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* 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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| * | | | Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experimentDavid Young2020-07-3050-1392/+1348
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| * | | | | I'm taking a guess that this code intended to point the 2-digit wideDavid Young2020-07-301-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.David Young2020-07-301-1/+1
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| * | | | | Add format string macros PRI[doxX]HID for hid_t and use PRIdHID.David Young2020-07-302-1/+7
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| * | | | | Use HDva_copy() and introduce a bunch of compatbility format-string constantsDavid Young2020-07-303-2/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | for uppercase hexadecimal strings, `PRIX...`. Should fix the VS2010 errors that Allen mentioned: H5system.obj : error LNK2019: unresolved external symbol va_copy referenced in function HDvasprintf [C:\autotest\hdf5trunk-StdShar-code-vs10\build\ctest\hdfbld\src\hdf5-shared.vcxproj] 2 ..\..\..\hdfsrc\test\h5test.c(2103): error C2146: syntax error : missing ')' before identifier 'PRIX64' [C:\autotest\hdf5trunk-StdShar-code-vs10\build\ctest\hdfbld\test\hdf5_test-static.vcxproj]
| * | | | | Provide an HDvasprintf implementation only if it isn't #defined. This shouldDavid Young2020-07-071-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | fix the mingw compilation issue that Allen reported.
| * | | | | Fix va_list usage in the vasprintf(3) implementation.David Young2020-07-071-2/+7
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| * | | | | Take pains to provide UINT64_MAX in all conditions.David Young2020-07-071-0/+6
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| * | | | | Fix fprintf arguments: "%p" expects a `void *` argument.David Young2020-07-071-3/+3
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