summaryrefslogtreecommitdiffstats
path: root/src/H5Apublic.h
Commit message (Collapse)AuthorAgeFilesLines
* Fix chid_t to hid_t (#3948)Glenn Song2024-02-141-1/+1
| | | Co-authored-by: Glenn Song <gsong@hdfgroup.org>
* 1.14 sync with develop (#3660)jhendersonHDF2023-10-121-11/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework tools.cmake and add C flags (#3110) * Fix gh pages so that the doxygen files are uploaded (#3102) * Add workspace path * add debug * Make one job so workspace files are available * Put doxygen docs under docs folder in gh-pages * Fix a misc warning in test/vol.c (#3112) The compiler complains about using integers instead of size_t for some sizes. * Remove H5detect and H5make_libsettings (#3104) Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file * clang-tidy clang-analyzer-core issues addressed (#3113) src/H5system.c:1293:13: warning: Dereference of null pointer [clang-analyzer-core.NullDereference] src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains uninitialized data (e.g., via the field chain: 'initial.user') [clang-analyzer-core.CallAndMessage] * Add note for issue 3056 (#3117) * Use 1.14 toolchain (#3116) * Remove the checkposix script (#3122) This script was used to ensure that all non-HDF5 calls were prefixed with 'HD'. We are removing this scheme so this script is no longer needed. * Remove unused HD macros (#3120) * Remove unused HD macros The library prefixes most C and POSIX API calls with 'HD'. We are going to start removing these so the code looks like normal C. This PR removes most of the unused HD markup macros. * Replace ntohl/ntohs * Adds an optional version arg to bin/format_source (#3119) * Clean up mirror VFD code in utils dir (#3121) * Remove dead code * Replace mybzero with memset * Replace hbool_t/TRUE/FALSE with bool/true/false * Fix spelling issues flagged by codespell (#3130) * Make autogen.sh output message consistent (#3128) * Add Python for HDF-EOS zoo description (#3129) * Fix function name in comment in ros3 VFD (#3131) * Revert long double checks (#3133) * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9. * Update comments to reflect newer systems * Add java options to build scripts (#3127) * Add java options to build scripts Previously, cmakehdf5 turned on compiling of the java interface by default due to a value set in cacheinit.cmake. Now, consistent with how Fortran and CPP interfaces are handled, the script overwrites this default value to disable the libraries, fixing #2958. I also implemented the --enable-java/--disable java options for cmakehdf5, and -java for buildhdf5. Allen said these scripts should mention that compilers are to be specified in environment variables, but missing compilers causes errors at the CMake level, and CMake's error messages are already pretty informative (See the one in #2958 about JAVA_COMPILER). * Removed .lnt linter files (#3143) These were last usefully modified in 2004 * Fix path to libhdf5.settings in cmakehdf5 (#3140) * Many clang -Wextra-semi-stmt fixes (#2537) * Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END * Remove HD prefix from network calls (#3142) HDsocket(), etc. Only affects the mirror VFD and its test code. * Remove hbool_t/TRUE/FALSE from java (#3145) Replaces with bool/true/false * CMake: (feature) ROS3 and cmake config file. (#3146) - Added a cmake variable to the hdf5-config.cmake file which indicate if the library has been build with or without the read-only S3 functionality. * Define minimal permissions for new GitHub workflows (#3147) * Track s3 i/o when S3COMMS_DEBUG enabled (#3139) * Track s3 i/o when S3COMMS_DEBUG enabled * Fix the snapshots workflow (#3148) * Add upload url as artifact * Change doxygen path and comment log-url upload * zip doxygen files for upload * add workspace var * chore: fix grammar (#3150) * chore: fix grammar * Removes the HD prefix from java C99 calls (#3149) POSIX calls (HDstrndup, etc.) are unchanged * Correct the zip usage (#3153) * Many fixes to various compiler warnings (#3124) * Fixed various -Wmissing-variable-declarations by adding static keyword * In a few cases, renamed the variable suffix from _g to _s. * Fixed some -Wmissing-variable-declarations by using different declaration macros * Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero * Fixed various -Wcomma warnings * Fixed clang -Wstrict-prototypes warnings * Fixed various -Wunused-variable warnings * Updated some casts to fix the only 3 -Wcast-qual warnings * Fixed the only -Wsometimes-uninitialized warning * Create Security Policy (#3152) * Fix #1978 h5vers usage message. (#3162) Update Platforms Tested in RELEASE.txt. * speed-up building HDF5 (#3087) Disables building the tests when building the netCDF, etc. * Remove dead code behind #ifdef OLD_WAY (#3163) * Remove H5F_evict_tagged_metadata() (#3165) The rest of the library just calls H5AC_evict_tagged_metadata() directly. * Add missing space in zip command (#3167) * Fixed check for a VOL's async compatibility (#3164) * cap flag fix in test * added async comp. output * Update Linux workflows (#3173) * Consolidate environment setup * Turn on ros3 VFD in CMake (Linux only) * Add gh-pages doxygen link (#3175) * Fix the doxygen to gh pages and artifact creation (#3176) * Tidy the list of options in main.yml (#3181) * Remove HD/hbool_t from fortran (#3182) * Remove HD/hbool_t from high-level lib (#3183) * Remove HDva_(arg|copy|end|start) (#3184) * Drop HD prefix & hbool_t from H5TS (#3180) * Remove HD from fork/exec*/wait* (#3190) These are not C99 but are hidden behind ifdefs and are highly unlikely to ever have non-POSIX equivalents. * Fix assertion failure when attempting to use IOC VFD directly (#3187) * Rename HDqsort() to qsort() (#3193) * Rename HDqsort() to qsort() * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Rename HDpipe() to pipe() (#3192) Pipe is