* Remove dummy comments that repeat function names. (#4775)
* Fix grammar in H5Odtype.c comment block (#4777)
* Add subfiling checks to the gcc action (#4776)
* Replace non-VOL calls with VOL calls - part 3 (#4771)
This PR switches H5I_object() to H5VL_vol_object() in H5O and H5T APIs. H5M is the last one and left out of this PR because it needs more work
in documentation and there is no test for the API functions.
Fixes GH-4730
* Add subfiling to CI more places where we test parallel (#4778)
* CMake: gcc,, AOCC
* Autotools: AOCC (gcc was added in a previous commit)
NVHPC generates a lot of tools errors for some reason
* Convert Collective Calls html file to doxygen (#4779)
* Fix grammar in H5Fint.c comment block (#4782)
* Improve the consistency of configure help messages (#4783)
Fix grammar in configure message
* Fixes Fortran parallel build race condition for tests (#4789)
* Update URL documentation links to support site (#4781)
* Fix grammar and simplify comment in H5Fint.c (#4790)
* Fix char-subscripts warnings in H5private.h (#4793)
* Bump the github-actions group with 3 updates (#4798)
Bumps the github-actions group with 3 updates: [actions/checkout](https://github.com/actions/checkout), [DoozyX/clang-format-lint-action](https://github.com/doozyx/clang-format-lint-action) and [github/codeql-action](https://github.com/github/codeql-action).
Updates `actions/checkout` from 4.1.1 to 4.1.7
- [Release notes](https://github.com/actions/checkout/releases)
- [Commits](https://github.com/actions/checkout/compare/v4.1.1...v4.1.7)
Updates `DoozyX/clang-format-lint-action` from 0.17 to 0.18
- [Release notes](https://github.com/doozyx/clang-format-lint-action/releases)
- [Commits](https://github.com/doozyx/clang-format-lint-action/compare/v0.17...v0.18)
Updates `github/codeql-action` from 3.25.15 to 3.26.6
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](afb54ba388...4dd16135b6)
---
updated-dependencies:
- dependency-name: actions/checkout
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: DoozyX/clang-format-lint-action
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: github-actions
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: github-actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix typo argueably in H5Cprivate.h (#4795)
* Fix typos in H5Cpkg.h (#4796)
* Add bounds checking to avoid Out-of-bounds Write for gif2h5 (#4786)
* Replace non-VOL calls with VOL calls - part 5 (#4788)
This PR switches H5I_object() and H5I_object_verify() to H5VL_vol_object() and H5VL_vol_object_verify(), respectively, in the H5M APIs and H5Gdeprec (was left out by mistake). This completes the fixes of issue GH-4730.
* Correct the URL paths (#4802)
* Fix a few issues with error reporting during sec2 reads/writes (#4794)
* Update windows and apple signing process (#4806)
* Use latest clang format action (#4807)
* Correct path to document (#4808)
* Detect invalid ID to H5Gmove2 (#4765)
User's application segfaulted because the returned value H5I_BADID wasn't
detected when H5I_get_type() was called. This PR adds checks for invalid
file/group identifiers passed into H5Gmove2.
This defect occurs in many other places, hence, issue GH-4764.
Fixes#4737
* Fix use of public API calls (#4809)
Switch public API calls to private ones. Root cause of #4672, which it fixes.
