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* Re-enable SZIP default to ON in CMake (#3414)Allen Byrne2023-08-236-11/+9
| | | The Autotools were handled in a separate commit
* Enable szip by default in Autotools (#3412)Dana Robinson2023-08-232-3/+14
| | | | | Since libaec is so prevalent and BSD-licensed for both encode and decode, we build the szip filter by default when the szip or aec libraries are found.
* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407)jhendersonHDF2023-08-223-9/+13
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* Fix for CVE-2016-4332 (#3406)Dana Robinson2023-08-222-9/+19
| | | | | | | | | | | | | This CVE issue was previously listed as fixed (via HDFFV-9950) back in 2016, but with no confirmation test. Now that test files exist for the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an assert in debug builds. This fix replaces the assert with pointer checks that don't raise errors or asserts. Since the function is in cleanup code, we do our best to close and free things, even when presented with partially- initialized structs. Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
* chore: fix typo (#3405)H. Joe Lee2023-08-221-1/+1
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* Fix serial to parallel chunked dataset file space allocation bug (#3394)jhendersonHDF2023-08-225-11/+315
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* Update presets, examples uncompress, szip cache (#3391)Allen Byrne2023-08-186-25/+34
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* Fix valgrind warning about write of uninitialized bytes in ScaleOffset ↵jhendersonHDF2023-08-181-1/+7
| | | | filter (#3390)
* Fix valgrind warning about write of uninitialized bytes (#3389)jhendersonHDF2023-08-181-3/+14
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* Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388)jhendersonHDF2023-08-182-2/+3
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* Fix assertion failure during file close on error (#3387)jhendersonHDF2023-08-185-1/+67
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* restore CI tarball name prefix to match bin/release (#3385)Allen Byrne2023-08-161-2/+2
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* Correct CI settings (#3384)Allen Byrne2023-08-162-26/+39
| | | | | * Correct CI settings * Correct plugin file name
* Correct script (#3377)Allen Byrne2023-08-161-1/+1
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* Fix possible performance regression introduced with in-place type conversion ↵Neil Fortner2023-08-151-0/+20
| | | | in 1.14.2 (#3376)
* Add RELEASE.txt notes for recent selection I/O work. (#3374)Neil Fortner2023-08-101-0/+23
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* set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with (#3364)Larry Knox2023-08-091-11/+13
| | | CMake to fix Fortran build failures.
* Work around a testphdf5 failure on Cray MPICH machines (#3361)jhendersonHDF2023-08-082-7/+21
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* Implementation of the mpio driver with selection I/O. (#3222)vchoi-hdfgroup2023-08-0712-295/+4182
| | | | * This changes the default selection I/O to on for MPIO.
* test(parallel): verify FALSE case (#3356)H. Joe Lee2023-08-051-11/+17
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* Add Fortran ES module to deploy list (#3341)Allen Byrne2023-08-043-61/+48
| | | | | * Add Fortran ES module to deploy list * Change fortran mod file export to use a list of names
* Fix for the bug exposed from running test/set_extent.c when selection… (#3319)vchoi-hdfgroup2023-08-046-137/+285
| | | | | * Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled. This is a fix from Neil. The test/set_extent.c is modified to test for selection I/O enabled.
