| Commit message (Collapse) | Author | Age | Files | Lines |
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* Includes hdf5dev.h in hdf5.h
* Removes hdf5dev.h
* Restores H5PLextern.h as an independent header
* H5PLextern.h missed in the null VOL connector
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* 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
* Apply patch for dynamically registering optional VOL operations
* (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.
* Remove H5Dwait & H5Fwait (moved to the async connector). Added H5atclose
routine. Updated 'optional op' operations.
* Fix missed merge marker, and reformatted line
* Update API tracing infrastructure for H5atclose callback
* Clean up some warnings
* Normalize against develop branch
* Correct level of indirection
* Add doxygen info for H5is_library_terminating and regression tests for it and H5atclose
* Relocate prototype (and doxygen info) for H5Aclose
* Align w/changes on develop
* Move group package initialization code to H5Gint.c, and update tracing macros
* Change non-static function declarations to be static
* Correct GCC diagnostic macro
* Ensure that H5TSpublic.h header gets installed (#129)
* Finish moving API routines that invoke VOL framework to main source files.
* Fix position of H5Fmount and H5Funmount
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Add wrappers for dynamically registered optional operations
* Fix typo
* Update doxygen comment for H5atclose with additional detail.
* Add H5VL\*_vararg versions of H5VL routines that use va_list parameters
* Implement and test H5S_BLOCK
* 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
* Finish another iteration on public H5ES routines, along with running the code reformatter
* Another round of reformatting
* 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)
* Remove H5Dwait and H5Fwait calls, which were incorrectly brought back in
* Tiny cleanup of H5Lcreate_hard_async
* Run source formatter
* Allow for canceled operation in wait_cb
* Attempt to fix switch on string value
* Re-run source formatter
* Add H5S_BLOCK testfile to CMake clean target
* Add H5Pset_vol_async API routine and 'get_cap_flags' VOL introspection callback
* Clean up warnings
* Add H5P(set\|get)_vol_implicit_async API routines to allow \/ disallow implicit asynchronous operations (default is disallowed)
* Run formatting script
* Remove H5VL_REQUEST_WAIT\*
* Warning cleanup
* Eliminate strdup()s on statically allocated strings
* Warning cleanup
* Split H5VLrestore_lib_state into H5VLstart_lib_state and H5VLrestore_lib_state, and rename H5VLreset_lib_state to H5VLfinish_lib_state.
* Duplicate strings when building err_info to return to applicatin
* Move connector author routines into seperate header files, all included in the new hdf5dev.h header
* Run bin/trace to add TRACE macros
* Allow H5ES_NONE as a valid, but no-op, parameter to all H5ES API routines that accept an event set ID
* Clean up formatting
* Remove H5Pset/get_vol_implicit_async
* Clean up warning
* Remove H5Pget_vol_async and replace with more generic H5Pget_vol_cap_flags
* Clean up warnings
* Add H5ESfree_err_info convenience routine
* Fix typo
* Correct matching for cached VOL plugins
* Add developer header file
* Update for C99 compatibility
* Add missing trace macro
* Stop clang-format from messing with the trace macros. Don't set up VOL wrappers for 'infrastructure' objects like requests and blobs
* Fix warning about formatting a directory
* Clean up formatting for H5E_BEGIN_TRY / H5E_END_TRY
* Reduce scope of H5ES__close
* Enable CMake checks for various types on MacOS
* Clean up properly when H5CX_retrieve_state() fails. Also clean up many compiler warnings.
* Committing clang-format changes
* Merge from develop
* Fix mis-placed assert
* Remove commented-out code
* Re-add macro for unsetenv on Windows (I think it accidentally was merged out)
* Strengthen sanity check from error report to assertion
* Committing clang-format changes
* Add units to the comments for a few fields
* Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it.
* Committing clang-format changes
* Remove H5ESget_time_estimate
* Committing clang-format changes
* Create developer header for datatype routines and move type conversion register/unregister routines there.
* Simplify internal H5VL_setup_name_args and H5VL_setup_idx_args routines
* Add H5VLlink_optional_op, allowing dynamicly registered optional operations for the link VOL subclass, also added H5VL_loc_params argument to the link 'optional' callback to allow them to work correctly.
* Run bin/format_source on current code
* Add H5VLobject_optional_op, allowing dynamicly registered optional operations for the object VOL subclass, also added H5VL_loc_params argument to the object 'optional' callback to allow them to work correctly.
* Run bin/format_source on current code
* Committing clang-format changes
* Revert "Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it."
This reverts commit 5ac92014da2682bdba62d7a2524b8d90e38f6b19.
