mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-26 04:09:39 +03:00
abe633d0a007897d8564b90724f005c708cd878b
442
Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
 Allen Byrne
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abe633d0a0 | Update clang format to get correct merge compares (#5253) | ||
 Larry Knox
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25fe253b7d |
Created new branch hdf5_1_14_6 (#5248)
* Created new branch hdf5_1_14_6 from hdf5_1.14.5 tag for HDF5 1.14.5 release. Incremented LT*VERS_REVISION for new code release with no API changes. Set version to 1.14.6-1 (h5vers -s 1.14.6-1 which ran autogen.sh). Updated HISTORY-1_14.txt and cleaned previous entries from RELEASE.txt. |
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Larry Knox
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922aaf30e5 |
1.14.5 release preparation (#4838)
* Updated release preparation branch version number t0 1.14.5-2 * Disable AM_MAINTAINER_MODE. Set HDF5GENERATE_HEADERS (CMAKE) to OFF. Change default build mode from debug to production. Ran autogen.sh to regenerate UNIX build system files. Added generated configure, Makefile.ins, etc to commit. |
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Allen Byrne
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6c5d47c95e | Merge changes from dev CMake and documentation (#4828) | ||
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Larry Knox
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4d135a0473 |
Sync develop changes 8/27 - 9/11 to hdf5_1_14. (#4822)
* 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](https://github.com/github/codeql-action/compare/afb54ba388a7dca6ecae48f608c4ff05ff4cc77a...4dd16135b69a43b6c8efb853346f8437d92d3c93) --- 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 |
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Larry Knox
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95fa8f15e8 |
Sync develop changes June 6 - July 2 to hdf5_1_14 (#4623)
* Fix typos in context/property documentation (#4550) * Fix CI markdown link check http 500 errors (#4556) Sites like GitLab can have internal problems that return http 500 errors while they fix their problems. Some sites also return http 200 OK, which is fine. This PR adds a config file to the markdown link check so those are considered "passing" and don't break the CI. * Simplify property copying between lists internally (#4551) * Add Python examples (#4546) These examples are referred to from the replacement page of https://portal.hdfgroup.org/display/HDF5/Other+Examples. * Correct property cb signatures in docs (#4554) * Correct property cb signatures in docs * Correct delete callback type name in docs * add missing word to H5P__free_prop doc * Move C++ and Fortran and examples to HDF5Examples folder (#4552) * Document 'return-and-read' field in API context (#4560) * Add compression includes to tests needing zlib support (#4561) * Allow usage of page buffering for serial file access from parallel HDF5 builds (#4568) * Remove old version of libaec (#4567) * Add property names to context field docs (#4563) * Document property shared name behavior (#4565) * Clarify H5CX macro documentation (#4569) * Document H5Punregister modifying default properties (#4570) * Update NVHPC to 24.5 (#4171) We don't test parallel in other GitHub actions, so this also converts the NVHPC check to configure and build only while we discuss how we'll test parallel HDF5 in GitHub. There is a blocking GitHub issue to address the test failures for HDF5 1.14.5 (#4571). * Clean up comments in H5FDros3.c (#4572) * Rename INSTALL_Auto.txt to INSTALL_Autotools.txt (#4575) * Clean up ros3 VFD stats code (#4579) * Removes printf debugging * Simplifies and centralizes stats code * Use #ifdef ROS3_STATS instead of #if * Other misc tidying * Turn off ros3 VFD stat collection by default (#4581) Not a new change - an artifact from a previous check-in. * Pause recording errors instead of clearing the error stack (#4475) An internal capability that's similar to the H5E_BEGIN_TRY / H5E_END_TRY macros in H5Epublic.h, but more efficient since we can avoid pushing errors on the stack entirely (and those macros use public API routines). This capability (and other techniques) can be used to remove use of H5E_clear_stack() and H5E_BEGIN_TRY / H5E_END_TRY within library routines. We want to remove H5E_clear_stack() because it can trigger calls to the H5I interface from within the H5E code, which creates a great deal of complexity for threadsafe code. And we want to remove H5E_BEGIN_TRY / H5E_END_TRY's because they make public API calls from within the library code. Also some other minor tidying in routines related to removing the use of H5E_clear_stack() and H5E_BEGIN_TRY / H5E_END_TRY from H5Fint.c * Add page buffer cache command line option to tools (#4562) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clarify documentation for H5CX_get_data_transform (#4580) * Correct comment for H5CX_get_data_transform * Document why data transform ctx field doesnt use macro * Remove public API call from ros3 VFD (#4583) * Remove printf debugging from H5FDs3comms.c (#4584) * Cleanup of ros3 test (#4587) * Removed JS* macro scheme (replaced w/ h5test.h macros) * Moved curl setup/teardown to main() * A lot of cleanup and simplification * Removed unused code