POSIX but implemented in Microsoft's CRT * Rename HDassert() to assert() (#3191) * Change HDassert to assert * Fix bin/make_err * Rename HD(f)printf() to (f)printf() (#3194) * Add note about HDF5_VOL_CONNECTOR to tools usage (#3159) * Rename HDsystem() to system() (#3197) system() is only used in the iopipe test and the things it calls (which are POSIX-y) are protected by an ifdef. * Remove HD from HDposix_memalign() (#3196) The posix_memalign call is only used in the direct VFD, which can only be built if posix_memalign() is available. * Remove HD from memory allocate/free calls (#3195) * HDcalloc * HDfree * HDmalloc * HDrealloc * chore: fix grammar (#3207) * docs: remove redundancy in Data Transfer section of user guide (#3208) * Remove checks for setsysinfo, which is unused (#3205) * Autotools * CMake * Remove HD from protected POSIX calls (#3203) These calls are non-C99 but protected by ifdefs and have no Windows equivalents: * HDalarm * HDasprintf * HDclock_gettime * HDfcntl * HDgethostname * HDgetrusage * HDsymlink * Rename HDato*() to ato*() (#3201) * Remove some "Programmer" comments (#3209) These are meaningless noise. Removes the "Programmer" lines on comment start lines: /* Programmer: John Smith These complicate my sed script that will rip out the rest of the comments. * Rename HDexit() and related to exit(), etc. (#3202) * HDatexit * HDexit * HD_exit * Remove HD from strto* calls (#3204) * HDstrtod * HDstrtol * HDstrtoll * HDstrtoul * HDstrtoull * HDstrtoumax * Remove HD from C std lib file ops (#3206) * HDfclose * HDferror * HDfeof * HDfflush * HDfopen * HDfread * HDfwrite * Remove programmer/date from comments (#3210) * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work * Remove HD from HDmem* calls (#3211) * Remove HD from HDis* (e.g., isalpha) (#3212) * HDisalnum * HDisalpha * HDiscntrl * HDisdigit * HDisgraph * HDislower * HDisprint * HDispunct * HDisspace * HDisupper * HDisxdigit * Update actions for release option, fix branch for daily build (#3185) * Update actions for release option, fix branch for daily build * Scheduled workflows run on latest commit on the develop * Add snapshots location * docs: improve consistency in verb form (#3076) (#3188) * fix gh action if statements (#3213) * Adjust presets timeout and fix build script VS versions (#3215) * Several ros3vfd logging improvements * Committing clang-format changes * Update COPYING (#3231) Fixed old support URL. * addresses compilation fortran warnings on Frontier (#3236) * Fix doc for H5allocate_memory (#3240) * merge bbrelease to release (#3232) * merge bbrelease to release * Fix pre-req workflow * Replace support.hdfgroup.org URLs for alternative COPYING file (#3228) * Replace support.hdfgroup.org URLs for alternative COPYING file locations in copyright headers with https://www.hdfgroup.org/licenses. Replace support.hdfgroup.org URL for alternative COPYING_LBNL_HDF5 with github URL. Tweak chkcopyright script for change from UICOPYRIGHTSTR to THGCOPYRIGHTSTR. * Replace 1_10 reference with develop branch (#3227) * Switch CI to use release script (#3242) * Subfiling VFD source cleanup (#3241) * Subfiling VFD source cleanup Modularize Subfiling CMake code into separate CMakeLists.txt file Update Mercury util code to latest version and update Copyright Generate mercury_util_config.h header file instead of using pre-generated file Remove unnecessary Mercury functionality Fix minor warning in Subfiling VFD code * Remove Mercury headers from Autotools publicly-distributed header list * install h5fuse.sh in bin dir. (#3244) * Disable h5py until fixed properly without spack (#3243) * ROS3: (feature) Temporary security credentials (#3030) - Implemented support for AWS temporary security credentials. For this kind of credentials also a session/security token should be included in the request by adding the x-amz-security-token header. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Avoid truncating at null byte when copying to std::string (#3083) --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix CMake builds when Subfiling VFD isn't enabled (#3250) * Fix CMake builds when Subfiling VFD isn't enabled * Add Subfiling VFD entry to hdf5-config.cmake.in * Fix some warnings in developer builds (#3247) * Fix some warnings in developer builds * Switch approach to Winline flag * Fixed more warnings about extra semicolons (#3249) * Require semi-colon after H5_CHECK_OVERFLOW calls Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro (#3259) Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning causing Werror Release builds to fail * Update DEFAULT_API_VERSION documentation for CMake (#3255) * Update DEFAULT_API_VERSION documentation for CMake * Fix hint --------- Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * changed the scope of #ifdef DOXYGEN to now include H5D multi-functions (#3254) * Option changed but not all references (#3252) * Option changed but not all references * remove quotes from binary var * Move 1.12.3 release to October (#3263) * Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized warning (#3260) * removed the use of encoded single apostrophe (#3261) * removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read * updated sanitizer paragraph * fixed brief description for H5Fget_info * ROS3: (fix) Replaced HDfprintf (#3266) - Replaced the HDfprintf() functions by fprintf() to be consistent with other parts of the library. * chore: make VRFY output consistent (#3268) * CMake: (fix) Threads dependency (#3267) - If the HDF5 library has been build with either thread-safety or subfiling VFD feature on it will have an additional dependency on a threading library. This dependency has been added to the hdf-config.cmake.in file. * chore: fix grammar - get hang -> get hung (#3272) * Another round of fixing -Wextra-semi-stmt warnings (#3264) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * chore: fix typo - persent -> present (#3273) * Remove py-pip from h5py action (#3265) * Update release schedule (#3317) * Move 1.12.3 to November * Add 1.14.3 in October * Update README.md w/ 1.4.3 info (#3318) * Switch parallel compression to use vector I/O (#3245) Updates parallel compression feature to use vector I/O instead of creating and passing down MPI derived types to VFD * Fix incorrect error check in H5Ofill.c for undefined fill values (#3312) * Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314) * Fix loading plugin fails with missing directory GH issue #3248 (#3315) * Made HGOTO_ERROR a do-while loop (#3308) * Made HGOTO_ERROR a do-while loop * Update files to skip list and ignore_words_list (#3321) * Update files to skip list and ignore_words_list for codespell to not check files generated by autotools. Autotools generate misspellings that can't be fixed in HDF5 code. * Windows runtime items go into the bin folder (#3320) * A couple of documentation items to fix (#3332) * Fix h5repack for variable-length datatyped datasets (#3331) * Fix CVE-2018-11202 (#3330) A malformed file could result in chunk index memory leaks. Under most conditions (i.e., when the --enable-using-memchecker option is NOT used), this would result in a small memory leak and and infinite loop and abort when shutting down the library. The infinite loop would be due to the "free list" package not being able to clear its resources so the library couldn't shut down. When the "using a memory checker" option is used, the free lists are disabled so there is just a memory leak with no abort on library shutdown. The chunk index resources are now correctly cleaned up when reading misparsed files and valgrind confirms no memory leaks. * Fix CVE-2018-13867 (#3336) * Fixes the last of the -Wextra-semi-stmt warnings (#3326) * Fixed extra semi warning by adjusting alternative macro definitions * Find-replace H5E_END_TRY; -> H5E_END_TRY * Made H5Epush_goto a do-while loop, fixed indentation * Made GOTOERROR and ERRMSG do-while loops * Made Hgoto_error and Hgoto_done do-while loops * Made vrfy_cint_type and vrfy_ctype do-while loops * Made TEST_TYPE_CONTIG and others do-while loops * Removed extraneous semi-colons * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix a typo in RELEASE.txt * Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340) * Make h5dump spacing consistent when printing VLEN datatype (#3351) * Fix for the bug exposed from running test/set_extent.c when selection… (#3319) * Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled. This is a fix from Neil. The test/set_extent.c is modified to test for selection I/O enabled. * Add Fortran ES module to deploy list (#3341) * Add Fortran ES module to deploy list * Change fortran mod file export to use a list of names * test(parallel): verify FALSE case (#3356) * Implementation of the mpio driver with selection I/O. (#3222) * This changes the default selection I/O to on for MPIO. * Work around a testphdf5 failure on Cray MPICH machines (#3361) * set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with (#3364) CMake to fix Fortran build failures. * Add RELEASE.txt notes for recent selection I/O work. (#3374) * Fix possible performance regression introduced with in-place type conversion in 1.14.2 (#3376) * Correct script (#3377) * Correct CI settings (#3384) * Correct CI settings * Correct plugin file name * restore CI tarball name prefix to match bin/release (#3385) * Fix assertion failure during file close on error (#3387) * Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388) * Fix valgrind warning about write of uninitialized bytes (#3389) * Fix valgrind warning about write of uninitialized bytes in ScaleOffset filter (#3390) * Update presets, examples uncompress, szip cache (#3391) * Fix serial to parallel chunked dataset file space allocation bug (#3394) * chore: fix typo (#3405) * Fix for CVE-2016-4332 (#3406) This CVE issue was previously listed as fixed (via HDFFV-9950) back in 2016, but with no confirmation test. Now that test files exist for the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an assert in debug builds. This fix replaces the assert with pointer checks that don't raise errors or asserts. Since the function is in cleanup code, we do our best to close and free things, even when presented with partially- initialized structs. Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo) * Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407) * Enable szip by default in Autotools (#3412) Since libaec is so prevalent and BSD-licensed for both encode and decode, we build the szip filter by default when the szip or aec libraries are found. * Re-enable SZIP default to ON in CMake (#3414) The Autotools were handled in a separate commit * Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368) * Add Intel oneAPI actions (#2949) (#2977) * ci: add Intel oneAPI actions (#2949) * ci: fix CMake installation * ci: use absolute paths for libtool installation * ci(oneAPI): update compiler versions and use cron * Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416) * chore: remove gubbins comment (#3420) * Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] (#3353) * Avoid H5Ocopy in h5repack for variable-length string types (#3419) * Skip atomicity tests for OpenMPI major versions < 5 (#3421) * Fix an issue with use of uninitialized memory in trefer_deprec.c test (#3422) * Add parallel examples in doxygen (#3413) * Fix use of uninitialized value in testpar/t_dset.c test (#3423) * Remove extraneous "33" in RELEASE.txt (#3425) * Revise file close assertion failure fix (#3418) * Remove intel oneapi warning (#3426) * Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with segmenetation fault. (#3427) It is because the object in the testfile points back to the root