* Committing clang-format changes
* Convert attribute 'get' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Update tracing macros
* Convert attribute 'specific' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert dataset 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to attribute 'get' and 'specific' operation parameters.
* Convert datatype 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to H5O_refresh_metadata arguments.
* Reduce warnings
* Reduce warnings
* Track change to datatype 'get' callback
* Fix bug with file pointer getting invalidated when object closed
* Reformat source
* Convert file and group VOL classes 'get' and 'specific' operations to use
struct-of-tagged-union pattern for VOL callback arguments, instead of using
varargs. Also small cleanup to the attribute get name operation. Also moved
'mount' and 'unmount' operations to be group specific operations, instead of
file specific, to better align with their behavior (mounted files are on
groups, so a group is what is operated on).
* Remove remainder of merge conflict marking
* Convert link VOL class 'create' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Remove some unused local variables
* Convert link VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor 'get name by idx' routines to return actual length of name with a parameter instead of the return value, and move some callback context structs for the link interface from the private header file into the source code module, to reduce their visibility scope.
* Update tracing macros
* Convert link VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert object VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert object VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor H5G_loc_exists, et al, to return 'exists' flag in a parameter and errors with the function return value, instead of overloading both into the return value. And, corrected logic error in test/links.c around non-existant objects in a file.
* Convert request VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert blob VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also removes the H5VL_BLOB_GETSIZE operation, as it's unused in the library and the blob ID size for a container is now returned with H5VL_FILE_GET_CONT_INFO.
* Add 'const' to several parameters that are only queried.
* Convert all VOL classes' 'optional' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Convert several 'get' routines to return the length of an array in a parameter instead of combining it into the return value. Move several routines to be in less public namespace. Correct direct_chunk test to verify that parameters aren't modified on error.
* Switch get/specific/optional VOL callback argument structures to be 'async-friendly'. Also other minor cleanups and bug-fixes.
* Add H5Pset_dataset_io_hyperslab_selection / H5S_PLIST feature, to allow skipping H5Dget_space + H5Sselect_hyperslab for async operation
* Add dynamic optional operations for request objects
* Update dynamic operation test for optional request operations
* Update a comment for an operation argument
* Run trace and format_source scripts
* Committing clang-format changes
* Committing clang-format changes
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>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER
* Rips out the BEGIN_FUNC, etc. macros
* Removes 'end if', etc. comments from H5HL package
* Committing clang-format changes
* Fixes an H5EA iterate issue
* Fixes an issue in the H5FA iterator code
* Further cleanup in bin/trace after macro removal
* Iterator changes in H5EA and H5FA
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Removes pre-C99 build and header cruft
* Assumes ANSI C headers exist
* Assumes stdbool.h, stdint.h, and inttypes.h are present
* Assumes the C++ compiler can handle stdint.h
* Removes all work-arounds for missing functionality, especially stdbool.h
* Formats source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Trivial warning fixes:
* Removes an unused done target in H5Tbit.c
* Add (void) to quiet "ignored return value" warnings in the generators
(which generally ignore errors)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fixed HDFFV-11223 (CVE-2018-14460)
Description
- Added checks against buffer size to prevent segfault, in case of data
corruption, for sdim->size and sdim->max.
- Renamed data files in an existing test to shorten their length
as agreed with other developers previously.
Platforms tested:
Linux/64 (jelly)
* Committing clang-format changes
* Updated for test files
* Updated for HDFFV-11223
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Purges UFAIL from the library
* H5HL_insert change requested in PR
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Removes gratuitous (double)x.yF casts
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fixed use of null pointer identified by UBSan
UBSan warned:
runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t')
with these two tests:
H5REPACK-committed_dt_DFF
H5REPACK-committed_dt
Reformulated per @gnuoyd suggestion.
* Fixed undefined float -> unsigned char conversion in HL_test_image
* Removed dead skip_overflow_tests_g global
The global `skip_overflow_tests_g` was being set but never read.
* Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5`
* Committing clang-format changes
* Remove extra ']' in line 730.
* Committing clang-format changes
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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(#561)
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING (license) file.
* Add release_docs/code-conventions.md file.
* Add script to test h5py.
* Fix script error.
* Add file h5pytest.yml.
* Test declaration of counter variables in for loops.
* Committing clang-format changes
* Committing clang-format changes
* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.
* Revert "Added [] to line 126 of H5LTanalyze.l."
This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266.
* Revert extra commits to match canonical develop.
* Update top-level COPYING file and remove COPYING files from
subdirectories.
* Remove subdirectory COPYING files from MANIFEST.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Brings the native VFD H5Fdelete() implementation from Bitbucket
Only brings the 'del' callbacks, not the 'open/close' scheme.
