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* Sync with develop (#1863)feature/onion_vfdDana Robinson2022-07-091-3/+3
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* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-23/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Add option for h5repack timing (#1142)Allen Byrne2021-11-081-14/+85
| | | | | | | | | | | | | | | | | * Add timing option to h5repack * Adjust help text * fix format * fix typos * Correct spacing * Change timing to use H5Timer * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD plugins (#602)jhendersonHDF2021-09-291-2/+2
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* Add support for parallel filters to h5repack (#832)jhendersonHDF2021-07-141-4/+21
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* File locks now work on Windows (#480)Dana Robinson2021-03-221-21/+46
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * File locks now work on Windows Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial). * Committing clang-format changes * Committing clang-format changes * Fixes commenting in h5repack * Reworks H5Fis_accessible() H5Fis_accessible() created a new file handle and attempted to read through it, which will fail when a file has been opened with an exclusive lock on operating systems that have mandatory locks. This change uses the same scheme we use in H5Fopen() to check if the file is already open and only tries to read the file signature if the file has not already been opened. Also adds a test for this behavior. * Committing clang-format changes * Trivial change to force github to run actions Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update clang config (#473)Quincey Koziol2021-03-171-1/+4
| | | | | | | * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)Sean McBride2021-03-091-3/+3
| | | | | | | | | | | | | * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Primary change is HDFFV-11212 - new refs and JNI (#372)Allen Byrne2021-02-251-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments
* Update license url part2 (#333)Larry Knox2021-02-171-1/+1
| | | | | | * 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.
* Clang-format of source filesAllen Byrne2020-09-301-728/+757
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* HDFFV-9984 Add options to merge/prune external links during repackAllen Byrne2020-08-141-11/+73
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* Trim trailing whitespaceQuincey Koziol2020-04-201-1/+1
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* Update Tools library to be better compatible with VOL connectorsJordan Henderson2020-03-171-19/+63
| | | | | | | | | | | | | | | | | | | | | Modify h5repack to integrate with VOL connectors Update tools library to accomodate VOL connectors Update logic in h5tools_fopen for VOL connectors Add command-line options to h5repack for specifying in/out VOL connectors Implement h5tools_set_vol_fapl Fix library shutdown issue Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme Avoid H5Ocopy in h5repack when using different VOL connectors Update h5tools_test_utils.c for ROS3 and HDFS integration
* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-1/+1
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* Update tools hid_t declarations with H5I_INVALID_HIDAllen Byrne2020-01-131-22/+22
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* Clean up tools warnings introduced by H5TOOLS_ERR_INIT macroJordan Henderson2019-12-311-116/+116
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* Refactor tools library error handling macrosJordan Henderson2019-12-281-111/+111
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* HDFFV-10980 - h5diff uses new ref APIsAllen Byrne2019-12-191-5/+5
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* HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-071-109/+109
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* Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-081-3/+3
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* HDFFV-10919 merge synchingAllen Byrne2019-10-021-108/+30
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* Merge branch 'develop' of ↵Jacob Smith2019-09-231-6/+9
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Add HD prefix to testsAllen Byrne2019-08-151-19/+19
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* | Change print calls to HD-wrapped.Jacob Smith2019-09-231-30/+36
| | | | | | | | Minor formatting tweaks (inc. regressions and in-file style-matching).
* | Merge branch 'develop' of ↵Jacob Smith2019-07-221-26/+4
|\ \ | |/ | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-26/+4
| | | | | | | | clean up warnings.
* | Undo some formatting modifications.Jacob Smith2019-06-211-17/+15
| | | | | | | | Update MANIFEST.
* | First pass at repack consolidating external storage if layout given.Jacob Smith2019-05-311-3/+12
| | | | | | | | Checks out manually, tests still complain.
* | Formatting changes, mostly.Jacob Smith2019-05-301-58/+125
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* TRILAB-81 coverity fixesAllen Byrne2018-10-171-3/+3
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* (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-164/+102
|\ | | | | | | | | | | (2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds. (3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check. (4) Add version bounds check for cache image feature.
| * Correct typoAllen Byrne2017-10-241-2/+2
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| * fix typoAllen Byrne2017-10-241-1/+1
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| * Fix typosAllen Byrne2017-10-241-1/+1
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| * HDFFV-10297 Free buffer inside loopAllen Byrne2017-10-231-0/+5
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| * HDFFV-10297 Cleanup, Initialize variablesAllen Byrne2017-10-231-14/+14
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| * Fix tools error handling and valgrind issuesAllen Byrne2017-10-181-8/+13
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| * HDFFV-10296 Update tools lib to use the error handling macros.Allen Byrne2017-10-131-132/+56
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* HDFFV-10297 - Fix test errors - five remainingAllen Byrne2017-10-091-3/+6
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* HDFFV-10297 - fix repack individual objectsAllen Byrne2017-10-061-104/+76
| | | includes H5Zfilter_avail() fix
* Update error handling to support ARGS and tools stackAllen Byrne2017-10-021-69/+38
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* HDFFV-10282 refactor out assert calls in toolsAllen Byrne2017-08-231-2/+0
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* Merge branch 'develop' into windows_openDana Robinson2017-05-311-107/+126
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| * HDFFV-8611 change h5repack to save the root group creation orderAllen Byrne2017-05-221-10/+29
| | | | | | Added test and new arguments to control the the input file parsing.
| * HDFFV-10186 Add endianess to bitfield and fix testsAllen Byrne2017-05-101-1/+1
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| * HDFFV-10186 Whitespace changeAllen Byrne2017-05-091-108/+107
| | | | | | | | Mostly tabs to spaces Remove Modifications comments
* | Rework of the POSIX file open permissions and macros to clean upDana Robinson2017-04-281-3/+3
|/ | | | | | HDopen() calls. Also fixed a minor const warning in the core VFD.
* 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.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-18/+56
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