from H5FDs3comms.c (#4588) * H5FD_s3comms_nlowercase() * H5FD_s3comms_trim() * H5FD_s3comms_uriencode() * Remove magic fields from s3comms structs (#4589) * Remove dead H5FD_s3comms_percent_encode_char() (#4591) * Rework the TestExpress usage and refactor dead code (#4590) * Skip examples if running sanitizers (#4592) * Clean up s3comms test code (#4594) * Remove JS* macros * Remove dead code * Bring in line with other test code * Add publish to bucket workflow (#4566) * Update abi report CI workflow for last release (#4596) * Update abi report workflow to handle 1.14.4.3 release * Update name of java report * Document that ctx VOL property isn't drawn from the FAPL (#4597) * Update macos workflow to 14 (keep 13 as alternate) (#4603) * Removed unnecessary call to H5E_clear_stack (#4607) H5FO_opened and H5SL_search don't push errors on the stack * Bring subfiling VFD code closer to typical library code (#4595) Remove API calls, use FUNC_ENTER/LEAVE macros, use the library's error macros, rename functions to have more standardized names, etc. * Correct documentation for return-and-read fields (#4598) * These two generators create strings without NUL for testing (#4608) * Fix Fortran pkconfig to indicate full path of modules (#4593) * Updated release schedule (#4615) 1.16 and 2.0 information * Document VOL object wrapping context (#4611) * Earray.c and farray.c in hdf5_1_14 still need time_t curr_time for HDsrandom. * Remove line to use future 116_API from CMakeListat.txt files in HDF5 examples directories |
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+1       
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ad50867d48 |
Sync develop changes May 20 - June 6 to hdf5_1_14 (#4553)
* 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](https://github.com/softprops/action-gh-release/compare/9d7c94cfd0a1f3ed45544c887983e9fa900f0564...69320dbe05506a9a39fc8ae11030b214ec2d1f87) 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](https://github.com/ossf/scorecard-action/compare/0864cf19026789058feabb7e87baa5f140aac736...dc50aa9510b46c811795eb24b2f1ba02a914e534) 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](https://github.com/github/codeql-action/compare/d39d31e687223d841ef683f52467bd88e9b21c14...f079b8493333aace61c81488f8bd40919487bd9f) --- 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> |
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Larry Knox
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86f603e6f9 |
Sync develop changes May 6 - May 20 to hdf5_1_14 (#4503)
* 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
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Larry Knox
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a3545767b4 |
Sync develop changes April 22 - May 7 to hdf5_1_14 (#4465)
* Split H5Tconv.c into modules by type (#4393) * Split H5Tconv.c into modules by type * Add new H5Tconv headers to list of private headers * Fix broken links in VOL API table (#4438) * Don't print thread ID when the library isn't multithreaded. (#4428) Corresponding changes to make error output for regression tests agnostic to thread setting. Signed-off-by: Quincey Koziol <quincey@koziol.cc> * Start refactoring H5E code to avoid using IDs internally (#4427) * Add support for builtin_expect compiler hint (#4425) * Add support for __builtin_expect extension And H5_LIKELY / H5_UNLIKELY macros to wrap it Signed-off-by: Quincey Koziol <quincey@koziol.cc> * Committing clang-format changes --------- Signed-off-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * sanitizer flags need set before compiler flags (#4444) * Add navigate chapters and use release_docs in Learn Basics (#4441) * Fix for github issue #3790: infinite loop closing library (#4445) * Fix for github issue #3790: infinite loop closing library Cause of the problem: When h5dump tries to open the user provided test file, the metadata cache will call the "get_final_load_size" callback to find out the actual size of the the root object header. The callback function will call H5O__prefix_deserialize() to allocate space for the object header data structure (via H5FL_CALLOC) and to deserialize the object header prefix in order to find the actual size of the object header. The metadata cache will then check whether the actual size obtained will exceed the file's EOA. Since the actual size obtained from the test file exceeds the EOA, the metadata cache throws an error and return. However, the oh structure that was allocated in H5O__prefix_deserialize() was not freed and hence causing the problem described in this issue. Fix: 1) Deallocate the oh structure after obtaining and saving the needed information in udata which will be used later on in the "verify_chksum" callback. 