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* 1.10: Fix weird characters in C2Cppfunction_map.htm (#2490)Dana Robinson2023-02-212-43/+43
| | | | | * Fix weird characters in C2Cppfunction_map.htm * Fix header.html
* Backport H5Dchunk_iter to 1.10 branch (#1968)Mark Kittisopikul2023-02-216-1/+659
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Backport H5Dchunk_iter to 1.10 branch * Add some accessory files, test still needs work * Apply proper formatting, and fix compile errors * Remove const from H5D__chunk_iter as per #1700 * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info * Modify chunk_info test to for unsigned / hsize_t types * Fix types in test * Add test_basic_query, helper functions to test/chunk_info.c 1_10 * 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 * Fix regression of #1419 * Add a note about return fail in 1.12 and older for invalid chunk index * Committing clang-format changes * Run clang-format on test/chunk_info.c --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove space from toolchain name #2482 (#2485)Allen Byrne2023-02-211-0/+0
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* 1.10 Merge Merge CMake generated pkg-config file is incorrect #2259 (#2479)Allen Byrne2023-02-179-16/+59
| | | | | * Merge Merge CMake generated pkg-config file is incorrect #2259 * Fix spacing
* Merge toolchain lowercase names and updates #2426 (#2469)Allen Byrne2023-02-165-14/+24
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* Merge Add build options for CMake packaging #2347 (#2466)Allen Byrne2023-02-161-24/+30
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* 1.10: Add spelling check to CI and fix errors. (#2442)Allen Byrne2023-02-16367-1305/+1345
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update CI and support files to match latest from 1.14 * Correct spelling * More spelling corrections * spelling fixes in testpar * Fix spelling errors in tools * More tools spelling fixes * Spelling fixes for rest of tools and some src * Fix spelling errors in src files, pt 2 * Fix spelling in src pt3 * Fix spelling errors pt4 * Fix spelling errors pt5 * Spelling fix pt6 * fix spelling error examples * fix spelling in tests * fix spelling errors in test pt2 * Fix spelling errors in test pt3 * fix spelling in test pt4 * Fix spelling errors in hl * fix spelling errors in c++ * Spelling fixes for fortran * spelling fixes for bin and java * Add relative path * Change spelling action to use a file for list of ignore words * Fix spelling ignore list * remove unused file
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion ↵vchoi-hdfgroup2023-02-132-14/+24
| | | | | | | | | | (#2153) (#2278) * 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.
* 1.10 Correct requires setting for pkgconfig files #2280 (#2284)Allen Byrne2023-02-136-10/+18
| | | | | --------- Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 1.10 h5repack should only print if verbose (#2275)Allen Byrne2023-02-135-31/+46
| | | | | --------- Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Bring generated file tidying from develop (#2451)Dana Robinson2023-02-122-10/+12
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* Add szip/libaec to GitHub CI and fix warnings (#2438) (#2450)Dana Robinson2023-02-125-20/+30
| | | | | | | | szip (or libaec) is currently not tested in CI. This adds szip to the the Autotools GitHub CI actions on Linux when building with the Autotools. This PR also cleans up a few warnings that remained in the szip- related code so the -Werror check will pass.
* Fixes an incorrect brief description for H5Dopen2 (#2452)Dana Robinson2023-02-121-1/+1
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* Bring `make install` GitHub action from develop (#2449)Dana Robinson2023-02-121-0/+14
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* Drop non-1.10 branches in main.yml (#2445)Dana Robinson2023-02-121-1/+1
| | | | | There's no reason to list develop, etc. in the list of branches where this flavor of main.yml applies. Those branches have their own main.yml files.
