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| * Update HISTORY-1_13.txt and clean RELEASE.txt (#1471)Larry Knox2022-03-072-139/+396
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Spelling of preceed was corrected to proceed, but should have been corrected to precede. * Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'. * Update version to 1.13.2-1 after 1.13.1 release. Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk. * Update VERS_RELEASE_EXCEPTIONS with new incompatible release version. * Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to HISTORY-1_13.txt. Clean entries from RELEASE.txt. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Disable memory alloc sanity checks by default for Autotools debug builds (#1468)jhendersonHDF2022-03-032-8/+28
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| * Create HISTORY-1_13.txt and update release.txt (#1466)Larry Knox2022-03-013-1419/+1775
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| * Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-0111-20/+24
| | | | | | | | | | | | to MANIFEST (#1460)
| * Fix install config and java test name conflict (#1467)Allen Byrne2022-03-012-3/+2
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| * fixed buf definition in h5dfill_f (#1465)Scot Breitenfeld2022-03-011-8/+4
| | | | | | | | | | | | | | * 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 * fixed buf definition in h5dfill_f
| * Remove targets PERMISSIONS setting (#1462)Allen Byrne2022-03-011-1/+0
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| * Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463)jhendersonHDF2022-03-012-15/+84
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| * Fix for parallel compression examples on Windows (#1459)jhendersonHDF2022-02-282-11/+23
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| * Amend RELEASE.txt with note about parallel compression testing assertion ↵jhendersonHDF2022-02-251-0/+9
| | | | | | | | failure (#1458)
| * Add release note for #1438 (#1457)Allen Byrne2022-02-252-1/+18
| | | | | | | | | | * Add release note for #1438 * fix typos.
| * Fix release check version logic (#1438)Allen Byrne2022-02-242-11/+11
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| * Parallel Compression improvements (#1302)jhendersonHDF2022-02-2428-3356/+9308
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| * Enable creation of RPM/DEB binaries GH#1394 (#1398)Allen Byrne2022-02-223-1/+17
| | | | | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
| * Oess 168 utils mirror vfd (#1444)Larry Knox2022-02-215-23/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Spelling of preceed was corrected to proceed, but should have been corrected to precede. * Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'. * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox and @gnuoyd reviews. * Eliminate clang warnings listed in PR #1310 without adding new ssize_t variables. * Committing clang-format changes * Add H5_ATTR_UNUSED to wait_for_child call. Remove unneeded casts in mirror_log calls. * Keep ssize_t in mirror_server.c line 479. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Hyo-Kyung Lee <hyoklee@hdfgroup.org>
| * Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix ↵David Young2022-02-2113-146/+139
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | issues (#1423) * Correct some conversion specifications. * Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few instances where PRIdHSIZE was appropriate. Remove a couple of casts and use correct format strings, instead. * Copy values from a possibly unaligned buffer to aligned local variables instead of casting and dereferencing pointers into the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Fix cache sanity checking code by moving functions to wider scope (#1435)jhendersonHDF2022-02-212-99/+88
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| * Fix issue with copying null new references (#1440)Neil Fortner2022-02-185-49/+57
| | | | | | | | | | | | | | | | * Fix issue with copying null new references. Fix assertion failure when reference copying fails. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Implement support for big I/O for independent reads (#1446)Neil Fortner2022-02-182-23/+64
| | | | | | | | | | | | | | | | | | | | * Implement big I/O support for independent reads. Add test for this. * Committing clang-format changes * Update big I/O code in H5FD__mpio_write() to match that in H5FD__mpio_read(). Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Updated reference for Multi Dataset RFC. (#1442)Gerd Heber2022-02-181-1/+1
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| * Add SZ filter and adjust compression file names to avoid conflicts (#1434)Allen Byrne2022-02-179-92/+90
| | | | | | | | | | | | | | | | | | * Updated plugins project required adjustments * Updated plugins need to distinguish external libs * Fix missed rename * Use same name for windows as linux - avoid name clash
| * Fixed AbstractDs::getVarLenType documentation (#1441)myd73492022-02-161-1/+1
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| * Creating FUNDING.yml (#1427)loricooperhdf2022-02-162-0/+4
| | | | | | | | | | | | | | | | | | | | | | * 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
| * Revert "Fix metadata cache bug when resizing a pinned/protected entry ↵Larry Knox2022-02-122-21/+4
| | | | | | | | | | (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
| * Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)Allen Byrne2022-02-112-1/+29
| | | | | | | | | | * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note
| * Make a buffer bigger: GCC 8.3.0 warned that a `snprintf` may be (#1403)David Young2022-02-111-1/+1
| | | | | | | | | | truncated because the recipient buffer was too small, and the warning is one that we promote to an error. Now there is a warning that the buffer is too big (-Wlarger-than=), but we don't promote those to errors, yet.
