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* 1.10: Add spelling check to CI and fix errors. (#2442)Allen Byrne2023-02-161-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update CI and support files to match latest from 1.14 * Correct spelling * More spelling corrections * spelling fixes in testpar * Fix spelling errors in tools * More tools spelling fixes * Spelling fixes for rest of tools and some src * Fix spelling errors in src files, pt 2 * Fix spelling in src pt3 * Fix spelling errors pt4 * Fix spelling errors pt5 * Spelling fix pt6 * fix spelling error examples * fix spelling in tests * fix spelling errors in test pt2 * Fix spelling errors in test pt3 * fix spelling in test pt4 * Fix spelling errors in hl * fix spelling errors in c++ * Spelling fixes for fortran * spelling fixes for bin and java * Add relative path * Change spelling action to use a file for list of ignore words * Fix spelling ignore list * remove unused file
* Add szip/libaec to GitHub CI and fix warnings (#2438) (#2450)Dana Robinson2023-02-121-3/+9
| | | | | | | | szip (or libaec) is currently not tested in CI. This adds szip to the the Autotools GitHub CI actions on Linux when building with the Autotools. This PR also cleans up a few warnings that remained in the szip- related code so the -Werror check will pass.
* 1.10 clang 13 format #1933 (#1940)Allen Byrne2022-07-291-2/+2
| | | | | * clang 13 format #1933 * Correct workflow
* Unify handling of collective metadata reads status (#1206) (#1418)jhendersonHDF2022-02-041-12/+2
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* Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)Allen Byrne2021-04-301-7/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 10 Update license url (#403)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. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Source formattedAllen Byrne2020-10-011-300/+264
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* Merge pull request #2772 in HDFFV/hdf5 from ↵Larry Knox2020-08-181-0/+67
|\ | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933_110 to hdf5_1_10 * commit '538bdb35ae932a1445f32a04e8173f8805d404f8': Updated for HDFFV-10933 Fixed HDFFV-10933
| * Fixed HDFFV-10933Binh-Minh Ribler2020-08-141-0/+67
| | | | | | | | | | | | | | | | | | | | | | Description: Fixed to allow the creation of a dataset when the combination of type, space, etc doesn't work for filter and the filter is optional. Currently, it was supposed to be skipped as indicated in the documentation, but it was not skipped and the creation failed. The function H5Z_ignore_filters was added and used in H5D__create. Platforms tested: Linux/64 (jelly)
* | Brings monotonic timer changes from developDana Robinson2020-08-151-89/+114
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* Brought H5I, H5Z, and some of H5PL in line with develop/1.12.Dana Robinson2020-05-201-57/+68
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* Moved H5MM_memcpy and H5MM_xfree_const from developDana Robinson2020-05-151-2/+2
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* Fix some collective metadata read issuesJordan Henderson2019-02-121-1/+1
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* Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-12-311-3/+3
| | | | orginally intended to support the full SWMR feature (from develop).
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-709/+631
|\ | | | | | | merge_hyperslab_updates
| * Cleanup API context function usage.Quincey Koziol2018-03-191-12/+0
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| * Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-23/+81
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| * Made a dcpl layout struct in H5Z.c dynamic to quiet a stack size warning.Dana Robinson2017-11-211-12/+19
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| * Fixed an uninitialized filter callback struct in H5Dchunk.c andDana Robinson2017-11-211-30/+32
| | | | | | | | | | | | unified the naming and initialization of said struct throughout the library. This was causing a crash on VS2015 in debug mode when the debug heap complained. Fixes HDFFV-10330.
| * Brings H5Z and H5PL packages in sync with VOL integration branch.Dana Robinson2017-11-171-84/+89
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| * HDFFV-10328 - fix typosAllen Byrne2017-11-171-5/+4
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| * HDFFV-10328 - remove allocation changesAllen Byrne2017-11-171-29/+4
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| * HDFFV-10328 merge allocation changes from 1.8Allen Byrne2017-11-161-336/+379
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| * HDFFV-10297 update calls to H5Zfilter_availAllen Byrne2017-10-091-1/+2
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| * HDFFV-10297 - fix repack individual objectsAllen Byrne2017-10-061-8/+7
| | | | | | includes H5Zfilter_avail() fix
| * Whitespace conversions and comment updatesAllen Byrne2017-10-041-535/+382
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| * Revert "Merge pull request #567 in HDFFV/hdf5 from ↵Dana Robinson2017-06-091-59/+15
| | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop to develop" This reverts commit 4242753848c44ab3b5d226e66225eac2f64db314, reversing changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
| * * Made STATIC free lists EXTERN for H5O_layout_t.Dana Robinson2017-06-071-1/+1
| | | | | | | | * Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
| * Updated H5O_layout_t dynamic work to use the H5FL interface.Dana Robinson2017-06-071-9/+48
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| * Made some H5O_layout_t stack allocations dynamic (quiets warnings).Dana Robinson2017-06-061-8/+13
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| * 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.
* | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-1/+1
|/ | | | improvements.
* Bring changes to I/O parameters from page_buffering branch.Quincey Koziol2017-03-131-1/+1
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* [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-1/+1
| | | | | | | | metadata optimizations. - rename H5AC_dxpl_id to H5AC_ind_read_dxpl_id and update all usage in the library tested on bb-8 with parallel and serial.
* [svn-r27811] Description:Quincey Koziol2015-09-161-3/+3
| | | | | | | | | | | Refactor property list code to "deep copy" properties in the correct way, retraining the rest of the library to copy & release things correctly. This cleans up another batch of memory leaks, etc. within the library. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (h5committest forthcoming)
* [svn-r27768] Description:Quincey Koziol2015-09-141-56/+61
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-3/+3
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r26329] Merge of r26069, r26070, and r26072 from the ↵Dana Robinson2015-02-271-20/+13
| | | | | | | | | | | | | | | | | | features/autotools_rework branch. Removed the configure option that allows selective disabling of individual internal filters (fletcher32, shuffle, etc.). This feature mucked up the code with a lot of #ifdefs, saved very little space, and was not scalable to a general scheme for library size reduction. We've decided to remove the feature while we investigate a more general scheme for decreasing the library size. Part of: HDFFV-9086 Tested on: h5committest
* [svn-r25766] Description:Quincey Koziol2014-11-031-1/+1
| | | | | | | | | | Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They are buggy and it's taking me a long time to correct the problem. I'll check in a revised form of the changes when I've got them straightened out. Tested on: Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN Linux 2.6.x (jam) w/parallel
* [svn-r25496] Description:Quincey Koziol2014-07-301-2/+2
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r25273] Description:Quincey Koziol2014-06-131-1/+1
| | | | | | | | | | | Bring in Chao/Neil/my changes to optimize hyperslab selection operations further, along with 3 new public API routines: H5Scombine_hyperslab(), H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to the code and fixing a few compiler warnings. Tested on: Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI (h5commttest forthcoming)
* [svn-r24725] HDFFV-8629: h5repack will not attempt to remove UD filters. ↵Allen Byrne2014-02-201-17/+21
| | | | | | h5repack requires a check for UD filters that also must check if the filter can be dynamically loaded. This require a change in the library that checks for this. Tested: locally and reviewed
* [svn-r24167] HDFFV-8513, HDFFV-8522 Plugin testing in h5repack, h5dump.Allen Byrne2013-09-191-4/+0
| | | | | | | Add more usage info for UserMacros. Add new option information about the Plugin default path. Tested: local linux, jam
* [svn-r23713] Description:Quincey Koziol2013-05-211-71/+164
| | | | | | | | | | Clean up warnings, switch library code to use Standard C/POSIX wrapper macros, remove internal calls to API routines, update checkapi and checkposix scripts. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN Big-Endian Linux/64 (ostrich)
* [svn-r23685] Issue 8380 H5Zunregister caused seg fault. I simplied the ↵Raymond Lu2013-05-081-49/+52
| | | | | | iteration process over datasets, groups, and files as Quincey suggested. I also removed H5I_search that I introduced in last commit but didn't actually used it. Tested on jam and koala - simple change.
* [svn-r23675] Issue 8380 - H5Zunregister caused seg fault. This is the ↵Raymond Lu2013-05-061-84/+116
| | | | | | | | | followup commit. Quincey reviewed my previous commit and suggested me to use H5I_iterate to iterate through all opened objects in H5Z_unregister. I changed it in this commit. Tested with h5committest.
* [svn-r23656] Issue 8380 H5Zunregister caused seg fault: I added some ↵Raymond Lu2013-04-291-8/+155
| | | | | | | | | protection measures: 1. If any opened object uses the filter, let it fail. 2. Flush all opened files to push any cached data to files. Tested with h5committest.
* [svn-r23549] Description:Quincey Koziol2013-04-041-2/+2
| | | | | | | | More misc. cleanups, but main change is to make an "extern" header file for the plugin interface. Tested on: Mac OSX/64 10.8.3 (amazon)
* [svn-r23543] Description:Quincey Koziol2013-04-041-24/+26
| | | | | | | | | Bring r23542 from desy_1_8 branch to trunk: Further revisions to dynamic library loading code, to clean it up. Tested on: Mac OSX/64 10.8.3 (amazon) w/parallel
* [svn-r23432] I added a new macro HDF5_PLUGIN_PRELOAD to skip plugin loading ↵Raymond Lu2013-03-221-3/+11
| | | | | | during data reading. Tested on koala and jam.
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