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* Hdf5 merge issue 435 (#460)Larry Knox2021-03-101-5/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Fixed clang-tidy readability-misleading-indentation warnings (#427) * Fixed clang-tidy readability-misleading-indentation warnings * Reformatted src/H5Zscaleoffset.c with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Fixed clang-tidy readability-redundant-control-flow warnings (#428) * 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> * Removed bad function pointer casts (#434) * 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> * fix block coordinate printing example (#437) Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Mike Smith <grimbough@gmail.com>
* 1 12 merges from develop (#412)Allen Byrne2021-03-031-17/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - src and test directories.
* 1 12 Whitespace changes after clang-format run (#288)Allen Byrne2021-01-291-38/+38
| | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version
* Basic alignment with async branch (#115) (#137)Quincey Koziol2020-11-301-38/+38
| | | | | | | * 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
* Merge available RM doxygen from develop to hdf5 1 12 (#131)Larry Knox2020-11-261-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
* Manual sync with develop (#95)Dana Robinson2020-11-171-0/+4
| | | | Brings all features from develop. Note that RELEASE.txt has not been updated (will be done in a future PR).
* Merge changes from developAllen Byrne2020-10-081-7/+11
| | | | | Comments and whitespace Skip file-locking and cache changes
* Source formattedAllen Byrne2020-10-011-1298/+1330
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* Add clang-format changes from develop.Allen Byrne2020-09-281-1/+1
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-1/+4
| | | | | | 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.
* Sync with developDana Robinson2020-08-011-52/+135
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* Reduce overhead for H5open, which is involved in the public symbols like ↵Quincey Koziol2020-06-181-2/+27
| | | | H5T_NATIVE_INT, etc.
* Make sure that H5TS_thread_id() is available as either a function or a macro inDavid Young2020-05-111-3/+5
| | | | | | | | | all configurations. Previously it was neither declared nor defined in --disable-threadsafety builds. The compiler's warning got lost in the noise---I first saw the issue because my -Werror branch stopped compiling cold---and the tests still linked and ran.
* Use a naked pthread_self() call in the HDF5 thread wrappers.David Young2020-05-111-4/+0
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* Replace pthread_self_ulong() with H5TS_thread_id(). The POSIX ThreadsDavid Young2020-05-061-5/+0
| | | | | implementation ought to be portable to any system that has POSIX Threads. On Windows, I use the same API call as before.
* Merge changes from develop to fix various issuesAllen Byrne2020-01-301-0/+3
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* Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to developKimmy Mu2020-01-281-1/+1
| | | | | | | | | * commit '406330addf45529ecdd088f4d22e9aab9a03661d': rename macro change condition pick up from Dave's fix leave Wswitch-default for later fix fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow
* prototype issuekmu2020-01-281-1/+1
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* Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-281-10/+17
| | | | | | | | | | | * commit '145ef3ceee20c28a443bd11507c58858bea3f889': more cleanup change it back pick up missing piece fix unused related warnings removed unused parameter more fix and address comments remove unsed var,function,macro, etc
* For portability, insulate the HDF5 library from some system macros.David Young2019-12-191-1/+18
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* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-161-7/+0
| | | | the Autotools and CMake.
* HDFFV-10876 Merge from developAllen Byrne2019-12-091-21/+17
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* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-091-19/+2
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-061-2/+19
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* Fixed the H5_set_bigio_count prototype by adding a missing input argument.Richard Warren2019-10-231-1/+1
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* Rename the set/get bigio_count functions. Also add the renamed prototypes ↵Richard Warren2019-10-231-1/+2
| | | | to H5private.h.
* Added the two missing files from the previous PR as requested by LesRichard Warren2019-10-151-0/+3
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* Added H5Pset/get_mpi_params calls and unified them with the MPI-I/ODana Robinson2019-08-261-0/+2
| | | | VFD info in H5FDmpio.c.
* Some refactoring prior to implementing new H5P MPI functions.Dana Robinson2019-08-141-0/+8
| | | | | | * Macro cleanup and obvious warning fixes in parallel code. * Moved H5FD comm and info dup/free wrapper code to a new H5mpi.c file and separated it to deal with each MPI type separately.
* Merge pull request #1860 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:map_api_merge ↵Dana Robinson2019-08-131-0/+3
|\ | | | | | | | | | | | | | | | | | | to develop * commit 'd95745235a468b17f697843adb3d0e54bd919893': Updated h5trav.c to emit output that doesn't require ddl changes for map support. Fixed Map API CMake option Renamed H5Mdelete_key to H5Mdelete and H5Mset to H5Mput. Added the map (H5M) API
| * Added the map (H5M) APIDana Robinson2019-08-131-0/+3
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* | Added ifdef for intel compilers, __GNUC__ has to be defined for header files ↵M. Scot Breitenfeld2019-08-131-1/+1
|/ | | | which use it to work with intel compilers. This gives a warning for intel compiler about fallthrough, so added a check not to include fallthrough if using intel compilers.
* Added gcc conditional for __attribute__((fallthrough)), removes 34 warnings ↵M. Scot Breitenfeld2019-08-081-0/+4
| | | | on theta (10% of warnings).
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-0/+3
| | | | clean up warnings.
* - Added H5MMprivate.h #includes where neededDana Robinson2019-03-161-5/+1
| | | | | - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
* Merge branch 'develop' into c_stdlib_posix_call_cleanupDana Robinson2019-02-191-0/+6
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| * Updated sec2, log, and core VFDs to use pread/pwrite whenDana Robinson2019-01-311-0/+6
| | | | | | | | available (can be controlled via a configure/CMake option)
* | C and POSIX call cleanupDana Robinson2019-01-111-2/+3
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* Further va_list improvements.Dana Robinson2018-12-171-0/+3
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* Fix plugin code from referencing invalid key ID value, and also switch fromQuincey Koziol2018-12-131-0/+3
| | | | | strtok() to strtok_r() to avoid possible interference with / to application use of strtok().
* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-5/+6
| | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-101-0/+10
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* Develop normalization with vol_integration.Dana Robinson2018-09-191-2/+1
| | | | | Mostly peripheral things like the tools and wrappers, with just enough core library code to support that.
* Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-09-181-50/+0
| | | | orginally intended to support the full SWMR feature.
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-2/+2
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-9/+29
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-28/+67
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* Normalization with VOL integration branch.Dana Robinson2017-11-301-84/+97
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* Rework of the POSIX file open permissions and macros to clean upDana Robinson2017-04-281-17/+4
| | | | | | HDopen() calls. Also fixed a minor const warning in the core VFD.