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* Update package scripts (#1744)Allen Byrne2022-05-072-4/+5
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* Fixes a bug where t_cache fails due to a string size being too small (#1720) ↵jhendersonHDF2022-05-051-4/+6
| | | | | | | | | | | | | (#1728) * Fixes a bug where t_cache fails due to a string size being too small Recent warning reductions led to an incorrect string size being passed to h5_fileaccess, causing the test to silently fail. In addition to fixing the bug, the test will now fail noisily on setup failures. * Updates the t_cache test to fail noisily on setup errors Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Implement support for big I/O for independent reads (#1446) (#1719)jhendersonHDF2022-05-031-16/+34
| | | | | | | | | | | | | * 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> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* [1.12 Merge]Hdf5 1 12 warnings fixes (#1715)jhendersonHDF2022-05-0360-4691/+3686
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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)jhendersonHDF2022-05-0315-64/+85
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Fix SWMR/refresh bug hidden by library free lists (#1702) (#1711)Larry Knox2022-05-021-4/+10
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* Add java clang-format (#1672)Allen Byrne2022-04-22162-10099/+13368
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* 1.12 merge: Removes HDF Group paths, adds shellcheck fixes (#1658)Dana Robinson2022-04-191-95/+41
| | | | | | For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* So number updates to match 1.12.2 release. (#1635)Larry Knox2022-04-151-17/+17
| | | | | | | | | * Undo increment of max_idx for addition of 1.14 verrsion from develop in make_vers. max_idx must match 1.12 version, otherwise build error results with --disable-deprecated-symbols. * Update Platforms tested and standardize indentation in RELEASE.txt. * Update so numbers to match 1.12.2 release.
* Update version to 1.12.3-1 after creating hdf5_1_12_2 releaseLarry Knox2022-04-089-407/+29
| | | | | preparation branch. Clean release note entries from RELEASE.txt.
* Hdf5 1 12 (#1625)Larry Knox2022-04-081-223/+153
| | | * Update Platforms tested and standardize indentation in RELEASE.txt.
* Undo increment of max_idx for addition of 1.14 verrsion from develop in (#1623)Larry Knox2022-04-081-2/+2
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* 1.12: Last round of normalizations for 1.12.2 (#1621)Dana Robinson2022-04-0826-218/+231
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* Minor doxygen changes from develop (#1617)Dana Robinson2022-04-082-2/+2
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* Brings minor changes from headers in develop (#1618)Dana Robinson2022-04-087-38/+0
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* Merge branch 'lrknox-spelling-corrections' into hdf5_1_12Larry Knox2022-04-07241-929/+946
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| * Merge branch 'spelling-corrections' of https://github.com/lrknox/hdf5 into ↵Larry Knox2022-04-07241-929/+946
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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 Knox2022-04-0736-4525/+438
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| * | Update .github/workflows/codespell.ymlLarry Knox2022-04-071-1/+1
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| * | Merge branch 'spelling-corrections' of https://github.com/lrknox/hdf5 into ↵Larry Knox2022-04-0713-63/+112
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| | * \ Merge branch 'hdf5_1_12' into spelling-correctionsLarry Knox2022-04-0710-58/+105
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| | * | | Committing clang-format changesgithub-actions2022-04-073-5/+7
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| * | | | Commit one more spelling correction.Larry Knox2022-04-071-1/+1
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| * | | Commit codespell spelling corrections.Larry Knox2022-04-07340-1327/+1342
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* | | | Brings free list debugging changes from develop (#1615)Dana Robinson2022-04-072-30/+72
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* | | | 1.12: Brings changes from testpar over from develop (#1614)Dana Robinson2022-04-0718-199/+232
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* | | | 1.12: Brings 1.12 compiler options in line with develop (#1611)Dana Robinson2022-04-0712-94/+78
| | | | | | | | | | | | | | | | | | | | * Brings 1.12 compiler options in line with develop * Revert 'since' doxygen field in H5public.h
* | | | Fixes H5E_ID error categores erroneously brought over from develop (#1613)Dana Robinson2022-04-073-3/+3
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* | | | Fix these Doxygen warnings #1581 (#1592)Allen Byrne2022-04-073-11/+10
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* | | | 1.12: Brings C++ wrappers in line with develop, minus C++11 bits (#1604)Dana Robinson2022-04-0774-1004/+670
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* | | Normalize Fortran code with develop (#1600)Dana Robinson2022-04-0748-189/+212
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* | | Normalization of Java with develop (#1607)Dana Robinson2022-04-073-13/+13
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* | | Normalization of HL library with develop (#1609)Dana Robinson2022-04-0720-122/+219
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* | | Brings skip list try_free_safe changes from develop (#1612)Dana Robinson2022-04-073-684/+206
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* | | Removes unused H5HP and H5MP packages (#1610)Dana Robinson2022-04-0716-3736/+4
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* | | Brings bin/restore.sh src/H5config.h.in cleanup from develop (#1608)Dana Robinson2022-04-071-0/+3
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* | Normalized configure.ac with develop (#1599)Dana Robinson2022-04-071-49/+23
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* | Normalization of 1.12 branch with develop (#1598)Dana Robinson2022-04-079-19/+24
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* | Brings release timeline and github action changes from develop (#1594)Dana Robinson2022-04-064-0/+68
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* | Remove c++11 keyword override. (#1587)Larry Knox2022-04-061-1/+1
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* Clang warning fixes from develop. (#1583)Larry Knox2022-04-0523-67/+77
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* Misc fixes from develop nov21 - feb22 (#1580)Larry Knox2022-04-0573-549/+594
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Add option for h5repack timing #1142 (#1575)Allen Byrne2022-04-047-51/+176
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* 1.12 New References for Dimension Scales (#1139) (#1574)Larry Knox2022-04-0218-418/+827
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * New references for Dimension Scale APIs (#1139) * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org> * Fix H5DS warnings related to new H5DSwith_new_ref and H5VLobject_is_native APIs (#1184) Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Elena <epourmal@hdfgroup.org>
* 1.12 Move error-stack text to top of usage display #1564 (#1566)Allen Byrne2022-04-0128-82/+136
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* Assume C99 fixed sized ints exist, use them (#470) (#1571)Larry Knox2022-04-0127-506/+199
| | | | | | | | | | | | | | | | * 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>
* October 2021 Pull Requests not previously merged to 1.12 (#1570)Larry Knox2022-04-014-65/+109
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* Update command format, avoid policy warning (#1551)Allen Byrne2022-04-011-3/+3
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* Remove old RELEASE.txt entries already in HISTORY-1_12.txt. (#1562)Larry Knox2022-04-011-33/+2
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