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* [1.10 Merge] Add Developer build mode to CMake (#2617)jhendersonHDF2023-03-2011-112/+110
| | | | | | | | | | | | | | | | | | | | | | * Add Developer build mode to CMake (#1659) * Add Developer build mode to CMake * Set a few CMake variables for Developer build modes * Refactor enabling of debug and developer-level compile definitions * Convert cache debugging macros to normal ifdef style Normal ifdef-style instead of if-style allows build system to define macros without warning about redefining macros with different values (0 vs. 1) * Add HDF5 Developer compile definitions to testing files * Temporarily disable -fanalyzer flag for GCC 12+ Developer builds * Fix Java tests for Developer build modes (#2079) * Minor adjustment of Developer build mode changes for 1.10 branch
* Normalize platform-independence code w/ develop (#2615)Dana Robinson2023-03-209-566/+230
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Normalize platform-independence code w/ develop * Use C99 types and functions in lieu of C89 work-arounds * Align key files with develop - H5public.h - H5private.h - H5system.c - H5win32defs.h * Minor fixes elsewhere to support changes in above files * Incidentally brings Fortran mod directory settings file change over This does NOT change the configure/build files. Those will still do the checks needed for the C89 work-around cruft until the perf and perform code gets cleaned up. * Add C++98 fixes * Explicitly set -std=c++98 in Autotools * Do not include cstdlib in H5public.h (requires C++11) * Remove redundant stdbool.h include * Fix alarm issues on Windows * Bring parallel alarm() changes from develop
* Gather latest CMake changes from develop (#2609)Allen Byrne2023-03-201-4/+4
| | | | Add HDF5_SRC_INCLUDE_DIRS variable cleanup cmake comments and documentation
* Bring warning fixes from develop (#2608)Dana Robinson2023-03-2012-67/+124
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* Bring mirror VFD test improvements from develop (#2597)Dana Robinson2023-03-201-3/+5
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* Bring warning macro changes from develop (#2594)Dana Robinson2023-03-202-52/+100
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* Remove unused H5MP and H5HP packages (#2591)Dana Robinson2023-03-189-1842/+1
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* Removes dmalloc support (#2239) (#2587)Dana Robinson2023-03-182-8/+0
| | | | | | | | | | This has not been used to debug the library in a very long time. Most developers use valgrind, -fsanitize=address, or some other memory checker instead of this library. This removes: * dmalloc.h include from H5private.h * --with-dmalloc= Autotools configure option * HDF5_ENABLE_USING_DMALLOC CMake option
* Minor merges to 1.10 (#2579)Larry Knox2023-03-182-8/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Elaborate how cd_values get stored (#2522) * Enclose MESG in do...while loop (#2576) Enclose MSG macro in a do...while loop * Add a clang-format comment about permissions (#2577) * Check for overflow when calculating on-disk attribute data size (#2459) * Remove duplicate code Signed-off-by: Egbert Eich <eich@suse.com> * Add test case for CVE-2021-37501 Bogus sizes in this test case causes the on-disk data size calculation in H5O__attr_decode() to overflow so that the calculated size becomes 0. This causes the read to overflow and h5dump to segfault. This test case was crafted, the test file was not directly generated by HDF5. Test case from: https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md --------- Co-authored-by: Mark (he/his) C. Miller <miller86@llnl.gov> Co-authored-by: glennsong09 <43005495+glennsong09@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Egbert Eich <eich@suse.com>
* Merge MD cache tag slist --> hash table change (#2580)Dana Robinson2023-03-174-129/+89
| | | PR #1925 from develop
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2547)Allen Byrne2023-03-141-4/+4
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* docs: in->out (#2514) (#2532)H. Joe Lee2023-03-121-1/+1
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* Update copyright headers. (#2527)Larry Knox2023-03-10403-405/+0
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* Fix 1.10 new codespell issues (#2521) (#2525)Larry Knox2023-03-093-3/+3
| | | | | | | | | | | | | * Fix new codespell issues (#2521) * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake * Fix typo in genparser --------- Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c ↵Mark Kittisopikul2023-03-081-26/+0
| | | | (#2513)
* Fix an errant bracket that confused formatter (#2511)Dana Robinson2023-03-061-4525/+4539
| | | An extra { in an ifdef'd-out block caused bad indentation in H5C.c
* 1.10 Merge doxygen plist tables changes #2470 from develop (#2506)Allen Byrne2023-03-0113-807/+183
| | | | | | | | | * Add new/moved files * Doxy corrections * Aother Doxy correction * Remove type not in 1.10
* Merge uthash version update from develop (#2502)Dana Robinson2023-02-263-68/+47
| | | * Merege uthash version update from develop
* Backport H5Dchunk_iter to 1.10 branch (#1968)Mark Kittisopikul2023-02-214-0/+240
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* 1.10 Merge Merge CMake generated pkg-config file is incorrect #2259 (#2479)Allen Byrne2023-02-171-4/+14
| | | | | * Merge Merge CMake generated pkg-config file is incorrect #2259 * Fix spacing
* 1.10: Add spelling check to CI and fix errors. (#2442)Allen Byrne2023-02-16139-383/+371
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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-hdfgroup2023-02-131-14/+11
| | | | | | | | | | (#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.