* Formatter changes
* Committing clang-format changes
* Fixes direct VFD callback name
* Removes UNUSED macro from family API call
* Adds barrier and rank 0 check to MPI-I/O VFD delete
* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"
This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143.
* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""
This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702.
* Adds a second barrier after the delete in MPI-I/O VFD
* Only delete files in the core VFD when the backing store flag is set
* Fixes string issues in multi VFD
Also, h5test.c cleanup code now uses H5Fdelete().
* Formatted source
* Rework fapl checks for MPI-I/O VFD delete callback
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Removes c99_(v)snprintf from standalone code
These internal API calls were removed in a previous commit but were
missed in the sio/pio_standalone code.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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>
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* 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>
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* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033)
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode
Platforms tested:
Linux/64 (jelly)
* Accidentally left in another occurrence of the previous patch from user
after a more correct fix was applied, that is the check now accounted
for the previous advance of the buffer pointer. Removed it.
* Typo
* Fixed format issues.
* Added test.
* Changed arguments to ADD_H5_TEST
* Fixing arguments to ADD_H5_TEST again.
* Fixing arguments again.
* Took out the CMake changes until Allen can help.
* Added files:
tCVE_2018_11206_fill_old.h5
tCVE_2018_11206_fill_new.h5
* Revert "Took out the CMake changes until Allen can help."
This reverts commit c21324d6e0044994c5cd24b0671e7d1dd41096cc.
* Revert "Fixing arguments again."
This reverts commit 5832a70674339e4b524749adde5a181f8c3a446a.
* Revert "Fixing arguments to ADD_H5_TEST again."
This reverts commit b45de823c22ce83a388d46466ef7c04b66ff05ed.
* Revert "Changed arguments to ADD_H5_TEST"
This reverts commit 16719824f57e52158451ddd261788c0dcaa3ec55.
* Added first argument to ADD_H5_TEST for HDFFV-10480 fix.
* Changed argument 0 to 1
* Revert "Changed argument 0 to 1"
This reverts commit b343d6613ba681b43248dd5820e96389984ebcf7.
* Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix."
This reverts commit b8a0f9a9e8ec8e6c6ff38d33195d63edff76a563.
* Added first argument and corrected the second.
* Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049
* Improved error messages.
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* 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
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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* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* Fixed clang-tidy readability-misleading-indentation warnings
* Reformatted src/H5Zscaleoffset.c with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* 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>
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* 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
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* 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
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* 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
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* 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
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* Drop the export attribute on forward declaration
They don't mean anything on forward declarations anyways.
* Fixed -Wunused-parameter warnings in some C++ files
Allowed all the attribute #defines to work in C++ also.
* Fixed -Wunused-variable warnings by removing dead code
* Fixed all -Wshorten-64-to-32 warnings by adjusting casts
There was no truncation in fact, since the unsigned result was upcast to size_t then implicitly downcast to uint32_t.
* Fixed all -Wcomma warnings by spliting statements onto own lines
* Fixed all -Wself-assign warnings with different unused param suppression
* Fixed all -Wextra-semi warnings
* Fixed all -Wswitch-enum warnings
Just added new explicit cases with the existing default case.
* Fixed all -Wmissing-prototypes warnings
Just made functions static. Moved them into an extern "C" block.
* Reformatted source with bin/format_source using clang version 10.0.1
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* Fixed various -Wincompatible-pointer-types-discards-qualifiers warnings by adding const
* Fixed various -Wincompatible-pointer-types-discards-qualifiers warning by removing extraneous consts
There were casts with const, but the function parameter doesn't actaully take const, so just modified the casts.
In the other case, a local variable was const that should not have been, becuase its source wasn't const either.
* Fixed a -Wincompatible-pointer-types-discards-qualifiers warning by strdup-ing a string
Create a duplicate string instead of mutating a supposedly const one.
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* Fixed all -Wsometimes-uninitialized warnings by initializing variables
* Fixed all -Wconditional-uninitialized warnings by initializing variables
* Commit alignment changes from running bin/format_source with clang
version 10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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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 - files not in src or test.
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* 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
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* 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
* Small changes plus merge of tools arg parse from 1.12
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* 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
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* Adds h5delete tool
* Fixed MANIFEST
* Added RELEASE.txt note
* Fix typo in RELEASE.txt
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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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The VOL_LIST variable used in the Autotools was duplicated in many
subdirectories. It's been moved to config/conclude.am to avoid
duplication. VFD_LIST was also moved to conclude.am.
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* Minor normalization with the async branch
* Update CMake and the Autotools to use the new pass-through VOL ID
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