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* Merge1 issue 839 PRs to hdf5 1 12 (#904)Larry Knox2021-08-121-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixes for a couple of trivial warnings (#676) * Committing clang-format changes * Trivial warning fixes: * Removes an unused done target in H5Tbit.c * Add (void) to quiet "ignored return value" warnings in the generators (which generally ignore errors) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Various CMake changes (#679) * Committing clang-format changes * Several CMake updates: * Removes unused HDF5_ENABLE_HSIZET * Switches TEST_SHELL_SCRIPTS to ON * Sets SH_PROGRAM to bash instead of sh * Set default build type back to RelWithDebInfo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * err_compat test cleanup (#681) * Committing clang-format changes * Cleans up err_compat test and output * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * CMake fix for sporadic flush2 failures (#692) * Committing clang-format changes * Runs the flush1/flush2 tests in their own directory Avoids file deletions by other tests. * Revert "Runs the flush1/flush2 tests in their own directory" This reverts commit 746c04882434cb502e4231de8f7dd5acb4949f54. Also pulls the flush files from the clean list, which is a simpler fix. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Ubsan fixes (#498) * Fixed use of null pointer identified by UBSan UBSan warned: runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t') with these two tests: H5REPACK-committed_dt_DFF H5REPACK-committed_dt Reformulated per @gnuoyd suggestion. * Fixed undefined float -> unsigned char conversion in HL_test_image * Removed dead skip_overflow_tests_g global The global `skip_overflow_tests_g` was being set but never read. * Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5` * Committing clang-format changes * Remove extra ']' in line 730. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * BUG: DataSet assignment operator is missing (#503) * BUG: DataSet assignment operator is missing * Some compilers complain if the copy constructor is given explicitly but the assignment operator is implicitly set to default. * Explicitly defining the assignment operator allows us to properly handle reference counters for shared resources. * BUG: DataSet assignment operator is missing. * Mimicking code of H5DataType::operator() as suggested by @bmribler. * Added test Description: Added test for DataSet::operator= that Leengit added Platform tested: Linux/64 (jelly) * Removed Author field. * Commit clang format changes. * Entry for Leengit's github PR #503 * Removed lines left by mistake Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Hdf5 merge pr7 (#516) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Add cmake variable HDF5_LIB_INFIX (#7) * Add cmake variable HDF5_LIB_INFIX This infix is added to all library names after 'hdf5'. e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' This name is used in packages on debian based systems. (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) This option is useful when testing projects on debian based systems with custom builds of hdf5 while trying to minimize differences between the custom setup and the environment created by installing system packages. * Added RELEASE.txt entry for HDF5_LIB_INFIX. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com> * Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601) * Committing clang-format changes * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times An internal string is incorrectly freed when the API call is invoked multiple times on a property list, which will usually cause a segfault to occur. On the first call the log location is NULL so the problem doesn't occur. Fixes HDFFV-11239 * Fixes typos Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607) * Committing clang-format changes * Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid fapl ID This was due to a pointer-containing struct being memset after the first internal API call. If the first call failed, the error condition would check if the pointer was not NULL and then attempt to free it if not. This would lead to the freeing of a wild pointer if an invalid fapl ID were passed in. This was fixed by reordering the memset and adding a test to ensure the problem stays fixed. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611) * Committing clang-format changes * Fixes incorrect size_hint handling in H5Gcreate1 * Updates the size hint type for group creation * Updates the RELEASE.txt note * Revert "Updates the RELEASE.txt note" This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff. * Reverts previous behavior to use a uint32_t struct field * Updates RELEASE.txt Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Lee Newberg <35611400+Leengit@users.noreply.github.com> Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org> Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) (#647)Larry Knox2021-05-161-1/+4
| | | Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
* Correct error test spelling and useAllen Byrne2019-08-131-1/+1
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* HDFFV-10879 fix reference fileAllen Byrne2019-08-121-1/+1
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* Remove core VFD-specific property list call and regenerate encoded propertyQuincey Koziol2018-12-2012-0/+0
| | | | lists.
* Clear driver properties before returning them to application.Quincey Koziol2018-12-1912-0/+0
| | | | | Move write_tracking and page_size properties to be inside the core VFD's driver properties.
* Refactor and standardize the link VOL callbacks. Also fix error stack forQuincey Koziol2018-11-011-7/+10
| | | | testing.
* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-1/+1
| | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-102-21/+15
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* Normalization with vol_integration (property lists, file drivers,Dana Robinson2018-09-211-2/+2
| | | | other misc).
* Normalization with vol_integration (test code and H5Xtest.c)Dana Robinson2018-09-201-1/+1
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* * Fixed the error testsDana Robinson2018-05-022-3/+3
| | | | * Moved common functionality into helper functions
* Update encoded DXPLs to reflect changes in properties.Quincey Koziol2018-03-208-0/+0
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-1820-0/+0
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Modifications made based on comments from pull request.Vailin Choi2018-02-0720-0/+0
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| * Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-271-1/+1
| |\ | | | | | | | | | Merge from develop to keeep the branch up-to-date.
| * | Initial checkin for library version boundsVailin Choi2017-10-0312-0/+0
| | | | | | | | | | | | Code changes to provide versioning support when adding to the enumerated defines for H5F_libver_t.
* | | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-1/+1
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* | Brings H5Z and H5PL packages in sync with VOL integration branch.Dana Robinson2017-11-171-1/+1
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* Final merge of page buffering branch to developQuincey Koziol2017-03-148-0/+0
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* Cache image feature and testingQuincey Koziol2017-01-2932-0/+0
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* [svn-r27806] Fix property list serialization for values encoded by ↵Neil Fortner2015-09-1698-0/+0
| | | | | | | | | | H5Pset_chunk_cache to be compatible between 32 and 64 bit systems. Expand cross platform property list encode/decode testing. Fix warning in H5P__fill_value_enc. Tested: jam, koala, ostrich (h5committest), ummon
* [svn-r27243] fix problem with encoding/decoding external fapl for lapls.Mohamad Chaarawi2015-06-186-0/+0
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* [svn-r25468] some code refactoring to align trunk with VOL branch.Mohamad Chaarawi2014-07-221-4/+1
| | | | tested with h5committest.
* [svn-r24993] Purpose:Dana Robinson2014-04-094-0/+0
| | | | | | | | | | | | | | | Adds write tracking to the core VFD, which can be configured via the H5Pset/get_core_write_tracking() API call. When enabled and writing to the backing store is enabled, this feature will track writes and only write out the changed bytes on flush/close. Tested on: 32-bit LE linux (jam) w/ Fortran and C++ 64-bit BE linux (ostrich) 64-bit Darwin 12.5.0 (kite) All were tested using the core VFD w/ paging on (core_paged in the VFD list). Make check-vfd was also tested on jam.
* [svn-r24646] HDFFV-8640: Remove xlate_utility by fixing reference files to ↵Allen Byrne2014-01-275-15/+0
| | | | | | not add extra lines. Tested: cmake and autotools local linux
* [svn-r24167] HDFFV-8513, HDFFV-8522 Plugin testing in h5repack, h5dump.Allen Byrne2013-09-191-0/+3
| | | | | | | Add more usage info for UserMacros. Add new option information about the Plugin default path. Tested: local linux, jam
* [svn-r23017] I added a prototype function H5DOwrite_chunk in HL library for ↵Raymond Lu2012-11-071-1/+4
| | | | | | | | | Dectris people to test performance. The library's API function H5PSIdirect_write is still in. I reorganized the internal library by adding H5D__pre_write function. Tested on koala.
* [svn-r22987] ported revisions from 22742 to 22986 from the trunkRaymond Lu2012-10-2924-0/+0
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* [svn-r22287] Description:Quincey Koziol2012-04-161-3/+3
| | | | | | | | Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r20934] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-061-1/+2
| | | | | | | | say which filter isn't registered. This is the follow-up commit (20929 and 20930). The check-vfd in Makefile has trouble with the file name. Because the test file is pre-generated, I use the default FAPL to create the full file name to avoid some driver test. Tested on jam - simple change.
* [svn-r20929] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-031-1/+20
| | | | | | say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output. Tested on jam, koala, and heiwa.
* [svn-r19782] Fix CMake testing for links_env test which requires an ↵Allen Byrne2010-11-151-0/+6
| | | | | | | | environment variable at test run-time. Modified runTest.cmake file to allow optional ENV_VAR and ENV_VALUE to be passed. runTest.cmake requires a reference file, added links_env.out to testfiles folder. Also updated root CMakeLists.txt to output a message when unsopported options are configured with the PARALLEL option. CMake will still generate files. Tested: windows and local linux
* [svn-r19507] Fix for bug 1707 - I changed the design from the previous fix ↵Raymond Lu2010-10-041-4/+28
| | | | | | | | | | as Quincey suggested. I added a flag IS_DEDAULT in the H5E_auto_t structure. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function. Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2. Tested on jam, heiwa, and amani.
* [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-211-1/+13
| | | | | | | | | | | | | application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a document for it. Tested on heiwa, jam, and amani. The property change in configure.in, config, and Makefile.am came from the merge of the 1.8 library change.
* [svn-r16835] Allow an error class to use other class's major or minor ↵Raymond Lu2009-04-221-2/+11
| | | | | | errors. Added a test for it, too. Tested on jam - simple change.
* [svn-r12345] Purpose: Codes for backward compatibility.Raymond Lu2006-05-121-1/+1
| | | | | | | | | | Description: Function prototype H5E_walk_t and structure H5E_error_t wasn't backward compatible. Solution: Make them compatible with v1.6 and provide new definitions of H5E_walk_stack_t and H5E_error_stack_t. Platforms tested: fuss and h5committest.
* [svn-r9839] Purpose:Quincey Koziol2005-01-191-4/+0
| | | | | | | | | | | Bug fix Description: Don't print very long description, check that it's correct internally. Platforms tested: Linux 2.4 (heping) Solaris 2.7 (arabica)
* [svn-r9825] Purpose:Quincey Koziol2005-01-141-0/+4
| | | | | | | | | | | | Bug fix Description: Fix possible overrun in error description string by allocating large enough string on the fly. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8484] Purpose: bug fixRaymond Lu2004-05-051-0/+6
| | | | | | | | | | Description: The error stack was accidentally cleared during the program. Solution: Change it to the correct output. Platforms tested: RH 8(fuss). Simple change. Misc. update:
* [svn-r7920] Purpose:Quincey Koziol2003-12-101-1/+1
| | | | | | | | | | | Bug fix Description: Correct a couple of minor problems with 1.6 compat mode. Platforms tested: FreeBSD 4.9 (sleipnir) not tested in h5committest
* [svn-r7524] *** empty log message ***Raymond Lu2003-09-292-15/+15
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* [svn-r7507] *** empty log message ***Raymond Lu2003-09-244-0/+59
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