2) Deserialize the object header prefix in the "object header's "deserialize" callback regardless. The original coding intends to keep the deserialized prefix so that the object header's "deserialize" callback does not need to deserialize the prefix again if the object header is coming through the "get_final_load_size" callback. * H5R Fortran wrappers and misc. H5R API/DOC updates (#4446) - Add Fortran H5R APIs: h5rcreate_attr_f, h5rcreate_object_f, h5rcreate_region_f, h5ropen_attr_f, h5ropen_object_f, h5ropen_region_f, h5rget_file_name_f, h5rget_attr_name_f, h5rget_obj_name_f, h5rcopy_f, h5requal_f, h5rdestroy_f, h5rget_type_f - Fixed function H5Requal actually to compare the reference pointers Fixed an issue with H5Requal always returning true because the function was only comparing the ref2_ptr to itself. * Fix heap-buffer-overflow in H5Fio.c (#4450) The buffer size for checksum was smaller than H5_SIZEOF_CHKSUM, causing an overflow while calculating the offset to the checksum in the buffer. A check was added so H5F_get_checksums would fail appropriately in all of its occurrences. Fix gh-4434 * Fix grammar in VOL guide (#4452) * Fix bug in MPI-IO VFD (#4456) Corrects incorrect usage of the vector_was_sorted parameter in H5FD__mpio_vector_build_types() * Bump the github-actions group with 3 updates (#4455) Bumps the github-actions group with 3 updates: [actions/download-artifact](https://github.com/actions/download-artifact), [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) and [github/codeql-action](https://github.com/github/codeql-action). Updates `actions/download-artifact` from 4.1.4 to 4.1.7 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/c850b930e6ba138125429b7e5c93fc707a7f8427...65a9edc5881444af0b9093a5e628f2fe47ea3b2e) Updates `peaceiris/actions-gh-pages` from 3.9.3 to 4.0.0 - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](https://github.com/peaceiris/actions-gh-pages/compare/373f7f263a76c20808c831209c920827a82a2847...4f9cc6602d3f66b9c108549d475ec49e8ef4d45e) Updates `github/codeql-action` from 3.24.9 to 3.25.3 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/1b1aada464948af03b950897e5eb522f92603cc2...d39d31e687223d841ef683f52467bd88e9b21c14) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major 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> * Fixed failures with xl compilers. (#4458) * type cast constant * fixed return types * Convert ERR test to use grep (#4451) * Convert ERR test to use grep * Eliminate use of .err files in CMake * Show error output if grep fails * Turn off cuda in NVHPC CI * Removed "function/code stack" debugging configure option (#4454) Easily replaced w/third-party tools, e.g. libbacktrace (https://github.com/ianlancetaylor/libbacktrace) * Clean up memory leaks in t_vfd (#4457) * Fixes and cleanup for ph5diff (#4460) * Fixes and cleanup for ph5diff Fixes concurrency issues in ph5diff that can cause interleaved output Fixes an issue where output can sometimes be dropped if it ended up in ph5diff's output overflow file Fixes an issue where MPI_Init is called after HDF5 has been initialized, preventing the library from setting up an MPI attribute to perform cleanup on MPI_Finalize Fixes an issue in config/cmake/runTest.cmake where the CMake logic would try to access an invalid list index if the number of lines in a test's output and reference files don't match * Add release note * Remove use of err files in autotools test scripts (#4461) * Fix typo in H5Rget_obj_type (#4463) Issue GH-1723 * Use ADD_H5_ERR_TEST to not compare output (#4464) |
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Larry Knox
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5086959778 |
Sync develop changes April 4 -April 22 to hdf5_1_14 (#4437)
* Fixed dead links in docs (#4334) * Revert "Fixed dead links in docs (#4334)" (#4335) This reverts commit |
||
 Glenn Song
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203cd53709 |
Update support branch (#4320)
Update support branch version number to 1.14.5-1 |
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Larry Knox
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3c86f0f0ce |
Sync develop changes March 20 - March 25 to hdf5_1_14. (#4241)
* Call memset before stat calls (#4202)
The buffers passed to stat-like calls are only partially filled in by
the call, leaving ununitialized memory areas when the stat buffers are
created on the stack.
This change memsets the buffers to 0 before the stat calls, quieting
the -fsanitze=memory complaints.
* Remove unused CMake configuration checks (#4199)
* Update link to Chunking in HDF5 page (#4203)
* Fix H5Pset_efile_prefix documentation error (#4206)
Fixes GH issue #1759
* Suggested header footer for NEWSLETTER (#4204)
* Suggested header footer for NEWSLETTER
* Updates
* Add NEWSLETTER.txt to h5vers script
* Fix grammar in README.md release template (#4201)
* Add back snapshot names (#4198)
* Use tar.gz extension for ABI reports (#4205)
* Fix issue with Subfiling VFD and multiple opens of same file (#4194)
* Fix issue with Subfiling VFD and multiple opens of same file
* Update H5_subfile_fid_to_context to return error value instead of ID
* Add helper routine to initialize open file mapping
* Reverts AC_SYS_LARGEFILE change (#4213)
We previously replaced local macros with AC_SYS_LARGEFILE, which is
unfortunately buggy on some systems and does not correctly set the
necessary defines, despite successfully detecting them.
This restores the previous macro hacks to acsite.m4
* Propagate group creation properties to intermediate groups (#4139)
* Add clarification for current behavior of H5Get_objtype_by_idx() (#4120)
* Addressed Fortran issues with promoted integers and reals via compilation flags (#4209)
* addressed issue wit promoted integers and reals
* added option to use mpi_f08
* Summarize the library version table (#4212)
Fixes GH-3773
* Fix URLs (#4210)
Also removed Copyright.html context because it's no longer valid.