Also minor code cleanups
* Remove call to H5E_clear_stack() (#4810)
Remove call to H5E_clear_stack() in H5G_node_debug()
Add misc. minor cleanups
* Enable win Intel signing (#4812)
* Remove unneeded file name part (#4814)
* Update NVHPC optimization settings (#4815)
* Use -gopt in Autotools/CMake instead of -g
* Autotools uses -O3 for release, -O1 for debug
* Remove CMake optimization flag removal hack
* Add mirror VFD to serial -Werror CI action (#4753)
* Add mirror VFD to serial -Werror CI action
* NUL terminate mirror_vfd.c strings
* Add THREADS check to configuration file (#4746)
* Cleanup threads package checks
* Check first if package was found
* Remove unnecessary dependent checks
* Remove Unused options and fix names of option prefix
* Rework RFC url in aliases (#4813)
* Update config/cmake/hdf5-config.cmake.in
_ENABLE_THREADS doesn't belong in hdf5_1_14
* Warning fix (#4682)
* warning fix
* warning fix
* CMake link line needs to use new HDF5_ENABLE_THREADS (#4685)
* Correct the properties for using THREADS library (#4690)
* Bump the github-actions group with 5 updates (#4688)
Bumps the github-actions group with 5 updates:
| Package | From | To |
| --- | --- | --- |
| [actions/download-artifact](https://github.com/actions/download-artifact) | `4.1.7` | `4.1.8` |
| [DoozyX/clang-format-lint-action](https://github.com/doozyx/clang-format-lint-action) | `0.13` | `0.17` |
| [softprops/action-gh-release](https://github.com/softprops/action-gh-release) | `2.0.6` | `2.0.8` |
| [ossf/scorecard-action](https://github.com/ossf/scorecard-action) | `2.3.3` | `2.4.0` |
| [github/codeql-action](https://github.com/github/codeql-action) | `3.25.11` | `3.25.15` |
Updates `actions/download-artifact` from 4.1.7 to 4.1.8
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](65a9edc588...fa0a91b85d)
Updates `DoozyX/clang-format-lint-action` from 0.13 to 0.17
- [Release notes](https://github.com/doozyx/clang-format-lint-action/releases)
- [Commits](https://github.com/doozyx/clang-format-lint-action/compare/v0.13...v0.17)
Updates `softprops/action-gh-release` from 2.0.6 to 2.0.8
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](a74c6b72af...c062e08bd5)
Updates `ossf/scorecard-action` from 2.3.3 to 2.4.0
- [Release notes](https://github.com/ossf/scorecard-action/releases)
- [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md)
- [Commits](dc50aa9510...62b2cac7ed)
Updates `github/codeql-action` from 3.25.11 to 3.25.15
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](b611370bb5...afb54ba388)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: DoozyX/clang-format-lint-action
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: github-actions
- dependency-name: softprops/action-gh-release
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: ossf/scorecard-action
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: github-actions
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
...
* Fix segfault when closing datatype during failure in H5Topen2 (#4683)
* Rework Dynamic Analysis and sanitize testing (#4681)
* Ignore predetermined failing test and check pointer before use
* Rework Analysis process
* Remove another H5E_BEGIN/END_TRY within the library (#4675)
* Update logic for (deprecated) H5Gget_objinfo() call to eliminate H5E_BEGIN_TRY
* Handle case for '.' at the end of a path
* Drop H5E_BEGIN/END_TRY and just check the error return from H5I_clear_types() (#4694)
Original case that the change in commit 2dc738a321
no longer applies.
* Add check of returned value from API calls. (#4702)
These were found while investigating GH-4672, but they were not related
to GH-4672.
* Add mac dmg binary and remove old macos-13 workflows (#4699)
* Add Windows SHLWAPI lib to public interface (#4701)
* Use local variable in btree2 and print value (#4679)
* Correct logic
* Technically, level 1 Express could skip tests
* Add windows signing (#4703)
* Add tests for H5R get name APIs (#4657)
Added functionality tests for the following APIs:
H5Rget_file_name
H5Rget_obj_name
H5Rget_attr_name
Also removed "+1" when returning a name length in H5R__get_attr_name().
The exter "+1" gave an incorrect value for the length of the referenced
object's attribute name.
Fixed GH-4447
* Fix Fortran test
The C API H5Rget_attr_name incorrectly added 1 to the length of the
referenced object's attribute name, so the Fortran API h5rget_attr_name_f
removed 1 from the returned value to accommodate the incorrectness.
This PR fixes H5Rget_attr_name so this workaround in h5rget_attr_name_f
is no longer needed.
* Add test H5Aget_name against H5Rget_attr_name
* Replace Visual Studio ???? with 2022 in MSI README file (#4709)
* Change logic for checking secrets exists (#4711)
* Change osx refs to macos (#4707)
* Replace alias \Code with \TText (#4714)
Fixed GH-2151
* Correct signing names and variables (#4713)
* Add secrets to release workflow (#4719)
* Add missing blosc2 info (#4717)
* Fix error return types in H5Rdeprec.c (#4722)
Copy-pasted code from elsewhere used FAIL instead of H5G_UNKNOWN
and H5I_INVALID_HID.
