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* Strip HD prefix from string/char C API calls (#3540)Dana Robinson2023-09-151-1/+1
| | | | | | | | | | | | | | | | | | | | | * Strip HD prefix from string/char C API calls * HD(f)(put|get)(s|c) * HDstr* * HDv*printf * HD(s)(print|scan)f * HDperror But NOT: * HDstrcase* * HDvasprintf * HDstrtok_r * HDstrndup As those are not C99 and have portability work-around implementations. They will be handled later. * Fix th5_system.c screwup
* hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491)Dana Robinson2023-09-051-23/+23
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* Add other types and full type to enum/str/vlen dataformat for ↵Allen Byrne2023-08-241-4/+12
| | | | structblock[begin/end] (#3353)
* Fix some warnings in developer builds (#3247)jhendersonHDF2023-07-181-0/+1
| | | | | * Fix some warnings in developer builds * Switch approach to Winline flag
* Remove programmer/date from comments (#3210)Dana Robinson2023-06-291-3/+0
| | | | * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work
* Remove HD from C std lib file ops (#3206)Dana Robinson2023-06-291-1/+1
| | | | | | | | | * HDfclose * HDferror * HDfeof * HDfflush * HDfopen * HDfread * HDfwrite
* Rename HD(f)printf() to (f)printf() (#3194)Dana Robinson2023-06-281-2/+2
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* Determine if native connector is terminal (#2397)Quincey Koziol2023-01-091-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths * Use API routine to determine if native connector is terminal. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Subfiling updates for release (#1963)jhendersonHDF2022-08-041-4/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built * Switch to MPI I/O driver for Subfiling HDF5 stub file * Rough first implementation for Subfiling file deletion * Subfiling VFD - get file dirname for file deletion * Subfiling VFD - set lock callback to NULL for now to avoid performance issues * Committing clang-format changes * Minor tidying up of Subfiling testing * Fixups for Subfiling VFD support in tools * Tidy up Subfiling public interface and add Doxygen * Respect Subfiling configuration settings from application * Add release note for Subfiling VFD * Committing clang-format changes * Committing clang-format changes * Shorten some Subfiling environment variable names Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD (#1953)Dana Robinson2022-08-021-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Onion VFD feature * Fixes onion VFD errors with non-sec2 backing store VFDs * Disables the onion VFD tests w/ ph5diff * Disables non-sec2 VFDs as onion VFD backing stores * Committing clang-format changes * Formatted source * Typo * Adds onion VFD tools tests to CMake * Fixes for v16 API compatibility * Memset structs to avoid bad frees on errors * H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE * Properly decodes checksums on BE machines * Be more careful about uint64_t to haddr_t/hsize_t conversions * Another fix for BE data comparison * Removed double underscores from onion constants * Replace hard-coded onion header string w/ constant * Fixes cleanup paths in H5FD__onion_ingest_history() * Fixed use of size_t revision numbers * Fix h5dump revision count format string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-23/+23
| | | | | * Update format source to clang 13 * More format changes
* Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix ↵David Young2022-02-211-3/+0
| | | | | | | | | | | | | | | | issues (#1423) * Correct some conversion specifications. * Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few instances where PRIdHSIZE was appropriate. Remove a couple of casts and use correct format strings, instead. * Copy values from a possibly unaligned buffer to aligned local variables instead of casting and dereferencing pointers into the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* VFD plugins (#602)jhendersonHDF2021-09-291-2/+7
| | | | | | | | | | | | | | | | | * 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
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)Sean McBride2021-03-091-3/+4
| | | | | | | | | | | | | * 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>
* Changes found during merge to 1.12 (#414)Allen Byrne2021-03-041-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup
* 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 Byrne2020-09-301-202/+214
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* Removes staff email addresses from the repositoryDana Robinson2020-08-071-1/+1
| | | | Removes redundant C library headers from hl library
* Tools refactorAllen Byrne2020-07-151-33/+34
| | | | | | Move error_stack setup to tools library Add structure for h5dump properties Eliminate duplicated h5diff functions Use properties structure in place of argument lists.