* 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 Robinson2023-02-122-10/+16
| | | | | | | | 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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* Merge #2198 CMake MPI link (#2216)Allen Byrne2022-11-051-6/+6
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* 1.10 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2222)Allen Byrne2022-11-051-2/+2
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-051-0/+4
| | | | | | | 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
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-051-2/+2
| | | | (#2138) (#2142)
* Main Getting Started page and the three HDF Resources have pages. (#2092)Allen Byrne2022-09-097-6/+30
| | | | | | | | 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 Fortner2022-09-091-9/+46
| | | | (#2069)
* Persist dataset access properties when using H5Fstart_swmr_write - merge to ↵Neil Fortner2022-08-234-30/+115
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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>
* [1.10 Merge] Hdf5 1 10 develop merges (#2013)jhendersonHDF2022-08-163-8/+23
| | | | | | | | | | | | | | | | | * 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 Byrne2022-08-0917-77/+35
| | | | | | | | | | | | | | | | | * 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 Byrne2022-07-29311-3058/+3066
| | | | | * clang 13 format #1933 * Correct workflow
* Port UG chapter 1 and some cleanup (#1924)Allen Byrne2022-07-223-4/+560
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* Port UG chapter 2 and fix LD bad ref warning (#1921)Allen Byrne2022-07-211-0/+803
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* Add doxygen chapter for files, fix autotools images (#1908)Allen Byrne2022-07-191-0/+1401
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* Add doxygen for high level modules to hdf51.10 (#1899)vchoi-hdfgroup2022-07-1614-14/+14
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* Port UG groups chapter to doxygen (#1850)Allen Byrne2022-07-065-6/+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 Byrne2022-07-054-7/+2932
| | | | | * Add datasets UG chapter, plus fix doxygen refs * Remove duplicates
* Port of datatypes UG. (#1829)Allen Byrne2022-06-2913-56/+3819
| | | | | * Port of datatypes UG. * Formatting fix
* Update version to 1.10.10-1 (#1783)Larry Knox2022-05-191-2/+2
| | | | Update so numbers to match 1.10.9 release. Clear 1.10.9 entries from RELEASE.txt.
* Add H5S UG chapter, adjust details (#1775)Allen Byrne2022-05-1711-29/+1523
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* Add H5P doxygen chapter (#1762)Allen Byrne2022-05-1423-80/+1155
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* INITIAL attempt at User Guide in doxygen (#1678)Allen Byrne2022-05-132-36/+872
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD * INITIAL attempt at User Guide in doxygen * Add quick H5E to show actual UG header sections * Add Error Handling chapter * Cleanup format changes * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for various warnings/alignment with develop branch (#1755)jhendersonHDF2022-05-0825-182/+129
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* [1.10 Merge] Hdf5 1 10 warnings merge (#1754)jhendersonHDF2022-05-0840-484/+544
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Fixes a bug where t_cache fails due to a string size being too small (#1720) * Fixes a bug where t_cache fails due to a string size being too small Recent warning reductions led to an incorrect string size being passed to h5_fileaccess, causing the test to silently fail. In addition to fixing the bug, the test will now fail noisily on setup failures. * Updates the t_cache test to fail noisily on setup errors * Fix a few Clang sanitizer warnings (#1727) * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.10 * Hdf5 1 12 Miscellaneous warnings fixes (#1718) * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix several warnings (#747) Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings random stuff over from develop (#1738)Dana Robinson2022-05-063-29/+32
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