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* Full set of current H5F documentation. (#105)Gerd Heber2020-11-211-13/+855
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Robinson2020-11-2110-1692/+1852
| | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Revert "Switch ID code to use a hash table instead of a skip list (#52)" (#104)Dana Robinson2020-11-202-1287/+28
| | | This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4.
* Add new files to CMake and MANIFEST (#100)Allen Byrne2020-11-191-0/+1
| | | | | * Add new header file * Add missing file
* First cut of the H5 public API documentation. (#80)Gerd Heber2020-11-1824-557/+6919
| | | | | | | | | | | | | | | | | | | | | * 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 Robinson2020-11-172-28/+1287
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 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 Knox2020-11-131-7/+3
|\ \ | | | | | | Downgrade m4 doxygen macros.
| * | Add missing entries, remove m4 referenceAllen Byrne2020-11-121-7/+3
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* | | Merge pull request #60 from bmribler/developLarry Knox2020-11-121-7/+12
|\ \ \ | |/ / |/| | Fix HDFFV-10590
| * | 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 Ribler2020-10-2649-10579/+10674
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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 #78 from gheber/developGerd Heber2020-11-103-103/+1230
|\ \ \ \ | | | | | | | | | | This is the first installment of Doxygen-based documentation for the H5F module.
| * | | | First cut of H5F.Gerd Heber2020-11-093-103/+1230
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* | | | Merge pull request #77 from byrnHDF/developLarry Knox2020-11-101-1/+3
|\ \ \ \ | |/ / / |/| | | Set doxygen default to normally disabled.
| * | | Update to latest doxygen.m4Allen Byrne2020-11-091-1/+3
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* | | | Merge pull request #73 from byrnHDF/developLarry Knox2020-11-082-3/+49
|\ \ \ \ | |/ / / | | | | Add doxygen autconf/cmake support
| * | | Change doxygen brief variableAllen Byrne2020-11-071-1/+1
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| * | | Doxygen correct PHONY targetAllen Byrne2020-11-031-1/+0
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| * | | Doxygen add new files and update docsAllen Byrne2020-11-031-0/+6
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| * | | Add doxygen auotoconf and cmake supportAllen Byrne2020-11-032-2/+43
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* | | | Change H5R__copy to not assume destination reference storage is initializedJordan Henderson2020-11-031-2/+4
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* | | Merge pull request #65 from derobins/minor/mpi_2gb_limitLarry Knox2020-10-301-14/+14
|\ \ \ | | | | | | | | Fixes a bit shift issue in an MPI constant
| * | | Fixes a bit shift issue in an MPI constantDana Robinson2020-10-291-14/+14
| | | | | | | | | | | | | | | | | | | | Redefines TWO_GIG_LIMIT to be INT32_MAX instead of 1 << 31, which fixes an issue revealed by compiling with -Wshift-overflow.
* | | | Replaces C std library calls with H5MM equivalentsDana Robinson2020-10-306-39/+39
|/ / / | | | | | | | | | Mostly H5MM_memcpy in newer VFDs
* | | Fixes minor issues in various virtual file driversDana Robinson2020-10-2910-49/+24
| |/ |/| | | | | | | | | | | | | | | | | | | | | - HDFS VFD files now ignored in the Autotools when the HDFS VFD is not being built. - All VFD init code uses idiomatic H5I_INVALID_HID instead of -1 or FAIL. - The HDFS VFD now includes H5FDdrvr_module.h in the right place. - The HDFS tests in test/hdfs.c no longer pass NULL to VERIFY macros, which raised warnings. - Minor tweaks to fix const, unused variables, etc. warnings in several VFDs.
* | Merge pull request #59 from derobins/trivial/HDprefixLarry Knox2020-10-244-11/+11
|\ \ | | | | | | HD prefix updates in src/ and test/
| * | Restores erroneously deleted key_id field from S3 VFDDana Robinson2020-10-241-1/+1
| | | | | | | | | | | | | | | Accidentally deleted while preparing the PR. Only existed in a branch.
| * | HD prefix updates in src/ and test/Dana Robinson2020-10-244-12/+12
| | | | | | | | | | | | | | | | | | | | | Adds missing HD prefixes to API calls in src and test. Adds some extra processing to bin/checkposix to keep the noise levels down when running the script (not comprehensive).
* | | Removes -Wimplicit-fallthrough=5 from the gcc warningsDana Robinson2020-10-226-2/+39
|/ / | | | | | | | | | | | | | | | | | | | | | | -Wimplicit-fallthrough=3 is added by -Wextra, which we already set. Bumping the warning level only changes how fall-through comments are parsed, with level 5 turning off fall-through comments entirely. This is unnecessary and results in having to do extra work to squash warnings when included external code uses fall-through. This change also adds /* FALLTHROUGH */ comments where H5_ATTR_FALLTHROUGH is used so compilers that don't use attributes but do respect fall-through comments don't raise spurious warnings.
