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* Various clang tidy warning fixes (#448)Sean McBride2021-03-102-4/+4
| | | | | | | | | | | | | | | | | | | | | | | * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)Sean McBride2021-03-097-30/+33
| | | | | | | | | | | | | * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed clang-tidy readability-redundant-control-flow warnings (#428)Sean McBride2021-03-053-8/+0
| | | | | | | | | * Fixed clang-tidy readability-redundant-control-flow warnings Just removed useless trailing return statements. * Removed blank lines from h5diffgentest.c with clang-format v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed clang-tidy readability-misleading-indentation warnings (#427)Sean McBride2021-03-053-158/+161
| | | | | | | * Fixed clang-tidy readability-misleading-indentation warnings * Reformatted src/H5Zscaleoffset.c with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes various warnings noticed on Windows (#425)Dana Robinson2021-03-053-12/+15
| | | | | | | | | | | | * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues
* Use do-while trick to force H5Epush_ret() to require trailing semi (#380)Sean McBride2021-03-043-174/+185
| | | | | | | | | | | | | | | * Use do-while trick to force H5Epush_ret() to require trailing semi Fixed ensuing compiler errors. * Commit format changes from running clang-format with clang version 10.0.1. * Use do-while trick to force H5Epush_ret() to require trailing semi Fixed ensuing compiler errors. Updated RELEASE.txt. This change was made to allow clang-format to correctly format the code. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Changes found during merge to 1.12 (#414)Allen Byrne2021-03-0416-49/+51
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup
* H5TS_win32_thread_exit (#396)Allen Byrne2021-03-011-25/+56
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int
* fixed error message typo (#401)Scot Breitenfeld2021-02-271-1/+1
| | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return
* Primary change is HDFFV-11212 - new refs and JNI (#372)Allen Byrne2021-02-251-1/+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 * 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 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments
* Patches from vtk (#358)Sean McBride2021-02-256-47/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Drop the export attribute on forward declaration They don't mean anything on forward declarations anyways. * Fixed -Wunused-parameter warnings in some C++ files Allowed all the attribute #defines to work in C++ also. * Fixed -Wunused-variable warnings by removing dead code * Fixed all -Wshorten-64-to-32 warnings by adjusting casts There was no truncation in fact, since the unsigned result was upcast to size_t then implicitly downcast to uint32_t. * Fixed all -Wcomma warnings by spliting statements onto own lines * Fixed all -Wself-assign warnings with different unused param suppression * Fixed all -Wextra-semi warnings * Fixed all -Wswitch-enum warnings Just added new explicit cases with the existing default case. * Fixed all -Wmissing-prototypes warnings Just made functions static. Moved them into an extern "C" block. * Reformatted source with bin/format_source using clang version 10.0.1 Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-23145-436/+436
| | | | | | | | | | | | | | | | * Fixed many -Wreserved-id-macro warnings by fixing header guard spelling Removed leading underscore(s) from header guard spelling. Used 2 regexes: ` _H5(.*)_H` ` __H5(.*)_H` Applied case-insensitively to only .h files. * Modified scripts that generate header files to not use underscore prefix Interestingly, there was already no leading underscore in the trailing comment at the end of the file * Fixed remaining -Wreserved-id-macro warning not caught by regex
* Fixed all -Wincompatible-pointer-types-discards-qualifiers warnings (#341)Sean McBride2021-02-227-27/+27
| | | | | | | | | | | | | * Fixed various -Wincompatible-pointer-types-discards-qualifiers warnings by adding const * Fixed various -Wincompatible-pointer-types-discards-qualifiers warning by removing extraneous consts There were casts with const, but the function parameter doesn't actaully take const, so just modified the casts. In the other case, a local variable was const that should not have been, becuase its source wasn't const either. * Fixed a -Wincompatible-pointer-types-discards-qualifiers warning by strdup-ing a string Create a duplicate string instead of mutating a supposedly const one.
* Fixed HDFFV-11150 (#356)bmribler2021-02-192-3/+4
| | | | | | | | Description Replaced an HDassert with a check for null pointer in H5O_dec_rc() to catch null pointer in corrupted data situation. As a result, removed the null check prior to H5O_dec_rc() calls. Platforms tested: Linux/64 (jelly)
* Fixed uninitialized warnings (#360)Sean McBride2021-02-1926-150/+151
| | | | | | | | | | * Fixed all -Wsometimes-uninitialized warnings by initializing variables * Fixed all -Wconditional-uninitialized warnings by initializing variables * Commit alignment changes from running bin/format_source with clang version 10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed various clang -Wformat-security warnings (#340)Sean McBride2021-02-192-2/+2
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* Update license url (#332)Larry Knox2021-02-17504-506/+506
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Fix for HDFFV-11109 - Copy MPI comm and info object into output FAPL from ↵jhendersonHDF2021-02-172-7/+23
| | | | | | | H5F_get_access_plist (#342) * Avoid freeing MPI_COMM_WORLD in H5_mpi_comm_free * Copy MPI Comm and Info to new FAPL in H5F_get_access_plist
* Check for wrap context before unwrapping file VOL object in H5F__dest (#325)jhendersonHDF2021-02-101-1/+9
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* Unwrap file VOL object when destroying file (#308)jhendersonHDF2021-02-061-9/+11
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* Fixes bin/trace so it doesn't dirty the repo when autogen runs (#295)Dana Robinson2021-02-032-6/+3
| | | | | * 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 Byrne2021-02-032-8/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Fortner2021-01-301-1/+29
| | | | 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 Robinson2021-01-301-1/+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 Byrne2021-01-2983-412/+412
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 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 Byrne2021-01-271-1/+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 * 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
* 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 Fortner2021-01-2212-36/+142
| | | | | | | | | | | | (#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 Fortner2021-01-202-7/+31
| | | | | | | | | * 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.
* 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 Robinson2021-01-144-16/+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 Byrne2021-01-131-2/+2
| | | | | | | | | | | | | * 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 Robinson2021-01-134-280/+19
| | | | | | | | | | * 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
* Reformat source (#244)Quincey Koziol2021-01-0719-785/+740
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* Fix error is H5Mclose_async. (#240)Neil Fortner2021-01-052-3/+3
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* Switch bool/true/false to hbool_t/TRUE/FALSE in a few places (#229)Dana Robinson2020-12-241-1/+1
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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)bmribler2020-12-234-8/+749
| | | | | | | * 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>
* Transferred RM blocks in H5D and H5G to develop (#213)bmribler2020-12-214-18/+1598
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* Avoid aligned access for references by decoding into temporary buffer and ↵Quincey Koziol2020-12-192-7/+14
| | | | 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>
* Fix datatype lookup in named datatype flush/refresh code and detect more ↵hdf5-1_13_0-rc3Quincey Koziol2020-12-171-2/+2
| | | | | | | | | | | 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
* 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.
* Enable H5Fopen to probe list of available VOL connectors when opening a (#182)jhendersonHDF2020-12-1610-49/+479
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* Transfer doxygen H5O RM blocks from doxygen branch to develop. (#174)vchoi-hdfgroup2020-12-162-0/+2502
| | | 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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