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* Changes for sanitize=address (#312)Allen Byrne2021-02-053-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3
* Fix DS examples (#307)Scot Breitenfeld2021-02-042-2/+5
| | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset
* Ensure processes always synchronize in t_shapesame test setup (#306)jhendersonHDF2021-02-031-16/+6
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* Fixes bin/trace so it doesn't dirty the repo when autogen runs (#295)Dana Robinson2021-02-033-7/+4
| | | | | * Fixes bin/trace so it doesn't dirty the repo when autogen runs * Put the trace max back to 110 and comment off H5O.c line
* Update supported platforms (#303)Allen Byrne2021-02-034-29/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace
* Modify VDS code to always open source files with H5F_CLOSE_WEAK close (#291)Neil Fortner2021-01-302-2570/+2689
| | | | degree. Add test cases to VDS test for this, and reduce the amount of output from that test.
* Remove unused AC_REVISION macro from configure.ac (#292)Dana Robinson2021-01-302-2/+2
| | | | | * Fixes a wayward parenthesis in H5TS.c * Removes unmaintained AC_REVISION macro from configure.ac
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-29146-724/+724
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction
* develop clang-format comments (#286)Allen Byrne2021-01-272-3/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes
* Jan ws changes (#282)Allen Byrne2021-01-2711-108/+114
| | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Whitespace fixes except for H5Tprivate.h typo fix
* Small fixes (#285)Allen Byrne2021-01-277-120/+133
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Small changes plus merge of tools arg parse from 1.12
* Java replace switch on string (#273)Allen Byrne2021-01-273-312/+374
| | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit
* Add H5ESpublic.h to main hdf5.h header (#278)Quincey Koziol2021-01-231-0/+1
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* Fix problems with vlens and refs inside compound using H5VLget_file_type() ↵hdf5-1_13_0-rc5Neil Fortner2021-01-2213-36/+151
| | | | | | | | | | | | (#274) * Fixed problems with vlens and refs inside compound using H5VLget_file_type() * Fix date in RELEASE.txt * Add assertions * Move some manipulation of H5VL_object_t struct fields into the H5VL package.
* Fixes a wayward parenthesis in H5TS.c (#262)hdf5-1_13_0-rc4Dana Robinson2021-01-201-1/+2
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* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270)Neil Fortner2021-01-203-7/+40
| | | | | | | | | * Cache the pointer to the next point to process after the last call to H5S__get_select_elem_pointlist. This allows the normal process of iterating over the points in batches to be much more efficient, as the library does not need to traverse the entirety of the preceding points every time the funciton is re-entered. * Update RELEASE.txt for point selection iteration performance fix.
* 11099 Add help text line (#259)Allen Byrne2021-01-153-0/+10
| | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text
* Fixes naked pthread usage in H5TS code added for async (#260)Dana Robinson2021-01-141-4/+8
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* Removes lock/unlock callbacks from ros3 and hdfs VFDs (#258)Dana Robinson2021-01-147-48/+164
| | | | | | | | | | | | | | | | * Removes no-op callback stubs from read-only VFDs Also changes VFD registration to allow read-only VFDs with no write callback to be registered. * Adds a RELEASE.txt note for HDFFV-11205 For the read-only VFD registration change * Revert "Removes no-op callback stubs from read-only VFDs" This reverts commit a7a95497305d64d2de783fdb0e3186a532446a4a. * Removes lock callbacks from ros3 and hdfs VFDs
* Reclassify CMake messages - HDFFV-11144 (#253)Allen Byrne2021-01-1325-116/+270
| | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages
* Allow read-only VFD registration (#257)Dana Robinson2021-01-135-280/+33
| | | | | | | | | | * Removes no-op callback stubs from read-only VFDs Also changes VFD registration to allow read-only VFDs with no write callback to be registered. * Adds a RELEASE.txt note for HDFFV-11205 For the read-only VFD registration change
* Keep doxygen comment length under 100 char line length (#247)Allen Byrne2021-01-081-31/+39
| | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace
* Fixes Autotools detection of the st_blocks field in stat (#246)Dana Robinson2021-01-082-3/+12
| | | | | | | | | * Fixes Autotools detection of the st_blocks field in stat The Autotools and CMake will now both correctly determine if the stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS appropriately. * Fixes a typo in configure.ac
* Reformat source (#244)Quincey Koziol2021-01-0727-813/+770
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* Fix error is H5Mclose_async. (#240)Neil Fortner2021-01-052-3/+3
