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* 1.14 sync with develop (#3660)jhendersonHDF2023-10-121-24/+24
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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 ---------
* Merge Fixes the last of the -Wextra-semi-stmt warnings #3326 (#3338)Allen Byrne2023-08-031-27/+27
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* Sync test dir w/ develop (#3303)Dana Robinson2023-07-281-4/+4
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* Brings over most of the HD prefix removal (#3293)Dana Robinson2023-07-271-16/+16
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* 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.
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-2/+2
| | | | | * Update format source to clang 13 * More format changes
* h5test.h testing macros get enclosed in do..while loops (#1721)Dana Robinson2022-05-041-103/+103
| | | | | | | * h5test.h testing macros get enclosed in do..while loops * Adds missed macro in hl C++ code * Fixes macro in Windows code
* Fixes stack size warnings in dtransform (#1696)Dana Robinson2022-04-271-10/+26
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* Implemented suggestion in #1381 for dtransform test (#1415)Allen Byrne2022-02-041-10/+7
| | | | | | | | | | | | | | | * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-081-4/+0
| | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD plugins (#602)jhendersonHDF2021-09-291-0/+2
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() … (#933)Jan-Willem Blokland2021-09-131-0/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() function - Made a small improvement for H5Z_xform_noop() function. Now, the function will also return TRUE if the data transform function expression = "x". For this case, the HDF5 library behaves in a similar fashion as the case when no data transform function has been specified. - Improved the inline documentation of the function H5Z_xform_create() such it is more inline with the rest of the code. * Committing clang-format changes * H5Ztrans: (feature) Added 3 tests for improved H5Z_xform_noop() function - Added serial test with data transform expression = "x" to verify the improved H5Z_xform_noop() function behaves as expected. - Added 2 parallel tests with data transform expression = "x" in combination with a filter. Before, these tests will fail but with the improved H5Z_xform_noop() function they work and result in the expected behavior. - Small bug fix for one of parallel filter tests. * Committing clang-format changes * H5Ztrans: (feature) Added release note about detection of the simple data transform function "x". - Added a brief explanation about the implemented improvement of the detection of the simple data transform function "x" to the RELEASE.txt file. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* More clang tidy (#908)Sean McBride2021-08-231-35/+35
| | | | | | | | | | | | | | | | | | | * Pacify clang-analyzer-unix.cstring.NullArg * Apply some bugprone-suspicious-string-compare * Apply some readability-simplify-boolean-expr * Apply some readability-make-member-function-const * Apple some bugprone-macro-parentheses * Changed an f suffix to L for `long double` * Applied some readability-uppercase-literal-suffix automatically * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update clang config (#473)Quincey Koziol2021-03-171-1/+4
| | | | | | | * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)Sean McBride2021-03-091-4/+4
| | | | | | | | | | | | | * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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.
* (fix) H5Z_xform_create function and scientific notation (#144)jwsblokland2020-12-021-0/+24
| | | | | | | | | | | | | | * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Clang-format of source filesAllen Byrne2020-09-301-449/+511
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* So that I can use PASSED(); anywhere a statement can go, #define PASSED() withDavid Young2020-02-281-6/+6
| | | | a do-while wrapper.
