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* Brings hash table IDs feature from develop/1.12 (#768)Dana Robinson2021-06-181-138/+242
| | | | | | | | | | | | | | | | | | | | | | | | | * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge issue 537 v110 (#545)Larry Knox2021-04-061-1/+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. * 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> * More warning fixes (#400) * Fixed -Wunused-local-typedef warning * Fixed -Wformat warnings In one case also removed a `z` character. There was a `z%d` that I think was supposed to be `%zd` * Fixed -Wshorten-64-to-32 warnings * Fixed -Wself-assign warnings * Fixed -Wreserved-id-macro warnings * Commit format changes from clang-format, clang version 10.0.1. * Fixed -Wself-assign warnings * Fixed -Wunused-local-typedef warning * Fixed -Wformat warnings In two cases also removed a `z` character. There was a `z%d` that was supposed to be `%zd`. * Fixed -Wshorten-64-to-32 warnings * Fixed -Wreserved-id-macro warnings * Fixed -Wself-assign warnings * Format source. * Remove blank lines to pass format check. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Changes found during merge to 1.12 (#414) * 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 * File locks now work on Windows (#480) * File locks now work on Windows Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial). * Committing clang-format changes * Committing clang-format changes * Fixes commenting in h5repack * Reworks H5Fis_accessible() H5Fis_accessible() created a new file handle and attempted to read through it, which will fail when a file has been opened with an exclusive lock on operating systems that have mandatory locks. This change uses the same scheme we use in H5Fopen() to check if the file is already open and only tries to read the file signature if the file has not already been opened. Also adds a test for this behavior. * Committing clang-format changes * Trivial change to force github to run actions Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * small edits (#481) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Adds an implementation for nanosleep on Windows (#483) * Adds an implementation for nanosleep on Windows * Committing clang-format changes * Fix insane formatter issue Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492) * Committing clang-format changes * Updates H5SYS_GOTO_ERROR to emit Win32's GetLastError() * Committing clang-format changes * Format source changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Updates that allow accum SWMR tests to work on Windows (#493) * Committing clang-format changes * Updates the accum test to work on Windows Uses CreateProcess() on Windows * Source formatting * Fix for Unix child result * Fixes process return code bug on Windows Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Disable long double tests and remove CMake flag groups (#494) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Misc warning fixes (#495) * Committing clang-format changes * Misc warning fixes from Visual Studio * Committing clang-format changes * Fixes warnings in swmr.c test * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Correct merge errors. * Committing clang-format changes Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> 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: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* 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 Byrne2020-10-011-176/+189
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* Some normalization with develop in testhdf5 files.Dana Robinson2020-05-281-10/+36
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* Cleanup when merging to other branchesAllen Byrne2019-07-301-3/+6
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-138/+137
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * More includes cleanupAllen Byrne2018-02-141-137/+136
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* Added CHECK_PTR_EQ macro to testhdf5 to quiet cast warnings on Windows.Dana Robinson2017-11-271-170/+172
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* Fixed misc Warnings flagged by VS2017.Dana Robinson2017-11-271-9/+9
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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.
* [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-r27415] Fix potential error with H5I_clear_type which could occur when ↵Neil Fortner2015-07-201-0/+199
| | | | | | | | | | | a callback closed a different ID in the same type. Added a new skiplist routine, H5SL_try_free_safe, which iterates over items, freeing some of them, and which intercepts and defers attempts to remove from the list outside of the main iteration. Changed H5I_clear_type to use this function. Tested: jam, koala, ostrich (h5committest); ummon
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-1/+1
| | | | | | | | * 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-r25496] Description:Quincey Koziol2014-07-301-7/+7
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r24376] Updated all code to use HDmalloc, HDcalloc, and HDfree.Dana Robinson2013-10-311-7/+7
| | | | | | | | | | | | | 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-r22582] Description:Quincey Koziol2012-07-161-9/+9
| | | | | | | | | Refactor ID class registration to be more like how other "class"s in the library are registered, and clean up compiler warnings. Tested on: Mac OSX/64 10.7.4 (amazon) w/debug (Too minor to require h5comittest)
* [svn-r19398] Descriptino:Quincey Koziol2010-09-161-2/+2
| | | | | | | | | | | | | | | | | | | | | | | Clean up the internal usage H5I_dec_ref() to eliminate the sequence of flags that has been creeping in. 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, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.4 (amazon) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
* [svn-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-091-2/+2
| | | | | | | couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. Tested with h5committest - jam, heiwa, amani.
