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* Develop HDFFV-11310 (#1811)Allen Byrne2022-07-111-0/+82
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework java vl check in read/write. Handle old refs in h5dump * Committing clang-format changes * Java changes allow default VL reads * Fix JNI utility for old refs * HDFFV-11310 - implement vlen read/write for atomic types. * format check fix * Mostly format fixes * More format issues * Two format changes * Use JNI names for sizeof * format change * fix size typo * Change to older method to initialize list * remove unused var * format fix * switch writeVL functions to use datatype instead of java type * Add VL option to generic read/write check * Correct function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Add release note and format changes * Another format update * Fix unreleased allocations * Fix format * format correction Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Misc clang warning fixes (#1869)Dana Robinson2022-07-111-2/+26
| | | | | | | | | | | | | | | | | * Minor clang warning fixes in src and test * Fixes clang warnings in high-level library * clang format-nonliteral warning fixes * Committing clang-format changes * Fixed int -> float clang cast warnings in h5diff * Quiets some warnings in flex/bison generated code * Suppress overlong string warning for libinfo on clang Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Various warning fixes (#1812)Sean McBride2022-06-221-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed -Wreserved-id-macro warnings from header include guards * Removed all __int64 and LL suffix stuff now that C99 is minimum requirement * Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings Double underscore is reserved in C++ and this public header should be C++ compatible. * Never define __STDC_FORMAT_MACROS anymore Defining it causes a -Wreserved-id-macro. Happily, according to the C++11 standard: "The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++." https://cplusplus.github.io/LWG/issue984 So looks like it's not necessary to define it with reasonably new toolchains. * Fixed some -Wunused-macros warnings, removed dead code * Fixed all -Wdouble-promotion warnings in C++ files * Fixed remaining -Wsuggest-destructor-override warnings * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for format string warnings raised by -Wformat=2/-Wformat-security (#1489)Dana Robinson2022-03-111-1/+1
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* Removes remaining register keywords (#1481)Dana Robinson2022-03-101-4/+4
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* Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix ↵David Young2022-02-211-12/+11
| | | | | | | | | | | | | | | | issues (#1423) * Correct some conversion specifications. * Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few instances where PRIdHSIZE was appropriate. Remove a couple of casts and use correct format strings, instead. * Copy values from a possibly unaligned buffer to aligned local variables instead of casting and dereferencing pointers into the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-081-2/+0
| | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix several warnings (#720)jhendersonHDF2021-09-141-1/+2
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* Cleanup tools debug build warnings (#627)Allen Byrne2021-05-051-7/+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 * 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 * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update clang config (#473)Quincey Koziol2021-03-171-2/+8
| | | | | | | * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)Sean McBride2021-03-101-1/+1
| | | | | | | | | * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code 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 McBride2021-03-091-1/+1
| | | | | | | | | | | | | * 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>
* #386 copyright corrections for java folder (#389)Allen Byrne2021-02-261-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 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
* Update license url part2 (#333)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - files not in src or test.
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-291-2/+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 * 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
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-2/+2
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Clang-format of source filesAllen Byrne2020-09-301-516/+508
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* Warnings reduction in toolsAllen Byrne2020-07-301-9/+7
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* Tools refactorAllen Byrne2020-07-151-52/+22
| | | | | | Move error_stack setup to tools library Add structure for h5dump properties Eliminate duplicated h5diff functions Use properties structure in place of argument lists.
* Misc changes for h5dump VOL changes.Dana Robinson2020-03-301-7/+7
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* Change tools debug macros to not use error stackAllen Byrne2020-01-231-6/+6
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-19/+27
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* Clean up tools warnings introduced by H5TOOLS_ERR_INIT macroJordan Henderson2019-12-311-15/+4
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* Refactor tools library error handling macrosJordan Henderson2019-12-281-39/+40
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* Fix compile statement orderAllen Byrne2019-12-201-1/+2
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* HDFFV-10976,-10980 Init obj_type before calling H5Rget_obj_type3Allen Byrne2019-12-201-1/+1
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* Add unknown define for h5dump ref objectsAllen Byrne2019-12-201-1/+2
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* Fix compile errors - mostly in jniAllen Byrne2019-12-061-20/+21
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* HDFFV-10876 Update dump to match DDL specAllen Byrne2019-12-051-1/+2
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* Update h5ls help and rework dump_mem routines for attrsAllen Byrne2019-12-041-2/+2
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* HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-071-80/+187
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* More whitespace changesAllen Byrne2019-10-031-46/+5
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+1
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-3/+3
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* TRILAB-81 check for func success before using valueAllen Byrne2018-10-191-27/+31
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* Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-1/+1
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* Fix for HDFFV-10180 Performance issues with H5Oget_info.Vailin Choi2018-04-241-1/+1
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* HDFFV-10297 Cleanup, Initialize variablesAllen Byrne2017-10-231-3/+5
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* Stripped C standard library headers (and a couple of macros)Dana Robinson2017-07-171-8/+0
| | | | | from the tools code. This is all handled in H5private.h, which should be included in all tools source files.
* Minor warning fixes in the tools.Dana Robinson2017-05-251-3/+4
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* HDFFV-10186 more whitespace formattingAllen Byrne2017-05-101-250/+204
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Bring SWMR-related tools changes from revise_chunks to develop.Quincey Koziol2016-12-111-1/+63
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* Merge pull request #48 in HDFFV/hdf5 from ↵Dana Robinson2016-12-071-1/+1
|\ | | | | | | | | | | | | | | | | HDFFV-9407-h5dump-fails-to-print-full-precision to develop Merged Kimmy's fix (still needs a test). * commit 'f76c3b56e1ccf81b16225fa6935adb45ac6d2f38': fix the issue of h5dump fails to print full precision
| * fix the issue of h5dump fails to print full precisionkmu2016-09-271-1/+1
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* | Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-0/+1
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* [svn-r30113] Description:Quincey Koziol2016-06-281-121/+119
| | | | | | | | Clean up warnings (from 2774 -> 1560, with my standard debug build) Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29534] Normalization w/ revise_chunks in preparation for big merge.Dana Robinson2016-03-231-0/+3
| | | | | | | | | tools directory Also fixes a minor Java test output error. Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial w/ Java, Fortran, & C++
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