| Commit message (Collapse) | Author | Age | Files | Lines |
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* Address nagfor exceptions stoppage. (#3658)
* added cmake ieee flag for nagfor
* generalized determining the nag compiler
* fixing some misc. NAG warnings
* Simplify. (#3659)
* Address @jhendersonHDF review
* Add expedited testing support to t_filters_parallel (#3665)
* Remove clang warnings (#3656)
* Fixes test failure for gfortran -O2 and -O3, -fdefault-real-16 (#3662)
* added cmake ieee flag for nagfor
* fixes gfortran -O2 and -O3, -fdefault-real-16
* fixed sync
* updated release notes
* Fix link error on clang17/gfortran13/macOS-13 (#3666) (#3671)
* Correct fortran CMake generator expressions (#3670)
* Add AOCC GitHub Action (#3504) (#3657)
* Fix uninitialized subfiling test variable (#3675)
Picked up by gcc 10 on skybridge. Probably spurious, but no harm in
initializing it to a "bad" value.
* Add support for AOCC & Flang w/ the Autotools (#3674)
* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
when using Flang, the MPI Fortran compiler wrappers, and building
the shared library. This would often result in unrecognized options
like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.
CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.
Fixes GitHub issues #3439, #1588, #366, #280
* Fix a strncpy call to use dest size not src (#3677)
A strncpy call in a path construction call used the size of the src
buffer instead of the dest buffer as the limit n.
This was switched to use the dest size and properly terminate the
string if truncation occurs.
* Remove CANBE_UNUSED() from subfiling VFD (#3678)
This macro was an attempt to quiet warnings about release mode unused
variables that only appear in asserts. It resolves to a void cast, which
doesn't quiet warnings when an assignment has already taken place.
* Suppress MPI_Waitall warnings w/ MPICH (#3680)
MPICH defines MPI_STATUSES_IGNORE (a pointer) to 1, which raises warnings
w/ gcc. This is a known issue that the MPICH devs are not going to fix.
See here:
https://github.com/pmodels/mpich/issues/5687
This fix suppresses those issues w/ gcc
* Fix a possible NULL pointer dereference in tests (#3676)
The dtypes test could dereference a NULL pointer if a strdup call
failed.
* Fix printf warnings in t_mpi (#3679)
* Fix printf warnings in t_mpi
The type of MPI_Offset varies with implementation. In MPICH, it's long,
which raises warnings when we attempt to use long long format
specifiers. Casting to long long fixes the warnings.
* Fix invalid memory access in S3 comms (#3681)
In the ros3 VFD, passing an empty string parameter to an internal
API call could result in accessing the -1th element of a string.
This would cause failures on big-endian systems like s390x.
This parameter is now checked before writing to the string.
Fixes GitHub #1168
* Add Doxygen for H5Pset_fapl_sec2() (#3685)
*
* switch to using time function instead of date function (#3690)
* Initialize API context MPI types to MPI_BYTE (#3688)
* Add test info output to t_filters_parallel (#3696)
* Suppress format string warnings in subfiling test (#3699)
* Fix unused variable in tselect.c (#3701)
* Fix unused variable warning in H5F_sfile_assert_num (#3700)
* Restore floating-point suffixes in tests (#3698)
A prior commit removed too many F suffixes. This restores the suffixes
for float variables.
* Sync with changes from develop
---------
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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* 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
---------
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* 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.
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* Fix typos found in the rest of the hdf5 code-base
* Typo in tool.cmake
* Revert "Typo in tool.cmake"
This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b.
* Fix clang-format styling
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* Update format source to clang 13
* More format changes
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* Replaced many uses of sprintf with safer snprintf
Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable.
* Removed unnecessary use of static on small buffers
This improves thread safety.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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>
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* 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
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* Fixes a few testhdf5 warnings raised in Visual Studio
Visual Studio is grumpier about treating pointers like integers than
gcc.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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>
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* Fixed all clang-tidy bugprone-suspicious-string-compare warnings
This change was generated entirely by clang-tidy itself.
* Reformat code with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* 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>
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* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
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Adds missing HD prefixes to API calls in src and test.
Adds some extra processing to bin/checkposix to keep the noise
levels down when running the script (not comprehensive).
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The API call used to set the internal H5S_NO_CLASS value which
produced errors when such a dataspace was passed to many other API
calls.
Fixes HDFFV-11027
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both selections, but with different selection types (i.e. one selection defined
as an 'all' type and the other as a hyperslab or point type), without falling
into the generic selection iteration case.
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(2) Add release notes
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1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace
to 1-d contiguous memory dataspace.
2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to
a separate routine.
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with tests and minor cleanups and refactorings.
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clean up warnings.
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share dataspace's selection with iterator (and with caution about not modifying
or closing the dataspace while the iterator is open).
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merge_hyperslab_updates
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