diff options
| author | jhendersonHDF <jhenderson@hdfgroup.org> | 2023-10-12 16:32:23 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-10-12 16:32:23 (GMT) |
| commit | ea3f92605761e1ff17d858df303dc375df7efc1c (patch) | |
| tree | 716311100f8d0f0dc77bca31245878546952aabc /tools/src/h5repack | |
| parent | 0feda66ff0dccdf77453b7c881c80be244e0ae12 (diff) | |
| download | hdf5-ea3f92605761e1ff17d858df303dc375df7efc1c.zip hdf5-ea3f92605761e1ff17d858df303dc375df7efc1c.tar.gz hdf5-ea3f92605761e1ff17d858df303dc375df7efc1c.tar.bz2 | |
1.14 sync with develop (#3660)
* Rework tools.cmake and add C flags (#3110)
* Fix gh pages so that the doxygen files are uploaded (#3102)
* Add workspace path
* add debug
* Make one job so workspace files are available
* Put doxygen docs under docs folder in gh-pages
* Fix a misc warning in test/vol.c (#3112)
The compiler complains about using integers instead of size_t
for some sizes.
* Remove H5detect and H5make_libsettings (#3104)
Removes H5detect and H5make_libsettings from the build and replaces
their functionality with things that don't affect cross-compiling.
H5detect --> floating-point types are now detected on library load
H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
* clang-tidy clang-analyzer-core issues addressed (#3113)
src/H5system.c:1293:13: warning: Dereference of null pointer
[clang-analyzer-core.NullDereference]
src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains
uninitialized data (e.g., via the field chain: 'initial.user')
[clang-analyzer-core.CallAndMessage]
* Add note for issue 3056 (#3117)
* Use 1.14 toolchain (#3116)
* Remove the checkposix script (#3122)
This script was used to ensure that all non-HDF5 calls were prefixed
with 'HD'. We are removing this scheme so this script is no longer
needed.
* Remove unused HD macros (#3120)
* Remove unused HD macros
The library prefixes most C and POSIX API calls with 'HD'. We are
going to start removing these so the code looks like normal C.
This PR removes most of the unused HD markup macros.
* Replace ntohl/ntohs
* Adds an optional version arg to bin/format_source (#3119)
* Clean up mirror VFD code in utils dir (#3121)
* Remove dead code
* Replace mybzero with memset
* Replace hbool_t/TRUE/FALSE with bool/true/false
* Fix spelling issues flagged by codespell (#3130)
* Make autogen.sh output message consistent (#3128)
* Add Python for HDF-EOS zoo description (#3129)
* Fix function name in comment in ros3 VFD (#3131)
* Revert long double checks (#3133)
* Revert "Remove long double conversion work-arounds (#3097)"
This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9.
* Update comments to reflect newer systems
* Add java options to build scripts (#3127)
* Add java options to build scripts
Previously, cmakehdf5 turned on compiling of the java interface
by default due to a value set in cacheinit.cmake.
Now, consistent with how Fortran and CPP interfaces are handled,
the script overwrites this default value to disable the libraries,
fixing #2958.
I also implemented the --enable-java/--disable java options for
cmakehdf5, and -java for buildhdf5.
Allen said these scripts should mention that
compilers are to be specified in environment variables, but missing
compilers causes errors at the CMake level, and
CMake's error messages are already pretty informative (See the one
in #2958 about JAVA_COMPILER).
* Removed .lnt linter files (#3143)
These were last usefully modified in 2004
* Fix path to libhdf5.settings in cmakehdf5 (#3140)
* Many clang -Wextra-semi-stmt fixes (#2537)
* Adds semicolons to function-like macros
* Adds a do..while(0) loop to some macros
* Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
* Remove HD prefix from network calls (#3142)
HDsocket(), etc. Only affects the mirror VFD and its test code.
* Remove hbool_t/TRUE/FALSE from java (#3145)
Replaces with bool/true/false
* CMake: (feature) ROS3 and cmake config file. (#3146)
- Added a cmake variable to the hdf5-config.cmake file which
indicate if the library has been build with or without the
read-only S3 functionality.
* Define minimal permissions for new GitHub workflows (#3147)
* Track s3 i/o when S3COMMS_DEBUG enabled (#3139)
* Track s3 i/o when S3COMMS_DEBUG enabled
* Fix the snapshots workflow (#3148)
* Add upload url as artifact
* Change doxygen path and comment log-url upload
* zip doxygen files for upload
* add workspace var
* chore: fix grammar (#3150)
* chore: fix grammar
* Removes the HD prefix from java C99 calls (#3149)
POSIX calls (HDstrndup, etc.) are unchanged
* Correct the zip usage (#3153)
* Many fixes to various compiler warnings (#3124)
* Fixed various -Wmissing-variable-declarations by adding static keyword
* In a few cases, renamed the variable suffix from _g to _s.
* Fixed some -Wmissing-variable-declarations by using different declaration macros
* Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero
* Fixed various -Wcomma warnings
* Fixed clang -Wstrict-prototypes warnings
* Fixed various -Wunused-variable warnings
* Updated some casts to fix the only 3 -Wcast-qual warnings
* Fixed the only -Wsometimes-uninitialized warning
* Create Security Policy (#3152)
* Fix #1978 h5vers usage message. (#3162)
Update Platforms Tested in RELEASE.txt.
* speed-up building HDF5 (#3087)
Disables building the tests when building the netCDF, etc.
* Remove dead code behind #ifdef OLD_WAY (#3163)
* Remove H5F_evict_tagged_metadata() (#3165)
The rest of the library just calls H5AC_evict_tagged_metadata()
directly.
* Add missing space in zip command (#3167)
* Fixed check for a VOL's async compatibility (#3164)
* cap flag fix in test
* added async comp. output
* Update Linux workflows (#3173)
* Consolidate environment setup
* Turn on ros3 VFD in CMake (Linux only)
* Add gh-pages doxygen link (#3175)
* Fix the doxygen to gh pages and artifact creation (#3176)
* Tidy the list of options in main.yml (#3181)
* Remove HD/hbool_t from fortran (#3182)
* Remove HD/hbool_t from high-level lib (#3183)
* Remove HDva_(arg|copy|end|start) (#3184)
* Drop HD prefix & hbool_t from H5TS (#3180)
* Remove HD from fork/exec*/wait* (#3190)
These are not C99 but are hidden behind ifdefs and are highly
unlikely to ever have non-POSIX equivalents.
* Fix assertion failure when attempting to use IOC VFD directly (#3187)
* Rename HDqsort() to qsort() (#3193)
* Rename HDqsort() to qsort()
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Rename HDpipe() to pipe() (#3192)
Pipe is POSIX but implemented in Microsoft's CRT
* Rename HDassert() to assert() (#3191)
* Change HDassert to assert
* Fix bin/make_err
* Rename HD(f)printf() to (f)printf() (#3194)
* Add note about HDF5_VOL_CONNECTOR to tools usage (#3159)
* Rename HDsystem() to system() (#3197)
system() is only used in the iopipe test and the things it calls
(which are POSIX-y) are protected by an ifdef.
* Remove HD from HDposix_memalign() (#3196)
The posix_memalign call is only used in the direct VFD, which can only
be built if posix_memalign() is available.
