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| * Replace usage of some standard library functions with HD- versionsJordan Henderson2020-03-261-2/+2
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| * Update Tools library to be better compatible with VOL connectorsJordan Henderson2020-03-175-71/+250
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modify h5repack to integrate with VOL connectors Update tools library to accomodate VOL connectors Update logic in h5tools_fopen for VOL connectors Add command-line options to h5repack for specifying in/out VOL connectors Implement h5tools_set_vol_fapl Fix library shutdown issue Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme Avoid H5Ocopy in h5repack when using different VOL connectors Update h5tools_test_utils.c for ROS3 and HDFS integration
* | Add extensive warnings to tools executablesAllen Byrne2020-03-251-0/+2
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* Fix standalone linkAllen Byrne2020-02-251-3/+3
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* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-211-1/+1
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* HDFFV-11014, fix the h5repack issue that misses a few attributes during the ↵Muqun Yang2020-02-071-1/+8
| | | | repacking. The flag that checks the object reference attribute is not updated properly. The fix is trivial. Just need to move the flag update line into the inner loop. Tested at Jelly. Also update the release.txt.
* testpar/t_2Gio.c: Fix a typo that I think was introduced by aDavid Young2020-01-291-5/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings.
* squash cast warning fixkmu2020-01-231-1/+1
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* merge and fixkmu2020-01-215-24/+37
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| * Squashed commit of the token_refactoring branch:Dana Robinson2020-01-165-24/+37
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* | merge and fix conflictkmu2020-01-194-73/+73
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| * Update tools hid_t declarations with H5I_INVALID_HIDAllen Byrne2020-01-134-73/+73
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* | merge and fix conflictskmu2020-01-146-380/+387
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| * Clean up tools warnings introduced by H5TOOLS_ERR_INIT macroJordan Henderson2019-12-316-354/+353
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| * Refactor tools library error handling macrosJordan Henderson2019-12-286-338/+339
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| * HDFFV-10980 - h5diff uses new ref APIsAllen Byrne2019-12-196-31/+38
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-12-021-8/+6
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0772b975d1d2bfa15aedeb4b6e2c2aac78c61a2f': Fix missing free in H5T__ref_mem_read() Fix bugs in H5VL file comparison code. Add short circuit success to H5VL_cmp_connector_cls(). Implement file comparison VOL callback. Other changes to allow references to work with non-native connectors. There is a bug somewhere. Add support for point selections to H5S_select_project_intersection. Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf3)" Revert "Oops, remove more C99 designated initializers for VS 2010 compatibility." H5R: fix H5Tconv to check for null references Trivial parameter renaming in VOL API calls. Move checking for zero offset in selection adjust calls to the selection callbacks. This makes the procedure for checking it consistent across selection types and between _s and _u, ensures it is always is performed even when called within the H5S package, and removes the redundant check that would occur when callins H5S_select_adjust_s() from outside the H5S package. Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() with H5Sselect_adjust. Implement "adjust_s" callback for all selection types. Add range checking to H5Sselect_adjust().
| * \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-261-6/+8
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9': (45 commits) Oops, remove more C99 designated initializers for VS 2010 compatibility. 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 *. ...
| * | | HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-076-326/+326
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* | | | remove unsed var,function,macro, etckmu2019-12-061-1/+1
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* | | Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings ↵David Young2019-11-271-8/+6
| |/ |/| | | | | level and fixing some code.' (commit 5c911d8baf3)"
* | Change some GCC warnings to errors. Fix code to quiet some warnings.David Young2019-11-051-6/+8
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* Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-083-6/+8
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* HDFFV-10919 merge synchingAllen Byrne2019-10-023-174/+63
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* Update versioning to next major versionAllen Byrne2019-09-251-1/+2
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* Revert else-if to single line.Jacob Smith2019-09-241-22/+12
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* Merge branch 'develop' of ↵Jacob Smith2019-09-234-25/+27
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Add HD prefix to testsAllen Byrne2019-08-153-59/+59
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| * Update libvers usageAllen Byrne2019-07-281-1/+2
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* | Change print calls to HD-wrapped.Jacob Smith2019-09-232-61/+68
| | | | | | | | Minor formatting tweaks (inc. regressions and in-file style-matching).
* | Add copyright/disclaimer to repack gentest.Jacob Smith2019-07-221-7/+0
| | | | | | | | Minor formatting tweaks.
* | Merge branch 'develop' of ↵Jacob Smith2019-07-224-54/+25
|\ \ | |/ | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Updates to warnhist script, along with a few cleanups, and add some commentsQuincey Koziol2019-07-101-1/+1
| | | | | | | | to warning cleanups that are a bit obscure.
| * Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-16/+8
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| * Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-213-38/+16
| | | | | | | | clean up warnings.
* | Minor formatting adjustments.Jacob Smith2019-07-222-20/+6
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* | Undo some formatting modifications.Jacob Smith2019-06-213-44/+40
| | | | | | | | Update MANIFEST.
* | Merge branch 'develop' into bugfix/repack_external_storageJacob Smith2019-06-202-10/+12
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| * HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-181-9/+11
| | | | | | | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
| * Modified Makefile.ams for h5repack, h5watch and gif2h5 to allowLarry Knox2019-06-121-1/+1
| | | | | | | | | | | | | | disabling tests. Moved h5cc.in from tools/src/misc to src directory to always create h5cc whether or not tools are enabled. Added configuration status of tools and tests to libhdf5.settings.
* | First pass at repack consolidating external storage if layout given.Jacob Smith2019-05-311-3/+12
| | | | | | | | Checks out manually, tests still complain.
* | Formatting changes, mostly.Jacob Smith2019-05-301-58/+125
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* | Modify code comments for clarity.Jacob Smith2019-05-281-145/+218
| | | | | | | | Some minor reformatting.
* | refactor h5repack_main.c -- remove some redundancy, formattingJacob Smith2019-05-241-173/+134
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* | Fit help message to 80 character width and clarify some details.Jacob Smith2019-05-141-27/+44
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* Invalid position of declaration fixed.Allen Byrne2019-01-251-1/+2
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* Fixed HDFFV-10586 and HDFFV-10588Binh-Minh Ribler2019-01-151-1/+2
| | | | | | | | | | | | | | | | | | Description: HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters Added a check for zero value HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper This is actually an Invalid read issue. It was found that the attribute name length in an attribute message was corrupted, which caused the buffer pointer to be advanced too far and later caused an invalid read. Added a check to detect attribute name and its length mismatch. The fix is not perfect, but it'll reduce the chance of this issue when a name length is corrupted or the attribute name is corrupted. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* TRILAB-81 coverity fixesAllen Byrne2018-10-172-3/+5
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Vailin Choi2018-05-231-2/+2
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '2b0fb7e3f1f7da5b23d430702493ed4fb7f87166': (21 commits) HDFFV-9739 only executes H5E tests in production Remove link flag from compile command fix typo Add release note Correct attribute location HDFFV-9739 fix copy testfiles command HDFFV-9739 remove obsolete test files HDFFV-9739 dup test file for concurrent tests HDFFV-9739 Fix autotools script HDFFV-9739 Change autotools test scripts Fix typo HDFFV-9739 Update test reference Update current windows test machines HDFFV-9739 Grab err number before API call HDFFV-9739 Add release note Adjust test names for concurrent tests Fix soversion HDFFV-9739 Fix copy name HDFFV-9739 factor out tests into separate JUnit Updated the threadsafety test to use error macros instead of asserts. ...
| * Fix MPI on Windows by adding MPI include folderAllen Byrne2018-05-091-2/+2
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