group. When the tool tries to traverse the object, it goes back to the root group and then back again. * chore: match function call and VRFY() output (#3428) * Fix the Fortran extension used in example links (#3430) * Put H5T_CONV_ab macros in do..while loops (#3432) Ever since a recent round of macro cleanup, bin/trace and clang-format have been bickering over what H5Tconv.c should look like and neither produces readable code. This change puts the top-level H5T_CONV_ab macros in do..while loops, adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros clang-format recognizes. H5Tconv.c is now readable and both bin/trace and clang-format are happy. * Convert some H5MM calls to standard C equivalents (#2382) * H5MM_calloc and malloc are now mapped to stdlib C calls * H5MM_memcpy now maps directly to memcpy in release builds * H5MM_memcpy is still implemented as a separate function that checks for buffer overlap when H5MM_DEBUG is defined (default w/ debug builds) * Switches many library memcpy calls to use H5MM_memcpy * Fixes a possible zero allocation in H5Olayout.c * Add 1.14.4 to the release schedule (#3434) * Output stderr file in CMake testing on failure (#3431) * Add Intel oneAPI badges (#3433) * Add a CVE regression test action (#3445) * * Disable SZIP for Intel oneAPI Action (#3449) * Disable SZIP for Intel oneAPI Action * Disable Fortran and parallel * Update VOL CMake for REST VOL (#3450) * Update VOL CMake for REST VOL * Prevent linking static libs to VOLs * Add an h5py badge to README.md (#3477) * Removed all the ranks printing out testing information (#3457) * Fix Subfiling VFD IOC assignment bug (#3456) * Correct java test dimension (#3482) * Support CMake VOL builds with FetchContent from local directory (#3455) * Update VOL CMake for REST VOL * Prevent linking static libs to VOLs * index on fetch_local: 5c5c3f1505 Prevent linking static libs to VOLs * index on (no branch): 9a36d3e7b1 On fetch_local: WIP:add source dir fetch option for vols * Allow building of VOL from local source * Move LOCAL_DIR option to HDF5_VOL_ALLOW_EXTERNAL * Fix the Fortran include dir in install config files (#3454) * Convert hbool_t --> bool in examples (#3492) * Fix some minor formatting for consistency (#3499) * Create scorecard.yml (#3508) Bring in OSSF Scorecard code scanner as a GitHub action * Convert hbool_t --> bool in testpar (#3495) * hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491) * Convert hbool_t --> bool in test (#3494) * Convert hbool_t --> bool in src (#3496) * hbool_t --> bool in src * Does not remove TRUE/FALSE * Public header files are unchanged * Public API calls are unchanged * TRUE/FALSE --> true/false in src * Add deprecation notice for hbool_t * Added new Fortran API wrappers (#3511) * Added new wrappers for h5get_free_list_sizes_f H5Sselect_intersect_block_f H5Sselect_shape_same_f h5pget_no_selection_io_cause_f h5pget_mpio_no_collective_cause_f H5Lvisit_by_name_f H5Lvisit_f H5Fget_info_f h5dwrite_chunk_f h5dread_chunk_f * added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests * added fortran tests * Update tH5F.F90 * misc. fortran fixes for failing CI dailty tests (#3523) * fixed H5Lvisit* interface * changed integer type for direct write * Consistent initialization of hid_t in the tests (#3521) * Fix windows cpack with debug (#3525) * Add missing row for the ROS3 VFD in table #3415 (#3517) * fixed nvidia compiler issue (#3527) * Identify functions in a subgroup (#3530) * quiet warning on sunspot (gcc 11.2.0) (#3534) * Add API examples doxygen page (#3500) * removed C_INT32_T from Fortran APIs (#3537) * Add NVHPC 23.7 GitHub Actions (#3509) * Add NVHPC 27.3 GitHub Actions * Address @derobins review * Remove HD prefix from math functions (#3538) * Remove HD prefix from HDlog10 calls (#3539) Was missed in a previous commit and causes building subfiling to fail. * fixed arg to C H5Dwrite_chunk (#3541) * Strip HD prefix from string/char C API calls (#3540) * Strip HD prefix from string/char C API calls * HD(f)(put|get)(s|c) * HDstr* * HDv*printf * HD(s)(print|scan)f * HDperror But NOT: * HDstrcase* * HDvasprintf * HDstrtok_r * HDstrndup As those are not C99 and have portability work-around implementations. They will be handled later. * Fix th5_system.c screwup * Convert main.yml CI into callable workflows (#3529) * Fix broken URL. (#3546) * Fix grammar (#3545) * Update oneAPI-C/A badge yml links. (#3564) * Check return values from HDF5 API calls. (#3556) * Adds link to h5fuse.sh in testpar for autotools (#3557) * Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped. * Some minor formatting and text changes (#3563) * Fix typos and grammar in t_pread. (#3565) * Fix typo (givin->given) in test/testframe.c. (#3567) * Fix ifx unused variable hdferr warning. (#3568) * Correct comments about H5Z_FILTER_NONE (#3572) * Update release script. (#3577) * fixed function declaration (#3579) * Fixed GH-3554 (#3584) Removed the extra condition * Remove h5dwalk.1 man page. (#3589) * Removed the use of -commons linking option on Darwin (#3581) Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used * Fix docs for H5Pset_dxpl_mpio_collective_opt() (#3594) * Fix typo: arange->arrange in src/H5Cmpio.c. (#3597) * Fix docs for H5Acreate2 and H5Acreate_by_name (#3598) * Use HDoff_t with lseek consistently (#3600) lseek on Windows uses __int64 for both the offset and return type instead of off_t like most POSIX systems. This changes ensures we use HDoff_t (which is typdef'd correctly on Windows) w/ lseek. * Replaces HDgetenv with getenv (#3599) * Develop tools move (#3580) Reorganizes the tools files to support the VOL tests * Clean up Subfiling VFD header doxygen formatting (#3601) * Remove `sh` to run bash script. (#3590) * Correct path name of ddl file to be changed (#3607) * Fix potential uninitialized variable (#3602) Moves a union initialization