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* 10 CVE fixes (#3440)Dana Robinson2023-08-299-98/+175
| | | | | | | | | | | | | * Fix for CVE-2018-15671 * Fix CVE-2016-4332 * Fix CVE-2018-11202 * Fix CVE-2018-11205 * Fix CVE-2018-13866 * Fix CVE-2018-13867 and CVE-2018-13871
* sync cmake and examples changes (#3438)Allen Byrne2023-08-2831-118/+192
| | | | | | | | | | | * sync cmake and examples changes * Add java lib changes * Update jave log files * Update java logger version * More logger version changes
* Bring strndup changes from develop (#3437)Dana Robinson2023-08-2811-30/+215
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* Misc normalization with develop (#3436)Dana Robinson2023-08-2617-84/+164
| | | Mostly .github and config directories
* Fix loading plugin fails with missing directory GH issue #3248 (#3325)Allen Byrne2023-08-025-16/+45
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* sync bin with develop (#3271)Allen Byrne2023-07-2515-65/+45
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* Duplicate function removed (#3256)Allen Byrne2023-07-201-23/+0
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* Merge changes from develop (#3239)Allen Byrne2023-07-186-399/+131
| | | | | | | * Merge changes from develop * Store name for last snapshot * Merge bbrelease into release
* Adjust presets timeout and fix build script VS versions (#3218)Allen Byrne2023-06-302-8/+8
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* Hdf5 1 10 release action (#3200)Allen Byrne2023-06-306-128/+240
| | | | * 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 (#3170)Allen Byrne2023-06-221-1/+1
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* Update github files/workflow from develop (#3156)Allen Byrne2023-06-193-5/+32
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* Various merges from develop (#3135)Allen Byrne2023-06-1941-559/+318
| | | | | | | | | * Merges from develop/1.14 * Fix doxygen warnings * Fix spelling * Fix doxygen ref * Add braces * Fix format * Remove unused file
* Add java options to build scripts (#3138)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).
* Update actions and change defaults of compression (fix vars) (#3044)Allen Byrne2023-06-0615-161/+326
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* Remove most unused options which are defaulted #2998 (#3047)Allen Byrne2023-06-0513-915/+21
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* Fix multiConfig variable usage and remove unused CMake vars (#3051)Allen Byrne2023-06-0510-31/+14
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* Add h5copy help test and verify consistency (#2905)Allen Byrne2023-05-219-23/+158
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* Prevent buffer overrun in H5S_select_deserialize (#2963)mattjala2023-05-2112-174/+471
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* Add DT workflows and update windows preset (#2967)Allen Byrne2023-05-2110-16/+1226
| | | | | * Add DT workflows and update windows preset * Stagger check time
* Fix CMake generator expression syntax (#2941)Allen Byrne2023-05-1211-56/+69
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* Update action uses version (#2942)Allen Byrne2023-05-121-1/+1
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* New 1 10 hdffv 11052 (#2932)vchoi-hdfgroup2023-05-116-28/+101
| | | | | | | | | | | | | | | | | | Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assertion failure for f->file_id > 0. Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5F__close_cb(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose().
* Correct usage of CMAKE_BUILD_TYPE (#2869)Allen Byrne2023-05-023-23/+20
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* Clean up memory allocated when reading messages in H5Dlayout on error (#2813)glennsong092023-04-302-4/+26
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* Add bug note to H5Dget_space_status documentation (#2788) (#2837)jhendersonHDF2023-04-301-0/+14
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* Add no subsets option to h5diff like h5dump (#2761)Allen Byrne2023-04-3016-269/+202
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* Fix v1 object header gap bug in H5Ocopy (#2785) (#2834)jhendersonHDF2023-04-303-2/+83
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* Add new version of COPYING_LBNL_HDF5. (#2773) (#2792)Larry Knox2023-04-221-48/+60
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* Fixed GH-2603, heap-buffer-overflow in H5O__linfo_decode (#2758)bmribler2023-04-182-7/+32
| | | | Verified with valgrind -v --tool=memcheck --leak-check=full h5dump POV-GH-2603 The several invalid reads shown originally are now gone.
* Remove author and date from RELEASE.txt entries (#2753)Dana Robinson2023-04-161-6/+3
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-154-54/+279
| | | | (#2679) (#2730)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-152-0/+46
| | | | (#2727)
* H5O__pline_decode() Make more resilient to out-of-bounds read (#2210) (#2734)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.
* Fix for github issue #2599: (#2665) (#2736)vchoi-hdfgroup2023-04-142-3/+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.
* Remove 1.10 release schedule (#2745)Dana Robinson2023-04-143-63/+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
* Add Elena to CODEOWNERS for FortranDana Robinson2023-04-141-1/+1
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* Fix memory leaks and aborts in H5O EFL decode (#2656) (#2708)Dana Robinson2023-04-131-48/+61
| | | | | | | | | | | | | | | | | | | | | * Convert asserts to error handling in efl decode 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
* [1.10 Merge] Avoid suppressing error output for non-tentative file opens ↵jhendersonHDF2023-04-081-20/+48
| | | | (#2632) (#2668)
* CMake - Match Autotools behavior for library instrumentation (#2648) (#2672)jhendersonHDF2023-04-082-2/+15
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* Update HDF5 version after 1.10.10 release. (#2681)Larry Knox2023-04-0710-311/+1178
| | | | | | | | * Update HDF5 version after 1.10.10 release. Update so numbers to match 1.10.10 release so numbers. Update HISTORY-1_10.txt. Clean RELEASE.txt entries. * Missed one version change.
* Check CMake version for correct option (#2650)Allen Byrne2023-03-291-1/+5
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* Revert the removal of HDF5GroupInfo class and deprecate. (#2636)Allen Byrne2023-03-275-0/+203
| | | | | | | | | * Revert the removal of HDF5GroupInfo class and deprecate. * revert H5_QUARTER_HADDR_MAX removal --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Undo revert 2615 (#2638)Larry Knox2023-03-2716-424/+206
| | | | | | * Revert "1 10 revert 2615 (#2629)" This reverts commit 43e4e64d886e9072a6075c6369e84c0e273fa44f.
* 1 10 revert 2615 (#2629)Larry Knox2023-03-2421-274/+602
| | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix a memory corruption issue in H5S__point_project_simple (#2627)jhendersonHDF2023-03-242-1/+15
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* Merge CMake cleanup process from develop (#2622)Allen Byrne2023-03-2385-1533/+2409
| | | | | * Merge CMake cleanup process from develop * Update test script files
* Remove getlogin work-arounds (#2620)Dana Robinson2023-03-234-22/+1
| | | Unused in the library
* Remove perf tool and standalone h5perf builds (#2619)Dana Robinson2023-03-2124-2439/+172
| | | | | | | | The small perf tool conflicts with the standard perf tool and is being removed from all HDF5 releases. Building h5perf in "standalone" mode (i.e., independently of the library) has been broken for some time, so the build code for that has also been removed.
* Add Option to not build gif tools and remove javadoc option (#2611)Allen Byrne2023-03-209-45/+58
| | | | | | | * Add Option to not build gif tools and remove javadoc option * Remove old option * Fix CMake command format
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