* Add HD prefix to testsAllen Byrne2019-08-151-204/+204
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* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-1/+1
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* 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-r27800] Minor warning fixes in the library tests.Dana Robinson2015-09-161-1/+1
| | | | Tested on: jam (too minor for h5committest)
* [svn-r26597] Description:Quincey Koziol2015-03-261-13/+0
| | | | | | | | | | | Bring r26500 from autotools_rework branch to trunk: Remove the LLONG_TO_FP_CAST_WORKS macro/define, as it targets problems with the Visual Studio 6 compilers. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26596] Description:Quincey Koziol2015-03-261-10/+0
| | | | | | | | | | | Bring r26499 from autotools_rework branch to trunk: Remove ULLONG_TO_FP_CAST_WORKS macro/define, as it only applies to older platforms we aren't supporting any longer. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26333] Eliminates gcc warnings due to -Wunsuffixed-float-constants.Dana Robinson2015-03-011-1/+1
| | | | | | | | | | | | - Adds 'F' suffixes for most float constants. - A few constants MUST be of type double. These now receive the long double L suffix and are then cast to double. I do this via a new H5_DOUBLE() macro which was added to H5private.h. Fixes: HDFFV-9148 Tested on: h5committest
* [svn-r24030] Description:Quincey Koziol2013-08-191-19/+19
| | | | | | | | Clean up more compiler warnings. Tested on: Mac OSX/64 10.8.4 (amazon) w/gcc, C++ & FORTRAN (too minor to require h5committest)
* [svn-r22076] #Issue 7922 - H5Pset_data_transform had seg fault with some ↵Raymond Lu2012-03-151-4/+176
| | | | | | | | | operations like x*-100. The parser mistaked "-" as substraction. I fixed it and also fixed another problem with some special cases like 100-x and 2/x. Tested on jam, koala, and ostrich.
* [svn-r19481] I'm backing out my fix for bug 1707 because there're some ↵Raymond Lu2010-09-271-14/+4
| | | | | | | | | | | unresolved issues - r19441 and 19467. Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with the 1.8 library to compile. I created a branch off the trunk called set_auto to continue working on the problem. Tested on jam - backing out, simple.
* [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-211-4/+14
| | | | | | | | | | | | | application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a document for it. Tested on heiwa, jam, and amani. The property change in configure.in, config, and Makefile.am came from the merge of the 1.8 library change.
* [svn-r19297] Description:Quincey Koziol2010-08-251-1/+1
| | | | | | | | | | Whack a few more memory errors exposed by valgrind. Make the debugging dump output a little bit prettier. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug (h5committest forthcoming)
* [svn-r18346] Description:Quincey Koziol2010-02-271-2/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity fixes back from branch to trunk: r18336: Fix coverity issues 275, 276, 277, 323, 432, 433, and 434 r18337: Fix Coverity issue #106: release free space section node on error r18338: Fixed Coverity #94 - In H5P_register, new_class wasn't closed when there's an error after it's created. r18339: Fix Coverity #185 - In test_conv_str_1, BUF wasn't freed when there's an error in this function. r18340: Correct error in r18337 that wasn't releasing indirect fractal heap block early enough. r18341: Close nodes if any failed in the middle of allocating new nodes. Coverity 140 and 141 r18342: Correct [another] problem w/r18337. r18343: Fix coverity items 185, 20, and 21. r18344: Fix Coverity 213 - In H5FD_family_close, the double pointer file->memb was dereferenced without NULL checking (We believe). r18345: Fix Coverity issue # 210; removed NULL check after pointer dereferenced in H5HFdblock.c. Also assigned NULL to pointer in H5Pint.c to fix segmentation fault. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, 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 Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18300] Description:Quincey Koziol2010-02-201-193/+248