* Fix the release reference name (#4721)
* Test creating unseekable file (#4720)
* Cleanup up tests (#4724)
* Add arch name to dmg file name (#4732)
The binaries in snapshot dmg file do not work on x86_64.
* Fix snapshot CI failure by adding arch name to dmg file (#4734)
See also #4732.
* Fix incorrect VOL vs. non-VOL calls partially (#4733)
* Fix incorrect VOL vs. non-VOL calls
H5Lget_info2() called H5I_object() instead of H5VL_vol_object() crashed
user application.
This is a wide-spread issue (GH-4730) but this PR only addresses GH-4705.
* Remove an incorrect change
* Fix segfault in ROS3 credential parsing (#4736)
* Fix segfault in s3 credential parsing
* Fix AWS cred parsing when >1 profile provided
* Revert gh-pages action hash to fix daily build (#4735)
* Revert gh-pages action hash to fix daily build
See also #4734
* Revert gh-pages action hash to fix daily build
* Eliminate another use of H5E_clear_stack() within the library (#4726)
* Remove call to H5E_clear_stack()
Also clean up a bunch of error macros and the return value from H5B_valid()
* Test fixes for log-based vol (#4618)
* fixes to address failures in the log-based VOL
* moved file cleanup to tests proper
* skipped index API test if not supported
* Add 'try' parameter to H5Z_find, and remove calls to H5E_clear_stack() (#4609)
* Bump the github-actions group with 4 updates (#4620)
Bumps the github-actions group with 4 updates: [actions/checkout](https://github.com/actions/checkout), [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials), [softprops/action-gh-release](https://github.com/softprops/action-gh-release) and [github/codeql-action](https://github.com/github/codeql-action).
Updates `actions/checkout` from 4.1.1 to 4.1.7
- [Release notes](https://github.com/actions/checkout/releases)
- [Commits](https://github.com/actions/checkout/compare/v4.1.1...v4.1.7)
Updates `aws-actions/configure-aws-credentials` from 1 to 4
- [Release notes](https://github.com/aws-actions/configure-aws-credentials/releases)
- [Changelog](https://github.com/aws-actions/configure-aws-credentials/blob/main/CHANGELOG.md)
- [Commits](https://github.com/aws-actions/configure-aws-credentials/compare/v1...v4)
Updates `softprops/action-gh-release` from 2.0.5 to 2.0.6
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](69320dbe05...a74c6b72af)
Updates `github/codeql-action` from 3.25.7 to 3.25.11
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](f079b84933...b611370bb5)
---
updated-dependencies:
- dependency-name: actions/checkout
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: aws-actions/configure-aws-credentials
dependency-type: direct:production
update-type: version-update:semver-major
dependency-group: github-actions
- dependency-name: softprops/action-gh-release
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix a stack size warning in ros3 VFD code (#4625)
Just makes a stack array dynamic. Valgrind shows no memory leaks.
* Reworked cleaning up API test files (#4626)
* Reworked cleaning up test files, only removing test files if present to account for skipped tests
* changed to using H5Fis_accessible
* update to full use of remove_test_file
* corrected offset type in C wrapper (#4622)
* Remove some internal use of API calls and H5E_BEGIN_TRY/H5E_END_TRY (#4624)
* Remove auto NSIS check because of issues with CI (#4646)
* Add python testing for examples (#4628)
* Clean up Fortran __float128 configure-time checks (#4649)
* Always use DECIMAL_DIG instead of LDBL_DIG. This was controlled by
an ifdef that is always true in C99 or greater
It's confusing to use float.h C constants as variable names in
configure.ac and the PAC_FC_LDBL_DIG macro.
* Directly compare MY_FLT128_DIG and MY_LDBL_DIG
* Make uniform across CMake and Autotools
* Don't export quadmath.h variables to H5pubconf.h
* Feature/awesome (#4604)
* Added Doxygen Awesome and fixed a few quirks.
* Fixed unterminated strings.
* Added Doxygen Awesome by copy.
