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* Hdf5 merge issue 435 (#460)Larry Knox2021-03-109-178/+176
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Merge #380 from develop (#438)Allen Byrne2021-03-054-179/+190
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry
* 1 12 Merges from develop (#421)Allen Byrne2021-03-0431-165/+166
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards
* 1 12 merges from develop (#412)Allen Byrne2021-03-03145-506/+493
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Fix for HDFFV-11109 - Copy MPI comm and info object into output FAPL from ↵jhendersonHDF2021-02-242-7/+23
| | | | | | | H5F_get_access_plist (#342) (#374) * Avoid freeing MPI_COMM_WORLD in H5_mpi_comm_free * Copy MPI Comm and Info to new FAPL in H5F_get_access_plist
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-20495-497/+497
| | | | file - src and test directories.
* Port PR 291 to 1.12 branch: Allow using virtual datasets in files opened ↵Neil Fortner2021-02-081-1/+29
| | | | | | | | | | | | with H5F_CLOSE_SEMI and H5F_CLOSE_STRONG (#322) * Modify VDS code to always open source files with H5F_CLOSE_WEAK close (#291) degree. Add test cases to VDS test for this, and reduce the amount of output from that test. * Run formatter on H5Dvirtual.c * Run formatter on test/vds.c
* Warnings merge 112 (#299)Allen Byrne2021-02-041-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Merge dev warnings changes from develop
* 1 12 Whitespace changes after clang-format run (#288)Allen Byrne2021-01-29100-755/+765
| | | | | | | | | | | | | | | | | | | | | * 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 PR #274 to 1.12 Branch (#283)Neil Fortner2021-01-2712-36/+182
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) * Cache the pointer to the next point to process after the last call to H5S__get_select_elem_pointlist. This allows the normal process of iterating over the points in batches to be much more efficient, as the library does not need to traverse the entirety of the preceding points every time the funciton is re-entered. * Update RELEASE.txt for point selection iteration performance fix. * Fix problems with vlens and refs inside compound using H5VLget_file_type() (#274) * Fixed problems with vlens and refs inside compound using H5VLget_file_type() * Fix date in RELEASE.txt * Add assertions * Move some manipulation of H5VL_object_t struct fields into the H5VL package. * Add fix that was mistakenly left off merge commit. * Update src/H5Tprivate.h Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) ↵Neil Fortner2021-01-222-7/+31
| | | | | | | | | | | (#275) * Cache the pointer to the next point to process after the last call to H5S__get_select_elem_pointlist. This allows the normal process of iterating over the points in batches to be much more efficient, as the library does not need to traverse the entirety of the preceding points every time the funciton is re-entered. * Update RELEASE.txt for point selection iteration performance fix.
* 1 12 merge of changes from dev (#271)Allen Byrne2021-01-191-2/+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
* Hdf5 1 12 - Fix unaligned access to reference buffer during datatype ↵Larry Knox2020-12-272-7/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | conversion on 64-bit Solaris (#231) * 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) 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>
* OESS-98 Update plugin build option - HDF5 1 12 (#173)Allen Byrne2020-12-151-1/+2
| | | | | | | | | | | | | * merge updates from develop * remove extension on command * Run autogen before chkmanifest * Update release text files and whitespace cleanup * Update list * OESS-98 Update plugin build option
* Merge VOL framework versioning to 1.12 (#154)Quincey Koziol2020-12-109-39/+106
| | | | | * Enforce VOL framework version compatibility when registering connectors. Also add a version for the connector itself, some refactoring on the register calls, and move the logic for matching / rejecting a VOL connector class from the plugin module to the VOL module. (#151) * Revise VOL framework version compatibility for the 1.12 release branch
* Basic alignment with async branch (#115) (#137)Quincey Koziol2020-11-30108-1169/+1171
| | | | | | | * 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 Knox2020-11-2631-596/+9322
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Cherry pick of Minor/id code cleanup (#114) (#124)Dana Robinson2020-11-2510-1684/+1844
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Switch ID code to use a hash table instead of a skip list (#52)" This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4. * H5I_id_type_t and H5I_class_t are no longer managed via free lists * Fixed commenting issues * Naming and commenting cleanup in H5I.c * H5I cleanup * Header cleanup * Commenting * More uniform naming * Renames H5I_id_type_t and related in H5I.c * Adds gcc pragmas to ignore H5I const casting * Split H5I code into multiple files * Rename id_type to simply type in H5I code * Minor typo in H5Itest.c
* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. (#116)Larry Knox2020-11-231-2/+2
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* Manual sync with develop (#95)Dana Robinson2020-11-1757-869/+3799
| | | | Brings all features from develop. Note that RELEASE.txt has not been updated (will be done in a future PR).