* Fix 'make check-vfd' target for Autotools (#4211)
Changes Autotools testing to use HDF5_TEST_DRIVER environment
variable to avoid running tests that don't work well with several
VFDs
Restores old h5_get_vfd_fapl() testing function to setup a FAPL
with a particular VFD
Adds a macro for the default VFD name
* Revert "Addressed Fortran issues with promoted integers and reals via compil…" (#4220)
This reverts commit
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||
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Larry Knox
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b69c6fcbf6 |
1 14 dev sync lrk (#4200)
* Added new H5E with tests. (#4049) Added Fortran H5E APIs: h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f, h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f, h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature) Addresses Issue #3987 * Don't load toolchain file in CMake workflows (#4077) * Add support for the new MSVC preprocessor (#4078) Microsoft has added a new, standards-conformant preprocessor to MSVC, which can be enabled with /Zc:preprocessor. This preprocessor trips over our HDopen() function-like variadic macro since it uses a hack that only works with the legacy MSVC preprocessor. This fix adds ifdefs to use the correct HDopen() macro depending on the MSVC preprocessor selected. Fixes #2515 * Increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096 to accommodate long AWS secret tokens (#4064) ros3: increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096; stratified the debugging statements so there is more control over the output * Close and reopen file during dset vlen IO API tests (#4050) - Close/reopen file and file objects to prevent cache from being used instead of actual I/O. - Moved vlen io test datasets under the dset container group instead of the root group - Moved the PASSED() invocation to after individual test cleanup in case an error occurs during H5Treclaim * New option for building with static CRT in Windows (#4062) * addressed compilation errors with gfortran 4.8 (#4082) * Fix bin/trace script w/ out params (#4074) The bin/trace script adds TRACE macros to public API calls in the main C library. This script had a parsing bug that caused functions that were annotated with /*out*/, etc. to be labeled as void pointers instead of typed pointers. This is mainly a developer feature and not visible to consumers of the public API. The bin/trace script now annotates public API calls properly. Fixes GH #3733 * Use H5T_STD_I32LE to create datatype in vds examples (#4070) Fixes issues when VDS examples are tested on BE systems * Remove printf debugging in H5HL code (#4086) * Fixed asserts due to H5Pset_est_link_info() values (#4081) * Fixed asserts due to H5Pset_est_link_info() values If large values for est_num_entries and/or est_name_len were passed to H5Pset_est_link_info(), the library would attempt to create an object header NIL message to reserve enough space to hold the links in compact form (i.e., concatenated), which could exceed allowable object header message size limits and trip asserts in the library. This bug only occurred when using the HDF5 1.8 file format or later and required the product of the two values to be ~64k more than the size of any links written to the group, which would cause the library to write out a too-large NIL spacer message to reserve the space for the unwritten links. The library now inspects the phase change values to see if the dataset is likely to be compact and checks the size to ensure any NIL spacer messages won't be larger than the library allows. Fixes GitHub #1632 * Fix copy-paste comments * update macOS support statement (#4084) * fixes compilation failures due to H5E additions (#4090) * Remove extra whitespaces from nvhpc-cmake action. (#4091) * Remove printf debugging in H5I package (#4088) * Add subfiling for h5dump filedriver option help message (#3878) * Merge HDF4 release workflow changes to hdf5 (#4093) * Update long double test with correct values (#4060) Update long double test with correct values * virtual creates must use the same datatype as the main file (#4092) * Fixed -Wdeprecated-copy-dtor warnings by implementing a copy assignment operator (#3306) Example warning was: warning: definition of implicit copy assignment operator for 'Group' is deprecated because it has a user-declared destructor [-Wdeprecated-copy-dtor] * Expand check for variable-length or reference types when clearing datatype conversion paths (#4085) When clearing out datatype conversion paths involving variable-length or reference datatypes on file close, also check for these datatypes inside compound or array datatypes * Remove H5B debug checks (#4089) The H5B (version 1 B-tree) package would add some computationally expensive integrity checks when H5B_DEBUG was defined. Due to their negative effects on performance, this option was rarely turned on, making the H5B__assert() check function stale, if not dead, code. This change: * Builds H5B__assert() when NDEBUG is not defined (the function relies on assert()) so it gets compiled more often. * Removes some printf debugging statements in the B-tree code * Removes all H5B "extra debug" checks that are leftover from past debugging sessions. Maintainers can add H5B__assert() selectively to perform integrity checks when debugging. * Removes the HDF5_ENABLE_DEBUG_H5B CMake option H5B_DEBUG now has no effect * Fix the last C++ stack size warning (#4099) * Clean up off_t usage (#4095) * Add comments to C++ and Fortran API calls that use off_t * Remove noise casts for small integers * Correct missing change of source path for S3 build (#4100) * Remove leading / from relative path. (#4101) * msvc: don't declare `HAVE_TIMEZONE` for older MSVC (#3956) It was introduced in MSVC 15 (Visual Studio 2017). * Remove a few H5O printf debugging statements (#4096) These were in H5Oint.c, were protected by H5O_DEBUG, and only dumped to stdout if the HDF5_DEBUG environment variable were set to do so. * Remove H5DEBUG() calls from H5Dmpio.c (#4103) Just use stdout when a stream is needed. * Remove printf debugging from H5Smpio.c (#4098) * Change how stats are printed in H5Z (#4097) H5Z used the soon-to-be-removed HDEBUG macro to decide if stats would be dumped and to what stream. This is now handled by a DUMP_DEBUG_STATS_g variable and the output is always sent to stdout. This