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* Remove duplicate setting (#236)Allen Byrne2021-01-051-1/+0
| | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Remove duplicate setting
* Modify temporary rpath for testing in java example scripts. (#230)Larry Knox2020-12-294-5/+37
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* Switch bool/true/false to hbool_t/TRUE/FALSE in a few places (#229)Dana Robinson2020-12-249-45/+45
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* Doxygen: Added more H5P RM entries (#226)bljhdf2020-12-241-40/+1058
| | | | | | | | | | | * Doxygen - RM entries for H5A, H5S, and H5P APIs * fix issues on ubuntu * added missing H5F_fspace_strategy_t_snip * Doxygen: Add more H5P functions Co-authored-by: hdfhelp <hdfhelp@jelly.ad.hdfgroup.org>
* RM blocks for H5R (#219)bmribler2020-12-235-8/+764
| | | | | | | * Transferred RM blocks in H5D and H5G to develop * Added RM blocks to H5R and added new aliases. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* dev -Update pkgconfig settings with version - #218 (#220)Allen Byrne2020-12-225-10/+10
| | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Pkgconfig fix - #218 * Update all pkgconfig settings with version
* Add compiler flags for GCC 10, along with updating warnhist script to ↵Quincey Koziol2020-12-218-52/+112
| | | | accommodate them. (#217)
* Transferred RM blocks in H5D and H5G to develop (#213)bmribler2020-12-214-18/+1598
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* Fixes a small memory leak in the chunk_cache test (#208)Dana Robinson2020-12-201-2/+6
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* Fixes a small memory leak in the h5jam test (#207)Dana Robinson2020-12-201-2/+3
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* Fixes a minor memory leak in hl/test/test_file_image.c (#209)Dana Robinson2020-12-201-0/+2
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* Update jni.h detection for OS version changes in Macos 11.x (#211)Quincey Koziol2020-12-201-6/+12
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* Avoid aligned access for references by decoding into temporary buffer and ↵Quincey Koziol2020-12-193-42/+46
| | | | then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* H5FD__mpio_read: Fix MPI_Bcast datatype (#205)Evan Ramos2020-12-181-1/+5
| | | Signed-off-by: Evan Ramos <evan@hpccharm.com>
* Restores maintainer mode in the autotools (#200)Dana Robinson2020-12-181-11/+39
| | | | | Maintainer mode should be enabled in development branches. Also adds helpful commenting.
* close #195. (#196)H. Joe Lee2020-12-171-2/+2
| | | | | * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake
* Fix datatype lookup in named datatype flush/refresh code and detect more ↵hdf5-1_13_0-rc3Quincey Koziol2020-12-176-12/+30
| | | | | | | | | | | core dumps in test scripts (#193) * Detect coredumps, and avoid printing a warning when creating a directory that already exists * Retrieve the actual datatype object correctly, in the face of possible pass-through VOL connectors * Detect more core dumps, and tiny formatting cleanup * Revert error status checks for mirror VFD test script
* OESS-98 fix hdf5 link target (#188)Allen Byrne2020-12-161-2/+1
| | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * OESS-98 fix hdf5 link target
* Adds h5delete tool (#187)Dana Robinson2020-12-165-2/+109
| | | | | | | | | * Adds h5delete tool * Fixed MANIFEST * Added RELEASE.txt note * Fix typo in RELEASE.txt
* Turns off clang formatter for H5ARGS_TRACE (#184)Dana Robinson2020-12-1610-94/+160
| | | | | | | | | The H5ARGS_TRACE macro was added during the async merge. These macros are updated by the bin/trace script, but conflict with the formatter so formatted code gets dirtied when autogen.sh is run. This change enshrines the bin/trace output as canonical and adds comments to turn clang formatting off for those lines containing H5ARGS_TRACE.
* OESS-98 convert plugin option to FetchContent, add tests (#155)Allen Byrne2020-12-1612-336/+325
| | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * Update other test machines * OESS-98 fix tools test for plugins * HDFFV-10865 performance improvement for java array
* Enable H5Fopen to probe list of available VOL connectors when opening a (#182)jhendersonHDF2020-12-1610-49/+479
| | | file
* Transfer doxygen H5O RM blocks from doxygen branch to develop. (#174)vchoi-hdfgroup2020-12-1613-322/+2662
| | | Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
* Doxygen - RM entries for H5A, H5S, and H5P APIs (#181)bljhdf2020-12-164-325/+6673
| | | | | | | * Doxygen - RM entries for H5A, H5S, and H5P APIs * fix issues on ubuntu * added missing H5F_fspace_strategy_t_snip
* Removes debug statement from H5R__open_attr_api_common() (#183)Dana Robinson2020-12-161-1/+0
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