* Merge pull request #89 from byrnHDF/hdf5_1_12Larry Knox2020-11-142-3/+47
|\ | | | | Hdf5 1 12 doxygen support framework
| * Add doxygen framework for CMake and autotoolsAllen Byrne2020-11-132-3/+47
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* | Merge pull request #93 from lrknox/hdf5_1_12Larry Knox2020-11-131-1/+1
|\ \ | | | | | | Merge pull request #91 from ksunden/patch-1
| * | Merge pull request #91 from ksunden/patch-1Larry Knox2020-11-131-1/+1
| |/ | | | | Fix spelling of metadata
* | Brings HDFS VFD binary compatibility stubs from 1.10Dana Robinson2020-11-132-21/+79
|/ | | | | | | | | | | The implementation of the HDFS VFD included no-op stubs for HDFS functionality, even when the HDFS VFD was not being built. These were removed in the develop branch and those changes were merged to the 1.12 development trunk after 1.12.0 was released. This would lead to binary compatibility problems if released in HDF5 1.12.1. This commit restores the no-op stubs.
* Mostly whitespace - reorder of inits.Allen Byrne2020-10-194-16/+17
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* OESS-98 add CMake option to build plugins project within hdf5Allen Byrne2020-10-161-22/+22
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* Remove 1 addition to src/H5Cmpio.c of member added to H5C_t struct in ↵Larry Knox2020-10-101-1/+1
| | | | | | develop branch inadvertently and partially merged to hdf5_1_12 branch. The addition breaks compile with parallel enabled; removing it restores compile, tested with MPICH 3.3 and OpenMPI 4.0.0. e with '#' will be ignored, and an empty message aborts the commit.
* Remove line referencing new cache feature not yet movedAllen Byrne2020-10-081-1/+0
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* Merge changes from developAllen Byrne2020-10-08114-11546/+11410
| | | | | Comments and whitespace Skip file-locking and cache changes
* Cleanup comments in tests, align comments better, update vfd testAllen Byrne2020-10-051-6/+6
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* Source formattedAllen Byrne2020-10-01489-107296/+100775
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* Src file format preventive updatesAllen Byrne2020-09-287-281/+293
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* Add clang-format changes from develop.Allen Byrne2020-09-2832-5771/+5855
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* Snapshot version 1.12 release 1-2. Update version to 1.12.1-3Larry Knox2020-09-181-2/+2
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* Merge pull request #2871 in HDFFV/hdf5 from ↵Quincey Koziol2020-09-038-232/+26
|\ | | | | | | | | | | | | | | | | | | | | fix_nil_collective_metadata_write_1_12 to hdf5_1_12 * commit '8b48ddb4c8d02aec2bc5e938fe7b789f6ad9c2b2': Add release note for collective metadata fix Fix mis-merge from develop Update buffer count Revert " Checkin of fix for CGNS bug" Revert "Removed commeted out code from H5C_dump_coll_write_list()"
| * Fix mis-merge from developQuincey Koziol2020-09-031-6/+1
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| * Update buffer countQuincey Koziol2020-09-031-29/+22
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| * Revert " Checkin of fix for CGNS bug"Quincey Koziol2020-09-038-207/+8
| | | | | | | | This reverts commit 94c34773ceae5b30c4afb227d0385ebf4ab6ce28.
| * Revert "Removed commeted out code from H5C_dump_coll_write_list()"Quincey Koziol2020-09-031-0/+5
| | | | | | | | This reverts commit eb75dc1bb02e13902d73a36caafe763eea585d02.
* | Bug fix to allow pass-through VOL connectors to set DXPL properties (like ↵Quincey Koziol2020-09-032-15/+13
|/ | | | requesting collective operations) on dataset I/O
* Merge pull request #2861 in HDFFV/hdf5 from ↵Quincey Koziol2020-08-287-47/+47
|\ | | | | | | | | | | | | hdf5_1_12_remove_unneeded_tagging to hdf5_1_12 * commit '4174fcb8c0a7f8f5ec5297f223c052eca039d5c3': Remove redundant calls to set the metadata cache tag
| * Remove redundant calls to set the metadata cache tagQuincey Koziol2020-08-277-47/+47
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* | Adds HDFS VFD stubs to prevent binary compatibility problemsDana Robinson2020-08-272-13/+72
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* Minor fixes to align w/state of 1.12 codeQuincey Koziol2020-08-222-11/+10
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* Correct typos w/HGOTO_DONE & HGOTO_ERRORQuincey Koziol2020-08-227-50/+47
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* Move H5T_vlen_reclaim to package scopeQuincey Koziol2020-08-224-6/+6
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* Switch H5VM inline routines back to single underscope and put a comment in ↵Quincey Koziol2020-08-2237-153/+201
| | | | their header about this naming
* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-22344-9947/+6657
| | | | | | 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.
* Simplify default use of MPI_BYTEQuincey Koziol2020-08-211-8/+3
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