* Add tools usage text as doxygen for Tools UG (#4602)
* Add h5* compiler wrapper testing for CMake #4605 (#4613)
* Add show option
* remove non-static libs and correct names of static libs
* Fixup the pkg-config libs and comp builds
* Fix commands and add fortran pkg-config test scripts
* Add help usage option
* Add temporary fix for ARM64 Mac _Float16 build failure (#4639)
* Correct H5VL_t ref count on H5O_refresh_metadata failure (#4636)
* Fix bad H5VL_t rc on H5O_refresh_metadata fail
* Decrement nrefs before raising error
* Update doxygen Learn Basics / example refs. Add Reference sections (#4640)
* Fixed messed up table captions. (#4653)
* Fixed messed up table captions. Browsers don't seem to respect relative values for width. Hardcoding 800px for now.
* Fixed FetchContent usage for new CMake reqs. (#4650)
CMake version 3.30 changed the behavior of the FetchContent module to deprecate
the use of FetchContent_Populate() in favor of FetchContent_MakeAvailable(). Therefore,
the copying of HDF specialized CMakeLists.txt files to the dependent project's source
was implemented in the FetchContent_Declare() call.
* Fixed usage issue with FindZLIB.cmake module (#4655)
* Add a comment on the FindZLIB.cmake module usage
* Allow choice of static/shared compression libs for Find Module
* Added new option to INSTALL_CMake file and changed option text
* Eliminate more H5E_BEGIN/END_TRY macros and H5E_clear_stack() calls (#4648)
* Correct name of zlib_ng option (#4658)
* Fix the examples for testing java with binaries (#4660)
* Update filename in RELEASE_PROCESS.md to current name
INSTALL_autotools.txt.
* Remove reference to V116 in tools/src/h5repack/h5repack.h.
* Fix daily-build CI and correct use of *_FOUND settings for filters (#4504)
* Correct examples tests to just run under dynamic analysis (#4505)
* Remove trailing extra whitespace in hyperlink (#4509)
* Set H5 specific vars immediately if legacy find (#4512)
* Set H5 specific vars immediately if legacy find
* Correct find process vars (vs in-line build)
* Correct SZIP find
* Everything is libaec 1.0.6 or newer
* Correct option help text
* Don't update 'pos' and 'op' fields when using pread/pwrite (#4492)
Instead of reading the absolute minimal possible, use the likely value of
a v2+ superblock w/8-byte addresses & lengths.
* Fix spelling (#4522)
* Fix typo in DAPL callback documentation (#4523)
* Move/rename libhdf5.settings input files (#4525)
Move without other changes:
src/libhdf5.settings.in -> src/libhdf5.settings.autotools.in
config/cmake/libhdf5.settings.cmake.in -> src/libhdf5.settings.cmake.in
* Disable UNITY_BUILD for now - globally (#4515)
* Fix function name in USAGE for H5Pencode2() (#4519)
* Allow HDF5_LIB_INFIX to work with DLL (#4500)
* Allow HDF5_LIB_INFIX to work with DLL
* Separate individual library name into parts and add suffix option
* Java cannot use alternative names and removed extra setting
* Incorporate the underscore into the CORE name
* Fix typos in property callback documentation (#4532)
* Fix wrong int type as some systems have int as 64-bit wide (#4534)
* H5FDquery return value (#4530)
* Switch H5FDquery() return values to use library's FAIL / SUCCEED macros
* Update return value also
* Refactor to reduce code duplication (#4531)
* Update error output w/new routine name
* Fix a few function names in USAGE comments that don't match the actual (#4533)
* Fix a few function names in USAGE comments that don't match the actual
function names.
* Remove typo '['
* Switch to working url for api-compatibility-macros.html.
* Remove julia CI actions (#4540)
These have been failing for a week or two for unclear reasons, both
in the Autotools and CMake. No obvious library changes triggered
this.
See GitHub issue #4539 for more info/discussion
The Julia tests will be disabled until the root cause is found.
* Bump the github-actions group with 3 updates (#4538)
Bumps the github-actions group with 3 updates: [softprops/action-gh-release](https://github.com/softprops/action-gh-release), [ossf/scorecard-action](https://github.com/ossf/scorecard-action) and [github/codeql-action](https://github.com/github/codeql-action).
