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* Hdf5 1 10 doxygen merges (#684)Allen Byrne2021-05-261-4/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 10 update license url part2 (#404)Larry Knox2021-03-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * 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. * Update license url (#332) * 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. * Update license url part2 (#333) * 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. * Update URL in source file Copyright headers for web. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* 1 10 merges from develop (#320)Allen Byrne2021-02-081-0/+45
| | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop
* Warnings merge 110 (#300)Allen Byrne2021-02-041-8/+39
| | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * Merge dev warnings refactor from develop
* Stat st blocks fix 110 (#249)Larry Knox2021-01-111-2/+2
| | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * 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: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Add doxygen framework for CMake and autotools (#90)Allen Byrne2020-11-201-5/+71
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* Update version to 1.8.0-1 for CMake test failure.Larry Knox2020-08-241-1/+1
| | | | | | | | | | | if (H5_VERS_SUBRELEASE) set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}-${H5_VERS_SUBRELEASE}") else () if (${H5_VERS_SUBRELEASE} STREQUAL "") set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}") else () set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}-${H5_VERS_SUBRELEASE}") endif ()
* Updated HDF5 1.10 support branch version number to 1.10.8-0Larry Knox2020-08-191-1/+1
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* 1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] afterLarry Knox2020-08-171-6/+6
| | | | | | | | AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
* Brings Mirror VFD to 1.10 from developDana Robinson2020-08-141-0/+48
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* Brings file locking changes from developDana Robinson2020-08-141-0/+50
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* Brought over thread-safety changes from develop.Dana Robinson2020-07-201-0/+1
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* Merge pull request #2686 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-131-1/+4
| | | | | * commit '800f93f7c994f88dfa716746153ded4b1e690e3a': Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
* Merge pull request #2670 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-061-3/+4
| | | | | * 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
* Merge pull request #2656 in HDFFV/hdf5 from ↵Larry Knox2020-06-211-0/+56
| | | | | | | | | ~LRKNOX/hdf5_lrk:changes_1_12_merge to hdf5_1_12 * commit '538b1317646f52658c2a896bbde4dce4246a9761': Squashed commit of the following: Addition of clang-warnings flags Update examples/teth5cc.sh.in for version 1.10.
* Misc fixes and changes from develop.Dana Robinson2020-05-161-0/+1
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* Normalization of high-level library with develop. Also brings theDana Robinson2020-05-151-1/+1
| | | | warnhist script over.
* Snapshot version 1.10 release 7 (snap0)hdftest2020-04-261-1/+1
| | | | Update version to 1.10.7-1
* TRILAB-192 merging warnings changes from developAllen Byrne2020-03-301-1/+30
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* Update version for HDF5_1_10Larry Knox2019-12-111-1/+1
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* Snapshot version 1.10 release 6 (snap3)Larry Knox2019-11-121-1/+1
| | | | Update version to 1.10.6-snap4
* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)Allen Byrne2019-09-181-1/+1
|\ | | | | | | | | * commit '2ca63e3890ebdaee7dc835e5d995ff03a182940f': Snapshot version 1.10 release 6 (snap2) Update version to 1.10.6-snap3
| * Snapshot version 1.10 release 6 (snap2)hdftest2019-09-171-1/+1
| | | | | | | | Update version to 1.10.6-snap3
* | Merge S3 code from develop to 1.10Allen Byrne2019-09-131-0/+130
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* Snapshot version 1.10 release 6 (snap1)hdftest2019-08-261-1/+1
| | | | Update version to 1.10.6-snap2
* Removed FORTRAN_SIZEOF_LONG_DOUBLE from public .h filesM. Scot Breitenfeld2019-08-051-1/+0
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* HDFFV-10658: setting and getting properties in API context. Porting the ↵Songyu Lu2019-07-261-0/+2
| | | | changes to the develop branch into the 1.10 branch: mainly the external file prefix and VDS prefix.
* Squash commit of options to build tools and testsDhvanil Popat2019-06-251-6/+53
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* Snapshot version 1.10 release 6 (snap0)\nUpdate version to 1.10.6-snap1)hdftest2019-04-011-1/+1
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* Update version on hdf5_1_10 branch to 1.10.6-snap0.Larry Knox2019-02-181-1/+1
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* Merge of changes from develop for 1.10.5.Dana Robinson2019-02-041-2/+44
| | | | Added RELEASE.txt entries for new features.