is an internal change, not normally visible to users. * Refactor datatype conversion code to use pointers rather than IDs (#4104) The datatype conversion code previously used IDs for the source and destination datatypes rather than pointers to the internal structures for those datatypes. This was mostly due to the need for an ID for these datatypes that can be passed to an application-registered datatype conversion function or datatype conversion exception function. However, using IDs internally caused a lot of unnecessary ID lookups and hurt performance of datatype conversions in general. This was especially problematic for compound datatype conversions, where the ID lookups were occuring on every member of every compound element of a dataset. The code has now been refactored to use pointers internally and only create IDs for datatypes when necessary. Fixed a test issue in dt_arith where a library datatype conversion function was being cast to an application conversion function. Since the two have different prototypes, this started failing after the parameters for a library conversion function changed from hid_t to H5T_t * and an extra parameter was added. This appears to have worked coincidentally in the past since the only different between a library conversion function and application conversion function was an extra DXPL parameter at the end of an application conversion function Fixed an issue where memory wasn't being freed in the h5fc_chk_idx test program. Even though the program exits quickly after allocating the memory, it still causes failures when testing with -fsanitize=address * Minimize use of abort() (#4110) The abort() call is used at several places where it probably shouldn't. * Clean up a few things in H5T.c (#4105) * remove (size_t) noise casts * replace (hid_t)FAIL with H5I_INVALID_HID * Convert H5B__assert to use error checks (#4109) Switches assert() calls to HGOTO_ERROR in H5B__assert() so it can be used in production mode. Also renames it to H5B__verify_structure() to better reflect what it checks. * Move common variables out of cache test blocks (#4108) Fixes a stack size warning w/ XCode * Remove lint comments (#4107) * Change compression tests reference files to use masking for compression ratios (#4083) Rework TEST_FILTER tests to handle slightly different compression ratios * Add Doxygen for HDFS VFD (#4106) * Add Doxygen for HDFS VFD * Fix Doxygen warning * Update H5FDhdfs.h * long double tests has problems setting precision with offset (#4102) * long double tests has problems setting precision with offset * Disable long double until more development fixes issues * Fix up dsets test for some platforms with different long double format (#4114) * Adjust aocc workflow to fit the autotools/cmake pattern of other callable workflows. (#4115) * Implement ID creation optimization for container datatype conversions (#4113) Makes the datatype conversion context object available during both the initialization and conversion processes for a datatype conversion function, allowing the compound, variable-length and array datatype conversion functions to avoid creating IDs for the datatypes when they aren't necessary Adds internal H5CX_pushed routine to determine if an API context is available to retrieve values from Also adds error checking to several places in H5T.c and H5Tconv.c where the code had previously assumed object close operations would succeed * Handle IBM long double issues in dsets.c test_floattypes test (#4116) * Handle IBM long double issues in dsets.c test_floattypes test * Remove old cmake check (#4117) * Use AC_SYS_LARGEFILE on Autotools (#4119) We previously used a hack introduced in 1.8.5 to paper over differences in off_t and off64_t when determining the type sizes. We no longer explicitly support off64_t in the library and AC_SYS_LARGEFILE works fine. * Initialize selection type in chunk struct (#4087) * Overhaul CMake LFS support (#4122) Externally visible: * The HDF_ENABLE_LARGE_FILE option (advanced) has been removed * We no longer run a test program to determine if LFS works, which will help with cross-compiling * On Linux we now unilaterally set -D_LARGEFILE_SOURCE and -D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since those options do nothing on 64-bit systems, this seems safe and covers all our bases. We don't set -D_LARGEFILE64_SOURCE since we don't use any of the POSIX 64-bit specific API calls like ftello64, as noted above. * We didn't test for LFS support on non-Linux platforms. We've added comments for how LFS should probably be supported on AIX and Solaris, which seem to be alive, though uncommon. PRs would be appreciated if anyone wishes to test this. Internal: * Drops off64_t size checks since this is unused (as in Autotools) * Remove HDF_EXTRA_FLAGS, which is now unused * Remove hack around deprecated LINUX_LFS Fixes #2395 * Update CMake comment about _POSIX_C_SOURCE (#4124) Was missng the 2008 pread/write info * Deprecate bin/cmakehdf5 (#4127) * Deprecate bin/cmakehdf5 * Add reference text * Don't set the rpath when linking statically (#4125) * Remove invalid compile flag (#4129) * Fix segfault in vlen io API test (#4130) * Update URLs in RELEASE.txt (#4132) * Add cygwin CI and update yaml files for consistency and accuracy (#4131) * Add cygwin CI * add cygwin packages * Correct option names * Cleanup yaml file and synch look and feel * Synch CI look and feel and correct path issues * Upgrade oneapi version * pwsh needs env: for vars * No continuation char for pwsh * restore correct pwsh step * Run subset of tests for cygwin workflow * Remove space chars in regex * restore full tests * Remove ros3 and hdfs VFDs from Autotools VFD list (#4142) These will never pass `make check` and would require a custom test suite for more comprehensive testing. * Skip part of dsets.c test for IBM long double type (#4136) * Capitalize option message for consistency. (#4141) * Fixed misc. H5E fortran failures due to previous PR (#4138) * fixed promotion of integers and reals tests and check-passthrough-vol failure * fixed cygwin issue * Fix Autotools -Werror cleanup (#4144) The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc. so configure checks don't trip over warnings generated by configure check programs. The sed line originally only scrubbed -Werror but not -Werror=something, which would cause errors when the '=something' was left behind in