up a bit so it's performed before code that can jump to the cleanup target, where file descriptors could be checked without being initialized. This could only happen in test code and only in an out-of-memory situation. Fixes Coverity 1542254 * Remove unnecessary assignment in test generator (#3603) Fixes what looks like a copy/paste/modify error in the format convert test file generator, where an array element is assigned one value and them immediately overwritten by another value. Fixes Coverity issue 1542285 * Remove useless define TRUE/FALSE statements. (#3604) * Fix typo behaviour and dependes. (#3605) * Fix typos (#3609) * Fixed unused variable in H5CS.c (#3552) (#3612) * Fixed #3552 * Fix grammar (#3614) * Cleanup unused statements (#3553) (#3617) Removed unnecessary assert statements and noise comments. * Fix Intel oneAPI icc warning (#3619) * Fix several spelling/grammar issues (#3621) * Add HPC CDash to README.md (#3623) * Disable static + thread-safe on Windows w/ CMake (#3622) The thread-safety feature on Windows requires a hook in DllMain() and thus is only available when HDF5 is built as a shared library. This was previously a warning, but has now been elevated to a fatal error that cannot be overridden with ALLOW_UNSUPPORTED. Fixes GitHub #3613 * Remove unused member from H5D_shared_t struct. (#3628) * Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624) * Fix grammar (#3635) * Disambiguate error output messages. (#3634) * Disambiguate error output messages. * Address @brtnfld review. * Fail CMake on Windows when sub-filing VFD is enabled (#3636) * Improve consistency in past tense usage (#3638) * Split out test logic to separate file (#3639) * Drop MPI-2 support (#3643) * Switch IEEE flags for NAG Fortran (#3644) Default is -ieee=stop, which causes problems when the H5T module performs floating-point type introspection. The new mode is -ieee=full * Remove 1.10.11 info from README.md (#3646) * Fixes GH#1027 compilation error (#3654) * Remove 1.10 badge (#3650) * Use real URLs and updated names for plugins (#3651) * synchronize TGZ naming convention/usage * Update parallel compression feature to support multi-dataset I/O (#3591) * Add more tests for selection I/O. (#3528) * Adjust 1.14 files after merging ---------
* Normalizes the public headers (#3292)Dana Robinson2023-07-271-14/+14
| | | * Also brings over the apostrophe fix
* Warn about changing collections during iteration (#2962)mattjala2023-05-161-0/+9
|
* Merge with develop (#2790)Dana Robinson2023-04-221-15/+15
|
* 1.14 Merge doxygen plist tables changes #2470 from develop (#2503)Allen Byrne2023-03-011-0/+3
| | | | | * Merge doxygen plist tables changes from develop * Doxy corrections
* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Removed the file, func, line args in the _async APIs fpr doxygen (#2179)Scot Breitenfeld2022-10-251-0/+61
| | | | | | | | | | | | | | | | | | | | | | | | | * Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean. * format fixes * fixed DOXYGEN_PREDEFINED * Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args * format fixes * Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN * reordered multidataset declarations * alt. for H5Aclose_async and H5Acreate_async * made doxgyen API into seperate blocks * updated codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* A batch of life-cycle examples for different modules (#654)Gerd Heber2021-09-011-205/+62
| | | | | | | | | * Create a tag file for permalinks. * Added DOXYGEN_TAG_FILE. * Added Doxygen life-cycle examples for different modules. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* doygen adjustments (#614)Allen Byrne2021-05-041-49/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge doxygen2 into develop (#553)Gerd Heber2021-04-261-67/+126
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed warnings and started H5Epublic.h. * Include H5FD* headers to correctly resolve references. * Doxygen2 (#330) * H5Eauto_is_v2. * Added a few more calls. * Added a few more H5E calls. * First cut of H5E v2. * Added the deprecated v1 calls. * Updated spacing. * Once more. * Taking some inspiration from Eigen3. * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352) * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2. * doxygen work. fixs format by using clang-format. * doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments. For Quincey's comments, since we are not supposed to change the source code. I leave this to future improvements. * added documentation for H5P APIs (#350) * add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios * format corrections * fixed grammer * fixed herr_t * Better name. * A fresh look. * add doxygen to H5Ppublic.h * use attention instead of warning * Add doxygen comments in H5Ppublic.h (#375) * Add doxygen comments in H5Ppublic.h * H5Pset_meta_block_size * H5Pset_metadata_read_attempts * H5Pset_multi_type * H5Pset_object_flush_cb * H5Pset_sieve_buf_size * H5Pset_small_data_block_size * H5Pset_all_coll_metadata_ops * H5Pget_all_coll_metadata_ops * Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt * Fix clang-format errors * Fix filenames in doxygen/examples * add doxygen to H5Ppublic.h (#378) * add doxygen to H5Ppublic.h * use attention instead of warning Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> * Revert "add doxygen to H5Ppublic.h (#378)" This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2. * Updated Doxygen variables. * I forgot to copy two images. * Enable desktop search by default. * Add my assigned Doxygen documentation. * Remove whitespace at EOL. Appease clang-format. * Addressed Chris' comments. * Added an alias for asynchronous functions. * One space is enough for all of us. * Slightly restructured RM page. * address some issues * reformatting * Style external links. * reformatting * reformatting * Added "Metadata