Commit Graph

20932 Commits

Author SHA1 Message Date
Dana Robinson
dcd4e2d7b9 Update CODEOWNERS given personnel changes (#2455) 2023-02-11 04:59:07 -08:00
Larry Knox
e2c71ed273 CMake: Find MPI in HDF5 CMake config (#2400) (#2411)
Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
2023-01-25 17:52:23 -06:00
Dana Robinson
cedd2a41f5 Brings mirror VFD test fixes from develop (#2392) 2023-01-05 12:51:25 -08:00
Dana Robinson
363b26fa0d Minor change to H5private.h to bring in line with develop (#2391) 2023-01-05 08:59:24 -08:00
Dana Robinson
bdf28749c9 Update README.md
Fixes incorrect version
2023-01-04 17:18:35 -08:00
Dana Robinson
6101a0cc83 Brings README.md changes from develop (#2389) 2023-01-04 16:28:26 -08:00
Dana Robinson
91aa02817a 1.12: Brings the updated CI in from develop (#2311)
* 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>
2022-12-16 13:42:48 -08:00
vchoi-hdfgroup
8ef713ae5d Fix for HDFFV-10840: Instead of using fill->buf for datatype conversi… (#2277)
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion (#2153)

* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion
if it is large enough, a buffer is allocated regardless so that the element
in fill->buf can later be reclaimed.
Valgrind is run on test/set_extent.c and there is no memory leak.

* Add information of this fix to release notes.

* Change macos version for CI to macos-11 until accum test failure is fixed for macos
12.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-12-12 10:40:30 -06:00
Allen Byrne
1dae8c805c 1.12 h5repack should only print if verbose (#2274)
* h5repack should only print if verbose

Also chage dump test to use long option

* Add note

* Update yaml workflows
2022-12-12 09:32:38 -06:00
Allen Byrne
1da36c90b6 1.12 Correct requires setting for pkgconfig files #2280 (#2283)
* Correct requires setting for pkgconfig files #2280

* Change macos for CI
2022-12-12 09:32:01 -06:00
Allen Byrne
52854566ec 1.12 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2221) 2022-11-04 10:37:17 -05:00
Allen Byrne
7a18854512 Merge #2198 correct CMake MPI linking (#2215) 2022-11-04 08:13:08 -05:00
Neil Fortner
66c8a48722 Fix problem with variable length attributes being accessed through multiple file handles (#2181) (#2207) 2022-11-04 07:51:21 -05:00
Scot Breitenfeld
1a81091b35 fixed fortran parallel testing with cmake (#2148) 2022-10-06 16:41:07 -07:00
Allen Byrne
04d11bfb2b 1.12 Fix some Java warnings (#2146)
* Fix some Java warnings

* Fix accidental change
2022-10-06 16:40:27 -07:00
Neil Fortner
1a20a9f342 Fixed an issue that could occur when combining hyperslab selections (#2122) (#2138) 2022-10-04 09:20:10 -07:00
Allen Byrne
50c1a9e483 Update examples reference to single-source version 2.0.1 (#2108)
Also fix github URL refs
2022-09-24 11:22:47 -05:00
jhendersonHDF
121bba8eec Cleanup some warnings in Java JNI code (#2034) (#2098) 2022-09-12 22:37:40 -05:00
Allen Byrne
9348ba920e 1 12 doxygen merge from 1.10 (#2094) 2022-09-12 22:37:01 -05:00
Neil Fortner
033b7ace5a Address review comments from downstream merge of #2016 (#2073) (#2081) 2022-09-01 08:19:01 -05:00
Neil Fortner
3cc7265e77 Fix bug in attribute type conversion wiith compound types - merge to 1.12 (#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>
2022-08-24 09:36:23 -07:00
Neil Fortner
955ac6a29e Persist dataset access properties when using H5Fstart_swmr_write - merge to 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>
2022-08-22 11:15:56 -07:00
Dana Robinson
82ebc9c370 Spelling fixes for codespell (#2038)
* Spelling fixes for codespell

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-18 10:48:17 -07:00
Allen Byrne
fab27c2529 Correct target name for szaec lib - merge #2000 (#2001) 2022-08-17 09:17:28 -07:00
Mark Kittisopikul
0c1898d6f5 Backport H5Dchunk_iter to 1.12 branch (#1970)
* Revert "Revert H5Dchunk_iter changes in hdf5_1_12_1 (#733)"

This reverts commit 10abe9a8b4.

