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* Snprintf2 (#1399)Sean McBride2022-01-281-75/+78
| | | | | | | | | | | | | * Replaced many uses of sprintf with safer snprintf Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable. * Removed unnecessary use of static on small buffers This improves thread safety. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* VFD plugins (#602)jhendersonHDF2021-09-291-36/+72
| | | | | | | | | | | | | | | | | * 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
* More various warnings (#958)Sean McBride2021-08-251-4/+3
| | | | | | | | | | | | | * Committing clang-format changes * Fixed various -Wdouble-promotion warnings * Fixed -Wshadow warning for `optopt` conflict On macOS at least, there is a global various named `optopt` in unistd.h. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes gratuitous (double)x.yF casts (#632)Dana Robinson2021-05-071-11/+11
| | | | | | | | | * 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>
* Update clang config (#473)Quincey Koziol2021-03-171-8/+32
| | | | | | | * 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 (#451)Sean McBride2021-03-101-23/+23
| | | | | | | | | * 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>
* Patches from vtk (#358)Sean McBride2021-02-251-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * 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.
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-291-8/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Bring async branch to develop (#166)Quincey Koziol2020-12-141-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 (#115)Quincey Koziol2020-11-231-4/+4
| | | | | | | * 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
* Clang-format of source filesAllen Byrne2020-09-301-1875/+1885
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-9/+2
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Revert "Revert "Moved -Wunsuffixed-float-constants to the developer warnings.""Dana Robinson2020-01-231-2/+2
| | | | This reverts commit 6486e06545bf637d46e18a787395542f4fca143a.
* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-85/+92
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* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-041-6/+6
| | | | the Autotools and CMake.
* OESS-29 Update HD prefix mostlyAllen Byrne2019-08-241-16/+13
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* Add HD prefix to testsAllen Byrne2019-08-151-136/+136
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* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-1/+1
| | | | clean up warnings.
* Added the creation and use of an attribute access property list toDana Robinson2019-06-151-49/+60
| | | | testhdf5.
* Change the checking to H5I_INVALID_HID in test_attr_dense_rename().Vailin Choi2019-04-161-10/+10
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* Fix for HDFFV-10579 H5Arename fails when creation order of attributes is ↵Vailin Choi2019-04-121-38/+55
| | | | | | | tracked. The attribute needs to be removed from the creation order index v2 B-tree before re-inserting the renamed attribute via H5A__dense_insert().
* Align behavior of H5Aget_name_by_idx with H5Aget_name when a NULL buffer is ↵Jordan Henderson2019-01-081-0/+57
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* Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-281-1/+95
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| * Add test for H5Arename NULL/empty attribute name fixJordan Henderson2018-12-171-1/+96
| | | | | | | | Split checking of NULL vs. empty string arguments
* | OHDR tests now accept h5_fileaccess() fapls.Jacob Smith2018-12-261-104/+107
| | | | | | | | Formatting, informative comments, and minor renaming.
* | Reformat to be more consistent with existing code.Jacob Smith2018-12-131-12/+3
| | | | | | | | Fix a few typos.
* | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-131-0/+64
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| * Add test for H5Aget_info(_by_name/_by_idx) NULL info pointerJordan Henderson2018-12-131-0/+65
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* | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-121-578/+576
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| * Normalization with vol_integration (test code and H5Xtest.c)Dana Robinson2018-09-201-578/+576
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* | Sidestep and hide&flag minor issues causing test failures.Jacob Smith2018-12-051-17/+57
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* | Incorporate minimized dset ohdr tests into extant suite.Jacob Smith2018-11-191-158/+272
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* Fix for HDFFV-9277: update the ainfo message after removing an attribute.Vailin Choi2018-07-201-0/+94
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* Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-10/+10
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* Fix for HDFFV-10180 Performance issues with H5Oget_info.Vailin Choi2018-04-241-25/+25
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-49/+47
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Cleanup overuse of include filesAllen Byrne2018-02-141-49/+47
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-121/+121
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* Fixed misc Warnings flagged by VS2017.Dana Robinson2017-11-271-7/+7
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* Fix some of the whitespaceAllen Byrne2017-11-161-127/+127
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* Fix Windows link errorAllen Byrne2017-11-141-379/+379
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* Initialize hid_t variables in test_Attr_bug9.Neil Fortner2017-11-131-4/+4
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* Fix HDFFV-10274. When deleting all (or almost all) of the messages inNeil Fortner2017-11-101-0/+98
| | | | | | an object header chunk, where the total amount deleted was greater than 64K, an error would occur due to an off by one error in the code that handled that case. Fixed this and added a test case.
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Description:Quincey Koziol2016-09-271-12/+32
| | | | Further warning cleanups: from 667 warnings to 503.
* [svn-r30017] Description:Quincey Koziol2016-06-061-20/+20
| | | | | | | | | Bring warning cleanusp in r29990, 29993, 29997, 29999, 30004 from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production. (h5committest forthcoming)
* [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-10-201-9/+9
| | | | | | | | | | | | | | available Fix tests accordingly and fix misuse of hbool_t in various places Fix initialization of H5Pgcpl/ocpl structs in property decoding routines Tested on: Linux/32 (jam) Linux/64 (platypus) Linux/PPC64 (ostrich) MacOSX/64 10.11
* [svn-r27800] Minor warning fixes in the library tests.Dana Robinson2015-09-161-6/+6
| | | | Tested on: jam (too minor for h5committest)
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