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* 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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* Align H5T code with develop to quiet warnings (#1717)jhendersonHDF2022-05-033-167/+176
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* Hdf5 1 10 parallel comp (#1644)jhendersonHDF2022-04-1413-1591/+4872
| | | | | * Hdf5 1 10 parallel compression merge
* Fix these Doxygen warnings #1581 (#1591)Allen Byrne2022-04-142-7/+10
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* Hdf5 1 10 merges (#1633)jhendersonHDF2022-04-1435-309/+594
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* 1.10 Merge doxygen changes from develop (#1543)Allen Byrne2022-03-3035-681/+672
| | | | | | | * Merge doxygen changes from develop * Remove 1.12 section * Minor comment cleanup
* 1.10 Fix release check version logic #1438 (#1494)Allen Byrne2022-03-121-8/+6
| | | | | * Fix release check version logic #1438 * Correct list comment
* Merge Mingw build fixes from develop (#1475)Baljak2022-03-091-2/+4
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* Unify handling of collective metadata reads status (#1206) (#1418)jhendersonHDF2022-02-048-81/+268
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* 1 10 Remove const from the argv tools/tests main sig. #1390 (#1405)Allen Byrne2022-01-312-2/+3
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* Merge cmake custom command changes (#1361)Allen Byrne2022-01-191-32/+36
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* Remove duplicate memcpy in chunk_file_cb (#1291)jhendersonHDF2021-12-131-1/+0
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* Initialize filter mask and chunk nbytes for 'Single' chunk index (#1261) (#1275)jhendersonHDF2021-12-131-1/+7
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* Fixed minor issues. (#1257)Gerd Heber2021-12-043-7/+6
| | | | | | | | | * Fixed minor issues. * Whoops. Forgot to commit these. * CMake update. * One more time.
* 1.10 TRILAB-266: Remove clang warnings. (#1200)H. Joe Lee2021-11-154-48/+58
| | | | | | | | | | | | | * OESS-99:Sync from develop. * TRILAB-266: Remove clang warnings. * Committing clang-format changes * TRILAB-266: Remove clang warnings. * TRILAB-266: Address @byrnHDF review. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-enable collective metadata reads after disabling for chunk lookup (#1175)jhendersonHDF2021-11-121-7/+21
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* 1 10 merge hdffv 10590 (#1128)Larry Knox2021-10-251-7/+12
| | | | | | | | | | * Merge pull request #60 from bmribler/develop Fix HDFFV-10590 * H5repack tests should fail if a corrupted file causes h5repack to segfault/core dump. * Remove test file, duplicate of h5repack_CVE-2018-17432.h5.
* Merge Remove clang warnings from develop (#1098)Allen Byrne2021-10-251-17/+17
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* Fixed HDFFV-11150 (#356) (#1095)Larry Knox2021-10-152-3/+4
| | | | | | | | | | Description Replaced an HDassert with a check for null pointer in H5O_dec_rc() to catch null pointer in corrupted data situation. As a result, removed the null check prior to H5O_dec_rc() calls. Platforms tested: Linux/64 (jelly) Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Update version to 1.10.9-1. (#1069)Larry Knox2021-10-031-3/+3
| | | Clear 1.10.8 entries out of RELEASE.txt.
* 1.10 Fixes a bad memory read and unfreed memory in fsinfo code (#893) (#1013)Larry Knox2021-09-152-14/+22
| | | | | | | | | | | | | | | | | | | | | * Fixes a bad memory read and unfreed memory in fsinfo code (#893) * Fixes a bad memory read and unfreed memory in fsinfo code The segfault from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() … ↵Larry Knox2021-09-141-5/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#933) (#1007) * H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() function - Made a small improvement for H5Z_xform_noop() function. Now, the function will also return TRUE if the data transform function expression = "x". For this case, the HDF5 library behaves in a similar fashion as the case when no data transform function has been specified. - Improved the inline documentation of the function H5Z_xform_create() such it is more inline with the rest of the code. * Committing clang-format changes * H5Ztrans: (feature) Added 3 tests for improved H5Z_xform_noop() function - Added serial test with data transform expression = "x" to verify the improved H5Z_xform_noop() function behaves as expected. - Added 2 parallel tests with data transform expression = "x" in combination with a filter. Before, these tests will fail but with the improved H5Z_xform_noop() function they work and result in the expected behavior. - Small bug fix for one of parallel filter tests. * Committing clang-format changes * H5Ztrans: (feature) Added release note about detection of the simple data transform function "x". - Added a brief explanation about the implemented improvement of the detection of the simple data transform function "x" to the RELEASE.txt file. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge Fix various warnings and issues in doxygen doc generation #994 (#997)Allen Byrne2021-09-103-42/+10
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* Update copyright headers with reproduction notice in 5 files (#993) (#1002)Larry Knox2021-09-092-17/+14
| | | | | | | | | | | * Update copyright headers with reproduction notice in 5 files that did not match terms in COPYING file . * 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>
* 1.10 Merge A batch of life-cycle examples for different modules #654 (#988)Allen Byrne2021-09-0728-1069/+1198
| | | | | * Merge A batch of life-cycle examples for different modules #654 * Change doxygen generated file location
* 1.10 Merge windows compiler fixes #912 (#915)Allen Byrne2021-08-202-0/+3
| | | | | | | | | * Merge windows compiler fixes #912 * Merge changes to check for pwd.h header * Add missing define * Merge Remove incorrect compiler check for windows clang sanitizer #942
* Add cast to relnum for merge of #812 (#932)Allen Byrne2021-08-191-1/+4
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* Brings doxygen changes from develop/1.12 for out-of-source builds (#936)Dana Robinson2021-08-191-8/+0
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* Rework version-check for relnum in H5checkversion function (#896)Allen Byrne2021-08-121-85/+143
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