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* 1 12 Merges from develop (#421)Allen Byrne2021-03-041-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Fix for HDFFV-11109 - Copy MPI comm and info object into output FAPL from ↵jhendersonHDF2021-02-241-0/+9
| | | | | | | 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
* Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf5_1_12Larry Knox2021-02-201-8/+17
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| * 1 12 Minor non-space formatting changes (#354)Allen Byrne2021-02-191-8/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* | Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
|/ | | | file - files not in src or test.
* 1 12 Merge #318 OSX changes from develop (#326)Allen Byrne2021-02-091-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 12 merges from develop (#319)Allen Byrne2021-02-081-0/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Warnings merge 112 (#299)Allen Byrne2021-02-041-0/+69
| | | | | | | | | | | | | | | | | | | | | | | | | * 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 minor merges from develop (#297)Allen Byrne2021-02-031-6/+12
| | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Merge PR #274 to 1.12 Branch (#283)Neil Fortner2021-01-271-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Fortner2021-01-221-0/+9
| | | | | | | | | | | (#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 Byrne2021-01-191-4/+33
| | | | | | | | | | | | | | | * 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
* Stat st blocks fix 112 (#248)Larry Knox2021-01-111-0/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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) * Fixes Autotools detection of the st_blocks field in stat (#246) * Fixes Autotools detection of the st_blocks field in stat The Autotools and CMake will now both correctly determine if the stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS appropriately. * Fixes a typo in configure.ac 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: Dana Robinson <43805+derobins@users.noreply.github.com>
* 1 12 HDFFV-10865 - merge from dev, HDFArray perf fix (#233)Allen Byrne2020-12-291-0/+14
| | | | | | | | | | | | | | | | | | | | | | | | | * 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 * OESS-98 fix tools test for plugins * Fix conflict * OESS-98 fix hdf5 link target * Update pkgconfig settings with version - #218 * HDFFV-10865 - merge from dev, HDFArray perf fix. * HDFFV-10865 - fix date
* OESS-98 Update plugin build option - HDF5 1 12 (#173)Allen Byrne2020-12-151-24/+40
| | | | | | | | | | | | | * 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 Koziol2020-12-101-0/+8
| | | | | * 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
* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. (#116)Larry Knox2020-11-231-1/+1
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* hdf5 1 12 release text (#110)hdf5-1.12.1-rc1Allen Byrne2020-11-217-4320/+9200
| | | | | | | | | | | * merge updates from develop * remove extension on command * Run autogen before chkmanifest * Update release text files and whitespace cleanup * Update list
* Add doxygen framework for CMake and autotoolsAllen Byrne2020-11-132-0/+12
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* Correct TARGET variable and CMake config file locationAllen Byrne2020-11-122-0/+19
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* HDFFV-10868 merge from developAllen Byrne2020-10-281-0/+8
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* OESS-98 - add option to build plugin library with hdf5Allen Byrne2020-10-231-5/+5
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* URL and options correctionsAllen Byrne2020-10-191-1/+1
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* OESS-98 add CMake option to build plugins project within hdf5Allen Byrne2020-10-163-8/+131
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* Correct entries related to --enable-build-mode and --enable-profiling inLarry Knox2020-10-031-4/+7
| | | | INSTALL file, and remove obsolete SZIP paragraph from COPYING file.
* Add clang-format changes from develop.Allen Byrne2020-09-281-0/+10
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* Snapshot version 1.12 release 1-2. Update version to 1.12.1-3Larry Knox2020-09-181-1/+1
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* Add release note for collective metadata fixQuincey Koziol2020-09-031-0/+6
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* Added release note for MPI type fixQuincey Koziol2020-08-211-0/+6
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* HDFFV-9989 Merge h5repack merge/prune from developAllen Byrne2020-08-151-0/+9
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* spellingAllen Byrne2020-08-131-3/+3
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* HDFFV-11127 - force RTLD_LOCAL in dlopenAllen Byrne2020-08-121-0/+9
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* Added RELEASE.txt note for HDFFV-11027Dana Robinson2020-08-111-0/+15
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* Merge pull request #2693 in HDFFV/hdf5 from ↵Vailin Choi2020-07-211-0/+14
| | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-11080-heap-use-after-free-by-the-call to develop * commit '3023b34272cc6ada84aebfa7441a6a55afa3621c': Update MANIFEST. Add new test to Cmake. Fix for jira issue HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
* Snapshot version 1.12.1-1hdftest2020-07-191-1/+1
| | | | Update version to 1.12.1-2
* CMake updates:Allen Byrne2020-07-152-0/+33
| | | | | | Add build folder as Include for generated files Add install option for copying Fortran mod files to include folder Add PRI defines to win32defs file Exclude mingw from extra flags
* Merge pull request #2670 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-061-0/+9
| | | | | * commit 'fc69de0e8ae30e80c1c3c542b156226a75444525': Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
* Add info to release notes.Quincey Koziol2020-06-181-0/+5
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* Update release notes for last ID caching.Quincey Koziol2020-06-111-0/+5
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* Add info to release notes about improvement for single element I/O.Quincey Koziol2020-06-111-1/+7
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* Add info to release notes about improvement to metdata cache tagging for ↵Quincey Koziol2020-06-101-0/+5
| | | | chunked datasets.
* Add info about optimization to release notesQuincey Koziol2020-06-071-0/+5
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* Add note about H5DOappend() optimization.Quincey Koziol2020-06-051-0/+6
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-05-081-1/+4
|\ | | | | | | | | | | | | | | | | | | * commit '943129f61000899e394b75405723a3f110a21205': Add note to release notes. Change thread IDs to uint64_t from unsigned long, per Quincey's suggestion. Add thread_id.c to the MANIFEST and the CMakeLists.txt per Allen's request. Replace pthread_self_ulong() with H5TS_thread_id(). The POSIX Threads implementation ought to be portable to any system that has POSIX Threads. On Windows, I use the same API call as before. Align contents of CMake and autotools testfile cleanup lists. Avoid allocating a chunk index for datasets with 0-sized dimensions, until the dataset is extended.
| * Add note to release notes.Quincey Koziol2020-05-071-1/+4
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* | OESS-65 Fix packagingAllen Byrne2020-05-081-0/+1
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* OESS-65 replace szip with aec libraryAllen Byrne2020-04-273-1/+20
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* Snapshot version 1.12 release 1 (snap0)hdftest2020-04-271-1/+1
| | | | Update version to 1.12.1-1
* TRILAB-192 - merge changes from developAllen Byrne2020-04-071-3/+5
| | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* Update release note for CMake warningsAllen Byrne2020-04-031-0/+2
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