Caching in HDF5" as a technical note example. * Revise this soon! * Added specification examples. * Fixed references. * Added H5AC cache image stuff and file format study. * Added older FMT versions. Where did 1.0 go? * Updated C/C++ note and replaced ambiguous labels. * Reformat source with clang v10.0.1. * Added the VFL technical note. * Added what I believe might be called version 1.0 of the format. * Added the remaining specs. * Added H5Z callback documentation and fixed a few mistakes. * Added dox for deprecated H5G calls and fixed a few snippet blockIDs. * clang-format happy? * Ok? * Bonus track: Deprecated H5D functions. * Carry over the more detailed group description. * Added documentation for the missing and deprecated H5R calls. * Life is easier and less repetitive w/ snippets. Use them! * Eliminate the snippet block ID artifacts in the HTML rendering. * Fixed snippet HTML artifacts and added a few missing calls. * Under 20 H5Ps to go! * Almost complete! * "This is a form of pedantry up with which I will not put." (Churchill) * Let's not waste as much space on bulleted lists! * First complete (?) draft of the Doxygen-based RM. * Completeness check and minor fixes along the way. * Pedantry. * Adding missing H5FD calls checkpoint. * Pedantry. * More pedantry. * Added H5Pset_fapl_log. * First draft of H5ES. * Fixed warnings. * Prep. for map module. * First cut of the map module. * Pedantry. * Possible H5F introduction. * Fix the indentation. * Pedantry. * Ditto. * Thanks to the reviewers for their comments. * Added missing images. * Line numbers are a distraction here. * More examples, references, and clean-up. Don't repeat yourself! * Clang pedantry. * Ditto. * More reviewer comments... * Templatized references and cleaned up \todos. * Committing clang-format changes * Fixed MANIFEST. * Addressed Quincey's comments. (OCPLs) * Fixed a few more \todo items. * Fixed more \todo items. * Added attribute life cycle. * Forgot the examples file. * Committing clang-format changes * Pedantry. * Live and learn! * Added a sample H5D life cycle. * Committing clang-format changes * Pedantry. Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com> Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-231-3/+3
| | | | | | | | | | | | | | | | * Fixed many -Wreserved-id-macro warnings by fixing header guard spelling Removed leading underscore(s) from header guard spelling. Used 2 regexes: ` _H5(.*)_H` ` __H5(.*)_H` Applied case-insensitively to only .h files. * Modified scripts that generate header files to not use underscore prefix Interestingly, there was already no leading underscore in the trailing comment at the end of the file * Fixed remaining -Wreserved-id-macro warning not caught by regex
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Reformat source (#244)Quincey Koziol2021-01-071-58/+54
|
* Doxygen - RM entries for H5A, H5S, and H5P APIs (#181)bljhdf2020-12-161-53/+819
| | | | | | | * Doxygen - RM entries for H5A, H5S, and H5P APIs * fix issues on ubuntu * added missing H5F_fspace_strategy_t_snip
* Bring async branch to develop (#166)Quincey Koziol2020-12-141-11/+76
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add H5Fwait, H5Dwait, and other changes for async vol connector * Revert temporary testing changes * Add H5Fwait to header file * Add H5VLreset_lib_state() routine. * Correct VOL wrap context when retrieving library state for file open & create. * Manage the API context's VOL connector state as part of the library state. * Set the 'VOL connector property valid' flag when restoring the library state. * Don't push new API context on stack when retrieving "current" one. * Check for NULL VOL wrap context before decrementing refcount on it, when freeing the API context state. * Manage recount of underlying connector for VOL wrap context. * Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and release the global lock on the HDF5 library. * Update library with new functions related to library global lock * Add asynchronous token API * Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the threadsafety (H5TS*) routines. * Sync w/develop * Initial event set code framework. * Elaborate on the H5ES routines, starting to add API routines. Update the "close ID" callbacks to allow asynchronous request tokens to be passed in from an asynchronous close API call. Refactor current asynchronous API routines (H5Fopen/H5Fclose and H5Dread/H5Dread) to use event sets instead of directly working with request tokens from the application. Clean up a few other minor warnings & code style issues. * Implement H5EScreate, H5ESget_count, and H5ESclose. It should be possible to write a simple application that creates an event set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and H5Fclose_async, then calls H5ESclose (which waits for all async events to complete). * Add source file for event set test. * Refactor sync & async API routines to call common routine. Move dataset API read / write routines to src/H5D.c, along with all the other API routines. Progress on "fake" async VOL connector, for testing. * Modify async implementation to wrap async requests in a H5VL_object_t struct so the VOL layer can find the connector when accessing the request at a later point. * Free the requests is H5ESclose. Remove comments implying that request wait, notify, and cancel callbacks should free the request. * Fix bug in error handling in H5Fclose. * Fix bugs in async file routines. Rename H5VL_create_object_generic to H5VL_create_object. * Add explicit async version of H5Fcreate. * Add more _async routines * Correct typo for return value from H5Awrite changes * Add H5EStest and H5ESwait routines * Updated with API tracing info * Fix NULL pointer dereference in H5ES__wait * Add H5is_library_terminating() routine, so that VOL connectors can detect when the library is shutting