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* Fix spelling (#3633)Dana Robinson2023-10-048-11/+11
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* Merge/update CMake, presets,java and tools (#3393)Allen Byrne2023-08-213-266/+308
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* Fix loading plugin fails with missing directory GH issue #3248 (#3324)Allen Byrne2023-08-021-10/+18
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* Add java options to build scripts (#3137)mattjala2023-06-152-2/+2
| | | | | | | | | | | | | | | | | 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).
* Move config/cmake_ext_mod content to config/cmake (#3062)Dana Robinson2023-06-071-11/+11
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* Bring key changesets from develop (#3052)Dana Robinson2023-06-062-17/+17
| | | | | | | | | * Bump GitHub action macOS version to 13 (#2999, #3009) * Bump GitHub action gcc/g++/gfortran version to 12 (#3015) * Bump Autoconf version to 2.71 (#2944) * Fix missing h5_reset() calls in accum test (#3001) * Only run ttsafe in GitHub thread-safe actions (#2777) * Fix Java debug asserts on Windows (#3012) * Fix long double dt_arith bug on macOS (#3038)
* Fix CMake generator expression syntax (#2940)Allen Byrne2023-05-121-3/+3
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* Fix v1 object header gap bug in H5Ocopy (#2785) (#2833)jhendersonHDF2023-04-301-0/+64
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* Port h5dchunk_iter_hsizet_size #2074 to hdf5_1_12 branch (#2329)Mark Kittisopikul2023-03-291-9/+9
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2546)Allen Byrne2023-03-142-3/+3
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* Fix up the H5Pencode2 test for virtual layout. (#2325) (#2356)vchoi-hdfgroup2023-03-141-115/+111
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* Update Copyright headers. (#2534)Larry Knox2023-03-13163-169/+4
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* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… ↵vchoi-hdfgroup2023-02-263-0/+40
| | | | | | | | | | | | | | | | | | | | | | | | (#2291) (#2496) * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings mirror VFD test fixes from develop (#2392)Dana Robinson2023-01-053-1566/+1428
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* 1.12: Brings the updated CI in from develop (#2311)Dana Robinson2022-12-161-2/+2
| | | | | | | | | | | | | | * Brings the updated CI in from develop Does not include the -Werror checks, changes 1.14 API to 1.12 where needed. * Fixes an API compat issue in the mirror VFD test * Committing clang-format changes * Removed pr-check.yml Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-041-1/+78
| | | | file handles (#2181) (#2207)
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-041-0/+52
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* Address review comments from downstream merge of #2016 (#2073) (#2081)Neil Fortner2022-09-011-1/+1
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* Fix bug in attribute type conversion wiith compound types - merge to 1.12 ↵Neil Fortner2022-08-241-0/+131
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#2061) * Fix bug in attribute type conversion wiith compound types (#2016) * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for GitHub #2016 (#2030) * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. * Add RELEASE.txt note for PR #2016 * Add GitHub number to release note Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Persist dataset access properties when using H5Fstart_swmr_write - merge to ↵Neil Fortner2022-08-221-0/+373
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1.12 branch (#2031) * Merge GitHub #1862 (HDFFV-11308) to 1.12 branch Persist dataset access properties when using H5Fstart_swmr_write (#1862) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix bug in swmr.c introduced with recent merge (double_t) (#1913) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes * Replace accidental use of double_t in swmr.c with double. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for HDFFV-11308 (#2029) * Add note to RELEASE.txt for HDFFV-11308 * Fix formatting error in RELEASE.txt * Committing clang-format changes * Fix inappropriate use of HGOTO_ERROR (#2055) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Spelling fixes for codespell (#2038)Dana Robinson2022-08-1821-57/+47
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Backport H5Dchunk_iter to 1.12 branch (#1970)Mark Kittisopikul2022-08-161-53/+171
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Revert H5Dchunk_iter changes in hdf5_1_12_1 (#733)" This reverts commit 10abe9a8b4985a18a0c88615686184d233d7b845. * Apply clang-format * Reincorporate spelling fix from #1166 * Incorporate H5Dchunk_iter changes from #161 * Backport to 1.12: Adds a quick for for some egregious chunk_info badness (#722) * Backport to 1.12: Converts testhdf5 macros to h5test macros in chunk_info.c (#1820) The two macro schemes were not designed to work together. Also quiets some MSVC warnings about comparing pointers and integers. * Backport to 1.12: H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969) * H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419 * Update docs for H5Dchunk_iter, H5Dget_chunk_info* Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following * offset Logical position of the chunk’s first element in units of dataset elements * filter_mask Bitmask indicating the filters used when the chunk was written * size Chunk size in bytes, 0 if the chunk does not exist * Sync H5Dchunk_iter documentation with develop * Remove H5VL_DATASET_WAIT references from 1.12 * Backport to 1.12 #161, #1474, review comments Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* clang 13 format #1933 (#1939)Allen Byrne2022-07-27107-1283/+1285
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* revert incorrect merge (#1912)Allen Byrne2022-07-191-1/+1
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* 1.12 eliminate unnecessary errors in the error stack (#1880)Allen Byrne2022-07-181-1/+1
| | | | | | | | | | | * Eliminate unnecessary error output * Fix merge typo * fix format * Fix object address to tokens * Fix conflict
* revert format of parallel getenv parameter (#1808)Allen Byrne2022-06-131-1/+1
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* Hdf5 1 12 sync (#1794)Allen Byrne2022-06-122-17/+17
