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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 Byrne2022-07-1839-7357/+604
| | | | | | | | | | | * Eliminate unnecessary error output * Fix merge typo * fix format * Fix object address to tokens * Fix conflict
* 1 12 Add utility JNI function for 1.10 style references (#1889)Allen Byrne2022-07-184-0/+98
| | | | | | | | | | | * Add utility JNI function for 1.10 style references * Clarify text * Correct signature * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add doxygen for high level modules to hdf5 1.12 (#1901)vchoi-hdfgroup2022-07-1714-14/+4476
| | | | | | | | * Add doxygen for high level modules to hdf5 1.12 * 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>
* Create CODE_OF_CONDUCT.md (#1894)Dana Robinson2022-07-141-0/+128
| | | Taken directly from GitHub's suggested CoC document. We may modify this in the future.
* Cherry-pick of deprecated symbols issue (#1884) from develop (#1886)Dana Robinson2022-07-132-14/+30
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* Cherry-pick of Autotools updates from develop (#1885)Dana Robinson2022-07-132-2/+6
| | | | * Suppress Autoconf "obsolete" warnings in Java checks (#1853) * Use AC_CHECK_LIB instead of AC_HAVE_LIBRARY for Winsock (#1837)
* 1.12 HDFFV-11310 implement JNI VL support for primitive types (#1856)Allen Byrne2022-07-1219-571/+2710
| | | | | | | | | | | | | | | * HDFFV-11310 - implement VL read/write using List of Lists * Fix function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations * Fix format
* revert format of parallel getenv parameter (#1808)Allen Byrne2022-06-131-1/+1
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* Hdf5 1 12 sync (#1794)Allen Byrne2022-06-1232-247/+310
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* Change TestExpress #1722 (#1776)Allen Byrne2022-05-2011-29/+79
| | | | | * Change TestExpress #1722 * Update comment
* Update VS2019 compilers (#1782)Allen Byrne2022-05-201-1/+1
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* Use windows ENV var for default install dir setting #1763 (#1767)Allen Byrne2022-05-172-2/+2
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* Replace obsolete docver arg with arg to supply branch name #1771 (#1772)Allen Byrne2022-05-151-31/+11
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* Use git command to get branch name (#1749)Allen Byrne2022-05-071-1/+1
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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
| |\ |/ / | | | | lrknox-spelling-corrections
| * 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
| |\ \ | | | | | | | | | | | | spelling-corrections
| | * \ 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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