down. * Fix typo * Remove event from event set's linked list * Move block of code so that vol_obj is valid * Avoid setting properties in the DXPL when reseting the library state (and in the test code). * Refactor argument tracing to implement new capability for tracing arguments of non-API routines, with the H5ARG_TRACE macro. This macro is updated automatically with the bin/trace script that runs as part of the autogen.sh process. Major changes were in src/H5trace.c and bin/trace, with the other changes being cleanups to the argument lists, to improve their presentation in the tracing output. Also - added the "managed string" routines, which can dynamically allocate strings, appending printf-formatted output to the string efficiently. * Release memory for managed strings * Fix printf() formats. * More printf() format fixes. * Add H5Eappend_stack routine and regression tests * Clean up a few missed merge conflicts and update the error stacks. * Remove unnecessary fork() operations and ten second sleep(). * Restore commented out attribute out, to better enable tracking down the previous failure * Allow multiple H5ARG_TRACE macros within a routine to be updated * Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert. * Merge "managed" string routines into "ref-counted" strings, and refactor code to use them. * Add missing file. * Add caller's name and arguments to event, for error reporting * Refactor event set setup for "API common" internal routines * Checkin async API routines for H5A* and H5G* modules as listed in ID-283. Fix couple h5dump expected output files due to the changes. * Add some of the error query routines needed for event sets. * Refactor to make async setup / teardown and "common" routines cleaner * (1) Add async APIs to H5L, H5F, and H5D modules (2) Fix errors in previous checkins of async APIs in H5A and H5G modules (3) h5dump expected output changes * Enhance event info, for better error handling * Change name of temporary vol_obj variable, to help reduce coding errors * Fix oversight with vol_obj pointer * Minor code cleanup * Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state * Run source formatter * Change H5TSmutex lock and release to include a lock count * Update error reporting ideas * Minor updates to improve sanity checking for retrieving / restoring library state * Updated with feedback from h5py team members * Refactor internal event set list and event handling, add implementation for H5ESget_err_info * Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines. * Update API tracing for new H5VL_request_status_t typedef * Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure * Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation * Remove 'canceled' event status from Java constants * Be safer about releasing resources when inserting a newly opened/created object or file into an event set * Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate". * Remove H5ES_STATUS_CANCELED from Java wrappers also * (a) Add async APIs for H5O module as listed in jira issue ID-283. (b) Remove verification of name parameter in async related routines for H55A and H5L modules because it is checked in H5VL_setup* routine. (c) Modify h5dump expected output due to the async changes. * Corrections based on PR feedback. * Further changes to make based on PR feedback. * Fix missed merge marker, and reformatted line * Clean up some warnings * Correct level of indirection * Relocate prototype (and doxygen info) for H5Aclose * Change non-static function declarations to be static * Ensure that H5TSpublic.h header gets installed (#129) * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c. * Add H5Iregister_future routine and tests. * Correct return value for H5Lexists_async * Add H5_DLL macro to public H5ES API routines * Update supported -> flags parameter for introspect_query callback * Remove my email address. Update passthrough VOL connector ID. * Fix comment for post_open_api_common * Remove unused non-blocking VOL connector * Minor cleanup in async branch in preparation for merge to develop * Update CMake and the Autotools to use the new pass-through VOL ID * Fix for SWMR daily test failures (#160) The H5I_register_using_existing_id() call did not initialize the future ID callbacks, causing the library to segfault when it tried to resolve those function pointers. * Added selective async APIs (#150) * Added selective async APIs Description: Added the following APIs: H5Ropen_attr_async H5Ropen_object_async H5Ropen_region_async H5Mcreate_async H5Mopen_async H5Mput_async H5Mget_async H5Mclose_async H5Tcommit_async H5Topen_async H5Tcopy_async H5Tclose_async - Updated an expected output file to include a new internal function in the error stack for the failure case. * Updated async APIs per reviews, including removing async version of H5Tcopy. * Removed statements that were added by mistake in the previous commit. * Fix compile issues in H5M and warnings elsewhere * Reformat code * Brings VOL_LIST changes from develop. (#163) Co-authored-by: Houjun Tang <htang4@lbl.gov> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <derobins@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Minor cleanups (#132)Quincey Koziol2020-11-261-21/+21
|
* Doxygen - added (mostly) beginner functions (#112)bljhdf2020-11-231-4/+337
| | | | | * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function
* Clang-format of source filesAllen Byrne2020-09-301-52/+41
|
* Moved the optional enums to H5VLnative.h and converted to an intDana Robinson2018-12-181-21/+13
| | | | typedef and a set of #defines.
* Moved the native VOL connector's optional enums to theDana Robinson2018-12-151-0/+16
| | | | | public headers and renamed to include native/NATIVE in the name.
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * 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.