* | Whitespace and url correctionAllen Byrne2020-10-193-15/+16
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* | Update javadoc comments to reduce warnings (#41)Allen Byrne2020-10-161-1/+1
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* | More general message about using description for errnoThomas Kluyver2020-10-151-2/+6
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* | Note that the description for system errors may be used by h5pyThomas Kluyver2020-10-151-0/+2
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* | Comment adjustmentsAllen Byrne2020-10-083-5/+4
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* | Update reformatting settings, trace wrapping, and printf-format strings (#22)Quincey Koziol2020-10-0630-10538/+10588
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add BEGIN_FUNC / CATCH / END_FUNC to macros * Remove incorrect trailing '{' * Update trace script to wrap H5TRACE macros at 110 characters and improve comments for code that performs this operation. * Clean up printf-formatting in H5public.h and correct some oversights in the code. * Reformat with BEGIN_FUNC / END_FUNC handled correctly by clang-format * Run clang-format on changes. * Correct H5_SIZEOF_HSIZE_T/H5_SIZEOF_HSSIZE_T macros to match typedef. * And make the undef value match also. * Update comment * Update clang-format actions to exclude generated files. * Post-process generated H5LTparse.h file as well as H5LTparse.c file. * Fix formatting * Update version of github clang-format action
* | Fix VFD h5repacktest (#20)Allen Byrne2020-10-061-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * h5repacktest VFD fix and formatting changes * Fix memory leak in H5PL__find_plugin_in_path When encountering a directory, the current loop iteration was skipped without freeing the memory allocated for the path. * Refactor parser GCC diagnostic statements * genparser on jelly with default bison/flex Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de>
* | Fix memory leak in H5PL__find_plugin_in_pathMichael Kuhn2020-10-051-1/+3
|/ | | | | When encountering a directory, the current loop iteration was skipped without freeing the memory allocated for the path.
* Clang-format of source filesAllen Byrne2020-09-30489-107614/+100931
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* Merge pull request #2650 in HDFFV/hdf5 from ↵David Young2020-09-2862-855/+479
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:rebased-fprintf-experiment to develop * commit 'c0fbc5c086566d5d3c1d1ef26baa81a53d59fc08': (24 commits) Use the right format string, "%zu", for size_t. Repair more format strings. Fix a bunch of format string errors reported by Larry. Fix some HDfprintf compilation errors: use the right format strings ("zu", PRIuHSIZE), avoid casting some printf arguments, pass the right number of arguments. Test the format string "ll" before "l", "L", and "q", like the ./configure script does. This ought to fix the compilation failure in test/dt_arith.c that Allen told me about: Cast a non-void pointer to void pointer for "%p". Use PRIu32 and "zu" formats. Delete some casts from `size_t`. I'm taking a guess that this code intended to point the 2-digit wide hexadecimal octet values, not 2 character-wide pointers to the bytes. The %02p format, which is a GNU-ism, disagreed with GCC 8.3.0 and the option flags we use. %08p is not portable, it's a GNU-ism. Use %8p, instead. Squashes a GCC error. Add format string macros PRI[doxX]HID for hid_t and use PRIdHID. Use HDva_copy() and introduce a bunch of compatbility format-string constants for uppercase hexadecimal strings, `PRIX...`. Should fix the VS2010 errors that Allen mentioned: Always #define HDfprintf as fprintf in this header. I believe this will fix the Windows build error that Allen reported. Provide an HDvasprintf implementation only if it isn't #defined. This should fix the mingw compilation issue that Allen reported. Fix va_list usage in the vasprintf(3) implementation. Promote format-string warnings to errors. Use the portable `-eq` operator instead of the bash-ism `==`. Fixes the tests on NetBSD, where /bin/sh != bash. Restore a literal percent sign ("%%") that I accidentally deleted. Fix code that made GCC complain about a NULL or `unsigned char *` arguments for "%s". Take pains to provide UINT64_MAX in all conditions. Correct a couple of format strings. ...
| * Use the right format string, "%zu", for size_t.David Young2020-09-271-1/+1
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| * Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experimentDavid Young2020-09-2724-5913/+6003
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| * | Repair more format strings.David Young2020-09-263-18/+19
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| * | Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experimentDavid Young2020-09-252-0/+51
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| * | | Cast a non-void pointer to void pointer for "%p".David Young2020-09-031-1/+1
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| * | | Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experimentDavid Young2020-09-03366-12087/+10698
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| * | | | Use PRIu32 and "zu" formats. Delete some casts from `size_t`.David Young2020-07-312-4/+4
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