| Commit message (Collapse) | Author | Age | Files | Lines |
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* 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>
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* Committing clang-format changes
* Brings over hash table code from Bitbucket
* Can be switched between skip list and hash table implementation
with H5_USE_ID_HASH_TABLE #define
* Not yet updated to use iterate-safe delete
* Fixes a warning and changes where the problematic test is
commented out.
* Adds mark-and-sweep flags and members
* Final fixes for hash table ID code
* Removes skip list ID code
* Committing clang-format changes
* Formatted source
* Adds a comment about the mark-and-sweep scheme.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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>
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* 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>
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* 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.
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* Add H5Fwait, H5Dwait, and other changes for async vol connector
* Revert temporary testing changes
* Add H5Fwait to header file
* Add H5VLreset_lib_state() routine.
* Correct VOL wrap context when retrieving library state for file open & create.
* Manage the API context's VOL connector state as part of the library state.
* Set the 'VOL connector property valid' flag when restoring the library state.
* Don't push new API context on stack when retrieving "current" one.
* Check for NULL VOL wrap context before decrementing refcount on it, when
freeing the API context state.
* Manage recount of underlying connector for VOL wrap context.
* Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and
release the global lock on the HDF5 library.
* Update library with new functions related to library global lock
* Add asynchronous token API
* Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the
threadsafety (H5TS*) routines.
* Sync w/develop
* Initial event set code framework.
* Elaborate on the H5ES routines, starting to add API routines.
Update the "close ID" callbacks to allow asynchronous request tokens to be
passed in from an asynchronous close API call.
Refactor current asynchronous API routines (H5Fopen/H5Fclose and
H5Dread/H5Dread) to use event sets instead of directly working with request
tokens from the application.
Clean up a few other minor warnings & code style issues.
* Implement H5EScreate, H5ESget_count, and H5ESclose.
It should be possible to write a simple application that creates an event
set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and
H5Fclose_async, then calls H5ESclose (which waits for all async events to
complete).
* Add source file for event set test.
* Refactor sync & async API routines to call common routine.
Move dataset API read / write routines to src/H5D.c, along with all the other
API routines.
Progress on "fake" async VOL connector, for testing.
* Modify async implementation to wrap async requests in a H5VL_object_t
struct so the VOL layer can find the connector when accessing the
request at a later point.
* Free the requests is H5ESclose. Remove comments implying that request
wait, notify, and cancel callbacks should free the request.
* Fix bug in error handling in H5Fclose.
* Fix bugs in async file routines. Rename H5VL_create_object_generic to
H5VL_create_object.
* Add explicit async version of H5Fcreate.
* Add more _async routines
* Correct typo for return value from H5Awrite changes
* Add H5EStest and H5ESwait routines
* Updated with API tracing info
* Fix NULL pointer dereference in H5ES__wait
* Add H5is_library_terminating() routine, so that VOL connectors can detect
when the library is shutting down.
* Fix typo
* Remove event from event set's linked list
* Move block of code so that vol_obj is valid
* Avoid setting properties in the DXPL when reseting the library state (and in
the test code).
* Refactor argument tracing to implement new capability for tracing arguments
of non-API routines, with the H5ARG_TRACE macro. This macro is updated
automatically with the bin/trace script that runs as part of the autogen.sh
process. Major changes were in src/H5trace.c and bin/trace, with the other
changes being cleanups to the argument lists, to improve their presentation
in the tracing output.
Also - added the "managed string" routines, which can dynamically allocate
strings, appending printf-formatted output to the string efficiently.
* Release memory for managed strings
* Fix printf() formats.
* More printf() format fixes.
* Add H5Eappend_stack routine and regression tests
* Clean up a few missed merge conflicts and update the error stacks.
* Remove unnecessary fork() operations and ten second sleep().
* Restore commented out attribute out, to better enable tracking down the previous failure
* Allow multiple H5ARG_TRACE macros within a routine to be updated
* Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert.
* Merge "managed" string routines into "ref-counted" strings, and refactor code to use them.
* Add missing file.
* Add caller's name and arguments to event, for error reporting
* Refactor event set setup for "API common" internal routines
* Checkin async API routines for H5A* and H5G* modules as listed in ID-283.
Fix couple h5dump expected output files due to the changes.
* Add some of the error query routines needed for event sets.
* Refactor to make async setup / teardown and "common" routines cleaner
* (1) Add async APIs to H5L, H5F, and H5D modules
(2) Fix errors in previous checkins of async APIs in H5A and H5G modules
(3) h5dump expected output changes
* Enhance event info, for better error handling
* Change name of temporary vol_obj variable, to help reduce coding errors
* Fix oversight with vol_obj pointer
* Minor code cleanup
* Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state
* Run source formatter
* Change H5TSmutex lock and release to include a lock count
* Update error reporting ideas
* Minor updates to improve sanity checking for retrieving / restoring library state
* Updated with feedback from h5py team members
* Refactor internal event set list and event handling, add implementation for H5ESget_err_info
* Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines.