* Separated VFD and VOL parameters in tools.Dana Robinson2020-04-211-10/+23
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* Changed identifiers and command-line options from "id" to "value" in toolsDana Robinson2020-04-141-3/+3
| | | | code to be in agreement with H5VL API terminology.
* Added support for passing connector info strings via the commandDana Robinson2020-04-091-2/+2
| | | | line to the tools internals.
* Minor renaming in the tools code.Dana Robinson2020-03-311-9/+9
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* Fix some missing symbols issues in tools libraryJordan Henderson2020-03-271-2/+3
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* Update Tools library to be better compatible with VOL connectorsJordan Henderson2020-03-171-1/+48
| | | | | | | | | | | | | | | | | | | | | 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
* Add unknown define for h5dump ref objectsAllen Byrne2019-12-201-0/+1
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* Fix issues found with ONLY_SHARED_LIBS optionAllen Byrne2019-12-111-14/+14
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* Fix compile errors - mostly in jniAllen Byrne2019-12-061-2/+2
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* Comment correctionAllen Byrne2019-11-211-1/+1
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* HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-071-23/+25
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* HDFFV-10384 Add optional arg to enable-error-stackAllen Byrne2018-02-141-1/+1
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* Minor warning fixes in the tools.Dana Robinson2017-05-251-1/+1
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* HDFFV-8611 change h5repack to save the root group creation orderAllen Byrne2017-05-221-0/+4
| | | 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/+0
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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.
* Bring SWMR-related tools changes from revise_chunks to develop.Quincey Koziol2016-12-111-0/+9
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* [svn-r30113] Description:Quincey Koziol2016-06-281-9/+9
| | | | | | | | Clean up warnings (from 2774 -> 1560, with my standard debug build) Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29889] HDFFV-9775: Add enable-error-stack to tools lib and refactor ↵Allen Byrne2016-05-041-5/+8
| | | | h5repack error handling.
* [svn-r29534] Normalization w/ revise_chunks in preparation for big merge.Dana Robinson2016-03-231-1/+1
| | | | | | | | | tools directory Also fixes a minor Java test output error. Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial w/ Java, Fortran, & C++
* [svn-r27835] Description:Quincey Koziol2015-09-211-0/+4
|\ | | | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27801] Minor warning fixes in the tools.Dana Robinson2015-09-161-0/+4
| | | | | | | | Tested on: jam (too minor for h5committest)
* | [svn-r26440] Added new structure, removed ";", used static hyperslab arrays.Allen Byrne2015-03-121-6/+7
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* | [svn-r26383] Add MAPPING to VDS outputAllen Byrne2015-03-061-0/+1
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* | [svn-r26353] Add VDS selection defines for ALL and NONEAllen Byrne2015-03-041-0/+2
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* | [svn-r26352] Update h5dump to latest BNF - reg vs irreg hyperslabs.Allen Byrne2015-03-041-1/+4
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* | [svn-r26318] Update virtual layout to latest changesAllen Byrne2015-02-261-6/+2
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* | [svn-r26297] Changed example and h5dump according to suggestions at today's ↵Elena Pourmal2015-02-251-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | code review VDS-176. BNF has been updated too. Now h5dump displays VDS like this: HDF5 "vds.h5" { GROUP "/" { DATASET "VDS" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) } STORAGE_LAYOUT { VIRTUAL { HYPERSLAB { (0,0)-(0,5) }; a.h5; A; ALL; HYPERSLAB { (1,0)-(1,5) }; b.h5; B; ALL; HYPERSLAB { (2,0)-(2,5) }; c.h5; C; ALL; } } } FILTERS { ....... I just commented the code with "EIP" and didn't delete to simplify the review with Allen tomorrow. Tested on jam
* | [svn-r26285] add virtual mapping output blank selections but actual file and ↵Allen Byrne2015-02-231-0/+9
| | | | | | | | dataset names.
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