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* Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2631)jhendersonHDF2023-04-042-1/+15
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* Update java logger version (#2644)Allen Byrne2023-04-0422-31/+34
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* Cherry-pick merges from develop to hdf5_1_14 (#2572)Larry Knox2023-03-164-9/+12
| | | | Co-authored-by: Mark (he/his) C. Miller <miller86@llnl.gov> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* 1.14 Fix H5Dchunk_iter doxygen example, cherry-pick of 04682f2 (#2519) (#2548)Larry Knox2023-03-161-3/+3
| | | | | * Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519) Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* Subfiling VFD - add option to specify config file prefix (#2495) (#2570)jhendersonHDF2023-03-157-25/+272
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* Update ReferenceManual.dox (#2517) (#2569)Larry Knox2023-03-151-1/+1
| | | Co-authored-by: mattjala <124107509+mattjala@users.noreply.github.com>
* docs: in -> out (#2514) (#2516) (#2568)Larry Knox2023-03-151-1/+1
| | | Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c ↵Larry Knox2023-03-151-26/+0
| | | | | | | (#2512) (#2566) Forward port of 9f252f1 from #2329 Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* Update cross compile checks and files #2497 (#2564)Allen Byrne2023-03-153-54/+138
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* Change libaec URL to actively maintained repo GH#2552 (#2560)Allen Byrne2023-03-153-6/+6
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* GH issue #2538, print must have verbose on first (#2541)Allen Byrne2023-03-151-4/+6
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* Add concurrency option to cancel in-progress jobs (#2539) (#2558)Larry Knox2023-03-151-1/+6
| | | Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Fix new codespell issues (#2521) (#2533)Larry Knox2023-03-1012-12/+12
| | | | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* 1.14 Merge doxygen plist tables changes #2470 from develop (#2503)Allen Byrne2023-03-0112-83/+5143
| | | | | * Merge doxygen plist tables changes from develop * Doxy corrections
* 1.14 Add fetchcontent for compression libs and fix cmake config #2487 (#2492)Allen Byrne2023-03-0121-153/+2149
| | | | | | | | | * Add fetchcontent for compression libs and fix cmake config #2487 * Update cmake doc for FetchContent * Add CI test for FetchContent * Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends
* Fix issue with collective metadata writes of global heap data (#2480) (#2486)jhendersonHDF2023-02-217-5/+104
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* Remove space from toolchain name #2482 (#2483)Allen Byrne2023-02-211-0/+0
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* Merge toolchain lowercase names and updates #2426 (#2467)Allen Byrne2023-02-179-24/+39
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* 1.14 Merge Correct pkgconfig variables and libraries #2259 (#2477)Allen Byrne2023-02-179-17/+58
| | | | | | | * Merge Correct pkgconfig variables and libraries #290 * Fix typo * Fix spacing
* Merge Add build options for CMake packaging #2347 (#2464)Allen Byrne2023-02-171-24/+30
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* 1.14 Correct VERS compatible (#2460)Allen Byrne2023-02-172-3/+2
| | | | | | | | | * Correct VERS compatible * Remove FAIL check in CMake test * Remove unnecessary value in vers array * revert empty list
* Update release_docs HISTORY scheme (#2443)Dana Robinson2023-02-1310-23560/+1007
| | | | | | | | We will no longer maintain HISTORY files for other maintenance branches, so those have been removed. Adds a README.md explaining the purpose and procedures of HDF5 HISTORY. Also adds a newsletter template and updates the RELEASE.txt note part of CONTRIBUTING.md. Also cleans out RELEASE.txt post-HDF5-1.14.0
* Drop non-1.14 branches in main.yml (#2448)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 (#2456)Dana Robinson2023-02-111-2/+2
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* CMake: Find MPI in HDF5 CMake config (#2400) (#2410)Larry Knox2023-01-191-0/+2
| | | Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
* Brings README.md changes from develop (#2388)Dana Robinson2023-01-053-25/+26
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* Adds RELEASE.txt notes and updates Doxygen (#2377) (#2378)Dana Robinson2022-12-293-8/+42
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* Adds Doxygen markup for H5FDdriver_query() (#2375)Dana Robinson2022-12-282-4/+23
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* Brings Doxygen changes from develop (#2366)Dana Robinson2022-12-2710-51/+104
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* Brings HL GIF tools configure changes from develop (#2361)Dana Robinson2022-12-247-56/+32
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* Fixed version info. (#2344)Gerd Heber2022-12-221-2/+2
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* Adds Doxygen VOL flag markup (#2340) (#2341)Dana Robinson2022-12-211-55/+63
| | | | | | | | | | | | | * Initial doxygen markup * Committing clang-format changes * Adds Doxygen comments to VOL flags * Committing clang-format changes 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>