* Remove HD from memory allocate/free calls (#3195)
* HDcalloc
* HDfree
* HDmalloc
* HDrealloc
* chore: fix grammar (#3207)
* docs: remove redundancy in Data Transfer section of user guide (#3208)
* Remove checks for setsysinfo, which is unused (#3205)
* Autotools
* CMake
* Remove HD from protected POSIX calls (#3203)
These calls are non-C99 but protected by ifdefs and have no Windows
equivalents:
* HDalarm
* HDasprintf
* HDclock_gettime
* HDfcntl
* HDgethostname
* HDgetrusage
* HDsymlink
* Rename HDato*() to ato*() (#3201)
* Remove some "Programmer" comments (#3209)
These are meaningless noise.
Removes the "Programmer" lines on comment start lines:
/* Programmer: John Smith
These complicate my sed script that will rip out the rest of
the comments.
* Rename HDexit() and related to exit(), etc. (#3202)
* HDatexit
* HDexit
* HD_exit
* Remove HD from strto* calls (#3204)
* HDstrtod
* HDstrtol
* HDstrtoll
* HDstrtoul
* HDstrtoull
* HDstrtoumax
* Remove HD from C std lib file ops (#3206)
* HDfclose
* HDferror
* HDfeof
* HDfflush
* HDfopen
* HDfread
* HDfwrite
* Remove programmer/date from comments (#3210)
* Removes Programmer: and Date: fields
* Fixes a few Modifications: fields leftover from previous work
* Remove HD from HDmem* calls (#3211)
* Remove HD from HDis* (e.g., isalpha) (#3212)
* HDisalnum
* HDisalpha
* HDiscntrl
* HDisdigit
* HDisgraph
* HDislower
* HDisprint
* HDispunct
* HDisspace
* HDisupper
* HDisxdigit
* Update actions for release option, fix branch for daily build (#3185)
* Update actions for release option, fix branch for daily build
* Scheduled workflows run on latest commit on the develop
* Add snapshots location
* docs: improve consistency in verb form (#3076) (#3188)
* fix gh action if statements (#3213)
* Adjust presets timeout and fix build script VS versions (#3215)
* Several ros3vfd logging improvements
* Committing clang-format changes
* Update COPYING (#3231)
Fixed old support URL.
* addresses compilation fortran warnings on Frontier (#3236)
* Fix doc for H5allocate_memory (#3240)
* merge bbrelease to release (#3232)
* merge bbrelease to release
* Fix pre-req workflow
* Replace support.hdfgroup.org URLs for alternative COPYING file (#3228)
* Replace support.hdfgroup.org URLs for alternative COPYING file
locations in copyright headers with https://www.hdfgroup.org/licenses.
Replace support.hdfgroup.org URL for alternative COPYING_LBNL_HDF5
with github URL.
Tweak chkcopyright script for change from UICOPYRIGHTSTR to
THGCOPYRIGHTSTR.
* Replace 1_10 reference with develop branch (#3227)
* Switch CI to use release script (#3242)
* Subfiling VFD source cleanup (#3241)
* Subfiling VFD source cleanup
Modularize Subfiling CMake code into separate CMakeLists.txt file
Update Mercury util code to latest version and update Copyright
Generate mercury_util_config.h header file instead of using
pre-generated file
Remove unnecessary Mercury functionality
Fix minor warning in Subfiling VFD code
* Remove Mercury headers from Autotools publicly-distributed header list
* install h5fuse.sh in bin dir. (#3244)
* Disable h5py until fixed properly without spack (#3243)
* ROS3: (feature) Temporary security credentials (#3030)
- Implemented support for AWS temporary security credentials.
For this kind of credentials also a session/security token
should be included in the request by adding the
x-amz-security-token header.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Avoid truncating at null byte when copying to std::string (#3083)
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix CMake builds when Subfiling VFD isn't enabled (#3250)
* Fix CMake builds when Subfiling VFD isn't enabled
* Add Subfiling VFD entry to hdf5-config.cmake.in
* Fix some warnings in developer builds (#3247)
* Fix some warnings in developer builds
* Switch approach to Winline flag
* Fixed more warnings about extra semicolons (#3249)
* Require semi-colon after H5_CHECK_OVERFLOW calls
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro (#3259)
Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning
causing Werror Release builds to fail
* Update DEFAULT_API_VERSION documentation for CMake (#3255)
* Update DEFAULT_API_VERSION documentation for CMake
* Fix hint
---------
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* changed the scope of #ifdef DOXYGEN to now include H5D multi-functions (#3254)
* Option changed but not all references (#3252)
* Option changed but not all references
* remove quotes from binary var
* Move 1.12.3 release to October (#3263)
* Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized warning (#3260)
* removed the use of encoded single apostrophe (#3261)
* removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read
* updated sanitizer paragraph
* fixed brief description for H5Fget_info
* ROS3: (fix) Replaced HDfprintf (#3266)
- Replaced the HDfprintf() functions by fprintf() to be consistent
with other parts of the library.
* chore: make VRFY output consistent (#3268)
* CMake: (fix) Threads dependency (#3267)
- If the HDF5 library has been build with either thread-safety or
subfiling VFD feature on it will have an additional dependency
on a threading library. This dependency has been added to the
hdf-config.cmake.in file.
* chore: fix grammar - get hang -> get hung (#3272)
* Another round of fixing -Wextra-semi-stmt warnings (#3264)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* chore: fix typo - persent -> present (#3273)
* Remove py-pip from h5py action (#3265)
* Update release schedule (#3317)
* Move 1.12.3 to November
* Add 1.14.3 in October
* Update README.md w/ 1.4.3 info (#3318)
* Switch parallel compression to use vector I/O (#3245)
Updates parallel compression feature to use vector I/O instead of
creating and passing down MPI derived types to VFD
* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312)
* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314)
* Fix loading plugin fails with missing directory GH issue #3248 (#3315)
* Made HGOTO_ERROR a do-while loop (#3308)
* Made HGOTO_ERROR a do-while loop
* Update files to skip list and ignore_words_list (#3321)
* Update files to skip list and ignore_words_list for codespell to not
check files generated by autotools. Autotools generate misspellings
that can't be fixed in HDF5 code.
* Windows runtime items go into the bin folder (#3320)
* A couple of documentation items to fix (#3332)
* Fix h5repack for variable-length datatyped datasets (#3331)
* Fix CVE-2018-11202 (#3330)
A malformed file could result in chunk index memory leaks. Under most
conditions (i.e., when the --enable-using-memchecker option is NOT
used), this would result in a small memory leak and and infinite loop
and abort when shutting down the library. The infinite loop would be
due to the "free list" package not being able to clear its resources
so the library couldn't shut down. When the "using a memory checker"
option is used, the free lists are disabled so there is just a memory
leak with no abort on library shutdown.
The chunk index resources are now correctly cleaned up when reading
misparsed files and valgrind confirms no memory leaks.
* Fix CVE-2018-13867 (#3336)
* Fixes the last of the -Wextra-semi-stmt warnings (#3326)
* Fixed extra semi warning by adjusting alternative macro definitions
* Find-replace H5E_END_TRY; -> H5E_END_TRY
* Made H5Epush_goto a do-while loop, fixed indentation
* Made GOTOERROR and ERRMSG do-while loops
* Made Hgoto_error and Hgoto_done do-while loops
* Made vrfy_cint_type and vrfy_ctype do-while loops
* Made TEST_TYPE_CONTIG and others do-while loops
* Removed extraneous semi-colons
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix a typo in RELEASE.txt
* Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340)
* Make h5dump spacing consistent when printing VLEN datatype (#3351)
* Fix for the bug exposed from running test/set_extent.c when selection… (#3319)
* Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled.