* [svn-r15628] Description:Quincey Koziol2008-09-161-2/+2
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r14234] Description:Quincey Koziol2007-11-011-1/+4
| | | | | | | | | | | | | | | | | | Add H5Aexists and H5Aexists_by_name API routines, to match H5Lexists. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14222] Description:Quincey Koziol2007-10-301-2/+2
| | | | | | | | | | | | | | | | | | Change H5Adelete2 -> H5Adelete_by_name and un-deprecate H5Adelete1 back to H5Adelete, for better consistency with new other API routiens. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14220] Description:Quincey Koziol2007-10-301-1/+3
| | | | | | | | | | | | | | | | | | | | Change H5Aiterate2 -> H5Aiterate_by_name to be more consistent with other new API routine names Re-add H5Aiterate2, to operate on a particular object Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14219] Description:Quincey Koziol2007-10-301-2/+2
| | | | | | | | | | | | | | | | | | Change H5Arename2 -> H5Arename_by_name and un-deprecate H5Arename1 back to H5Arename. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14218] Description:Quincey Koziol2007-10-301-2/+4
| | | | | | | | | | | | | | | | | | | | | Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with other new API routines. Re-added simpler form of H5Acreate2, which creates attributes directly on an object. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14217] Description:Quincey Koziol2007-10-301-2/+3
| | | | | | | | | | | | | | | | | | | | | Change H5Aopen -> H5Aopen_by_name, in order to be more consistent with other new API routines. Re-add H5Aopen as a simpler routine, to open attributes on a particular object. (Much like the old H5Aopen_name routine). Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14187] Description:Quincey Koziol2007-10-041-8/+2
| | | | | | | | | | | | | | | | | | | | Put H5Acreate() under API versioning, with all internal usage shifted to H5Acreate2(). Add regression tests for H5Acreate1(). Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14185] Description:Quincey Koziol2007-10-041-1/+1
| | | | | | | | | | | | | | | | | | | | | Move H5Aopen_name() routine to deprecated symbol section and replace internal usage with H5Aopen(). Add simple regression test for H5Aopen_name() to deprecated routine test. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14184] Description:Quincey Koziol2007-10-041-1/+1
| | | | | | | | | | | | | | | | | | | | Move H5Aopen_idx() into deprecated symbols section, replacing all internal usage with H5Aopen_by_idx(). Add simple regression test for H5Aopen_idx(). Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14183] Description:Quincey Koziol2007-10-041-1/+1
| | | | | | | | | | | | | | | | | | Move H5Aget_num_attrs() into deprecated routines section, replacing all internal usage with H5Oget_info(). Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14180] Description:Quincey Koziol2007-10-041-6/+6
| | | | | | | | | | | | | | | | | | | Make H5Aiterate() versioned and change all internal use to H5Aiterate2() Leave some regression tests that exercise H5Aiterate1() Fix attribute display in h5dump & h5ls to be "by name" by default Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14163] Description:Quincey Koziol2007-09-271-1/+1
| | | | | | | | | | | | | | | | | | | Make H5Arename() versioned and switch internal usage to use H5Arename2() Add regression test for H5Arename1() Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14162] Description:Quincey Koziol2007-09-271-1/+17
| | | | | | | | | | | | | | | | | | Make H5Adelete versioned and switch internal library use to H5Adelete2. Add regression test for H5Adelete1 Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r13361] Description:Quincey Koziol2007-02-211-4/+9
| | | | | | | Add H5Aopen(), H5Aopen_by_idx() and H5Acreate2() routines. Tested on: Mac OS X/32 10.4.8 (amazon)
* [svn-r13360] Description:Quincey Koziol2007-02-211-5/+11
| | | | | | | | | | | | Finish H5Aiterate2() Add H5Arename2() and mark H5Arename as deprecated. Started on H5Oopen_by_idx(). Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13353] Description:Quincey Koziol2007-02-201-3/+10
| | | | | | | | | | | | Checkpoint progress on H5Aiterate2(). Mark H5Aiterate() as deprecated. Various code cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13347] Description:Quincey Koziol2007-02-201-1/+3
| | | | | | | | | Deprecate H5Adelete in favor of H5Adelete2, which corresponds to the new pattern of specifying an object's location. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13341] Description:Quincey Koziol2007-02-201-1/+4
| | | | | | | Checkpoint "delete by index" code, which is partially finished. Tested on: FreeBSD/32 6.2 (duty)
* [svn-r13304] Description:Quincey Koziol2007-02-141-4/+5
| | | | | | | | Fix new API routines to use same pattern of arguments for specifying an object as the new H5G/L/O API routines. Tested on: Linux/32 2.6 (chicago)
* [svn-r13287] Description:Quincey Koziol2007-02-131-0/+3
| | | | | | | | | | | | | Add H5Aget_info_by_idx & H5Aget_name_by_idx routines, along with refactoring underlying indices code to handle those sort of queries. Simplify the link callback routines a bit. Minor other cleanups. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13272] Description:Quincey Koziol2007-02-081-2/+4
| | | | | | | | Checkpoint attribute creation order coding on "by index" routines. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r13248] Description:Quincey Koziol2007-02-061-1/+13
| | | | | | | | | More progress on creation order for attribbutes - they are now basically working for "compact" attribute storage. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.8 (amazon)
* [svn-r12976] Description:Quincey Koziol2006-11-271-1/+7
| | | | | | | | | | | Add # of attributes to the object info struct and deprecate H5Aget_num_attrs(). Tested on: FreeBSd/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12700] Alert:Quincey Koziol2006-10-021-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | File format is not stable, don't keep files produced! Description: First stage of checkins modifying the format of groups to support creation order. Implement "dense" storage for links in groups. Try to clarify some of the symbols for the H5L API. Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest file format options (including "dense" link storage in groups) Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation order tracking in groups (although no index on creation order yet). Remove --enable-group-revision configure flag, as file format issues are now handled in a backwardly/forwardly compatible way. Clean up lots of compiler warnings and other minor formatting issues. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-v1.6 compa Mac OSX/32 10.4.8 (amazon) AIX 5.3 (copper) w/parallel & FORTRAN
* [svn-r12221] Purpose:Quincey Koziol2006-04-101-0/+2
| | | | | | | | | | | | | | | "Hide" file format changes (for now) Description: Add ifdef's (controlled by the --enable-group-revision configure flag) to disable group revision changes to the file format, in order to allow alpha release to go ahead without releasing an unsupported version into the wild. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 32-bit (heping) Linux 2.4 64-bit (mir) Solaris 2.9 (shanti)
generated by cgit v0.12 at 2024-11-25 01:31:48 (GMT)