* Implement support for loading of Virtual File Drivers as plugins
Fix plugin caching for VOL connector and VFD plugins
Fix plugin iteration to skip paths that can't be opened
* Enable dynamic loading of VFDs with HDF5_DRIVER environment variable
* Temporarily disable error reporting during H5F_open double file open
* Default to using HDstat in h5_get_file_size for unknown VFDs
* Use macros for some environment variables that HDF5 interprets
* Update "null" and "ctl testing" VFDs
* Pacify clang-analyzer-unix.cstring.NullArg
* Apply some bugprone-suspicious-string-compare
* Apply some readability-simplify-boolean-expr
* Apply some readability-make-member-function-const
* Apple some bugprone-macro-parentheses
* Changed an f suffix to L for `long double`
* Applied some readability-uppercase-literal-suffix automatically
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* C++ build and warning updates
* Fixes all warnings on C++ (with gcc 9.3)
* Updates CMake and Autotools C++ builds
* Undo warning clobber
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* BUG: DataSet assignment operator is missing
* Some compilers complain if the copy constructor is given explicitly
but the assignment operator is implicitly set to default.
* Explicitly defining the assignment operator allows us to properly
handle reference counters for shared resources.
* BUG: DataSet assignment operator is missing.
* Mimicking code of H5DataType::operator() as suggested by @bmribler.
* Added test
Description:
Added test for DataSet::operator= that Leengit added
Platform tested:
Linux/64 (jelly)
* Removed Author field.
* Commit clang format changes.
* Entry for Leengit's github PR #503
* Removed lines left by mistake
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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>
* 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>
* 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>
* Fixed clang-tidy bugprone-reserved-identifier warnings
* Fixed clang-tidy bugprone-assert-side-effect warnings
* Fixed clang-tidy bugprone-copy-constructor-init warning
* Fixed clang-tidy readability-redundant-preprocessor warning
For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.
Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.
* Fixed clang-tidy readability-redundant-string-init warnings
* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings
* Fixed clang-tidy performance-unnecessary-value-param warnings
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removed 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>
* 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>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling
Removed leading underscore(s) from header guard spelling. Used 2 regexes:
` _H5(.*)_H`
` __H5(.*)_H`
Applied case-insensitively to only .h files.
* Modified scripts that generate header files to not use underscore prefix
Interestingly, there was already no leading underscore in the trailing comment at the end of the file
* Fixed remaining -Wreserved-id-macro warning not caught by regex
* 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.
* 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
* 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
* 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>
* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
Description:
Added wrappers for H5Pset/get_create_intermediate_group:
// Specifies in property list whether to create missing
// intermediate groups
void setCreateIntermediateGroup(bool crt_intmd_group) const;
// Determines whether property is set to enable creating missing
// intermediate groups
bool getCreateIntermediateGroup() const;
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
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)
Description:
- Added a wrapper for H5Ovisit2 to class H5Object
// Recursively visit elements reachable from this object.
void visit(H5_index_t idx_type, H5_iter_order_t order,
visit_operator_t user_op, void *op_data, unsigned int fields);
- Fixed various typos in documentation
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
Description:
- Added class DSetAccPropList for the dataset access property list.
- Added wrapper for H5Dget_access_plist to class DataSet
// Gets the access property list of this dataset.
DSetAccPropList getAccessPlist() const;
- Added wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class
DSetAccPropList
// Sets the raw data chunk cache parameters.
void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0)
// Retrieves the raw data chunk cache parameters.
void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
- Added two more arguments to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
- Added one more argument to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Description:
Moved the new H5Object::getInfo member functions to H5Location and
made them overloaded with the existing H5Location::getObjinfo. This
way is cleaner than the previous approach.
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