* Onion VFD header cleanup (#2337) (#2338)Dana Robinson2022-12-213-112/+85
| | | | | | | | | | | * Partial work towards cleaning up the onion VFD code * Committing clang-format changes * A few minor tweaks to the onion VFD public header 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>
* Fix up the H5Pencode2 test for virtual layout. (#2325) (#2335)Dana Robinson2022-12-211-91/+87
| | | | | | | | | | | | | * Fix up the H5Pencode2 test for virtual layout. * Committing clang-format changes * Remove VERIFY and use TEST_ERROR. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.14 Fix some doxygen warnings (#2323)Allen Byrne2022-12-2117-62/+29
| | | | | | | | | | | | | | | * Fix some doxygen warnings * Remove javadocs * Fix spelling * Fix section format * Correct doxygen function name * Remove duplicate Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Brings the following changesets over from develop: (#2328)Dana Robinson2022-12-2117-66/+153
| | | | | | | | | | | | b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) 70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320) 8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319) 784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321) 6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315) 10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html 0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303) a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295) 502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293) a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* 1.14 Disable hl tools by default #2313 (#2318)Allen Byrne2022-12-175-6/+48
| | | | | | | * Disable hl tools by default #2313 * Only gif tools are deprecated * Update autotools
* Fixes duplicated build mode name in -Werror GitHub actions (#2316)Dana Robinson2022-12-161-2/+2
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* Converts the YAML build mode arrays to objects in special runs (#2308) (#2309)Dana Robinson2022-12-161-37/+41
| | | | | | | | | | | | | * Converts the YAML build mode arrays to objects in special runs * Adds a dump of the matrix context for each test This would have made it a LOT easier to debug the build_mode issues... * Disable the mirror VFD in the -Werror checks We can re-enable this after we fix the warnings, but I don't want to conflate code and GitHub changes, so this is a better way to get the CI to pass for now.
* Adds 'unused' hints for MDS io_info parameters (#2301) (#2306)Dana Robinson2022-12-163-18/+17
| | | | | | | | | | | | | | | | | * Adds 'unused' hints for MDS io_info parameters * Committing clang-format changes * Fix issue with formatter * Committing clang-format changes * Final fix for formatter * Committing clang-format changes 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>
* Updates the special Autotools builds in main.ymlDana Robinson2022-12-151-7/+7
| | | The missing leading space causes the builds to always use the default instead of the specified build mode.
* Hdf5 1 14 (#2296)Larry Knox2022-12-147-26/+29
| | | | | | | | | | | | | | | | * Update versions for hdf5_1_14 develop branch after creation of hdf5_1-14_0 branch for 1.14.0 release. * Update windows worker compilers (#2286) * Update windows worker compilers * Update bin and test issues * Update script and revert java test * Update scripts and versions in java files. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Update versions for hdf5_1_14 develop branch after creation of (#2294)Larry Knox2022-12-1310-25/+25
| | | hdf5_1-14_0 branch for 1.14.0 release.
* added doc. warning for H5Oflush in parallel (#2289)Scot Breitenfeld2022-12-101-0/+3
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* fixed unclosed objects in test (#2290)Scot Breitenfeld2022-12-101-6/+10
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* Check for size==0 for all datatypes read from disk, not just compound (#2287)Neil Fortner2022-12-081-9/+5
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* Compound datatypes may not have members of size 0 (#2243)Egbert Eich2022-12-072-69/+125
| | | | | | | | | | | | | | | | | | | | | | * Compound datatypes may not have members of size 0 A member size of 0 may lead to an FPE later on as reported in CVE-2021-46244. To avoid this, check for this as soon as the member is decoded. This should probably be done in H5O_dtype_decode_helper() already, however it is not clear whether all sizes are expected to be != 0. This fixes CVE-2021-46244 / Bug #2242. Signed-off-by: Egbert Eich <eich@suse.com> * Rework error recovery code in H5O__dtype_decode_helper() and H5O__dtype_decode(). * Format changes for src/H5Odtype.c. Signed-off-by: Egbert Eich <eich@suse.com> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Correct requires setting for pkgconfig files (#2280)Allen Byrne2022-12-076-10/+18
| | | | | * Correct requires setting for pkgconfig files * Add issue number
* Fixes warnings in H5Opline.c error messages (#2281)Dana Robinson2022-12-061-3/+5
| | | | | | | * Fixes warnings in H5Opline.c error messages * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add text about release notes (#2246)Allen Byrne2022-12-061-10/+67
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