* 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>
2022-08-16 14:59:55 -07:00
jhendersonHDF
d9247ec17e [1.12 Merge] Hdf5 1 12 develop merges (#2012)
* Fix invalid comment about character encoding in H5Fint.c (#1845)

* Convert assertion on (possibly corrupt) file contents to normal error check (#1861)

* Convert assertion on (possibly corrupt) file contents to normal error check

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Avoid allocating chunk map for contiguous and compact dataset I/O (#1927)

* Add documentation for parallel compression feature (#1981)

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-16 14:08:52 -07:00
Allen Byrne
75baddbf62 Fix Error examples (#1997) 2022-08-11 09:24:32 -07:00
Allen Byrne
4c66bf627e Merge UG from 1.10 and add prelim vol section (#1980)
* Merge UG from 1.10 and add prelim vol section

* Spelling fixes

* Merge format and autotools javadoc from 1.10
2022-08-09 16:11:14 -07:00
Allen Byrne
fc9f31ad8c fortran module folder from GH#1411 #1922 (#1942) 2022-07-27 10:29:22 -07:00
Allen Byrne
a0a1959c58 clang 13 format #1933 (#1939) 2022-07-27 10:28:11 -07:00
Allen Byrne
f0690f13fb eliminate unnecessary errors in the error stack (#1937) 2022-07-26 14:49:46 -07:00
Larry Knox
d0739f13c1 Revert "1.12 eliminate unnecessary errors in the error stack (#1880)" (#1935)
This reverts commit f699768133.
2022-07-26 14:30:04 -05:00
Allen Byrne
6eaa59d2f8 revert incorrect merge (#1912) 2022-07-19 14:19:20 -07:00
Allen Byrne
f699768133 1.12 eliminate unnecessary errors in the error stack (#1880)
* Eliminate unnecessary error output

* Fix merge typo

* fix format

* Fix object address to tokens

* Fix conflict
2022-07-18 10:23:37 -07:00
Allen Byrne
7f9a5f0b6e 1 12 Add utility JNI function for 1.10 style references (#1889)
* 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>
2022-07-18 06:18:47 -07:00
vchoi-hdfgroup
0b337cb093 Add doxygen for high level modules to hdf5 1.12 (#1901)
* 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>
2022-07-16 22:20:45 -07:00
Dana Robinson
33d968668a Create CODE_OF_CONDUCT.md (#1894)
Taken directly from GitHub's suggested CoC document. We may modify this in the future.
2022-07-14 14:20:26 -07:00
Dana Robinson
26d8e760b6 Cherry-pick of deprecated symbols issue (#1884) from develop (#1886) 2022-07-13 14:14:59 -07:00
Dana Robinson
d6ff0ff657 Cherry-pick of Autotools updates from develop (#1885)
* Suppress Autoconf "obsolete" warnings in Java checks (#1853)
* Use AC_CHECK_LIB instead of AC_HAVE_LIBRARY for Winsock (#1837)
2022-07-13 12:13:53 -07:00
Allen Byrne
21b8d65c2c 1.12 HDFFV-11310 implement JNI VL support for primitive types (#1856)
* 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
2022-07-12 08:46:26 -07:00
Allen Byrne
65ee1ec549 revert format of parallel getenv parameter (#1808) 2022-06-13 08:25:23 -05:00
Allen Byrne
2a147be72f Hdf5 1 12 sync (#1794) 2022-06-11 23:06:49 -05:00
Allen Byrne
4466a30825 Change TestExpress #1722 (#1776)
* Change TestExpress #1722

* Update comment
2022-05-20 10:07:09 -07:00
Allen Byrne
60820abcbe Update VS2019 compilers (#1782) 2022-05-20 10:06:12 -07:00
Allen Byrne
e67e1f8cb6 Use windows ENV var for default install dir setting #1763 (#1767) 2022-05-17 07:13:03 -05:00
Allen Byrne
13fbd85284 Replace obsolete docver arg with arg to supply branch name #1771 (#1772) 2022-05-15 06:58:50 -05:00
Allen Byrne
2aef4ba50c Use git command to get branch name (#1749) 2022-05-07 18:19:51 -05:00
Allen Byrne
aef939b0bd Update package scripts (#1744) 2022-05-07 07:08:33 -05:00
jhendersonHDF
b4ffea5011 Fixes a bug where t_cache fails due to a string size being too small (#1720) (#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>
2022-05-05 11:18:53 -05:00
jhendersonHDF
a1b8141e26 Implement support for big I/O for independent reads (#1446) (#1719)
* 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>
2022-05-03 11:56:44 -07:00