This is a fix from Neil.
The test/set_extent.c is modified to test for selection I/O enabled.
* Add Fortran ES module to deploy list (#3341)
* Add Fortran ES module to deploy list
* Change fortran mod file export to use a list of names
* test(parallel): verify FALSE case (#3356)
* Implementation of the mpio driver with selection I/O. (#3222)
* This changes the default selection I/O to on for MPIO.
* Work around a testphdf5 failure on Cray MPICH machines (#3361)
* set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with (#3364)
CMake to fix Fortran build failures.
* Add RELEASE.txt notes for recent selection I/O work. (#3374)
* Fix possible performance regression introduced with in-place type conversion in 1.14.2 (#3376)
* Correct script (#3377)
* Correct CI settings (#3384)
* Correct CI settings
* Correct plugin file name
* restore CI tarball name prefix to match bin/release (#3385)
* Fix assertion failure during file close on error (#3387)
* Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388)
* Fix valgrind warning about write of uninitialized bytes (#3389)
* Fix valgrind warning about write of uninitialized bytes in ScaleOffset filter (#3390)
* Update presets, examples uncompress, szip cache (#3391)
* Fix serial to parallel chunked dataset file space allocation bug (#3394)
* chore: fix typo (#3405)
* Fix for CVE-2016-4332 (#3406)
This CVE issue was previously listed as fixed (via HDFFV-9950) back in
2016, but with no confirmation test. Now that test files exist for
the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an
assert in debug builds.
This fix replaces the assert with pointer checks that don't raise
errors or asserts. Since the function is in cleanup code, we do our
best to close and free things, even when presented with partially-
initialized structs.
Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407)
* Enable szip by default in Autotools (#3412)
Since libaec is so prevalent and BSD-licensed for both encode and
decode, we build the szip filter by default when the szip or aec
libraries are found.
* Re-enable SZIP default to ON in CMake (#3414)
The Autotools were handled in a separate commit
* Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368)
* Add Intel oneAPI actions (#2949) (#2977)
* ci: add Intel oneAPI actions (#2949)
* ci: fix CMake installation
* ci: use absolute paths for libtool installation
* ci(oneAPI): update compiler versions and use cron
* Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416)
* chore: remove gubbins comment (#3420)
* Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] (#3353)
* Avoid H5Ocopy in h5repack for variable-length string types (#3419)
* Skip atomicity tests for OpenMPI major versions < 5 (#3421)
* Fix an issue with use of uninitialized memory in trefer_deprec.c test (#3422)
* Add parallel examples in doxygen (#3413)
* Fix use of uninitialized value in testpar/t_dset.c test (#3423)
* Remove extraneous "33" in RELEASE.txt (#3425)
* Revise file close assertion failure fix (#3418)
* Remove intel oneapi warning (#3426)
* Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with segmenetation fault. (#3427)
It is because the object in the testfile points back to the root group.
When the tool tries to traverse the object, it goes back to the root group and then back again.
* chore: match function call and VRFY() output (#3428)
* Fix the Fortran extension used in example links (#3430)
* Put H5T_CONV_ab macros in do..while loops (#3432)
Ever since a recent round of macro cleanup, bin/trace and clang-format
have been bickering over what H5Tconv.c should look like and neither
produces readable code.
This change puts the top-level H5T_CONV_ab macros in do..while loops,
adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF
and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros
clang-format recognizes. H5Tconv.c is now readable and both bin/trace
and clang-format are happy.
* Convert some H5MM calls to standard C equivalents (#2382)
* H5MM_calloc and malloc are now mapped to stdlib C calls
* H5MM_memcpy now maps directly to memcpy in release builds
* H5MM_memcpy is still implemented as a separate function that
checks for buffer overlap when H5MM_DEBUG is defined
(default w/ debug builds)
* Switches many library memcpy calls to use H5MM_memcpy
* Fixes a possible zero allocation in H5Olayout.c
* Add 1.14.4 to the release schedule (#3434)
* Output stderr file in CMake testing on failure (#3431)
* Add Intel oneAPI badges (#3433)
* Add a CVE regression test action (#3445)
*
* Disable SZIP for Intel oneAPI Action (#3449)
* Disable SZIP for Intel oneAPI Action
* Disable Fortran and parallel
* Update VOL CMake for REST VOL (#3450)
* Update VOL CMake for REST VOL
* Prevent linking static libs to VOLs
* Add an h5py badge to README.md (#3477)
* Removed all the ranks printing out testing information (#3457)
* Fix Subfiling VFD IOC assignment bug (#3456)
* Correct java test dimension (#3482)
* Support CMake VOL builds with FetchContent from local directory (#3455)
* Update VOL CMake for REST VOL
* Prevent linking static libs to VOLs
* index on fetch_local: 5c5c3f1505 Prevent linking static libs to VOLs
* index on (no branch): 9a36d3e7b1 On fetch_local: WIP:add source dir fetch option for vols
* Allow building of VOL from local source
* Move LOCAL_DIR option to HDF5_VOL_ALLOW_EXTERNAL
* Fix the Fortran include dir in install config files (#3454)
* Convert hbool_t --> bool in examples (#3492)
* Fix some minor formatting for consistency (#3499)
* Create scorecard.yml (#3508)
Bring in OSSF Scorecard code scanner as a GitHub action
* Convert hbool_t --> bool in testpar (#3495)
* hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491)
* Convert hbool_t --> bool in test (#3494)
* Convert hbool_t --> bool in src (#3496)
* hbool_t --> bool in src
* Does not remove TRUE/FALSE
* Public header files are unchanged
* Public API calls are unchanged
* TRUE/FALSE --> true/false in src
* Add deprecation notice for hbool_t
* Added new Fortran API wrappers (#3511)
* Added new wrappers for
h5get_free_list_sizes_f
H5Sselect_intersect_block_f
H5Sselect_shape_same_f
h5pget_no_selection_io_cause_f
h5pget_mpio_no_collective_cause_f
H5Lvisit_by_name_f
H5Lvisit_f
H5Fget_info_f
h5dwrite_chunk_f
h5dread_chunk_f
* added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests
* added fortran tests
* Update tH5F.F90
* misc. fortran fixes for failing CI dailty tests (#3523)
* fixed H5Lvisit* interface
* changed integer type for direct write
* Consistent initialization of hid_t in the tests (#3521)
* Fix windows cpack with debug (#3525)
* Add missing row for the ROS3 VFD in table #3415 (#3517)
* fixed nvidia compiler issue (#3527)
* Identify functions in a subgroup (#3530)
* quiet warning on sunspot (gcc 11.2.0) (#3534)
* Add API examples doxygen page (#3500)
* removed C_INT32_T from Fortran APIs (#3537)
* Add NVHPC 23.7 GitHub Actions (#3509)
* Add NVHPC 27.3 GitHub Actions
* Address @derobins review
* Remove HD prefix from math functions (#3538)
* Remove HD prefix from HDlog10 calls (#3539)
Was missed in a previous commit and causes building subfiling to
fail.
* fixed arg to C H5Dwrite_chunk (#3541)
* Strip HD prefix from string/char C API calls (#3540)
* 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
* Convert main.yml CI into callable workflows (#3529)
* Fix broken URL. (#3546)
* Fix grammar (#3545)
* Update oneAPI-C/A badge yml links. (#3564)
* Check return values from HDF5 API calls. (#3556)
* Adds link to h5fuse.sh in testpar for autotools (#3557)
* Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.