* Update API tracing for new H5VL_request_status_t typedef
* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure
* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation
* Remove 'canceled' event status from Java constants
* Be safer about releasing resources when inserting a newly opened/created object or file into an event set
* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".
* Remove H5ES_STATUS_CANCELED from Java wrappers also
* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.
* Corrections based on PR feedback.
* Further changes to make based on PR feedback.
* Fix missed merge marker, and reformatted line
* Clean up some warnings
* Correct level of indirection
* Relocate prototype (and doxygen info) for H5Aclose
* Change non-static function declarations to be static
* Ensure that H5TSpublic.h header gets installed (#129)
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c.
* Add H5Iregister_future routine and tests.
* Correct return value for H5Lexists_async
* Add H5_DLL macro to public H5ES API routines
* Update supported -> flags parameter for introspect_query callback
* Remove my email address. Update passthrough VOL connector ID.
* Fix comment for post_open_api_common
* Remove unused non-blocking VOL connector
* Minor cleanup in async branch in preparation for merge to develop
* Update CMake and the Autotools to use the new pass-through VOL ID
* Fix for SWMR daily test failures (#160)
The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.
* Added selective async APIs (#150)
* Added selective async APIs
Description:
Added the following APIs:
H5Ropen_attr_async
H5Ropen_object_async
H5Ropen_region_async
H5Mcreate_async
H5Mopen_async
H5Mput_async
H5Mget_async
H5Mclose_async
H5Tcommit_async
H5Topen_async
H5Tcopy_async
H5Tclose_async
- Updated an expected output file to include a new internal function
in the error stack for the failure case.
* Updated async APIs per reviews, including removing async version of
H5Tcopy.
* Removed statements that were added by mistake in the previous commit.
* Fix compile issues in H5M and warnings elsewhere
* Reformat code
* Brings VOL_LIST changes from develop. (#163)
Co-authored-by: Houjun Tang <htang4@lbl.gov>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
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operations (#135)
* Expand ID dec_ref and close callbacks to allow for asynchronous close operations.
* Fix typo
* Rename token -> request, remove programmer name
* H5E_ATOM to H5E_ID
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This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4.
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* Brings hash table ID code over from Bitbucket branch
* Includes reformatting via clang.
* Excludes uthash.h from reformatting.
* Still has the failing test issue in tid.c. This should only be a
problem if a custom ID type is used and its free function deletes
other IDs.
* Fixes munged H5_GCC_DIAG_ON/OFF macros in H5I.c
The H5_GCC_DIAG_ON/OFF macros used to turn off fallthrough warnings
in uthash.h (external code) were munged when formatting with clang
due to their lack of quotes.
e.g.;
H5_GCC_DIAG_OFF(implicit-fallthrough)
was munged to:
H5_GCC_DIAG_OFF(implicit - fallthrough)
which compiles, but is useless. So, with quotes, this is now:
H5_GCC_DIAG_OFF("implicit-fallthrough")
which survives reformatting with clang.
* Fixes issues with user callbacks in the ID hash tables
The skip lists (previously) used to handle IDs use a mark-and-sweep
scheme to deal with user-defined ID delete callbacks which themselves delete
other IDs in the list. The uthash hash table implementation used to manage
the IDs in this feature branch does not have this ability.
This commit restores the skip lists for non-library ID types in lieu of
significantly modifying the uthash code. The hash tables are used to
manage the library IDs as those do not delete other IDs when they are
closed.
* Adds uthash.h to MANIFEST
* Removes implicit-fallthrough diagnostic disable
Removing -Wimplicit-fallthrough=5 means that the uthash code
no longer raises warnings so the H5_GCC_DIAG_OFF/ON macros
that disabled those warnings have been removed from H5I.c.
* Adds a test to ensure you can delete IDs in the H5Iiterate() callback
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level and fixing some code.' (commit 5c911d8baf3)"
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Description
Moved the new tests to a more appropriate test function.
Platforms tested:
Linux/64 (jelly)
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Description:
- Added parameter validation (HDFFV-10210)
- Added detection of division by zero (HDFFV-10587 - CVE-2018-17438)
- Fixed typos in various tests
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
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merge_func_enter_vol
Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
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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.
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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
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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
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* 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.
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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)
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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.
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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)
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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
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couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure.
Tested with h5committest - jam, heiwa, amani.
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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.
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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)
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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.
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Clean up more compiler warnings, esp. on Linux/64 platform.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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
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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.... :-)
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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
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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
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Bug fix
Description:
Fix a typo in my last checkin. Should make some compilers happier
about "operand types."
Platforms tested:
sleipnir, heping, kelgia
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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)
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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:
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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)
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Purpose:
Fixed problem in tid.c that broke daily tests.
Description:
Solution:
Platforms tested:
Sleipnir
Misc. update:
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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:
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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:
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allow users to register IDs and ID types at runtime.
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