CFLAGS. The sed line has been updated to handle -Werror=something lines. Fixes one issue raised in #3872 * Fix doxygen link to example function usage (#4133) * Remove useless headers (#4145) Removes unnecessary headers from C library source files. * Clean up some hbool_t/TRUE/FALSE stragglers (#4143) It looks like most of these snuck in via selection I/O work * Fix error when overwriting an indirectly nested vlen with a shorter sequence (#4140) * defined CMAKE_H5_HAVE_DARWIN (#4146) * Make the newsletter scheme work like HDF4 (#4149) * Remove at the end of list item. (#4151) * Fix buffer size calculation in the deflate filter (#4147) * Remove H5O header and friend status from H5A.c (#4150) * Remove HDF from Fortran 2003 configuration check message. (#4157) * Suppress H5Dmpio debugging output unless HDF5_DEBUG=d is set (#4155) * Header cleanup in C library (#4154) * Ensure H5FL header is included everywhere * Ensure H5SL header is included everywhere * Ensure H5MM header is included everywhere * Add Doxygen to H5FDmirror.h (#4158) * Remove lseek64 and stat64 symbols from CMake (#4163) We don't use these in the library. * Remove HAVE_IOEO checks from CMake (#4160) This was intended to check for thread-safety functionality on Windows. The required functionality has been standard since Windows Vista, so these checks can be removed. * Fix some minor warnings (#4165) * Bump the size of the mirror VFD IP field (#4167) The IP address string isn't big enought to hold an IPv4-mapped IPv6 address. * Fix mirror VFD script (#4170) This had directory problems when running locally. * Fix an issue where the Subfiling VFD's context cache grows too large (#4159) * Address code page issues w/ Windows file paths (#4172) On Windows, HDF5 attempted to convert file paths passed to open() and remove() to UTF-16 in order to handle Unicode file paths. This scheme does not work when the system uses code pages to handle non-ASCII file names. As suggested in the forum post below, we now also try to see if we can open the file with open(), which should handle systems where non-ASCII code pages are in use. https://forum.hdfgroup.org/t/open-create-hdf5-files-with-non-utf8-chars-such-as-shift-jis/11785 * Add Doxygen to API calls in H5VLnative.h (#4173) * Allow H5Soffset_simple to accept NULL offsets (#4152) The reference manual states that the offset parameter of H5Soffset_simple() can be set to NULL to reset the offset of a simple dataspace to 0. This has never been true, and passing NULL was regarded as an error. The library will now accept NULL for the offset parameter and will correctly set the offset to zero. Fixes HDFFV-9299 * Add filter plugin user guide text. Fix registered URL in docs (#4169) * Add support for _Float16 16-bit floating point type (#4065) Fixed some conversion issues with Clang due to problematic undefined behavior when casting a negative floating-point value to an integer Fixed a bug in the library's software integer to floating-point conversion function where a user's conversion exception function returning H5T_CONV_UNHANDLED in the case of overflows would result in incorrect data after conversion Added configure checks for functions and macros related to _Float16 usage since some compilers expose the datatype but not the functions or macros Fixed a dt_arith test failure when H5_WANT_DCONV_EXCEPTION isn't defined Fixed a few warnings from not explicitly casting some _Float16 variables upwards * Remove some H5T_copy calls that are now unnecessary (#4164) Removes some datatype copying calls that are now unnecessary after refactoring the datatype conversion code to use pointers internally rather than IDs Rewrites the enum conversion function so that it uses cached copies of the source and destination datatypes in order to avoid modifying the datatypes passed in Adds a 'recursive' field to the datatype conversion context which allows the conversion functions for members of a container datatype to skip unnecessary repetitive conversion setup code Changes internal datatype conversion callback functions so that the source and destination datatype structure pointers are const Removes some unused and unnecessary internal IDs registered with H5I_register * Add RELEASE.txt note for cmpd segfault fix (#4175) RELEASE notice for the fix in #3842 * Clean up CMake direct VFD handling (#4161) There's no need to build and run programs, or even check the operating system. We just need to check for O_DIRECT and posix_memalign(). * Capitalize linux for consistency (#4178) * Reworked H5Epush_f (#4153) * Add const to new _Float16 conversion routine parameters (#4181) * Update Release Specific Information link. (#4179) * Filter plugins updates for registration URL (#4180) * Update filter plugin URL to new location * Adjust test array size * Add daily VFD CI workflow (#4176) Adds testing of Subfiling VFD * Exclude shell tests from sanitizers (#4186) * Add a missing period at the end of sentence. (#4184) * last-file.txt should not be created for release workflow (#4185) * Skip part of dtypes.c _Float16 file size check for certain VFDs (#4182) * Fixes several MinGW + Autotools issues (#4190) * Fixes detection of various Windows libraries, etc. * Corrects alarm(2) configure checks * Uses Win32 threads by default w/ Pthreads override, if desired * Set _WIN32_WINNT correctly for MinGW * Fix setenv(3) wrapper for MinGW, which does not have getenv_s() MinGW Autotools support is still not Amazing, but this at least allows the library and tools build and is better about thread-safety * Add semicolons to the end of HSYS_GOTO_ERROR (#4193) Looks like we forgot these when we did the other macros. * Remove broken links (#4187) * Skip vlen IO API test for cache VOL (#4135) * Fix cache VOL segfault in vlen io test * Skip vlen IO API test * Handle certain empty subfiling environment variables (#4038) * h5diff compares attribute data like dataset data (#4191) Updates tools docs to indicate that dataset and attribute data are compared in the same way * A path component may include a dot with other characters (#4192) * Add RELEASE.txt note for recent datatype conversion improvements (#4195) * Add NEWSLETTER item about _Float16 support (#4197) * Correct download link for develop doxygen (#4196) * Update version in new .yml files. |
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 Sean McBride