| * Fixed H5Dget_storage_size_f for zero sized datasets (#1430)Scot Breitenfeld2022-02-111-4/+4
| | | | | | | | | | | | | | | | | | | | | | * 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 * fixed handling size 0 datasets * fixed handling size 0 datasets * format
| * Fix issue with H5_now_usec() with 32 bit systems (#1416)Neil Fortner2022-02-102-6/+39
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Implement H5ESget_requests() to retrieve request pointers and corresponding connector IDs from an event set. Add tests for this function. * Add "order" parameter to H5ESget_requests, to allow the user to specify the order in which requests are returned. * Fix bugs with H5ESinsert_request() * Change H5ESget_requests() API to have separate input and output parameters for the allocated array length(s) (in) and the number of events in the event set (out). * Fix issue with H5_now_usec() with 32 bit systems. Also improve event set test. * Committing clang-format changes * Add comments to H5_now_usec() explaining rationale for uint64_t casts. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Fix metadata cache bug when resizing a pinned/protected entry (#1358)jhendersonHDF2022-02-082-4/+21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | When resizing a pinned/protected cache entry, the metadata cache code previously would wait until after resizing the entry to attempt to log the newly-dirtied entry. This would cause H5C_resize_entry to mark the entry as dirty and make H5AC_resize_entry think that it doesn't need to add the newly-dirtied entry to the dirty entries skiplist. Thus, a subsequent H5AC__log_moved_entry would think it needs to allocate a new entry for insertion into the dirty entry skip list, since the entry doesn't exist on that list. This causes an assertion failure, as the code to allocate a new entry assumes that the entry is not dirty.
| * Implemented suggestion in #1381 for dtransform test (#1415)Allen Byrne2022-02-042-11/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name
| * Fix a few issues noted by LGTM (#1421)jhendersonHDF2022-02-0410-32/+38
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| * Don't use a nonliteral format string in test/fheap.c:begin_test(). (#1401)David Young2022-02-031-87/+60
| | | | | | | | | | | | | | | | | | * Avoid using a non-literal formatting string with sprintf in begin_test. Use snprintf. Don't duplicate a string on the heap unnecessarily. * Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format string any more. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Update doc with HDF5_ROOT usage. (#1414)Allen Byrne2022-02-023-14/+16
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| * Unify handling of collective metadata reads status (#1206)jhendersonHDF2022-01-2911-136/+357
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| * Added another missing override keyword on a dtor (#1384)Sean McBride2022-01-291-1/+1
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| * Fix some spelling. (#1402)David Young2022-01-281-3/+3
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| * Snprintf2 (#1399)Sean McBride2022-01-2841-425/+467
| | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
| * Remove const from the argv tools/tests main sig. (#1390)Allen Byrne2022-01-2838-78/+82
| | | | | | | | | | | | | | | | | | * Remove const from the argv tools/tests main sig. * also remove const from H5_get_option and parse_command_line. * 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)Sean McBride2022-01-2824-46/+43
| | | | | | | | | | | | | | * 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)Sean McBride2022-01-286-8/+8
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| * Revert 61464d7e (#1396)Larry Knox2022-01-261-10/+22
| | | | | | | | | | | | | | | | Commit 61464d7e was a fix for a compiler error on OpenBSD where int_fast8_t is in fact larger than 1 byte. However, the changes broke H5detect.c generation of H5Tinit.c on Power8 big-endian, and probably on all big-endian machines. Switching DETECT_BYTE to DETECT_I for 8 byte types doesn't work on our big-endian Power8 machine because switching the last parameter of DETECT_I_BYTE_CORE from "int" to the 8 byte type incorrectly sets dt->shared->u.atomic.order = H5T_ORDER_LE on a big-endian machine. A different fix to accomodate both big-endian and OpenBSD is needed. See commit 61464d7e for OpenBSD info. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Update code owners file with more names (#1386)Allen Byrne2022-01-261-15/+15
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| * Fix cmake dynamic analysis on windows (#1373)Allen Byrne2022-01-242-5/+21
| | | | | | | | | | * Fix sanitizer flag form on windows * Add search paths to windows code-coverage
| * Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-229-71/+180
| | | | | | | | | | | | | | * 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>
| * Open bsd fixes (#1195)Sean McBride2022-01-203-82/+70
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| * Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-207-18/+659
| | | | | | | | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Fix documentation for H5D_space_status_t enum values (#1372)jhendersonHDF2022-01-191-3/+3
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| * Do not set CMAKE_INSTALL_PREFIX when built externally (#1380)Matt McCormick2022-01-191-1/+1
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| * various cleanup java test, test files, comments (#1363)Allen Byrne2022-01-185-12/+17
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| * Develop java newrefs fixes for obj ref datasets (#1354)Allen Byrne2022-01-183-249/+207
| | | | | | | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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