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* Hdf5 1 12 release action (#3199)Allen Byrne2023-06-307-129/+241
| | | | * Update actions for release option, fix branch for daily build * Scheduled workflows run on latest commit on the develop
* Add missing space in zip command (#3169)Allen Byrne2023-06-221-1/+1
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* Remove duplicate code (#3161)Allen Byrne2023-06-201-23/+0
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* Update github files/workflow from develop (#3155)Allen Byrne2023-06-193-5/+32
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* Add java options to build scripts (#3137)mattjala2023-06-154-3/+18
| | | | | | | | | | | | | | | | | Previously, cmakehdf5 turned on compiling of the java interface by default due to a value set in cacheinit.cmake. Now, consistent with how Fortran and CPP interfaces are handled, the script overwrites this default value to disable the libraries, fixing #2958. I also implemented the --enable-java/--disable java options for cmakehdf5, and -java for buildhdf5. Allen said these scripts should mention that compilers are to be specified in environment variables, but missing compilers causes errors at the CMake level, and CMake's error messages are already pretty informative (See the one in #2958 about JAVA_COMPILER).
* Merges from develop/1.14 (#3118)Allen Byrne2023-06-1542-567/+320
| | | | | | | | | | | | * Fix release action that allows files to be uploaded. Add autotools h5copy help test. Update cmake tools.cmake file for clang-tidy. CMake build is missing H5FDsubfiling.h macros improved for configure output capture. Remove obsolete files * Revert parallel config with TS * Fix doxygen warnings
* Bring MD cache uthash tag list from develop (#3099)Dana Robinson2023-06-123-216/+75
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* Adds a release note for Autoconf 2.71 bump (#3092)Dana Robinson2023-06-101-1/+24
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* Minor normalization w/ develop (#3073)Dana Robinson2023-06-0712-54/+75
| | | | | | | Mostly bin directory * bin/release uses sha256 * bin/h5vers whitespace changes * bin/genparser warning fixes + HL changes * Add bin directory for make distclean
* Add autotools generated files to codespell (#3075)Larry Knox2023-06-071-2/+2
| | | | | Add autotools files for codespell to skip in order to avoid codespell failing for misspelled words in files generated by autotools when running autogen.sh.
* Update uthash and move to H5private.h (#3074)Dana Robinson2023-06-074-86/+57
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* Remove unused cruft from bin dir (#3071)Dana Robinson2023-06-0713-593/+5
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* Bring HDF-EOS5 and netCDF actions from develop (#3064)Dana Robinson2023-06-072-0/+103
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* Bring gcc/clang attribute and warning macros over (#3063)Dana Robinson2023-06-072-47/+89
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* Move config/cmake_ext_mod content to config/cmake (#3062)Dana Robinson2023-06-0750-846/+821
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* Bring key changesets from develop (#3052)Dana Robinson2023-06-0612-39/+85
| | | | | | | | | * Bump GitHub action macOS version to 13 (#2999, #3009) * Bump GitHub action gcc/g++/gfortran version to 12 (#3015) * Bump Autoconf version to 2.71 (#2944) * Fix missing h5_reset() calls in accum test (#3001) * Only run ttsafe in GitHub thread-safe actions (#2777) * Fix Java debug asserts on Windows (#3012) * Fix long double dt_arith bug on macOS (#3038)
* Update actions and change defaults of compression (fix vars) (#3043)Allen Byrne2023-06-0520-201/+367
| | | | | | | | | * Update actions and change defaults of compression (fix vars) * disable TS and parallel * remove parallel for TS * Correct list of default options
* Remove most unused options which are defaulted #2998 (#3046)Allen Byrne2023-06-0517-923/+30
| | | | | | | * Remove most unused options which are defaulted #2998 * Correct doxygen predefined list * Correct doxygen list of predefineds
* Hdf5 1 12 dt action (#2965)Allen Byrne2023-05-184-4/+354
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* Add h5copy help test and verify consistency (#2903)Allen Byrne2023-05-189-50/+142
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* Update 1.12 release_docs/README_HPC (#2976)Larry Knox2023-05-181-14/+12
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* Prevent buffer overrun in H5S_select_deserialize (#2956)mattjala2023-05-1812-213/+560
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* Update action uses version (#2939)Allen Byrne2023-05-121-1/+1
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* Fix CMake generator expression syntax (#2940)Allen Byrne2023-05-1211-38/+57
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* Add configure_file commands for batch (#2882)Allen Byrne2023-05-031-0/+8
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* Correct usage of CMAKE_BUILD_TYPE (#2868)Allen Byrne2023-05-023-23/+20
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* Correct compression install files (#2847)Allen Byrne2023-04-302-8/+22
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* Add bug note to H5Dget_space_status documentation (#2788) (#2836)jhendersonHDF2023-04-301-0/+14
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* Add support for CMakePresets and fix example download (#2819)Allen Byrne2023-04-306-12/+893
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* Clean up memory allocated when reading messages in H5Dlayout on error (#2811)glennsong092023-04-302-5/+26
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* Fix v1 object header gap bug in H5Ocopy (#2785) (#2833)jhendersonHDF2023-04-303-2/+83
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* H5Spoint.c: Comment fix (#2782)Dave Allured2023-04-201-1/+1
| | | Comment should be "point", not "hyperslab".