* Some minor formatting and text changes (#3563)
* Fix typos and grammar in t_pread. (#3565)
* Fix typo (givin->given) in test/testframe.c. (#3567)
* Fix ifx unused variable hdferr warning. (#3568)
* Correct comments about H5Z_FILTER_NONE (#3572)
* Update release script. (#3577)
* fixed function declaration (#3579)
* Fixed GH-3554 (#3584)
Removed the extra condition
* Remove h5dwalk.1 man page. (#3589)
* Removed the use of -commons linking option on Darwin (#3581)
Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Fix docs for H5Pset_dxpl_mpio_collective_opt() (#3594)
* Fix typo: arange->arrange in src/H5Cmpio.c. (#3597)
* Fix docs for H5Acreate2 and H5Acreate_by_name (#3598)
* Use HDoff_t with lseek consistently (#3600)
lseek on Windows uses __int64 for both the offset and return type
instead of off_t like most POSIX systems. This changes ensures we
use HDoff_t (which is typdef'd correctly on Windows) w/ lseek.
* Replaces HDgetenv with getenv (#3599)
* Develop tools move (#3580)
Reorganizes the tools files to support the VOL tests
* Clean up Subfiling VFD header doxygen formatting (#3601)
* Remove `sh` to run bash script. (#3590)
* Correct path name of ddl file to be changed (#3607)
* Fix potential uninitialized variable (#3602)
Moves a union initialization up a bit so it's performed before code
that can jump to the cleanup target, where file descriptors could
be checked without being initialized.
This could only happen in test code and only in an out-of-memory
situation.
Fixes Coverity 1542254
* Remove unnecessary assignment in test generator (#3603)
Fixes what looks like a copy/paste/modify error in the format convert
test file generator, where an array element is assigned one value
and them immediately overwritten by another value.
Fixes Coverity issue 1542285
* Remove useless define TRUE/FALSE statements. (#3604)
* Fix typo behaviour and dependes. (#3605)
* Fix typos (#3609)
* Fixed unused variable in H5CS.c (#3552) (#3612)
* Fixed #3552
* Fix grammar (#3614)
* Cleanup unused statements (#3553) (#3617)
Removed unnecessary assert statements and noise comments.
* Fix Intel oneAPI icc warning (#3619)
* Fix several spelling/grammar issues (#3621)
* Add HPC CDash to README.md (#3623)
* Disable static + thread-safe on Windows w/ CMake (#3622)
The thread-safety feature on Windows requires a hook in DllMain() and
thus is only available when HDF5 is built as a shared library.
This was previously a warning, but has now been elevated to a fatal
error that cannot be overridden with ALLOW_UNSUPPORTED.
Fixes GitHub #3613
* Remove unused member from H5D_shared_t struct. (#3628)
* Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624)
* Fix grammar (#3635)
* Disambiguate error output messages. (#3634)
* Disambiguate error output messages.
* Address @brtnfld review.
* Fail CMake on Windows when sub-filing VFD is enabled (#3636)
* Improve consistency in past tense usage (#3638)
* Split out test logic to separate file (#3639)
* Drop MPI-2 support (#3643)
* Switch IEEE flags for NAG Fortran (#3644)
Default is -ieee=stop, which causes problems when the H5T
module performs floating-point type introspection.
The new mode is -ieee=full
* Remove 1.10.11 info from README.md (#3646)
* Fixes GH#1027 compilation error (#3654)
* Remove 1.10 badge (#3650)
* Use real URLs and updated names for plugins (#3651)
* synchronize TGZ naming convention/usage
* Update parallel compression feature to support multi-dataset I/O (#3591)
* Add more tests for selection I/O. (#3528)
* Adjust 1.14 files after merging
---------
Diffstat (limited to 'tools/src/h5repack')
| -rw-r--r-- | tools/src/h5repack/h5repack.c | 8 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.h | 10 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_copy.c | 76 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_filters.c | 6 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_main.c | 84 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_opttable.c | 40 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_parse.c | 48 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 2 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_verify.c | 4 |
9 files changed, 139 insertions, 139 deletions
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c index 7849e29..6747c25 100644 --- a/tools/src/h5repack/h5repack.c +++ b/tools/src/h5repack/h5repack.c @@ -67,7 +67,7 @@ h5repack(const char *infile, const char *outfile, pack_opt_t *options) *------------------------------------------------------------------------- */ int -h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) +h5repack_init(pack_opt_t *options, int verbose, bool latest) { int k, n; @@ -373,7 +373,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ H5O_info2_t oinfo; /* object info */ int j; unsigned u; - hbool_t is_ref = 0; + bool is_ref = 0; H5T_class_t type_class = -1; int ret_value = 0; @@ -523,7 +523,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ /* Check if we have VL data and string in the attribute's datatype that must * be reclaimed */ - if (TRUE == h5tools_detect_vlen(wtype_id)) + if (true == h5tools_detect_vlen(wtype_id)) H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf); free(buf); @@ -562,7 +562,7 @@ done: /* Check if we have VL data and string in the attribute's * datatype that must be reclaimed */ - if (TRUE == h5tools_detect_vlen(wtype_id)) + if (true == h5tools_detect_vlen(wtype_id)) H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf); /* Free buf */ diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h index 0387c68..fa79c6f 100644 --- a/tools/src/h5repack/h5repack.h +++ b/tools/src/h5repack/h5repack.h @@ -35,7 +35,7 @@ /* File space default information */ #define FS_PAGESIZE_DEF 4096 #define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR -#define FS_PERSIST_DEF FALSE +#define FS_PERSIST_DEF false #define FS_THRESHOLD_DEF 1 /*------------------------------------------------------------------------- @@ -111,11 +111,11 @@ typedef struct { chunk_info_t chunk_g; /* global chunk INFO for the ALL case */ H5D_layout_t layout_g; /* global layout information for the ALL case */ int verbose; /* verbose mode */ - hbool_t merge; /* Merge external file. */ - hbool_t prune; /* Don't follow external file. */ + bool merge; /* Merge external file. */ + bool prune; /* Don't follow external file. */ hsize_t min_comp; /* minimum size to compress, in bytes */ int use_native; /* use a native type in write */ - hbool_t latest; /* pack file with the latest file format */ + bool latest; /* pack file with the latest file format */ H5F_libver_t low_bound; /* The file's low bound as in H5Fset_libver_bounds() */ H5F_libver_t high_bound; /* The file's high bound as in H5Fset_libver_bounds() */ hid_t fin_fapl; /* FAPL to use for opening the input file */ @@ -153,7 +153,7 @@ extern "C" { int h5repack(const char *infile, const char *outfile, pack_opt_t *options); int h5repack_addfilter(const char *str, pack_opt_t *options); int h5repack_addlayout(const char *str, pack_opt_t *options); -int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest); +int h5repack_init(pack_opt_t *options, int verbose, bool latest); int h5repack_end(pack_opt_t *options); int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options); int h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, hid_t fname2_fapl); diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c