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* Merge of mostly clang-tidy changes from 1.12 (#965)Allen Byrne2021-08-251-3/+3
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* Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)Allen Byrne2021-04-301-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge issue 487 v110 (#533)Larry Knox2021-04-011-5/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up a couple of MSVC warnings in testhdf5 (#475) * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix typos and grammar errors. (#476) * Suppresses the tcheck_version test's abort dialog on Windows (#477) * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* Hdf5 merge issue 458 v110 (#465)Larry Knox2021-03-121-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * 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. * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * 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> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * 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> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * 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> * Fix clang-tidy suspicious string compare in H5A.c missed in merge. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Hdf5 merge issue 435 v110 (#462)Larry Knox2021-03-101-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * 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. * Fixed clang-tidy readability-misleading-indentation warnings (#427) * Fixed clang-tidy readability-misleading-indentation warnings * Reformatted src/H5Zscaleoffset.c with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Fixed clang-tidy readability-redundant-control-flow warnings (#428) * 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> * Removed bad function pointer casts (#434) * Removed bad function pointer casts In one case fixed the actual function signature to be correct. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * fix block coordinate printing example (#437) Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Mike Smith <grimbough@gmail.com>
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * 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. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Source formattedAllen Byrne2020-10-011-972/+914
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* Minor normalizations with developDana Robinson2020-08-161-1/+1
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* Normalization and warning fixes from developDana Robinson2020-07-311-2/+1
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* Merge of --Wc++-compat changes from developDana Robinson2020-01-091-1/+1
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* Merge HD prefix and whitespace changes from developAllen Byrne2019-08-181-894/+542
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* Needs to sync with lib version and Sencode.M. Scot Breitenfeld2018-03-071-5/+35
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* Change copyright headers to replace url referring to file to be removedlrknox2017-04-141-6/+4
| | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771)Vailin Choi2017-04-121-18/+0
| | | | | 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in. See pull request #396 review comments.
* Re-enabled fixed array index testing in the test_random_rank4_vl() testDana Robinson2017-04-051-8/+13
| | | | | in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-3/+15
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* [svn-r30189] Description:Quincey Koziol2016-07-181-4/+2
| | | | | | | | | Clean up more warnings: drop the warning count from ~1310 down to ~940, with only 31 types of warnings in 148 files (down from 38 types in 167 files). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r29722] Description:Quincey Koziol2016-04-171-18/+380
| | | | | | | | Bring over more dataset tests from the revise_chunks branch. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29607] Description:Quincey Koziol2016-04-021-13/+41
| | | | | | | | | Bring "don't filter partial edge chunks" capability from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/debug, production & parallel (h5committest forthcoming)
* [svn-r29545] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-269/+97
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-10-201-2/+2
| | | | | | | | | | | | | | available Fix tests accordingly and fix misuse of hbool_t in various places Fix initialization of H5Pgcpl/ocpl structs in property decoding routines Tested on: Linux/32 (jam) Linux/64 (platypus) Linux/PPC64 (ostrich) MacOSX/64 10.11
* [svn-r27548] Revert r27545Jerome Soumagne2015-08-211-2/+2
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* [svn-r27545] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-08-211-2/+2
| | | | | | available Fix tests accordingly
* [svn-r26333] Eliminates gcc warnings due to -Wunsuffixed-float-constants.Dana Robinson2015-03-011-2/+2
| | | | | | | | | | | | - Adds 'F' suffixes for most float constants. - A few constants MUST be of type double. These now receive the long double L suffix and are then cast to double. I do this via a new H5_DOUBLE() macro which was added to H5private.h. Fixes: HDFFV-9148 Tested on: h5committest
* [svn-r20529] Purpose: Add testing for bug 1864Neil Fortner2011-04-151-0/+3
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r19352] Description:Quincey Koziol2010-09-041-21/+10
| | | | | | | | Align w/changes on revise_chunks branch Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19297] Description:Quincey Koziol2010-08-251-2/+2
| | | | | | | | | | Whack a few more memory errors exposed by valgrind. Make the debugging dump output a little bit prettier. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug (h5committest forthcoming)
* [svn-r18894] Purpose: Improve allocation performance of filtered datasets ↵Neil Fortner2010-05-251-4/+3
| | | | | | | | | | | | | with non-default VL fill values. Description: Previously, H5D_chunk_allocate would, if a dataset were filtered and had a non-default VL fill value, allocate a new buffer for every chunk. Changed H5D_chunk_allocate to reuse the existing buffer if possible. Also other miscellaneous cleanup. Tested: jam, linew, amani (h5committest)
* [svn-r18868] Purpose: Fix bug in dataset shrinking algorithmNeil Fortner2010-05-201-48/+90