Updates `softprops/action-gh-release` from 2.0.4 to 2.0.5
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](9d7c94cfd0...69320dbe05)
Updates `ossf/scorecard-action` from 2.3.1 to 2.3.3
- [Release notes](https://github.com/ossf/scorecard-action/releases)
- [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md)
- [Commits](0864cf1902...dc50aa9510)
Updates `github/codeql-action` from 3.25.3 to 3.25.7
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](d39d31e687...f079b84933)
---
updated-dependencies:
- dependency-name: softprops/action-gh-release
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: ossf/scorecard-action
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: github-actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix various mistakes in doxygen docs (#4541)
* Fix a dead link and example file names
* Add the missing content of a section
* Export HDF5 parallel status for CMake FetchContent'ed VOL connectors (#4542)
* Remove an unnecessary check for parallel and thread-safety from examples (#4543)
* Add option to use zlib-ng as zlib library (#4487)
* Export HDF5 version for CMake FetchContent'ed VOL connectors (#4548)
* Adjust h5repack userblock option to allow reserve size (#4544)
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: mattjala <124107509+mattjala@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Peter Chang <peter.chang@diamond.ac.uk>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* win32defs: Fix Wundef warning (#4467)
* Refactor error handling code to eliminate internal ID calls (#4453)
All calls to the H5I routines are now made in API routines (sometimes in
FUNC_ENTER/LEAVE_* macros), except for some calls to H5E_clear_stack() within
the library, but I'm planning to remove those over time.
Also, made all the library internal error messages into static const variables,
instead of malloc'ing them, which means that they can just be referenced
and not copied.
Several new and updated auto-generated header files were necessary to enable
this.
* CMake: Fix mingw/fortran build (#4466)
* Update for blosc2 in plugins and prefix hdf5 cmake varnames (#4468)
* Fix an issue where compound datatype member IDs can be leaked during conversion (#4459)
Also fixes issues with handling of partially initialized datatypes during library shutdown
* H5Group: Fix operator= (#4473)
Closes#4472
* Fix github issue #2523: doxygen -- fix grammatically incorrect sentence alias (#4474)
* Remove env step not used by CI in testing (#4476)
* Add H5fortkit dependecy for H5Rff.F90 (#4482)
* Properly clean up cache when failing to load an object header (#4477)
* Properly clean up cache when failing to load an object header
* Don't check message type a second time in H5G__open_oid if the first attempt returns error
* Add more asserts to H5O__assert() to avoid segfaults
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add a missing image from the original document (#4490)
* Disable EOF checks for SWMR readers in more cases. (#4489)
Fixes a race condition where the reader opens the file and sets its EOF from the
file's size (from the stat() call in the driver open callback). Then, before
the reader can read the file's superblock, a SWMR writer races in, extends the
file, and closes the file, writing an updated superblock with the 'writer' and
'SWMR writer' flags in the superblock off (appropriately). Then the reader
proceeds to read the superblock, and flags the EOF as wrong. Taking out the
check for the 'writer' and 'SWMR writer' flags will cause SWMR readers to avoid
flagging the file as incorrect.
* Remove unnecessary fortran install (#4498)
* Only one version of binaries is produced for platforms (#4496)
* Fix for github issue #2220. (#4497)
Document the limitation in the Passthrough Conncector section of the VOL Connector Author Guide.
The limitation is posted by Neil in the github issue on Dec 22, 2022.
* Release asset tarballs with no version filenames (#4494)
* Improve spec. reading superblock into cache (a little) by using v2 size (#4491)
* Improve spec. reading superblock into cache (a little) by using v2 size
Instead of reading the absolute minimal possible, use the likely value of
a v2+ superblock w/8-byte addresses & lengths.
* Fix for github Issue #1388 can't delete renamed dense attribute with corder tracking enabled (#4462)
* Fix for github issue #1388: can't delete renamed dense attribute with corder tracking enabled
The problem occurs in step 3(b) below which will delete the attribute with corder x
from the creation order index v2 B-tree.
