.
Ignore Coverity's dead code warnings as the checks that lead to the code
are machine dependent.
r18006:
Coverity 63,70,73: Checked result of function before assigning to an unsigned
variable.
r18007:
Coverity 78,79: added continue statement if H5Pget_filter2 returns negative.
r18008:
Fixed Coverity issue # 138:
Added support in error handling to free dst pointer (if allocated) on error.
r18009:
Whitespace & coding style cleanup