index dd32a3c..3921913 100644 --- a/tools/src/h5repack/h5repack_copy.c +++ b/tools/src/h5repack/h5repack_copy.c @@ -67,11 +67,11 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options) trav_table_t *travt = NULL; hsize_t ub_size = 0; /* size of user block */ H5F_fspace_strategy_t set_strategy; /* Strategy to be set in output file */ - hbool_t set_persist; /* Persist free-space status to be set in output file */ + bool set_persist; /* Persist free-space status to be set in output file */ hsize_t set_threshold; /* Free-space section threshold to be set in output file */ hsize_t set_pagesize; /* File space page size to be set in output file */ H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ - hbool_t in_persist; /* Persist free-space status from input file */ + bool in_persist; /* Persist free-space status from input file */ hsize_t in_threshold; /* Free-space section threshold from input file */ hsize_t in_pagesize; /* File space page size from input file */ unsigned crt_order_flags; /* group creation order flag */ @@ -274,7 +274,7 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options) if (options->fs_persist == -1) /* A default "persist" is specified by user */ set_persist = FS_PERSIST_DEF; else if (options->fs_persist != 0) /* Set "persist" as specified by user */ - set_persist = (hbool_t)options->fs_persist; + set_persist = (bool)options->fs_persist; if (options->fs_threshold == -1) /* A "0" threshold is specified by user */ set_threshold = (hsize_t)0; @@ -654,7 +654,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti int is_ref = 0; htri_t is_named; htri_t is_vlen = 0; - hbool_t limit_maxdims; + bool limit_maxdims; hsize_t size_dset; int ret_value = 0; @@ -683,7 +683,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti for (i = 0; i < travt->nobjs; i++) { /* init variables per obj */ buf = NULL; - limit_maxdims = FALSE; + limit_maxdims = false; switch (travt->objs[i].type) { case H5TRAV_TYPE_UNKNOWN: @@ -725,7 +725,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti * and copy its attributes using that ID *------------------------------------------------------------------------- */ - if (HDstrcmp(travt->objs[i].name, "/") == 0) { + if (strcmp(travt->objs[i].name, "/") == 0) { if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); } @@ -763,7 +763,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti *------------------------------------------------------------------------- */ case H5TRAV_TYPE_DATASET: { - hbool_t use_h5ocopy; + bool use_h5ocopy; read_time = 0.0; write_time = 0.0; @@ -778,7 +778,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti /* check if filters were requested for individual objects */ if (options->op_tbl->objs) { for (u = 0; u < options->op_tbl->nelems; u++) { - if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) + if (strcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) for (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) { if (options->op_tbl->objs[u].filter[ifil].filtn > 0) req_filter = 1; @@ -867,7 +867,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); if (in_vol_id != out_vol_id) - use_h5ocopy = FALSE; + use_h5ocopy = false; if (in_vol_id != default_vol_id) if (H5VLclose(in_vol_id) < 0) @@ -979,15 +979,15 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti if (options->op_tbl->nelems > 0) { /* if current obj match specified obj */ if (options_get_object(travt->objs[i].name, options->op_tbl)) - limit_maxdims = TRUE; + limit_maxdims = true; } else /* no dataset is specified */ - limit_maxdims = TRUE; + limit_maxdims = true; /* if convert to COMPACT */ if (options->layout_g == H5D_COMPACT) if (size_dset > MAX_COMPACT_DSIZE) - limit_maxdims = FALSE; + limit_maxdims = false; /* unset unlimited max dims */ if (limit_maxdims) @@ -1032,7 +1032,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti /* Set up collective write if using filters in parallel */ { #ifdef H5_HAVE_PARALLEL - hbool_t parallel = (H5FD_MPIO == H5Pget_driver(options->fout_fapl)); + bool parallel = (H5FD_MPIO == H5Pget_driver(options->fout_fapl)); if (parallel && apply_s && apply_f) { if ((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0) @@ -1070,7 +1070,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti /* Check if we have VL data in the dataset's * datatype that must be reclaimed */ - if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) + if (true == H5Tdetect_class(wtype_id, H5T_VLEN)) if (H5Treclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Treclaim failed"); @@ -1104,8 +1104,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti H5I_INVALID_HID; /* dataset creation property list ID */ /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; + if (H5Tdetect_class(wtype_id, H5T_VLEN) == true) + vl_data = true; /* check first if writing dataset is chunked, * if so use its chunk layout for better performance. */ @@ -1420,7 +1420,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti } /* Set flag for intermediate group creation */ - if (H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) + if (H5Pset_create_intermediate_group(lcpl_id, true) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_create_intermediate_group failed"); if (H5Ocopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, ocpl_id, @@ -1528,7 +1528,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr, pack_opt_ char f_objname[256]; /* filter objname */ int i; - HDstrcpy(strfilter, "\0"); + strcpy(strfilter, "\0"); /* get information about input filters */ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) @@ -1539,65 +1539,65 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr, pack_opt_ if ((filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, sizeof(f_objname), f_objname, NULL)) < 0) { - HDstrcat(strfilter, "ERROR "); + strcat(strfilter, "ERROR "); continue; } switch (filtn) { case H5Z_FILTER_NONE: - HDstrcat(strfilter, "NONE "); + strcat(strfilter, "NONE "); break; case H5Z_FILTER_DEFLATE: - HDstrcat(strfilter, "GZIP "); + strcat(strfilter, "GZIP "); #if defined(PRINT_DEBUG) { unsigned level = cd_values[0]; - HDsnprintf(temp, sizeof(temp), "(%d)", level); - HDstrcat(strfilter, temp); + snprintf(temp, sizeof(temp), "(%d)", level); + strcat(strfilter, temp); } #endif break; case H5Z_FILTER_SZIP: - HDstrcat(strfilter, "SZIP "); + strcat(strfilter, "SZIP "); #if defined(PRINT_DEBUG) { unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/ unsigned ppb = cd_values[1]; - HDsnprintf(temp, sizeof(temp), "(%d,", ppb); - HDstrcat(strfilter, temp); + snprintf(temp, sizeof(temp), "(%d,", ppb); + strcat(strfilter, temp); if (options_mask & H5_SZIP_EC_OPTION_MASK) - HDstrcpy(temp, "EC) "); + strcpy(temp, "EC) "); else if (options_mask & H5_SZIP_NN_OPTION_MASK) - HDstrcpy(temp, "NN) "); + strcpy(temp, "NN) "); } - HDstrcat(strfilter, temp); + strcat(strfilter, temp); #endif break; case H5Z_FILTER_SHUFFLE: - HDstrcat(strfilter, "SHUF "); + strcat(strfilter, "SHUF "); break; case H5Z_FILTER_FLETCHER32: - HDstrcat(strfilter, "FLET "); + strcat(strfilter, "FLET "); break; case H5Z_FILTER_NBIT: - HDstrcat(strfilter, "NBIT "); + strcat(strfilter, "NBIT "); break; case H5Z_FILTER_SCALEOFFSET: - HDstrcat(strfilter, "SCALEOFFSET "); + strcat(strfilter, "SCALEOFFSET "); break; default: - HDstrcat(strfilter, "UD "); + strcat(strfilter, "UD "); break; } /* end switch */ } /* end for each filter */ @@ -1610,10 +1610,10 