* Merge pull request #1450 in HDFFV/hdf5 from ↵Ray Lu2019-01-181-0/+24
| | | | | | | | | ~SONGYULU/hdf5_ray:TRILAB-98-dt_arith-and-cpp_testhdf5-tests to develop * commit 'b02de315b93ac29d2483a91d526b110a25073505': NNSA Tri-LabsTRILAB-98: Another two test cases out. NNSA Tri-Labs TRILAB-98: Taking out a few more test cases. NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on sierra.llnl.gov: According to the group decision, simply provide a macro to disable some failing test cases on sierra (IBM power9 cpu). All failing cases involve long double data type.
* merged:M. Scot Breitenfeld2019-01-101-0/+9
| | | | | HDFFV-10652 HDFFV-10443
* Merge pull request #1442 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:hdf5_1_10 to ↵Vailin Choi2019-01-071-1/+1
|\ | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit '1a50622733c14d89b3fd8c6bab684af9205a3b96': Fix for daily test failure: too many arguments to function 'H5Gopen1'. Fix the git merge leftover in RELEASE.txt. Fix the git merge leftovers in RELEASE.txt. Fix for HDFFV-10659: The library aborts with "infinite loop closing library" after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
| * Fix for HDFFV-10659: The library aborts with "infinite loop closing library"Vailin Choi2019-01-061-1/+1
| | | | | | | | | | | | | | | | after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
* | Merged the rest of the parallel flush test code.Dana Robinson2019-01-071-0/+1
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* Merge of logging framework updates.Dana Robinson2018-12-311-34/+0
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* Snapshot version 1.10 release 5 (snap1)hdftest2018-11-081-1/+1
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* Merge CMake changes from developAllen Byrne2018-10-231-9/+9
| | | Improved cross-compiling and toolchains
* Update versionLarry Knox2018-09-051-1/+1
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* HDFFV-10552 Add missing HDF5_USE_110_API_DEFAULT optionAllen Byrne2018-08-171-0/+2
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* Rearrange issues by date orderJordan Henderson2018-08-091-1/+1
| | | | | Update version. Update .so versions to match 1.10.3.
* Add Autotools and CMake checks for big I/O MPI-3 functionsJordan Henderson2018-08-021-0/+32
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* Add configure check for MPI_Mprobe and MPI_Imrecv functionsJordan Henderson2018-08-021-0/+31
| | | | | | | | | | | | | | | Add line to libhdf5settings file for status of Parallel writes to filtered datasets status Surround Parallel Compression code in MPI_VERSION >= 3 checks Add disabled message for Parallel Compression built w/ MPI-2 Modify Parallel Compression tests to only run the parallel filtered read tests when parallel filtered writes are disabled Update big I/O code to handle being built with MPI-2 Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
* Apply Cygwin pathches from Marco Atzeri.Larry Knox2018-07-261-13/+0
| | | | Commit Joe Lee's typo corrections for src/H5MF.c.
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-261-1/+1
| | | | | | | | | 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
* Snapshot version 1.10 release 3 (snap3)hdftest2018-06-241-1/+1
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)hdftest2018-06-161-4/+4
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '87829e06189cd9b29583b5ca8065b52b1f4cd523': (30 commits) HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly Cleaned up H5Fmount/unmount code. Normalization with vol_integration branch. Add fortran MPI to test and example Add mpi include folders for fortran C objects Normalization with the vol_integration branch. Fixed MANIFEST Fix usage of compression lib in shared tests Fix jni function call version Fix the error found after earlier checkin. H5O_info fixes for java and examples Added a RELASE.txt entry for HDFFV-10505. Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags. (1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463. Normalize with vol_integration. Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c. Restored some unused #defines to the deprecated section of H5Dpublic.h. Changes made based on feedback from pull request #1039. ...
| * Merge pull request #1111 in HDFFV/hdf5 from hdf5_1_10.sync to hdf5_1_10Scot Breitenfeld2018-06-151-4/+4
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '57f64b92d19fed2879ee9bafe1d29bfac865d54c': (30 commits) HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly Cleaned up H5Fmount/unmount code. Normalization with vol_integration branch. Add fortran MPI to test and example Add mpi include folders for fortran C objects Normalization with the vol_integration branch. Fixed MANIFEST Fix usage of compression lib in shared tests Fix jni function call version Fix the error found after earlier checkin. H5O_info fixes for java and examples Added a RELASE.txt entry for HDFFV-10505. Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags. (1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463. Normalize with vol_integration. Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c. Restored some unused #defines to the deprecated section of H5Dpublic.h. Changes made based on feedback from pull request #1039. ...
| | * Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-06-041-4/+4
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