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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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| * | | | | Squash my changes on branch `fprintf-experiment` into one commit forDavid Young2020-07-0756-852/+445
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | reapplication to my new warnings branch, `warnings-again`. These changes are included: commit 915551b7bf64e777dd2007386ec77b1d117770da Merge: 63858c2 a8892bb Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:39:49 2019 -0600 Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment commit a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9 Merge: 5c911d8 f907b51 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:33:54 2019 -0600 Merge pull request #2055 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop * commit 'f907b511d06612dafc7814a7c30f2f3d2b76d52b': Oops, remove more C99 designated initializers for VS 2010 compatibility. commit 63858c22e168acaec0af8ced6641f26102cc6bb0 Merge: 20ae787 5c911d8 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:04:42 2019 -0600 Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment commit 5c911d8baf3ee7fe654269088eebdf07f59a8192 Merge: b8a5671 62208b0 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 16:58:27 2019 -0600 Merge pull request #2030 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop * commit '62208b056a09c01855fbac7f75146be58ad6bfe5': (44 commits) Add an #include to get a function declaration. Don't use C99 designated initializers, they're not compatible with Visual Studio 2010. Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*. Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using. Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check. Only use -Werror=cast-function-type with GCC 8 and later. Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags. Add new source files to CMakeLists.txt. Mention the -Werror= flags in libhdf5.settings.in. free -> HDfree Promote decleration-after-statement warnings to errors. Quiet decleration-after-statement warnings. Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements. Document H5D__chunk_mem_xfree_wrapper(). Undo accidental test deletion. Oops, delete a debug printf that snuck in here. Undo my changes to the HD macros, hadn't really intended those to be on this branch.... Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options. Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *. Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. ... commit 20ae7877e33931b95e8c3502b027d6c3fe94a11f Merge: 46f8c61 edd5297 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:34:09 2019 -0600 Merge remote-tracking branch 'origin/add-werror-and-squash-some' into fprintf-experiment commit 46f8c613d5117a8be5bc8385a072daa0b4262f06 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:29:00 2019 -0600 GCC really wants us to use `ll` to format `long long`, so try to make that work before any other format modifier. Seems like we're not compiling the autoconf test program with -Werror=format ? Probably should. commit eee35b8ef3759c391327cd48a9b3c56b6f8abc99 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:28:05 2019 -0600 It's hard to know just how wide an HDoff_t will be, and I don't think POSIX or C standards provide a PRI macro for it, so cast to intmax_t and format using PRIdMAX. commit 86eab12df7a89b546a38e99f8178dd2adbcb3433 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:26:25 2019 -0600 URemove some casts.se the right format string for the argument. Here and there stop casting a printf argument. commit f722f7cbecbaa99449941484b014426f62f1bed5 Merge: 58e3743 6d5ec83 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 14:44:16 2019 -0600 Merge branch 'add-werror-and-squash-some' into fprintf-experiment commit 58e3743b7faa9836606ee91798fe80dfc0040da7 Author: David Young <dyoung@hdfgroup.org> Date: Wed Nov 20 21:07:21 2019 -0600 Remove custom HDfprintf implementation, using the standard library's, instead. Take a swipe at repairing fprintf format strings, mainly replacing "%Hu" with "%" PRIuHSIZE, "%a" with "%" PRIuHADDR, "%Zu" with "%zu". Here and there remove an awkward cast of a printf argument to `long long` and use PRI[doux]8, PRI[doux]32, or PRI[doux]64, instead. Change occurrences of "%t" to "%s" and perform a suitable change of argument, `cond` -> `cond ? "TRUE" : "FALSE"`. Some occurrences of %Hu, %a, and %t remain, they just weren't flagged by the compiler because of #ifdef'age. commit d4366909293fa970c23512ac80e5d865d76cddbf Author: David Young <dyoung@hdfgroup.org> Date: Wed Nov 20 20:54:32 2019 -0600 Promote format-string warnigns to errors.
* | | | | | OESS-98 merge with clang-format changesAllen Byrne2020-09-251-22/+22
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* | | | | Merge pull request #2882 in HDFFV/hdf5 from ↵Allen Byrne2020-09-2524-5918/+6009
|\ \ \ \ \ | |_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BYRN/hdf5_adb:feature/cmakeV2-clang-format to develop * commit '571a5e9250ca69adb54ef956361a5cf77059f67c': Add h5ls test plugin format target Fix manifest Add code owners file Update actions - split push/pull-request commits Change to executable Change to based on LLVM format Fix comment formatting due to tabs conversion Disable formatting for file File changes to affect formatting CMake and script changes for clang-format
| * | | | Fix comment formatting due to tabs conversionAllen Byrne2020-09-248-386/+384
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| * | | | Disable formatting for fileAllen Byrne2020-09-051-30/+4
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