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* Change TestExpress #1722 (#1776)Allen Byrne2022-05-206-24/+43
| | | | | * Change TestExpress #1722 * Update comment
* [1.12 Merge]Hdf5 1 12 warnings fixes (#1715)jhendersonHDF2022-05-039-4183/+3030
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in ntypes (#1695) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.12 Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 12 Miscellaneous warnings fixes (#1718)jhendersonHDF2022-05-032-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12: Last round of normalizations for 1.12.2 (#1621)Dana Robinson2022-04-087-123/+119
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* Merge branch 'spelling-corrections' of https://github.com/lrknox/hdf5 into ↵Larry Knox2022-04-0775-437/+437
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| * Apply suggestions from code reviewLarry Knox2022-04-073-6/+6
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| * Merge branch 'hdf5_1_12' into spelling-correctionsLarry Knox2022-04-078-2096/+3
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| * | Committing clang-format changesgithub-actions2022-04-071-2/+2
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| * | Commit codespell spelling corrections.Larry Knox2022-04-0775-435/+435
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* | | 1.12: Brings changes from testpar over from develop (#1614)Dana Robinson2022-04-072-9/+19
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* | Brings skip list try_free_safe changes from develop (#1612)Dana Robinson2022-04-071-208/+0
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* | Removes unused H5HP and H5MP packages (#1610)Dana Robinson2022-04-077-1888/+3
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* Clang warning fixes from develop. (#1583)Larry Knox2022-04-052-9/+13
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* Misc fixes from develop nov21 - feb22 (#1580)Larry Knox2022-04-0524-267/+287
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Make default to build high-level tools the same as default for (#1234) high-level library. * Updated README.txt to README.md (#1375) * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * Converted README.txt to README.md and updated files referring to README.txt to README.md. * removed references to README.txt * updated MANIFEST * Snprintf2 (#1399) * Replaced many uses of sprintf with safer snprintf Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable. * Removed unnecessary use of static on small buffers This improves thread safety. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Replaced several uses of sprintf with safer snprintf (#1383) * Replaced several uses of sprintf with safer snprintf * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Used clang-tidy to change all floating point f suffixes to F (#1359) * Added another missing override keyword on a dtor (#1384) * Creating FUNDING.yml (#1427) * Creating FUNDING.yml Will add sponsor this project widget to the repo's page. * Correct file name Add sponsor widget; filename typo fixed. * Update MANIFEST * Fixed AbstractDs::getVarLenType documentation (#1441) * Committing clang-format changes * Open bsd fixes (#1195) * Fix end of line alignment. Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: loricooperhdf <lori.cooper@hdfgroup.org> Co-authored-by: myd7349 <myd7349@gmail.com>
* Assume C99 fixed sized ints exist, use them (#470) (#1571)Larry Knox2022-04-014-133/+25
| | | | | | | | | | | | | | | | * 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> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12 Merge doxygen changes from develop (#1542)Allen Byrne2022-03-301-2/+2
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* Hdf5 1 12 merges (#1528)jhendersonHDF2022-03-253-11/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Add support for parallel filters to h5repack (#832) * Allow parallel filters feature for comm size of 1 (#840) * Avoid popping API context when one wasn't pushed (#848) * Fix several warnings (#720) * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fix free list tracking and cleanup cast alignment warnings (#1288) * Fix free list tracking and cleanup cast alignment warnings * Add free list tracking code to H5FL 'arr' routines * Fix usage of several HDfprintf format specifiers after HDfprintf removal (#1324) * Use appropriate printf format specifiers for haddr_t and hsize_t types directly (#1340) * Fix H5ACmpio dirty bytes creation debugging (#1357) * Fix documentation for H5D_space_status_t enum values (#1372) * Parallel rank0 deadlock fixes (#1183) * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix a few issues noted by LGTM (#1421) * Fix cache sanity checking code by moving functions to wider scope (#1435) * Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463) * Disable memory alloc sanity checks by default for Autotools debug builds (#1468) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12 Fix release check version logic #1438 (#1493)Allen Byrne2022-03-121-1/+1
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* Implemented suggestion in #1381 for dtransform test (#1490)Allen Byrne2022-03-111-11/+10
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* Merge Mingw fixes from develop (#1477)Baljak2022-03-105-30/+30
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* 1 12 Remove const from the argv tools/tests main sig. #1390 (#1404)Allen Byrne2022-01-2910-11/+11
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* Merge Fix directory variable in shell scripts #1273 (#1278)Allen Byrne2021-12-117-101/+31
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* 1.12 TRILAB-266: Remove clang warnings. (#1193)H. Joe Lee2021-11-134-60/+61
| | | | | | | | | | | | | | | | | | | | | | | * TRILAB-266: Remove clang warnings in src/H5Zscaleoffset.c. (PR #1105) * Committing clang-format changes * TRILAB-266: Remove clang warnings in H5private.h and uthash.h. (PR #1124) * TRILAB-266: Remove clang warnings in H5FDcore.c. (PR #1127) * Committing clang-format changes * TRILAB-266: Remove clang warnings in test/testmeta.c. (PR #1135) * TRILAB-266: Remove clang warnings in test/swmr.c. (PR #1136) * TRILAB-266: Remove clang warnings in test/cork.c. (PR #1137) * Committing clang-format changes * TRILAB-266: Remove clang warnings in test/cork.c. (PR #1146) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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