* Make h5dump spacing consistent when printing VLEN datatype (#3351)jhendersonHDF2023-08-0412-26/+26
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* Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340)jhendersonHDF2023-08-031-3/+3
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* Fix a typo in RELEASE.txtAleksandar Jelenak2023-08-031-1/+1
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* Fixes the last of the -Wextra-semi-stmt warnings (#3326)Sean McBride2023-08-0263-1551/+1561
| | | | | | | | | | | | | | | | | | | | | | | * Fixed extra semi warning by adjusting alternative macro definitions * Find-replace H5E_END_TRY; -> H5E_END_TRY * Made H5Epush_goto a do-while loop, fixed indentation * Made GOTOERROR and ERRMSG do-while loops * Made Hgoto_error and Hgoto_done do-while loops * Made vrfy_cint_type and vrfy_ctype do-while loops * Made TEST_TYPE_CONTIG and others do-while loops * Removed extraneous semi-colons * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix CVE-2018-13867 (#3336)Dana Robinson2023-08-022-0/+15
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* Fix CVE-2018-11202 (#3330)Dana Robinson2023-08-022-0/+23
| | | | | | | | | | | | | A malformed file could result in chunk index memory leaks. Under most conditions (i.e., when the --enable-using-memchecker option is NOT used), this would result in a small memory leak and and infinite loop and abort when shutting down the library. The infinite loop would be due to the "free list" package not being able to clear its resources so the library couldn't shut down. When the "using a memory checker" option is used, the free lists are disabled so there is just a memory leak with no abort on library shutdown. The chunk index resources are now correctly cleaned up when reading misparsed files and valgrind confirms no memory leaks.
* Fix h5repack for variable-length datatyped datasets (#3331)jhendersonHDF2023-08-022-1/+28
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* A couple of documentation items to fix (#3332)Allen Byrne2023-08-022-5/+4
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* Windows runtime items go into the bin folder (#3320)Allen Byrne2023-08-021-1/+1
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* Update files to skip list and ignore_words_list (#3321)Larry Knox2023-08-022-3/+3
| | | | | * Update files to skip list and ignore_words_list for codespell to not check files generated by autotools. Autotools generate misspellings that can't be fixed in HDF5 code.
* Made HGOTO_ERROR a do-while loop (#3308)Sean McBride2023-08-02320-13946/+14084
| | | | | * Made HGOTO_ERROR a do-while loop
* Fix loading plugin fails with missing directory GH issue #3248 (#3315)Allen Byrne2023-08-023-3/+15
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* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314)jhendersonHDF2023-08-024-36/+72
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* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312)jhendersonHDF2023-08-023-4/+41
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* Switch parallel compression to use vector I/O (#3245)jhendersonHDF2023-08-022-816/+544
| | | | | Updates parallel compression feature to use vector I/O instead of creating and passing down MPI derived types to VFD
* Update README.md w/ 1.4.3 info (#3318)Dana Robinson2023-08-011-1/+2
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* Update release schedule (#3317)Dana Robinson2023-08-012-2/+4
| | | | * Move 1.12.3 to November * Add 1.14.3 in October
* Remove py-pip from h5py action (#3265)H. Joe Lee2023-07-271-4/+2
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* chore: fix typo - persent -> present (#3273)H. Joe Lee2023-07-254-4/+4
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* Another round of fixing -Wextra-semi-stmt warnings (#3264)Sean McBride2023-07-24186-1205/+1216
| | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* chore: fix grammar - get hang -> get hung (#3272)H. Joe Lee2023-07-248-15/+15
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* CMake: (fix) Threads dependency (#3267)Jan-Willem Blokland2023-07-241-0/+5
| | | | | | - If the HDF5 library has been build with either thread-safety or subfiling VFD feature on it will have an additional dependency on a threading library. This dependency has been added to the hdf-config.cmake.in file.
* chore: make VRFY output consistent (#3268)H. Joe Lee2023-07-241-1/+1
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* ROS3: (fix) Replaced HDfprintf (#3266)Jan-Willem Blokland2023-07-241-3/+3
| | | | - Replaced the HDfprintf() functions by fprintf() to be consistent with other parts of the library.
* removed the use of encoded single apostrophe (#3261)Scot Breitenfeld2023-07-2055-369/+369
| | | | | | * removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read * updated sanitizer paragraph * fixed brief description for H5Fget_info
* Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized ↵Sean McBride2023-07-203-4/+1
| | | | warning (#3260)
* Move 1.12.3 release to October (#3263)Dana Robinson2023-07-202-2/+2
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* Option changed but not all references (#3252)Allen Byrne2023-07-183-5/+4
| | | | | * Option changed but not all references * remove quotes from binary var
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