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* Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-2329-67/+96
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* HDFFV-11014, fix the h5repack issue that misses a few attributes during the ↵Muqun Yang2020-02-101-1/+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.
* Squashed commit of the following:David Young2020-01-315-101/+112
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit ff7a9a34de2fcd78f5d32a1532f3d0e224b20d94 Author: Kimmy Mu <kmu@hdfgroup.org> Date: Wed Jan 29 14:12:18 2020 -0600 Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12 * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop commit 9f3d808c05d2a3b308f32c958c6671fcac0a432c Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 11:43:55 2020 -0600 testpar/t_2Gio.c: Fix a typo that I think was introduced by a 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. commit 43a4b80b21c0329fbc1f9a0e2854795189f0bb50 Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 10:47:30 2020 -0600 Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required. Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c. commit 035bfa0769a4012881fc659b673bacf44d146537 Author: David Young <dyoung@hdfgroup.org> Date: Tue Jan 28 20:35:28 2020 -0600 Reduce differences between my -Werror branch and `develop`: Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* Merge changes from develop to fix various issuesAllen Byrne2020-01-3024-487/+324
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* Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-2920-396/+426
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop
| * Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to developKimmy Mu2020-01-288-71/+105
| | | | | | | | | | | | | | | | | | * commit '406330addf45529ecdd088f4d22e9aab9a03661d': rename macro change condition pick up from Dave's fix leave Wswitch-default for later fix fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow
| * Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to developKimmy Mu2020-01-2811-150/+160
| | | | | | | | | | | | * commit 'af5c33afabdae2e39bb45eb1b3e9c8366da01145': remove unnecessary stuff squash cast warning fix
| * Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized ↵Kimmy Mu2020-01-281-1/+1
| | | | | | | | | | | | | | to develop * commit '2de0ce0d8ba2fb58fadefc5d718a3c0fedab25c8': fix uninitizlized warning
| * Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to developKimmy Mu2020-01-282-3/+7
| | | | | | | | | | | | | | * commit '9afaf94bef740f89958a1a8aae369d5f607845f4': not use hdf5 private header fix float type cmp warning fix float type cmp warning
| * Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to ↵Kimmy Mu2020-01-281-2/+0
| | | | | | | | | | | | | | develop * commit '9f80ffa1f1908975b3100814b2529bf779521e13': fix missing prototype warning
| * Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-2811-171/+155
| | | | | | | | | | | | | | | | | | | | | | * commit '145ef3ceee20c28a443bd11507c58858bea3f889': more cleanup change it back pick up missing piece fix unused related warnings removed unused parameter more fix and address comments remove unsed var,function,macro, etc
* | Update version to 1.12.1-snap0 for hdf5_1_12 branch.Larry Knox2020-01-281-7/+7
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* Merge pull request #2238 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-244-8/+8
|\ | | | | | | | | | | | | * commit '48cc850199901c5b67a40183262f4ead975b884f': fix test assert fail error Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop Merge pull request #2234 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
| * fix test assert fail errorkmu2020-01-101-2/+2
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| * Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-0810-28/+28
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '0a2bb11b248df6841daabca3970df5d8504adfc7': address problems from comments fix and address comments change according to previous comments add missing piece remove unnecessary check macro fix intel compile warnings Revert "fix warnings from Intel compiler" Revert "fix warnings and some text alignment" Revert "let hdf5 pick up the right compiler in Intel environment" Revert "fix issues from previous PR comments" Revert "using a different MACRO" using a different MACRO fix issues from previous PR comments let hdf5 pick up the right compiler in Intel environment fix warnings and some text alignment fix warnings from Intel compiler
* | Change tools debug macros to not use error stackAllen Byrne2020-01-2310-203/+142
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* | Improved CMake options for testsAllen Byrne2020-01-1914-199/+226
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-01-1927-376/+570
|\ \ | | | | | | | | | | | | | | | | | | * commit '29efed58a861346be122b1ff0c50741206742322': Squashed commit of the token_refactoring branch: Add test for reference shutdown issue H5R: set app ref when incrementing ref_count on location held by reference (fix HDFFV-10992)