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr, pack_opt_ else { char str[512], temp[512]; - HDstrcpy(str, "dset "); - HDstrcat(str, strfilter); - HDsnprintf(temp, sizeof(temp), " (%.3f:1)", ratio); - HDstrcat(str, temp); + strcpy(str, "dset "); + strcat(str, strfilter); + snprintf(temp, sizeof(temp), " (%.3f:1)", ratio); + strcat(str, temp); if (options->verbose == 2) printf(FORMAT_OBJ_TIME, str, read_time, write_time, objname); else diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c index 512e4fa..9669d0c 100644 --- a/tools/src/h5repack/h5repack_filters.c +++ b/tools/src/h5repack/h5repack_filters.c @@ -57,7 +57,7 @@ aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */ } objout->nfilters = nfilters; - HDstrcpy(objout->path, name); + strcpy(objout->path, name); if ((layout = H5Pget_layout(dcpl_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_layout failed"); @@ -92,7 +92,7 @@ aux_find_obj(const char *name, /* object name from traverse list */ unsigned int i; for (i = 0; i < options->op_tbl->nelems; i++) { - if (HDstrcmp(options->op_tbl->objs[i].path, name) == 0) { + if (strcmp(options->op_tbl->objs[i].path, name) == 0) { *obj = options->op_tbl->objs[i]; return (int)i; } @@ -104,7 +104,7 @@ aux_find_obj(const char *name, /* object name from traverse list */ if (pname[0] == '/') pname++; - if (HDstrcmp(pdest, pname) == 0) { + if (strcmp(pdest, pname) == 0) { *obj = options->op_tbl->objs[i]; return (int)i; } diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index 85bc15d..85ab93a 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -400,11 +400,11 @@ read_info(const char *filename, pack_opt_t *options) /* cycle until end of file reached */ while (1) { - if (EOF == HDfscanf(fp, "%9s", stype)) + if (EOF == fscanf(fp, "%9s", stype)) break; /* Info indicator must be for layout or filter */ - if (HDstrcmp(stype, "-l") != 0 && HDstrcmp(stype, "-f") != 0) { + if (strcmp(stype, "-l") != 0 && strcmp(stype, "-f") != 0) { error_msg("bad file format for %s", filename); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; @@ -415,7 +415,7 @@ read_info(const char *filename, pack_opt_t *options) i = 0; c = '0'; while (c != ' ') { - if (HDfscanf(fp, "%c", &c) < 0 && ferror(fp)) { + if (fscanf(fp, "%c", &c) < 0 && ferror(fp)) { error_msg("fscanf error\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; @@ -427,7 +427,7 @@ read_info(const char *filename, pack_opt_t *options) c = '0'; /* go until end */ while (c != ' ') { - if (HDfscanf(fp, "%c", &c) < 0 && ferror(fp)) { + if (fscanf(fp, "%c", &c) < 0 && ferror(fp)) { error_msg("fscanf error\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; @@ -441,7 +441,7 @@ read_info(const char *filename, pack_opt_t *options) } comp_info[i - 1] = '\0'; /*cut the last " */ - if (!HDstrcmp(stype, "-l")) { + if (!strcmp(stype, "-l")) { if (h5repack_addlayout(comp_info, options) == -1) { error_msg("could not add chunk option\n"); h5tools_setstatus(EXIT_FAILURE); @@ -481,9 +481,9 @@ set_sort_by(const char *form) { H5_index_t idx_type = H5_INDEX_UNKNOWN; - if (!HDstrcmp(form, "name")) + if (!strcmp(form, "name")) idx_type = H5_INDEX_NAME; - else if (!HDstrcmp(form, "creation_order")) + else if (!strcmp(form, "creation_order")) idx_type = H5_INDEX_CRT_ORDER; return idx_type; @@ -504,9 +504,9 @@ set_sort_order(const char *form) { H5_iter_order_t iter_order = H5_ITER_UNKNOWN; - if (!HDstrcmp(form, "ascending")) + if (!strcmp(form, "ascending")) iter_order = H5_ITER_INC; - else if (!HDstrcmp(form, "descending")) + else if (!strcmp(form, "descending")) iter_order = H5_ITER_DEC; return iter_order; @@ -525,10 +525,10 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) h5tools_vol_info_t out_vol_info; h5tools_vfd_info_t in_vfd_info; h5tools_vfd_info_t out_vfd_info; - hbool_t custom_in_vol = FALSE; - hbool_t custom_in_vfd = FALSE; - hbool_t custom_out_vol = FALSE; - hbool_t custom_out_vfd = FALSE; + bool custom_in_vol = false; + bool custom_in_vfd = false; + bool custom_out_vol = false; + bool custom_out_vfd = false; hid_t tmp_fapl = H5I_INVALID_HID; int bound, opt; int ret_value = 0; @@ -620,7 +620,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) break; case 'L': - options->latest = TRUE; + options->latest = true; break; case 'j': @@ -646,30 +646,30 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) break; case 'X': - options->merge = TRUE; + options->merge = true; break; case 'W': - options->prune = TRUE; + options->prune = true; break; case 'c': options->grp_compact = atoi(H5_optarg); if (options->grp_compact > 0) - options->latest = TRUE; /* must use latest format */ + options->latest = true; /* must use latest format */ break; case 'd': options->grp_indexed = atoi(H5_optarg); if (options->grp_indexed > 0) - options->latest = TRUE; /* must use latest format */ + options->latest = true; /* must use latest format */ break; case 's': { int idx = 0; int ssize = 0; - char *msgPtr = HDstrchr(H5_optarg, ':'); - options->latest = TRUE; /* must use latest format */ + char *msgPtr = strchr(H5_optarg, ':'); + options->latest = true; /* must use latest format */ if (msgPtr == NULL) { ssize = atoi(H5_optarg); for (idx = 0; idx < 5; idx++) @@ -678,18 +678,18 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) else { char msgType[10]; - HDstrcpy(msgType, msgPtr + 1); + strcpy(msgType, msgPtr + 1); msgPtr[0] = '\0'; ssize = atoi(H5_optarg); - if (!HDstrncmp(msgType, "dspace", 6)) + if (!strncmp(msgType, "dspace", 6)) options->msg_size[0] = ssize; - else if (!HDstrncmp(msgType, "dtype", 5)) + else if (!strncmp(msgType, "dtype", 5)) options->msg_size[1] = ssize; - else if (!HDstrncmp(msgType, "fill", 4)) + else if (!strncmp(msgType, "fill", 4)) options->msg_size[2] = ssize; - else if (!HDstrncmp(msgType, "pline", 5)) + else if (!strncmp(msgType, "pline", 5)) options->msg_size[3] = ssize; - else if (!HDstrncmp(msgType, "attr", 4)) + else if (!strncmp(msgType, "attr", 4)) options->msg_size[4] = ssize; } } break; @@ -723,14 +723,14 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) case 'S': { char strategy[MAX_NC_NAME]; - HDstrcpy(strategy, H5_optarg); - if (!HDstrcmp(strategy, "FSM_AGGR")) + strcpy(strategy, H5_optarg); + if (!strcmp(strategy, "FSM_AGGR")) options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR; - else if (!HDstrcmp(strategy, "PAGE")) + else if (!strcmp(strategy, "PAGE")) options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE; - else if (!HDstrcmp(strategy, "AGGR")) + else if (!strcmp(strategy, "AGGR")) options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR; - else if (!HDstrcmp(strategy, "NONE")) + else if (!strcmp(strategy, "NONE")) options->fs_strategy = H5F_FSPACE_STRATEGY_NONE; else { error_msg("invalid file space management strategy `%s`\n", H5_optarg); @@ -792,13 +792,13 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) case '1': in_vol_info.type = VOL_BY_VALUE; in_vol_info.u.value = (H5VL_class_value_t)atoi(H5_optarg); - custom_in_vol = TRUE; + custom_in_vol = true; break; case '2': in_vol_info.type = VOL_BY_NAME; in_vol_info.u.name = H5_optarg; - custom_in_vol = TRUE; + custom_in_vol = true; break; case '3': @@ -808,13 +808,13 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) case '4': out_vol_info.type = VOL_BY_VALUE; out_vol_info.u.value = (H5VL_class_value_t)atoi(H5_optarg); - custom_out_vol = TRUE; + custom_out_vol = true; break; case '5': out_vol_info.type = VOL_BY_NAME; out_vol_info.u.name = H5_optarg; - custom_out_vol = TRUE; + custom_out_vol = true; break; case '6': @@ -824,13 +824,13 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) case '7': in_vfd_info.type = VFD_BY_VALUE; in_vfd_info.u.value = (H5FD_class_value_t)atoi(H5_optarg); - custom_in_vfd = TRUE; + custom_in_vfd = true; break; case '8': in_vfd_info.type = VFD_BY_NAME; in_vfd_info.u.name = H5_optarg; - custom_in_vfd = TRUE; + custom_in_vfd = true; break; case '9': @@ -840,13 +840,13 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) case '0': out_vfd_info.type = VFD_BY_VALUE; out_vfd_info.u.value = (H5FD_class_value_t)atoi(H5_optarg); - custom_out_vfd = TRUE; + custom_out_vfd = true; break; case 'Y': out_vfd_info.type = VFD_BY_NAME; out_vfd_info.u.name = H5_optarg; - custom_out_vfd = TRUE; + custom_out_vfd = true; break; case 'Z': @@ -864,7 +864,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) infile = argv[H5_optind]; outfile = argv[H5_optind + 1]; - if (!HDstrcmp(infile, outfile)) { + if (!strcmp(infile, outfile)) { error_msg("file names cannot be the same\n"); usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); @@ -886,7 +886,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options) } /* If the input file uses the onion VFD, get the revision number */ - if (in_vfd_info.u.name && !HDstrcmp(in_vfd_info.u.name, "onion")) { + if (in_vfd_info.u.name && !strcmp(in_vfd_info.u.name, "onion")) { if (in_vfd_info.info) { errno = 0; onion_fa_in_g.revision_num = strtoull(in_vfd_info.info, NULL, 10); @@ -981,7 +981,7 @@ main(int argc, char **argv) } /* initialize options */ - if (h5repack_init(&options, 0, FALSE) < 0) { + if (h5repack_init(&options, 0, false) < 0) { printf("Error occurred while initializing repack options\n"); h5tools_setstatus(EXIT_FAILURE); goto done; diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c index 2018527..8a9042d 100644 --- a/tools/src/h5repack/h5repack_opttable.c +++ b/tools/src/h5repack/h5repack_opttable.c @@ -28,7 +28,7 @@ init_packobject(pack_info_t *obj) { int j, k; - HDstrcpy(obj->path, "\0"); + strcpy(obj->path, "\0"); for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) { obj->filter[j].filtn = -1; obj->filter[j].cd_nelmts = CD_VALUES; @@ -181,7 +181,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac { unsigned i, j, I; unsigned added = 0; - hbool_t found = FALSE; + bool found = false; int ret_value = 0; /* increase the size of the collection by N_OBJS if necessary */ @@ -196,7 +196,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac /* linear table search */ for (i = 0; i < table->nelems; i++) { /*already on the table */ - if (HDstrcmp(obj_list[j].obj, table->objs[i].path) == 0) { + if (strcmp(obj_list[j].obj, table->objs[i].path) == 0) { /* already chunk info inserted for this one; exit */ if (table->objs[i].chunk.rank > 0) { H5TOOLS_INFO("chunk information already inserted for <%s>\n", obj_list[j].obj); @@ -205,7 +205,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac /* insert the layout info */ else { aux_tblinsert_layout(table, i, pack); - found = TRUE; + found = true; break; } } /* if */ @@ -215,7 +215,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac /* keep the grow in a temp var */ I = table->nelems + added; added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); + strcpy(table->objs[I].path, obj_list[j].obj); aux_tblinsert_layout(table, I, pack); } /* cases where we have an already inserted name but there is a new name also @@ -223,11 +223,11 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 dset1 is already inserted, but dset2 must also be */ - else if (found && HDstrcmp(obj_list[j].obj, table->objs[i].path) != 0) { + else if (found && strcmp(obj_list[j].obj, table->objs[i].path) != 0) { /* keep the grow in a temp var */ I = table->nelems + added; added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); + strcpy(table->objs[I].path, obj_list[j].obj); aux_tblinsert_layout(table, I, pack); } } /* j */ @@ -238,7 +238,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac for (j = 0; j < n_objs; j++) { I = table->nelems + added; added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); + strcpy(table->objs[I].path, obj_list[j].obj); aux_tblinsert_layout(table, I, pack); } } @@ -261,7 +261,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa { unsigned int i, j, I; unsigned added = 0; - hbool_t found = FALSE; + bool found = false; /* increase the size of the collection by N_OBJS if necessary */ if (table->nelems + n_objs >= table->size) @@ -275,10 +275,10 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa /* linear table search */ for (i = 0; i < table->nelems; i++) { /*already on the table */ - if (HDstrcmp(obj_list[j].obj, table->objs[i].path) == 0) { + if (strcmp(obj_list[j].obj, table->objs[i].path) == 0) { /* insert */ aux_tblinsert_filter(table, i, filt); - found = TRUE; + found = true; break; } /* if */ } /* i */ @@ -287,7 +287,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa /* keep the grow in a temp var */ I = table->nelems + added; added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); + strcpy(table->objs[I].path, obj_list[j].obj); aux_tblinsert_filter(table, I, filt); } /* cases where we have an already inserted name but there is a new name also @@ -295,11 +295,11 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 dset1 is already inserted, but dset2 must also be */ - else if (found && HDstrcmp(obj_list[j].obj, table->objs[i].path) != 0) { + else if (found && strcmp(obj_list[j].obj, table->objs[i].path) != 0) { /* keep the grow in a temp var */ I = table->nelems + added; added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); + strcpy(table->objs[I].path, obj_list[j].obj); aux_tblinsert_filter(table, I, filt); } } /* j */ @@ -311,7 +311,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa for (j = 0; j < n_objs; j++) { I = table->nelems + added; added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); + strcpy(table->objs[I].path, obj_list[j].obj); aux_tblinsert_filter(table, I, filt); } } @@ -338,15 +338,15 @@ options_get_object(const char *path, pack_opttbl_t *table) for (i = 0; i < table->nelems; i++) { /* make full path (start with "/") to compare correctly */ - if (HDstrncmp(table->objs[i].path, "/", 1) != 0) { - HDstrcpy(tbl_path, "/"); - HDstrcat(tbl_path, table->objs[i].path); + if (strncmp(table->objs[i].path, "/", 1) != 0) { + strcpy(tbl_path, "/"); + strcat(tbl_path, table->objs[i].path); } else - HDstrcpy(tbl_path, table->objs[i].path); + strcpy(tbl_path, table->objs[i].path); /* found it */ - if (HDstrcmp(tbl_path, path) == 0) { + if (strcmp(tbl_path, path) == 0) { return (&table->objs[i]); } } diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c index f88ba6f..0317ef7 100644 --- a/tools/src/h5repack/h5repack_parse.c +++ b/tools/src/h5repack/h5repack_parse.c @@ -41,7 +41,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t { size_t i, m, u; char c; - size_t len = HDstrlen(str); + size_t len = strlen(str); int f, k, l, p, q, end_obj = -1, no_param = 0; unsigned j, n; char sobj[MAX_NC_NAME]; @@ -94,7 +94,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t else sobj[k + 1] = '\0'; - HDstrcpy(obj_list[n].obj, sobj); + strcpy(obj_list[n].obj, sobj); memset(sobj, 0, sizeof(sobj)); n++; k = -1; @@ -123,7 +123,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * example SZIP=8,NN *------------------------------------------------------------------------- */ - if (HDstrcmp(scomp, "SZIP") == 0) { + if (strcmp(scomp, "SZIP") == 0) { l = -1; /* mask index check */ for (m = 0, u = i + 1; u < len; u++, m++) { if (str[u] == ',') { @@ -146,9 +146,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t if (l == 2) { smask[l] = '\0'; i = len - 1; /* end */ - if (HDstrcmp(smask, "NN") == 0) + if (strcmp(smask, "NN") == 0) filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK; - else if (HDstrcmp(smask, "EC") == 0) + else if (strcmp(smask, "EC") == 0) filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK; else { error_msg("szip mask must be 'NN' or 'EC' \n"); @@ -173,7 +173,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * SOFF=3,DF *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "SOFF") == 0) { + else if (strcmp(scomp, "SOFF") == 0) { l = -1; /* mask index check */ for (m = 0, u = i + 1; u < len; u++, m++) { if (str[u] == ',') { @@ -196,9 +196,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t if (l == 2) { smask[l] = '\0'; i = len - 1; /* end */ - if (HDstrcmp(smask, "IN") == 0) + if (strcmp(smask, "IN") == 0) filt->cd_values[j++] = H5Z_SO_INT; - else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE) + else if (strcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE) filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE; else { error_msg("scale type must be 'IN' or 'DS' \n"); @@ -216,7 +216,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * UD=307,0,1,9 *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "UD") == 0) { + else if (strcmp(scomp, "UD") == 0) { l = -1; /* filter number index check */ f = -1; /* filter flag index check */ p = -1; /* CD_VAL count check */ @@ -298,7 +298,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_NONE *------------------------------------------------------------------------- */ - if (HDstrcmp(scomp, "NONE") == 0) { + if (strcmp(scomp, "NONE") == 0) { filt->filtn = H5Z_FILTER_NONE; filt->cd_nelmts = 0; } @@ -307,7 +307,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_DEFLATE *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "GZIP") == 0) { + else if (strcmp(scomp, "GZIP") == 0) { filt->filtn = H5Z_FILTER_DEFLATE; filt->cd_nelmts = 1; if (no_param) { /*no more parameters, GZIP must have parameter */ @@ -322,7 +322,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_SZIP *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "SZIP") == 0) { + else if (strcmp(scomp, "SZIP") == 0) { filt->filtn = H5Z_FILTER_SZIP; filt->cd_nelmts = 2; if (no_param) { /*no more parameters, SZIP must have parameter */ @@ -337,7 +337,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_SHUFFLE *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "SHUF") == 0) { + else if (strcmp(scomp, "SHUF") == 0) { filt->filtn = H5Z_FILTER_SHUFFLE; filt->cd_nelmts = 0; if (m > 0) { /*shuffle does not have parameter */ @@ -351,7 +351,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_FLETCHER32 *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "FLET") == 0) { + else if (strcmp(scomp, "FLET") == 0) { filt->filtn = H5Z_FILTER_FLETCHER32; filt->cd_nelmts = 0; if (m > 0) { /*shuffle does not have parameter */ @@ -365,7 +365,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_NBIT *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "NBIT") == 0) { + else if (strcmp(scomp, "NBIT") == 0) { filt->filtn = H5Z_FILTER_NBIT; filt->cd_nelmts = 0; if (m > 0) { /*nbit does not have parameter */ @@ -379,7 +379,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * H5Z_FILTER_SCALEOFFSET *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "SOFF") == 0) { + else if (strcmp(scomp, "SOFF") == 0) { filt->filtn = H5Z_FILTER_SCALEOFFSET; filt->cd_nelmts = 2; if (no_param) { /*no more parameters, SOFF must have parameter */ @@ -393,7 +393,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t * User Defined Filter *------------------------------------------------------------------------- */ - else if (HDstrcmp(scomp, "UD") == 0) { + else if (strcmp(scomp, "UD") == 0) { /* parameters does not match count */ if (filt->cd_nelmts != j) { if (obj_list) @@ -448,7 +448,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t error_msg("pixels_per_block is too large in <%s>\n", str); exit(EXIT_FAILURE); } - if ((HDstrcmp(smask, "NN") != 0) && (HDstrcmp(smask, "EC") != 0)) { + if ((strcmp(smask, "NN") != 0) && (strcmp(smask, "EC") != 0)) { if (obj_list) free(obj_list); error_msg("szip mask must be 'NN' or 'EC' \n"); @@ -486,7 +486,7 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about obj_list_t *obj_list = NULL; unsigned i, j, n; char c; - size_t len = HDstrlen(str); + size_t len = strlen(str); int k, end_obj = -1, c_index; char sobj[MAX_NC_NAME]; char sdim[10]; @@ -527,7 +527,7 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about sobj[k] = '\0'; else sobj[k + 1] = '\0'; - HDstrcpy(obj_list[n].obj, sobj); + strcpy(obj_list[n].obj, sobj); memset(sobj, 0, sizeof(sobj)); n++; k = -1; @@ -546,11 +546,11 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about for (j = (unsigned)(end_obj + 1), n = 0; n <= 5; j++, n++) { if (n == 5) { slayout[n] = '\0'; /*cut string */ - if (HDstrcmp(slayout, "COMPA") == 0) + if (strcmp(slayout, "COMPA") == 0) pack->layout = H5D_COMPACT; - else if (HDstrcmp(slayout, "CONTI") == 0) + else if (strcmp(slayout, "CONTI") == 0) pack->layout = H5D_CONTIGUOUS; - else if (HDstrcmp(slayout, "CHUNK") == 0) + else if (strcmp(slayout, "CHUNK") == 0) pack->layout = H5D_CHUNKED; else { error_msg("in parse layout, not a valid layout in <%s>\n", str); @@ -604,7 +604,7 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about else if (i == len - 1) { /*no more parameters */ sdim[k] = '\0'; k = 0; - if (HDstrcmp(sdim, "NONE") == 0) { + if (strcmp(sdim, "NONE") == 0) { pack->chunk.rank = -2; } else { diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index ce4a5cf..e71d6db 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -451,7 +451,7 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) / unsigned u, i, j; int rank; H5T_class_t type_class = -1; - hbool_t is_ref = 0, is_ref_vlen = 0, is_ref_array = 0, is_ref_comp = 0; + bool is_ref = 0, is_ref_vlen = 0, is_ref_array = 0, is_ref_comp = 0; void *refbuf = NULL; void *buf = NULL; unsigned *ref_comp_index = NULL; diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c index 572aa48..819dd94 100644 --- a/tools/src/h5repack/h5repack_verify.c +++ b/tools/src/h5repack/h5repack_verify.c @@ -49,7 +49,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options hid_t fcpl_in = H5I_INVALID_HID; /* file creation property for input file */ hid_t fcpl_out = H5I_INVALID_HID; /* file creation property for output file */ H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */ - hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ + bool in_persist, out_persist; /* free-space persist status for in/output file */ hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ int ret_value = 0; @@ -234,7 +234,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * the same as the input file's free-space persist status */ if (options->fs_persist) { - if (out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) + if (out_persist != (bool)(options->fs_persist == (-1) ? false : options->fs_persist)) H5TOOLS_GOTO_ERROR((-1), "free-space persist status not set as unexpected"); } else { |