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* FreeBSD autotools changes (#142)Dana Robinson2020-11-302-4/+38
| | | | | | | | | | | | | | | | * Updates to allow autotools builds on recent FreeBSD * Switches the default C compiler to cc from gcc (this may need a version string check if we want to support FreeBSD 9 and earlier. FreeBSD 10 was released in 2014) * Makes the default C++ compiler c++ (no previous setting) * Both of these resolve to Clang on FreeBSD 10+ * Added a note about flang being unsuitable on FreeBSD (the port uses an ancient build of flang that lacks Fortran 2003 support) * Autotools only - CMake appears to use different CPP flags which cause compilation errors * Adds a RELEASE.txt note for new FreeBSD autotools changes
* Fixes clang debug optimization level w/ Autotools (#141)Dana Robinson2020-11-301-1/+1
| | | | NOTE: This was only released in HDF5 1.10.7, so only the 1.10 branch needs a note in RELEASE.txt.
* Removed H5_ECXXFLAGS from libhdf5.settings (#140)Dana Robinson2020-11-301-1/+1
| | | This variable is unused and was missed in the -Werror changes.
* Minor cleanups (#132)Quincey Koziol2020-11-263-27/+27
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* Minor refactoring in tid.c (#127)Dana Robinson2020-11-261-137/+239
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* Enhance API tracing (#120)Quincey Koziol2020-11-2661-2735/+3524
| | | Enhance API tracing to handle more types, and to put tracing info in a string, allowing it to be used when reporting errors. Also refactor ref-counted strings (H5RS) module to add capabilities needed for the tracing. Refactored H5Gname.c routines to use new H5RS routines also. Added /*out*/ tags to API routines that are returning information to the application. Updated H5TRACE macros from running updated trace script over library code. Added tests for new H5RS routines.
* Refactor to avoid using fork to create initial file (#122)Quincey Koziol2020-11-251-331/+19
| | | | | * Refactor to avoid using fork to create initial file * Use correct exit value on failure
* Update H5TS code to reflect library's coding style (#123)Quincey Koziol2020-11-252-42/+178
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* Move package initialization code for H5A and H5G to internal source file. (#125)Quincey Koziol2020-11-255-353/+343
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* Add else choice to error flags option (#128)Allen Byrne2020-11-2514-0/+279
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* Minor/solaris gcc fix (#126)Dana Robinson2020-11-252-4/+21
| | | | | | | * Adds gnu99 as the standard when building with gcc on Solaris * Adds a note to RELEASE.txt and improves comments For Solaris + gcc fix (HDFFV-11191)
* Adds a configure/CMake option to control -Werror behavior (#119)Dana Robinson2020-11-256-19/+95
| | | | | * Works in both Autotools and CMake * OFF by default * Reverts "always on" -Werror behavior released in 1.10.7
* Doxygen - added (mostly) beginner functions (#112)bljhdf2020-11-236-27/+1551
| | | | | * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function
* Update release text files (#109)Allen Byrne2020-11-238-2449/+7659
| | | | | | | * Update release text files * spelling correction * Update list
* Basic alignment with async branch (#115)Quincey Koziol2020-11-23170-1452/+1443
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Full set of current H5F documentation. (#105)Gerd Heber2020-11-215-44/+1311
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Minor/id code cleanup (#114)Dana Robinson2020-11-2111-1692/+1854
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Switch ID code to use a hash table instead of a skip list (#52)" This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4. * H5I_id_type_t and H5I_class_t are no longer managed via free lists * Fixed commenting issues * Naming and commenting cleanup in H5I.c * H5I cleanup * Header cleanup * Commenting * More uniform naming * Renames H5I_id_type_t and related in H5I.c * Adds gcc pragmas to ignore H5I const casting * Split H5I code into multiple files * Rename id_type to simply type in H5I code * Minor typo in H5Itest.c
* Corrects use of unitialized bytes in the chunk_info test (#106)Dana Robinson2020-11-201-2/+2
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* chkmanifest will run autogen (#102)Allen Byrne2020-11-202-0/+2
| | | | | | | * chkmanifest will run autogen * remove extension on command * run autogen first
* Revert "Switch ID code to use a hash table instead of a skip list (#52)" (#104)Dana Robinson2020-11-207-1367/+30
| | | This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4.
* Add new files to CMake and MANIFEST (#100)Allen Byrne2020-11-192-0/+3
| | | | | * Add new header file * Add missing file
* First cut of the H5 public API documentation. (#80)Gerd Heber2020-11-1825-562/+6930
| | | | | | | | | | | | | | | | | | | | | * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch.