* Add no subsets option to h5diff like h5dump (#2760)Allen Byrne2023-04-1917-270/+205
| | | * reorder argument in alpha order
* Add new version of COPYING_LBNL_HDF5. (#2776)Larry Knox2023-04-181-48/+60
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* Fixed GH-2603, heap-buffer-overflow in H5O__linfo_decode (#2763)bmribler2023-04-182-8/+33
| | | | Verified with valgrind -v --tool=memcheck --leak-check=full h5dump POV-GH-2603 The several invalid reads shown originally are now gone.
* Check for invalid AAPL in H5Aopen (#2712) (#2771)jhendersonHDF2023-04-181-5/+9
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* Remove author and date from RELEASE.txt entries (#2752)Dana Robinson2023-04-161-43/+15
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-154-53/+278
| | | | (#2679) (#2729)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-152-0/+46
| | | | (#2726)
* H5O__pline_decode() Make more resilient to out-of-bounds read (#2210) (#2733)jhendersonHDF2023-04-153-2/+28
| | | | | | | | | Malformed hdf5 files may have trunkated content which does not match the expected size. When this function attempts to decode these it may read past the end of the allocated space leading to heap overflows as bounds checking is incomplete. Make sure each element is within bounds before reading. This fixes CVE-2019-8396 / HDFFV-10712 / github bug #2209.
* Remove 1.12 release schedule (#2744)Dana Robinson2023-04-143-64/+0
| | | | | | There is no need to maintain the release schedule in each branch, so it's being removed from all branches aside from develop. Also removes the badges that don't pertain to 1.12
* Fix for github issue #2599: (#2665) (#2735)vchoi-hdfgroup2023-04-142-1/+20
| | | | | | | | | | | | As indicated in the description, memory leak is detected when running "./h5dump pov". The problem is: when calling H5O__add_cont_msg() from H5O__chunk_deserialize(), memory is allocated for cont_msg_info->msgs. Eventually, when the library tries to load the continuation message via H5AC_protect() in H5O_protect(), error is encountered due to illegal info in the continuation message. Due to the error, H5O_protect() exits but the memory allocated for cont_msg_info->msgs is not freed. When we figure out how to handle fuzzed files that we didn't generate, a test needs to be added to run h5dump with the provided "pov" file.
* Add Elena to CODEOWNERS for FortranDana Robinson2023-04-141-1/+1
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* CMake - Match Autotools behavior for library instrumentation (#2648) (#2673)jhendersonHDF2023-04-132-1/+17
| | | Enable library instrumentation by default for parallel debug builds
* Avoid suppressing error output for non-tentative file opens (#2632) (#2669)jhendersonHDF2023-04-131-7/+43
| | | | | * Avoid suppressing error output for non-tentative file opens * Update comment about tentative file opens
* Fix #2598 sanitize leak (#2676)Allen Byrne2023-04-132-4/+11
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* Change name of test file to avoid conflict (#2705)Allen Byrne2023-04-131-2/+2
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* * Convert asserts to error handling in efl decode (#2709)Dana Robinson2023-04-131-48/+61
| | | | | | | | | | | | | | | | | | | The function that decodes external data files object header messages would call assert() when parsing malformed files, causing applications to crash when linked against the debug library. This change converts these assert() calls to HDF5 error checks, so the messages are sanity checked in both release and debug mode and debug mode no longer crashes applications. Also cleaned up some error handling usage and debug checks. * Free memory on H5O efl decode errors * Add buffer size checks to efl msg decode * Add parentheses to math expressions Fixes GitHub #2605
* Fix CMake for version less then 3.18 (#2651)Allen Byrne2023-03-3018-62/+112
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* Port h5dchunk_iter_hsizet_size #2074 to hdf5_1_12 branch (#2329)Mark Kittisopikul2023-03-294-38/+12
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