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* Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)Allen Byrne2021-04-301-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2021-04-011-44/+176
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2021-03-121-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2021-03-101-3/+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 Byrne2020-10-011-1105/+1055
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* Normalization and warning fixes from developDana Robinson2020-07-311-3/+134
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* Merge HD prefix and whitespace changes from developAllen Byrne2019-08-181-17/+17
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* Cleanup when merging to other branchesAllen Byrne2019-07-301-16/+14
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* Update system commands with HD prefix and whitespaceAllen Byrne2018-08-281-1/+1
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* Fix test_misc33() in test/tmisc.cVailin Choi2018-07-261-1/+1
| | | | Open the test file read-only so that it can be accessed for testing.
* Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-8/+8
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* Fix for HDFFV-10180 Performance issues with H5Oget_info.Vailin Choi2018-04-241-12/+12
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* More includes cleanupAllen Byrne2018-02-141-52/+51
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* Fixed misc Warnings flagged by VS2017.Dana Robinson2017-11-271-18/+18
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* Removed asserts from H5MM calls that conflict with stated behaviorDana Robinson2017-11-091-1/+61
| | | | and added a test to ensure that this doesn't happen in the future.
* Modifications based on comments from pull request reviewVailin Choi2017-08-231-1/+1
| | | | | (1) Remove unnecessary asserts (2) Add code to insert bad offset values to the test file in gen_bad_offset.c
* Fix for HDFFV-10216 segfault in H5G_node_cmp3 with corrupt h5 fileVailin Choi2017-08-221-0/+55
| | | | | Fix H5HL_offset_into() to return error when offset exceeds heap data block size. Also fix other places that call this routine to detect error return.
* * Yanked the smoke check that was recently introduced to testDana Robinson2017-07-051-142/+140
| | | | | | | | | | | the unused H5I_REFERENCE ID type in test_misc19(). This fails when running testhdf5 and skipping the reference test since the H5R package won't be initialized. H5I_REFERENCE will be going away soon and the ID type is unused so there's really no point to doing anything to test it. * Cleaned up test_misc13(), which is a basic test of userblock functionality, to not emit warnings due to the large global array.
* * Reverted removal of H5I_REFERENCE to avoid breaking binaryDana Robinson2017-07-031-0/+29
| | | | | | compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c.
* Added missing free() call to test_misc19().Dana Robinson2017-07-011-0/+2
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* Purged the unused H5I_REFERENCE from the library.Dana Robinson2017-07-011-2/+0
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* Added a test for VFD IDs to testhdf5.Dana Robinson2017-07-011-14/+55
| | | | | | | This required adding some code to generate a fake VFD class to pass to H5FDregister(). Also, a bunch of whitespace and comment tidying.
* 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.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-7/+9
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* Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-5/+5
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* [svn-r28761] Description:Quincey Koziol2016-01-011-3/+13
| | | | | | | | | | | | Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also make H5Ocopy use a private version of H5Lexists, which doesn't internally throw (and suppress) errors when an object (or the path to it) isn't found in the destination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-10-201-1/+1
| | | | | | | | | | | | | | 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-r27773] Description:Quincey Koziol2015-09-141-8/+8
| | | | | | | Correct typos in fix. Tested on: Linux 2.6/32 (jam) w/gcc
* [svn-r27772] Description:Quincey Koziol2015-09-141-17/+30
| | | | | | | | Clean up warnings, address HDFFV-9524 Tested on: MacOSX/64 10.10.5 (amazon) w/serial (Too minor to require h5committest)
* [svn-r27768] Description:Quincey Koziol2015-09-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r27626] Various minor warning fixes before major SWMR and VDS merges.Dana Robinson2015-08-311-21/+21
| | | | | | | | | | | gcc 4.9.2 was used to create the warning list - implicit casts - shadowed variables - various enum issues - other minor fixes (comments, unused macros, etc.) Tested on: h5committest
* [svn-r27548] Revert r27545Jerome Soumagne2015-08-211-1/+1
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* [svn-r27545] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-08-211-1/+1
| | | | | | available Fix tests accordingly
* [svn-r27204] Description:Quincey Koziol2015-06-151-8/+8
| | | | | | | | | Clean up compiler warnings before merging in v3 metadata cache changes from branch. Tested on: MacOSX/64 10.10.3 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-2/+2
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r26514] Fix for HDFFV-9173:Vailin Choi2015-03-201-0/+12
| | | | | | H5Pset_istore_k() will validate the "ik" value to not exceed the max v1 btree entries (2 bytes) The same check for H5Pset_sym_k() "ik" value. h5committested.