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity fixes from branch to trunk: r18282: Fix Coverity issue #428 by wrapping testing calls with if(pass) {} block. r18283: Fix Coverity issue #425 by wrapping test calls in if(pass) {} block r18284: Issue 166: init_error() malloc'd 3 pointers in initialization and never freed inc ase of errors. Init pointers to NULL, check allocation results and free allocations in error block r18285: Fix Coverity issue #410 by wrapping test calls with if(pass) {} block. r18286: Issue 165: custom_print_cb() needed allocations freed in error block. r18287: Fix coverity issue # 409 Added if (pass) checks around calls to flush_cache. Additionally, added a check for file_ptr = NULL after call to setup_cache. r18288: Fix coverity# 107 free fh in H5HF_close() correctly before exit the function even when failure occurs. r18289: Fix Coverity issue #429: correct failure return values to match return type from routine. r18290: Fix Coverity issue #103: release allocated indirect section on error r18294: Issue 153, 152: Check allocations and free allocations in error block. Also cleaned up hid_t identifer that were opened in error block. r18295: Fix coverity# 101 free new_loc in H5HF_man_iter_start_entry() correctly before exit the function even when failure occurs r18296: Fix coverity# 100 free down_loc in H5HF_man_iter_down() before exit the function when failure occurs r18297: Fixed coverity issues 54, 55 and 216. Correctly handle the various ways that allocation of attr_name can fail in test_attr_basic_write. r18298: Fix coverity# 119 free object in H5HG_read() before exit the function when failure occurs r18299: Fix coverity issue #112: Add cleanup during error handling of H5MP_create. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & production Misc. Linux configurations (on original checkins)
* [svn-r16803] Purpose: Fix bug 1548Neil Fortner2009-04-201-24/+35
| | | | | | | | | Description: When writing data to a dataset, the data transform was performed after type conversion. This caused an error if the file type was non-native. This has been changed so data transforms are always performed on the memory type. Tested: jam, linew. smirom (h5committest)
* [svn-r16560] Description:Quincey Koziol2009-03-101-12/+18
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r16489] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-181-4/+4
| | | | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 Vista 32, VS2005, IVF101 XP32, Cygwin
* [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-r14199] Description:Quincey Koziol2007-10-111-79/+79
| | | | | | | | | | | | | | | | | | | | | Add H5Dcreate to API versioned routines, replacing internal usage with H5Dcreate2 Fix thread-safe error stack initialization for API versioned error stack printing routines. 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-r13648] Description:Quincey Koziol2007-04-121-4/+4
| | | | | | | | | | Rename new error handling API routines from H5E<foo>_stack() to H5E<foo>2(). Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty)
* [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-r12880] Purpose: Bug fixLeon Arber2006-11-081-27/+28
| | | | | | | Description: Fix some memory-related bugs in the data transform code Tested: kagiso w/ valgrind 3.2.1
* [svn-r12803] Description:Quincey Koziol2006-10-231-0/+2
| | | | | | | | | | | | | | Finish new version of the I/O pipeline message, which is much smaller than the previous version. This version is used with the "use the latest version of the format" flag. Closed several memory leaks/overruns (found with valgrind). Also, lots of compiler & formatting cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r11771] Purpose:Quincey Koziol2005-12-081-6/+6
| | | | | | | | | | | | Code cleanup Description: Fix a bunch of warnings flagged by Windows compilers. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11524] Purpose:Albert Cheng2005-10-111-0/+14
| | | | | | | Inserted copyright notice. Platforms tested: Tested in heping only since only a comment block was added.
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-54/+54
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11144] Purpose:Quincey Koziol2005-07-231-0/+4
| | | | | | | | | | | New port Description: Elena asked me to check in her NEC SX-6 work, so here it is! :-) Platforms tested: FreeBSD 4.11 (sleipnir) NEC SX-6 (by Elena)
* [svn-r10699] Purpose:Quincey Koziol2005-04-291-2/+2
| | | | | | | | | | | | Code cleanup Description: Switch name & logic from H5_LLONG_TO_FP_CAST_BROKEN to H5_LLONG_TO_FP_CAST_WORKS, to better match the rest of the library. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10661] Purpose:Leon Arber2005-04-251-2/+2
| | | | | | | | | | | | | | | | Bug fix.... Description: Despite passing all tests, the previous checkin had a copy/paste typo that resulted in the tests being run under the wrong conditions. Solution: Fixed typo. Platforms tested: yet another minor change... copper only. Misc. update:
* [svn-r10660] Purpose:Leon Arber2005-04-251-4/+4
| | | | | | | | | | | | | | | | | bug fix (sorta) Description: Rename H5_LLONG_TO_FP_CAST_WORKS to H5_LLONG_TO_FP_CAST_BROKEN Solution: Since a test for H5_LLONG_TO_FP_CAST_WORKS is not present in the configure script, the dtransform test would assume that this cast doesn't work and skip the test. Change the variable around so that, by default, it is assumed a long long to double cast does work. Platforms tested: minor change: copper, sol Misc. update:
generated by cgit v0.12 at 2024-11-18 03:17:52 (GMT)