| * | Squashed commit of the token_refactoring branch:Dana Robinson2020-01-1927-376/+570
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* | | Merge perform standalone changes from developAllen Byrne2020-01-173-4/+20
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* | Merge tools changes from developAllen Byrne2020-01-1355-2376/+2379
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* | Update file with changes from developAllen Byrne2020-01-121-46/+39
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* | Fix CMake test macros and perform standalone testsAllen Byrne2020-01-126-10/+144
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-01-074-6/+12
|\ \ | |/ | | | | | | | | | | | | | | | | | | * commit '7116d82f6b685261b5b4e64fada1a0a031cd7341': Remove mismerged code Cherry pick of 0225e6d5969 Cleanups from PR reviews Remove unnecessary H5CX call Refactor H5Dvlen_get_buf_size to use optional dataset operation, with generic fallback for VOL connectors that don't implement operation Refactor all the 'H5VL_*_optional' callbacks to move the type of operation out of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Update h5debug to retrieve file pointer through VOL framework
| * Cherry pick of 0225e6d5969Quincey Koziol2020-01-043-5/+5
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| * Update h5debug to retrieve file pointer through VOL frameworkQuincey Koziol2020-01-041-1/+7
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* | Add MPI libs for standalone perfAllen Byrne2019-12-221-2/+2
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* | Fix autotools test scriptsAllen Byrne2019-12-224-7/+45
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* | Add ref files to test scriptAllen Byrne2019-12-212-5/+18
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* | h5diff test script fixesAllen Byrne2019-12-212-1/+8
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* | Fix compile statement orderAllen Byrne2019-12-203-4/+5
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* | HDFFV-10976,-10980 h5dump, h5ls, h5diff use new ref APIsAllen Byrne2019-12-2049-469/+1460
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* Standalone doesn't use h5test implementation.Allen Byrne2019-12-201-0/+3
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* In portable shell scripts (using #!/bin/sh) we have to use single squareDavid Young2019-12-191-1/+1
| | | | brackets, [ ], instead of the bash-ism double square brackets, [[ ]].
* For portability, use the POSIX sh(1) string-comparison operator `=`David Young2019-12-191-2/+2
| | | | instead of `==`.
* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2019-12-173-10/+3
|\ | | | | | | | | | | | | | | | | | | * commit '1097ac60c2b95a2b958a3150b537c75f512cacca': Merge t_2Gio test into hdf5_1_12. This will eventually be refactored out after merging the test functionality into the testphdf5 test. Merge t_2Gio test into hdf5_1_12. This will eventually be refactored out after merging the test functionality into the testphdf5 test. Minor tweaks noticed while going over VOL documentation. Yanked -Wc++-compat from the flags used to build the C library in both the Autotools and CMake. Fixed missing blob callbacks in test VOL connectors. Trivial parameter renaming in VOL API calls.
| * Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-163-10/+3
| | | | | | | | the Autotools and CMake.
* | Remove duplicate instanceAllen Byrne2019-12-161-6/+0
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* Revert and move declarationAllen Byrne2019-12-131-3/+5
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* Correct compile and test Windows errorsAllen Byrne2019-12-131-5/+4
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* Fix issues when using ONLY_SHARED_LIBSAllen Byrne2019-12-112-2/+2
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* Change defines to not conflict with windowsAllen Byrne2019-12-111-14/+14
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* Fix reference fileAllen Byrne2019-12-101-1006/+1009
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* HDFFV-10876 Merge from developAllen Byrne2019-12-0968-3605/+4257
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* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-097-23/+12
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-067-12/+23
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* Fix MPI test namesAllen Byrne2019-10-231-1/+1
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* Fix missing HD and whitespaceAllen Byrne2019-10-211-185/+112
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* Merge branch 'hdf5_1_12' of ↵Larry Knox2019-10-0912-65/+71
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12
| * Fix reference type comparison in h5dumpJerome Soumagne2019-10-081-1/+5
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