* Switch ID code to use a hash table instead of a skip list (#52)Dana Robinson2020-11-177-30/+1367
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings hash table ID code over from Bitbucket branch * Includes reformatting via clang. * Excludes uthash.h from reformatting. * Still has the failing test issue in tid.c. This should only be a problem if a custom ID type is used and its free function deletes other IDs. * Fixes munged H5_GCC_DIAG_ON/OFF macros in H5I.c The H5_GCC_DIAG_ON/OFF macros used to turn off fallthrough warnings in uthash.h (external code) were munged when formatting with clang due to their lack of quotes. e.g.; H5_GCC_DIAG_OFF(implicit-fallthrough) was munged to: H5_GCC_DIAG_OFF(implicit - fallthrough) which compiles, but is useless. So, with quotes, this is now: H5_GCC_DIAG_OFF("implicit-fallthrough") which survives reformatting with clang. * Fixes issues with user callbacks in the ID hash tables The skip lists (previously) used to handle IDs use a mark-and-sweep scheme to deal with user-defined ID delete callbacks which themselves delete other IDs in the list. The uthash hash table implementation used to manage the IDs in this feature branch does not have this ability. This commit restores the skip lists for non-library ID types in lieu of significantly modifying the uthash code. The hash tables are used to manage the library IDs as those do not delete other IDs when they are closed. * Adds uthash.h to MANIFEST * Removes implicit-fallthrough diagnostic disable Removing -Wimplicit-fallthrough=5 means that the uthash code no longer raises warnings so the H5_GCC_DIAG_OFF/ON macros that disabled those warnings have been removed from H5I.c. * Adds a test to ensure you can delete IDs in the H5Iiterate() callback
* obsolete CMAKE_BUILD_TOOL => CMAKE_MAKE_PROGRAM (#97)Michael Hirsch2020-11-171-1/+1
| | | CMAKE_BUILD_TOOL has been [replaced](https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TOOL.html) by CMAKE_MAKE_PROGRAM
* Merge pull request #91 from ksunden/patch-1Larry Knox2020-11-131-1/+1
|\ | | | | Fix spelling of metadata
| * Fix spelling of metadataKyle Sunden2020-11-131-1/+1
|/ | | was spelled "metadatda"
* Merge pull request #82 from derobins/minor/skip_list_errorLarry Knox2020-11-131-1/+1
|\ | | | | H5SL_release() returns SUCCEED on errors
| * H5SL_release() returns SUCCEED on errorsDana Robinson2020-11-121-1/+1
| | | | | | | | | | H5SL_release() erroneously returned SUCCEED on errors. It now correctly returns ret_value.
* | Merge pull request #84 from byrnHDF/developLarry Knox2020-11-135-57/+62
|\ \ | | | | | | Downgrade m4 doxygen macros.
| * | Correction for location of doxygen folderAllen Byrne2020-11-121-1/+1
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| * | downgrade doxygen.m4 macro file to previous version.Allen Byrne2020-11-121-43/+43
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| * | Add missing entries, remove m4 referenceAllen Byrne2020-11-125-15/+20
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* | | Merge pull request #60 from bmribler/developLarry Knox2020-11-125-7/+53
|\ \ \ | | | | | | | | Fix HDFFV-10590
| * | | Fixed typo!!Binh-Minh Ribler2020-11-121-1/+1
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| * | | Fixed typo!Binh-Minh Ribler2020-11-121-1/+1
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| * | | Added line for new fileBinh-Minh Ribler2020-11-121-0/+2
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| * | | Removed the line, added by mistake.Binh-Minh Ribler2020-11-121-1/+0
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| * | | Added a missing line.Binh-Minh Ribler2020-11-121-0/+1
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| * | | Fixed typo again.Binh-Minh Ribler2020-11-111-1/+1
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| * | | Fixed typoBinh-Minh Ribler2020-11-111-1/+1
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| * | | Miscellaneous updateBinh-Minh Ribler2020-11-114-1/+8
| | | | | | | | | | | | | | | | | | | | - added test for CMake - renamed new input file to conform to the existing files
| * | | Added test for the fix HDFFV-10590Binh-Minh Ribler2020-10-282-0/+32
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| * | | Fix HDFFV-10590Binh-Minh Ribler2020-10-2627-205/+125
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description This is to fix the CVE issue CVE-2018-17432. h5repack produced a segfault on a corrupted file. This fix modified the dataspace encode and decode functions per Quincey's suggestion to prevent the segfault and h5repack only failed for the corrupted file now. Platforms tested: Linux/64 (jelly)
| * | | Merge branch 'develop' of https://github.com/HDFGroup/hdf5 into developBinh-Minh Ribler2020-10-26193-15258/+18024
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| * | | | Fix HDFFV-10590Binh-Minh Ribler2020-10-2627-127/+212
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description This is to fix the CVE issue CVE-2018-17432. h5repack produced a segfault on a corrupted file. This fix modified the dataspace encode and decode functions per Quincey's suggestion to prevent the segfault. h5repack only failed for the corrupted file now. Platforms tested: Linux/64 (jelly)
* | | | | Merge pull request #81 from jhendersonHDF/developLarry Knox2020-11-121-8/+4
|\ \ \ \ \ | |_|_|/ / |/| | | | Fix non-collective metadata read in t_mdset with collective metadata reads enabled
| * | | | Fix non-collective metadata read in t_mdset with collective metadata reads ↵Jordan Henderson2020-11-111-8/+4
| | | | | | | | | | | | | | | | | | | | enabled
* | | | | Merge pull request #79 from byrnHDF/developLarry Knox2020-11-123-5/+6
|\ \ \ \ \ | | | | | | | | | | | | Correct TARGET variable and CMake config file location
| * | | | | Correct TARGET variable and CMake config file locationAllen Byrne2020-11-113-5/+6
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* | | | | Merge pull request #78 from gheber/developGerd Heber2020-11-107-115/+2143
|\ \ \ \ \ | | | | | | | | | | | | This is the first installment of Doxygen-based documentation for the H5F module.
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