* [svn-r26392] Reinstates r26327-8, which had been reverted due to failures onDana Robinson2015-03-091-0/+68
| | | | | | | | | | | | | | Solaris and OS X. Added public API functions that expose the C library's memory allocator for use in filter functions that need to allocate or resize buffers. Intended for use with filter plugins, particularly on Windows, where C runtime (CRT) issues can cause problems. Fixes: HDFFV-9100 Tested on: h5committest + OS X (quail) + Solaris (emu)
* [svn-r26333] Eliminates gcc warnings due to -Wunsuffixed-float-constants.Dana Robinson2015-03-011-12/+12
| | | | | | | | | | | | - 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-r26331] Revert checking r 26327&8, which added new code and test that ↵Larry Knox2015-02-281-68/+0
| | | | | | fails on solaris and macs. Tested h5committest + emu and quail.
* [svn-r26328] Fixed a typo in tmisc.c.Dana Robinson2015-02-271-1/+1
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* [svn-r26327] Added public API functions that expose the C library's memory ↵Dana Robinson2015-02-271-0/+68
| | | | | | | | | | | | allocator for use in filter functions that need to allocate or resize buffers. Intended for use with filter plugins, particularly on Windows, where C runtime (CRT) issues can cause problems. Fixes: HDFFV-9100 tested on: jam (minor, localized change)
* [svn-r24998] Description:Quincey Koziol2014-04-091-0/+110
| | | | | | | | Check in Neil's changes for correctly handling case where library is reinitialized through a deprecated routine. Tested on: Linux 2.4.x/32 (jam)
* [svn-r24376] Updated all code to use HDmalloc, HDcalloc, and HDfree.Dana Robinson2013-10-311-1/+1
| | | | | | | | | | | | | Prep work for adding a memory free function, part of HDFFV-8551. Tested on: 32-bit LE linux (jam) * with C++, Fortran * with thread safety on These are minor changes (almost entirely renaming foo functions to HDfoo) that don't change functionality. This should not require a full commit test.
* [svn-r22287] Description:Quincey Koziol2012-04-161-42/+42
| | | | | | | | Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r22024] Add HD prefix to tools library based tests. Cleaned ↵Allen Byrne2012-03-051-41/+37
| | | | | | allocation/free in tests. Tested: local linux/ changes h5committetest against 1.8 version
* [svn-r21561] Description:Quincey Koziol2011-10-141-3/+91
| | | | | | | | | | | | Correct error in loading local heap prefix & data block from the file. Sometimes the local heap's prefix could be loaded before the data block (e.g. using H5Oget_info), but then when the data block was loaded later, the free list information would get lost, causing the heap's size to grow larger than necessary. This is Jira bug #HDFFV-7767 Tested on: Mac OS X/32 10.7.2 (amazon) w/debug (h5committest coming up)
* [svn-r18650] Description:Quincey Koziol2010-04-271-1/+1
| | | | | | | | | | | | | | | | | | | Bring back various minor tweaks & cleanups from the revise_chunks branch. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r18419] Description:Quincey Koziol2010-03-181-0/+1
| | | | | | | | | Clean up srcdir querying code more, extracting it into single header file, to avoid compiler warnings. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & prod Linux/32 2.6 (jam)
* [svn-r18413] Description:Quincey Koziol2010-03-171-36/+4
| | | | | | | | | | | | | | Unify srcdir handling for test executables and allow them to use the srcdir setting from configure time without requiring the 'srcdir' environment variable be set (although you still can, to override the built in setting). Attempted to get this right for Windows builds also. Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so that the test/testcheck_version.sh script works correctly. Tested on: Linux/32 2.6 (jam) Mac OS X/32 10.6.2 (amazon)
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