* [svn-r16653] Bug fix #1503 - H5Iget_type failed unexpected when an invalid ↵Raymond Lu2009-04-011-1/+42
| | | | | | | | | ID was passed in. I put some argument check in the internal function H5I_find_id and took out the assertion check. I also removed the argument check in H5Iis_valid because it's in H5I_find_id now. Tested on jam - simple change. Tested v1.8 already.
* [svn-r16036] Purpose: add H5Iis_valid functionNeil Fortner2008-11-051-4/+82
| | | | | | | | | Description: H5Iis_valid function added. This function checks if the id is valid (i.e. it is currently registered and visible to the application), and returns TRUE if it is valid, or FALSE otherwise. It should never return an error. Tested: kagiso, linew, smirom (h5committest)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r12829] Description:Quincey Koziol2006-10-301-9/+9
| | | | | | | | Clean up more compiler warnings, esp. on Linux/64 platform. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r11838] Purpose:Quincey Koziol2005-12-261-1/+1
| | | | | | | | | | | | | | | | Bug fix Description: Retrieving an object's name could fail (in various ways) under certain circumstances (mostly having to do with mounted files). Solution: Re-write & simplify "get object name" code to fix error in a better way than adding yet another hack to the previous pile of hacks... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-2/+2
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10944] Purpose:James Laird2005-06-171-42/+77
| | | | | | | | | | | | | | | Bug fix Description: tid.c is a test for user-defined hid_t's. It should be part of the testhdf5 tests, but was not being run. It also had a couple of minor bugs. Solution: Added id test to testhdf5 and fixed bugs. Platforms tested: mir, sleipnir, modi4
* [svn-r10217] Purpose:James Laird2005-03-151-2/+2
| | | | | | | | | | | Bug fix Description: Fix a typo in my last checkin. Should make some compilers happier about "operand types." Platforms tested: sleipnir, heping, kelgia
* [svn-r10216] James Laird2005-03-141-1/+26
| | | | | | | | | | | | | | | | Purpose: Bug fix Description: Calling H5Iobject_verify on an invalid type of ID (e.g., H5I_BADID) triggers an assert. Solution: Test for this condition and return an error instead of an assert. Added tests for this case. Platforms tested: sleipnir (minor change)
* [svn-r8892] Purpose:Quincey Koziol2004-07-161-7/+5
| | | | | | | | | | | | | | Code cleanup Description: Clean up a bunch of warnings and bring new code better inline with current library coding practice. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest Misc. update:
* [svn-r8844] Purpose:Quincey Koziol2004-07-091-0/+1
| | | | | | | | | | | | | | | | | | Bug fix Description: The "shared" raw B-tree node can get freed before all the B-tree nodes had been flushed out to disk and released by the cache. Solution: Implement a simple reference counting wrapper for objects in the library and use it to hold the shared raw B-tree nodes so they aren't freed before all references to them in memory are released. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) IRIX64 6.5 (modei4)
* [svn-r8779] Nat Furrer2004-07-011-1/+1
| | | | | | | | | | | | | | Purpose: Fixed problem in tid.c that broke daily tests. Description: Solution: Platforms tested: Sleipnir Misc. update:
* [svn-r8772] Nat Furrer2004-06-301-1/+2
| | | | | | | | | | | | | | | Purpose: Needed to change the type of a variable in tid.c from int to hsize_t to accomodate the change in H5Inmembers. Description: I lied... this is the last commit. Really, it is. Solution: Platforms tested: Misc. update:
* [svn-r8766] Nat Furrer2004-06-301-13/+33
| | | | | | | | | | | | | | | | | | | Purpose: Small H5I API changes. Description: Changed public version of H5Inmembers to return the number of IDs in a type by reference. This allows the user to differentiate between the case when H5Inmembers has an error and when the ID type is just empty. Added a new API function, H5Itype_exists, which allows the user to find out whether an ID type exists or not, without throwing an error. Solution: Platforms tested: Copper Misc. update:
* [svn-r8707] Changed the way HDF5 handles hid_t's and added API functions to ↵James Laird2004-06-181-0/+344
allow users to register IDs and ID types at runtime.