* Update CODEOWNERS given personnel changes (#2454)Dana Robinson2023-02-111-34/+3
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* CMake: Find MPI in HDF5 CMake config (#2400) (#2412)Larry Knox2023-01-201-0/+2
| | | Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
* Update README.mdDana Robinson2023-01-051-1/+1
| | | Fixes incorrect version number
* Brings README.md changes from develop (#2390)Dana Robinson2023-01-053-42/+43
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* 1.10: Brings the updated CI in from develop (#2312)Dana Robinson2022-12-163-393/+334
| | | | | | | | | | | | | | * 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 compatibility 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>
* Merge #2198 CMake MPI link (#2216)Allen Byrne2022-11-057-19/+25
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* 1.10 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2222)Allen Byrne2022-11-0519-64/+164
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-053-1/+92
| | | | | | | file handles (merge to 1.10) (#2223) * Fix problem with variable length attributes being accessed through multiple file handles (#2181) (#2207) * Fix bug in merge of vlen attr fix (#2181) from 1.12
* 1.10 Fix some Java warnings (#2147)Allen Byrne2022-10-066-184/+187
| | | | | * Fix some Java warnings * fix formatting
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-053-2/+61
| | | | (#2138) (#2142)
* Update examples reference to single-source version 2.0.1 (#2109)Allen Byrne2022-10-016-42/+43
| | | Also fix github URL refs
* Cleanup some warnings in Java JNI code (#2034) (#2099)jhendersonHDF2022-09-164-108/+146
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* 1.10 Port "learn HDF5" tutorial to doxygen (#2093)Allen Byrne2022-09-0932-99/+6216
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* Main Getting Started page and the three HDF Resources have pages. (#2092)Allen Byrne2022-09-0984-15352/+9791
| | | | | | | | HDFView is still under construction, but mostly there. Merge the Fortran doxygen changes from develop PR, updated RM index. Adjusted references to UG and created some TODOs for missing UG modules Some may just need a reference back to a section of the user guide. Made some Fortran doxygen changes for overall consistency.
* Fix bug in attribute type conversion wiith compound types - merge to 1.10 ↵Neil Fortner2022-09-093-9/+186
| | | | (#2069)
* Persist dataset access properties when using H5Fstart_swmr_write - merge to ↵Neil Fortner2022-08-236-30/+498
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1.10 (#2058) * 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> * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct target name for szaec lib - merge #2000 (#2003)Allen Byrne2022-08-174-15/+16
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* [1.10 Merge] Hdf5 1 10 develop merges (#2013)jhendersonHDF2022-08-165-9/+346
| | | | | | | | | | | | | | | | | * 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>
* Fix Error examples (#1996)Allen Byrne2022-08-111-267/+211
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* Update java code with doxygen tags, add menu files. (#1972)Allen Byrne2022-08-0986-1480/+2762
| | | | | | | | | | | | | | | | | * Update java code with doxygen tags, add menu files. * Add -Xdoclint:none to autotools javadoc command * Committing clang-format changes * Add fortran RM list descriptions * delete empty file * doc tag location changes * Spelling corrections Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.10 clang 13 format #1933 (#1940)Allen Byrne2022-07-29629-5947/+5972
| | | | | * clang 13 format #1933 * Correct workflow
* fortran module folder from GH#1411 #1922 (#1943)Allen Byrne2022-07-2910-21/+78
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* Merge changes between branches (#1930)Allen Byrne2022-07-267-16/+19
| | | | | * Merge changes between branches * More merge synchs
* Port UG chapter 1 and some cleanup (#1924)Allen Byrne2022-07-2225-4/+560
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* Port UG chapter 2 and fix LD bad ref warning (#1921)Allen Byrne2022-07-2110-3/+806
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* Add doxygen chapter for files, fix autotools images (#1908)Allen Byrne2022-07-198-1/+1405
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* 1.10 eliminate unnecessary errors in the error stack (#1881)Allen Byrne2022-07-182-16/+19
| | | | | | | * Eliminate unnecessary error output * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 10 Add utility JNI function for 1.10 style references (#1890)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 hdf51.10 (#1899)vchoi-hdfgroup2022-07-1628-24/+4421
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* Cherry-pick of Autotools updates from develop (#1885) (#1893)Dana Robinson2022-07-152-2/+6
| | | | * Suppress Autoconf "obsolete" warnings in Java checks (#1853) * Use AC_CHECK_LIB instead of AC_HAVE_LIBRARY for Winsock (#1837)
* Create CODE_OF_CONDUCT.md (#1895)Dana Robinson2022-07-141-0/+128
| | | Taken directly from GitHub's suggested CoC document. We may modify this in the future.
* 1 10 HDFFV-11310 implement JNI VL support for primitive types (#1858)Allen Byrne2022-07-1215-502/+2415
| | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-11310 - implement vlen read/write for atomic types. * HDFFV-11310 - VL read/write function for primitive types * Add read/write VL option * fix function name typo * remove debugging prints * Remove more debugging code * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations, fix debug * Fix format * Fix formatting * Correct typo
* Port UG groups chapter to doxygen (#1850)Allen Byrne2022-07-0623-6/+903
| | | | | | | * Port UG groups chapter to doxygen. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add datasets UG chapter, plus fix doxygen refs (#1841)Allen Byrne2022-07-0524-37/+2984
| | | | | * Add datasets UG chapter, plus fix doxygen refs * Remove duplicates
* Port of datatypes UG. (#1829)Allen Byrne2022-06-2958-229/+3824
| | | | | * Port of datatypes UG. * Formatting fix
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