| | | | | | | | | | | | | | | | Description: Previously, it was possible for a chunk to be flushed due to chunk operations in the callback from H5B_iterate in H5D_chunk_prune_by_extent. Because flushing the chunk can force it to be reallocated if it is filtered, this can change the contents of the chunk b-tree in the middle of H5B_iterate. Because H5B_iterate uses a locally cached copy of the b-tree, this causes subsequent operations to be passed incorrect data. Rewrote H5D_chunk_prune_by_extent to avoid H5B_iterate entirely. Also fixed a bug in the dataset expand algorithm that could cause extra chunks to be created. Tested: jam, linew, smirom (h5committest)
* [svn-r18445] Purpose: Fix bug 1637Neil Fortner2010-03-241-0/+48
| | | | | | | | | | Description: Modified algorithm for extending a dataset with early allocation so it only deals with the new chunks. Formerly, it would loop over all chunks, checking to see if each existed in cache and on disk, causing major performance issues with large numbers of chunks. Tested: jam, linew, amani (h5committest)
* [svn-r18262] Purpose: Fix bug in b-tree codeNeil Fortner2010-02-161-438/+544
| | | | | | | | | | | | Description: In certain cases, removal of an object in a v1 b-tree would cause the leftmost key in the right neighbor to be overwritten. While this did not pose a problem for group b-trees, with chunked datasets it would overwrite the offset value of the neighbor's leftmost child, causing corruption. Reworked the code to differentiate between b-trees whose children are fundamentally associated with their left key and those who are associated with their right key. Tested: jam, linew, amani (h5committest)
* [svn-r18197] Description:Quincey Koziol2010-01-301-633/+633
| | | | | | | | | Trim trailing whitespace from source code files with this command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r16523] Purpose: Fix bugs related to H5Dset_extent and fill valuesNeil Fortner2009-02-271-19/+48
| | | | | | | | | Description: In some situations it was possible for the fill value to not be written to parts of a chunked dataset, particularly when extending and/or shrinking. Prior to the fix for the chunk cache (1015) these bugs would have been exceedingly rare. Tested: jam, smirom, linew (h5committest)
* [svn-r16511] bug fix: TESTING2 macro introduced recently for the test suite ↵Pedro Vicente Nunes2009-02-231-7/+7
| | | | | | (it adds an extra space at the beginning of output, for indentation) was already available for HL and caused compilation problems on AIX. Replaced the name with TESTING_2 tested: h5committest
* [svn-r16431] Uncomment a h5cleanup() call previously accidently left commented Pedro Vicente Nunes2009-02-051-1/+1
| | | | Tested: linux
* [svn-r16423] bug fix: a open call was not made the expected FAPLPedro Vicente Nunes2009-02-041-9/+11
| | | | tested: windows, linux (split, sec2)
* [svn-r16419] #1449 Change set_extent test to use standard standalone test ↵Pedro Vicente Nunes2009-02-041-28/+40
| | | | | | | | | | | | | | | | | | framework Call h5_fixname (with an array of test filenames) for generating the filename to create and then call h5_cleanup() when the tests pass, to delete the files created and close the FAPL from h5_fileaccess(). Defined a macro #define TESTING2(WHAT) {printf(" Testing %-62s",WHAT); fflush(stdout);} Similar to TESTING, except that it has a initial indentation space. The effect is for nested loop tests Testing with old file format: Testing with fill value, no compression PASSED tested: windows, linux
* [svn-r16417] Description:Quincey Koziol2009-02-041-83/+69
| | | | | | | | | | | Bring r16416 from revise_chunks branch to trunk: Bring closer to standard standalone test format, add checks for using the latest file format and close dataset ID leaked. Tested on: FreeBSD/32 6.3 (duty) (too minor to require h5committest)
* [svn-r16405] #1449 Change set_extent test to use standard standalone test ↵Pedro Vicente Nunes2009-02-031-61/+66
| | | | | | | | | | | | | | | | framework use a fapl obtained by h5_fileaccess to the call of H5Fcreate and redo the test calls with h5_reset(); fapl = h5_fileaccess(); nerrors += do_ranks( fapl ) < 0 ? 1 : 0; nerrors += test_external( fapl ) < 0 ? 1 : 0; nerrors += do_layouts( fapl ) < 0 ? 1 : 0; tested: windows, linux
* [svn-r16372] Description:Quincey Koziol2009-01-291-6/+13
| | | | | | | | Clean up files produced from set_extent testing. Tested on: FreeBSD/32 6.3 (duty) (too minor to require h5committest)
* [svn-r16273] Added a test for shrinking to 0 dimemsionsPedro Vicente Nunes2009-01-081-226/+351
| | | | Tested: windows, linux
* [svn-r16229] merge 16228Pedro Vicente Nunes2008-12-291-20/+20
| | | | | cleaned more linux warnings tested: linux
* [svn-r16227] cleaned some linux warningsPedro Vicente Nunes2008-12-291-3/+1
| | | | tested: linux
* [svn-r16225] removed some debug messagesPedro Vicente Nunes2008-12-291-18/+0
| | | | tested: windows, linux
* [svn-r16223] Modified H5Dset_extent so that it fails when called for compact ↵Pedro Vicente Nunes2008-12-291-159/+1693
| | | | | | | | datasets and contiguous with no external storage new test program: It adds tests for several ranks, use of fill value or not, compression, different fill value allocation times, use of different storage layouts, and external files tested: windows, linux
* [svn-r16158] Test the non deletion of a chunk for the case chunk_offset == ↵Pedro Vicente Nunes2008-12-041-2/+240
| | | | | | dimension by shrinking first, then expanding to original size and compare buffers of initialized values Tested: windows, linux
* [svn-r16156] close & re-open the file for the test of non-default B-tree ↵Pedro Vicente Nunes2008-12-041-0/+29
| | | | | | | internal 'K' value (There was a bug where a non-default B-tree internal 'K' value was not being stored in the file) this is a rewrite of the old set_extent.c test program tested: windows, linux
* [svn-r16152] added comments and removed unnecessary codePedro Vicente Nunes2008-12-021-16/+63
| | | | tested: windows, linux
* [svn-r16148] reorganized the set_extent test to be more modularPedro Vicente Nunes2008-12-021-83/+116
| | | | tested: windows, linux
* [svn-r16143] add a test for recent fixes of H5Dset_extentPedro Vicente Nunes2008-12-011-625/+541
| | | | tested: windows, linux
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