The rename sequence in H5A__dense_rename() occurs in the following order:
1) The old attribute with corder x was removed from the creation order index v2 B-tree
2) The new renamed attribute was inserted via H5A__dense_insert():
(a) insert the attribute with new name j into the name index v2 B-tree
(b) insert the attribute with corder x into the creation order index v2 B-tree
3) The old attribute was removed via H5A__dense_remove():
(a) remove the attribute with old name k from the name index v2 B-tree
(b) remove the attribute with coorder x from the creation order index v2 B-tree
Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove()
won't delete the attribute with corder x from the creation order index v2 B-tree.
* Fix/revert a libtool sed hack (#4501)
* Revert "Remove Autotools sed hack (#3848)"
This reverts commit 8b3ffdef30.
* Fix libtool sed cleanup on MacOS
Convert sed -i line to sed > libtool.bak && mv libtool.bak libtool
to avoid non-portable -i option.
* Update src/H5public.h
* Set H5 specific vars immediately if legacy find (#4512)
* Correct find process vars (vs in-line build)
* Correct SZIP find
* Everything is libaec 1.0.6 or newer
* Correct option help text
* Reorg and update options for doc and cmake config
* Correct subfiling depends
* Add linux S3 binaries to GH published files
* Correct path
* Try reducing parallel jobs in tests
* Change examples jobs for test from 8 to 4
* Correct ld in format strings in cmpd_dset.c (#3697)
Removes clang warnings
* Clean up comments. (#3695)
* Add NVidia compiler support and CI (#3686)
* Work around Theta system issue failure in links test (#3710)
When the Subfiling VFD is enabled, the links test may
try to initialize the Subfiling VFD and call MPI_Init_thread.
On Theta, this appears to have an issue that will cause
the links test to fail. Reworked the test to check for
the same conditions in a more roundabout way that doesn't
involved initializing the Subfiling VFD
* Fix issue with unmatched messages in ph5diff (#3719)
* provide an alternative to mapfile for older bash (#3717)
* Attempt to quiet some warnings with cray compilers. (#3724)
* Fix CMake VOL passthrough tests by copying files to correct directory (#3721)
* Develop intel split (#3722)
* Split intel compiler flags into sub-folders
* Update Intel options for warnings
* Mostly CMake, Autotools needs additional work
* Fixes and adjustments to t_filters_parallel (#3714)
Broadcast number of datasets to create in multi-dataset I/O cases
so that interference with random number generation doesn't cause
mismatches between ranks
Set fill time for datasets to "never" by default and adjust on a
per-test basis to avoid writing fill values to chunks when it's
unnecessary
Reduce number of loops run in some tests when performing multi-dataset
I/O
Fix an issue in the "fill time never" test where data verification
could fill if file space reuse causes application buffers to be
filled with chosen fill value when reading from datasets with
uninitialized storage
Skip multi-chunk I/O test configurations for multi-dataset I/O
configurations when the TestExpress level is > 1 since those
tests can be more stressful on the file system
Disable use of persistent file free space management for now
since it occasionally runs into an infinite loop in the library's
free space management code
* Suppress cast-qual warning in H5TB Fortran wrapper (#3728)
This interface is fundamentally broken, const-wise.
* Add new API function H5Pget_actual_select_io_mode() (#2974)
This function allows the user to determine if the library performed selection I/O, vector I/O, or scalar (legacy) I/O during the last HDF5 operation performed with the provided DXPL. Expanded existing tests to check this functionality.
* Test scripts now execute in-source with creation of tmp dir (#3723)
Fixes a few issues created in #3580:
* Fixes a problem where committed tools test files were deleted when cleaning after an in-source build
* Fixes issues with test file paths in Autotools tools test scripts
* Add -h and --help as flags in h5cc & h5fc (#3729)
Adds these common help flags in addition to -help
* Update the library version matrix for H5Pset_libver_bounds() (#3702)
* Fixed#3524
Added 1.12, 1.14, and 1.16 to the table for libver bounds in the H5Pset_libver_bounds docs.
* Remove references to LIBVER_V116
---------
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Neil Fortner <fortnern@gmail.com>
Co-authored-by: Glenn Song <43005495+glennsong09@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* 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 1e1dac1dac.
* 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
---------
Larry Knox
Allen Byrne
jhendersonHDF
Dana Robinson