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4aeaa9c2d4 | Issue #1824: Replaced most remaining sprintf with safer snprint (#4003) | ||
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Allen Byrne
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fed6e095e5 | Add abi-complience check and upload to releases (#3996) | ||
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Allen Byrne
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56d9be146f |
Fix doxygen errors (#3962)
* Switch warnings as errors to default OFF * Enable mac docs * Add doxygen action uses step * Use html div around snippet * Allow preset name to be an argument to cmake-ctest.yml |
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Allen Byrne
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72e33ad772 | Merge examples and workflows from develop (#3918) | ||
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jhendersonHDF
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fb84c696a4 |
Sync 1.14 branch with develop (#3887)
* Preserve MPI-I/O file hints when fapl is closed (#3755) * Fix for issue #3025: Save the MPI info in the file struct so H5Fget_access_plist() can retrieve it from there. * Add compression tests for subfiling (#3769) * Fix typo in comment (#3775) * Fixed a file handle leak in the core VFD (#3779) When opening a file with the core VFD and a file image, if the file already exists, the file check would leak the POSIX file handle. Fixes GitHub issue #635 * Fix a format string warning in the C++ examples (#3776) * Cancel running GitHub workflows on push to same PR (#3772) * Cancel running GitHub workflows on push to same PR * Remove github.sha from workflow concurrency groups * Print some messages in parallel tests on MPI rank 0 only (#3785) Avoids overly verbose output from all processes emitting progress, etc. info. * Avoid attempted use of NULL pointer in parallel compression code (#3786) The parallel compression test code tests for the case where all MPI ranks have no selection in a dataset when writing to it. Add an early exit to the code to avoid attempting to use a NULL pointer due to there being no work to do. * Don't install h5tools_test_utils test program on system (#3793) * Add Doxygen to H5FDsplitter.h (#3794) * H5FD_CURR_SPLITTER_VFD_CONFIG_VERSION * H5FD_SPLITTER_PATH_MAX * H5FD_SPLITTER_MAGIC * H5FD_splitter_vfd_config_t * H5Pset_fapl_splitter() * H5Pget_fapl_splitter() * Update Doxygen initializers & identifiers in VFDs (#3795) * Add Doxygen for all H5FD_<VFD> initializers * Add Doxygen for all H5FD_<VFD>_VALUE values * Mark H5FD_<vfd>_init() calls private in Doxygen * Fix memory corruption in 'MPI I/O FAPL preserve' test (#3806) * Fix usage of h5_clean_files in t_pflush2.c (#3807) * Fix parallel driver check in h5_fixname_real (#3808) * Fix a couple usages of MPI_Info_get (#3809) * Remove H5system.c warning on Windows oneAPI. (#3812) * Add processing of NVHPC flags in linux-gnulibc1 file (#3804) * Disable testing as tests are failing the same as in CMake * Use the current toolchain for examples as default (#3810) * Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787) * Set NVHPC maximum optimization level to -O1 for now (#3800) * Set NVHPC maximum optimization level to -O1 for now Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved. * Disable nvhpc Java testing in CMake and amend known issues * Re-enable testing of Autotools nvhpc * Update some doxygen links to local refs (#3814) * Rework MPI Info FAPL preserve PR to use VFD 'ctl' operations (#3782) * Removed the use of C wrappers from H5P APIs. (#3824) * fix seg fault on frontier/cray * fix seg fault on frontier/cray * fix seg fault on frontier/cray * removed the use of h5pclose_c * removed the use of h5pclose_c * Fortran Wrappers H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f (#3801) * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests * Create test for H5Pget_dxpl_mpio (#3825) * Create test and add to testphdf5 * Renamed h5fuse.sh to h5fuse (#3834) * provide an alternative to mapfile for older bash * Disable FP exceptions in H5T init code (#3837) The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. Fixes #3831 * Add intel oneapi windows build to CI CMake (#3836) * Remove printf format warning on Windows oneAPI. (#3838) * Correct ENV variables (#3841) * Remove Autotools sed hack (#3848) configure.ac contains a sed line that cleans up incorrect library flags which was added to paper over some bugs in earlier versions of the Autotools. These issues are not a problem with the current versions of the Autootols. The sed line causes problems on MacOS, so it has been removed. Fixes #3843 * Make filter unregister callbacks safe for VOL connectors (#3629) * Make filter callbacks use top-level API functions When using VOL connectors, H5I_iterate may not provide valid object pointers to its callback. This change keeps existing functionality in H5Zunregister() without using potentially unsafe pointers. * Filter callbacks use internal API * Skip MPI work on non-native VOL * Add extra space in comments for consistency (#3852) * Add extra space in comments for consistency * uncomment tfloatsattrs test * Update Actions badges to link to relevant workflow (#3850) * Add CMake long double cross-compile defaults (#3683) HDF5 performs a couple of checks at build time to see if long double values can be converted correctly (IBM's Power architecture uses a special format for long doubles). These checks were performed using TRY_RUN, which is a problem when cross-compiling. These checks now use default values appropriate for most non-Power systems when cross-compiling. The cache values can be pre-set if necessary, which will preempt both the TRY_RUN and the default. Affected values: H5_LDOUBLE_TO_LONG_SPECIAL (default no) H5_LONG_TO_LDOUBLE_SPECIAL (default no) H5_LDOUBLE_TO_LLONG_ACCURATE (default yes) H5_LLONG_TO_LDOUBLE_CORRECT (default yes) H5_DISABLE_SOME_LDOUBLE_CONV (default no) Fixes GitHub #3585 * Updates for building and testing VOL connectors * Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable * Initialize parallel testing with MPI_THREAD_MULTIPLE when testing API * Add CMake variable to allow specifying a VOL connector's package name * Remove call to MPI_Init in serial API tests While previously necessary, it now interferes with VOL connectors that may need to be initialized with MPI_THREAD_MULTIPLE * Fixes for CI and presets (#3853) * Change dest for doxygen (#3856) * Implement selection vector I/O with collective chunk filling (#3826) * Changes for ECP-344: Implement selection vector I/O with collective chunk filling. Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization when computing max address. * Fixes based on PR review comments: For H5Dchunk.c: fix H5MM_xfree() For H5FDmpio.c: 1) Revert the fix to H5FD__mpio_write_vector() 2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types() * Put back the logic of dividing up the work among all the mpi ranks similar to the original H5D__chunk_collective_fill() routine. * Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector(). * Do not publish compression headers or docs (#3865) * Fix typo: look -> loop (#3866) * Moved the README to markdown and expanded its overview of the files, file generation, and other Fortran wrapper development practices as mentioned in the HDF5 architectural document. I added a new figure and included the SVG file and the original xfig file it was generated from. (#3862) * Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859) * Fix typo in error message for `MPI_Type_dup`. (#3867) * Complete the `if command line option` sentence. (#3868) * Fix h5dump segmentation fault when --vfd-value option is used (#3873) * Updated URL in funding.yml (#3882) Using new shortened URL, might look better. * Remove unused variable from unmerged changes * Update src/H5Tinit_float.c |
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Allen Byrne
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528a8e7f46 |
Sync CMake changes from develop (#3811)
Guard test dirs with HDF5_EXTERNALLY_CONFIGURED Add toolchain support to examples testing |
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Larry Knox
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71d8975b54 |
Update version to 1.14.4-1. (#3799)
Clean 1.14.3 entries from RELEASE.txt. Add hdf5-1.14.3-RELEASE.txt contents to HISTORY-1_14.txt. |
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jhendersonHDF
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a91be87f07 |
Sync with develop (#3764)
* Add missing test files to distclean target (#3734) Cleans up new files in Autotools `make distclean` in the test directory * Add tools/libtest to Autotools builds (#3735) This was only added to CMake many years ago and tests the tools library. * Clean up onion VFD files in tools `make clean` (#3739) Cleans up h5dump and h5diff *.onion files in the Autotools when runing `make clean`. * Clean Java test files on Autotools (#3740) Removes generated HDF5 and text output files when running `make clean`. * Clean the flushrefresh test dir on Autotools (#3741) The flushrefresh_test directory was not being cleaned up w/ `make clean` under the Autotools * Fix file names in tfile.c (#3743) Some tests in tfile.c use h5_fileaccess to get a VFD-dependent file name but use the scheme from testhdf5, reusing the FILE1 and FILE8 names. This leads to files like test1.h5.h5 which are unintended and not cleaned up. This changes the filename scheme for a few tests to work with h5test, resulting in more informative names and allowing the files to be cleaned up at the end of the test. The test files have also been added to the `make clean` target for the Autotools. * Clean Autotools files in parallel tests (#3744) Adds missing files to `make clean` for parallel, including Fortran. * Add native VOL checks to deprecated functions (#3647) * Add native VOL checks to deprecated functions * Remove unneeded native VOL checks * Move native checks to top level calls * Fix buffer overflow in cache debugging code (#3691) * update stat arg for apple (#3726) * update stat arg for apple * use H5_HAVE_DARWIN for Apple ifdef * fix typo * removed duplicate H5_ih_info_t * added fortran async test to cmake * Fix windows cpack error in WiX package. (#3747) * Add a simple cache to the ros3 VFD (#3753) Adds a small cache of the first N bytes of a file opened with the read-only S3 (ros3) VFD, where N is 4kiB or the size of the file, whichever is smaller. This avoids a lot of small I/O operations on file open. Addresses GitHub issue #3381 * Update Autotools to correctly configure oneAPI (#3751) * Update Autotools to correctly configure oneAPI Splits the Intel config files under the Autotools into 'classic' Intel and oneAPI versions, fixing 'unsupported option' messages. Also turns off `-check uninit` (new in 2023) in Fortran, which kills the H5_buildiface program due to false positives. * Enable Fortran in oneAPI CI workflow * Turn on Fortran in CMake, update LD_LIBRARY_PATH * Go back to disabling Fortran w/ Intel For some reason there's a linking problem w/ Fortran error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory * Add h5pget_actual_selection_io_mode fortran wrapper (#3746) * added h5pget_actual_selection_io_mode_f test * added tests for h5pget_actual_selection_io_mode_f * fixed int_f type conversion * Update fortran action step (#3748) * Added missing DLL for H5PGET_ACTUAL_SELECTION_IO_MODE_F (#3760) * add missing H5PGET_ACTUAL_SELECTION_IO_MODE_F dll * Bump the ros3 VFD cache to 16 MiB (#3759) * Fix hangs during collective I/O with independent metadata writes (#3693) * Fix some issues with collective metadata reads for chunked datasets (#3716) Add functions/callbacks for explicit control over chunk index open/close Add functions/callbacks to check if chunk index is open or not so that it can be opened if necessary before temporarily disabling collective metadata reads in the library Add functions/callbacks for requesting loading of additional chunk index metadata beyond the chunk index itself * Fix failure in t_select_io_dset when run with more than 10 ranks (#3758) * Fix H5Pset_evict_on_close failing regardless of actual parallel use (#3761) Allow H5Pset_evict_on_close to be called regardless of whether a parallel build of HDF5 is being used Fail during file opens if H5Pset_evict_on_close has been set to true on the given File Access Property List and the size of the MPI communicator being used is greater than 1 |
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4a028905e4 |
Sync 1.14 branch with develop (#3705)
* 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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jhendersonHDF
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ea3f926057 |
1.14 sync with develop (#3660)
* Rework tools.cmake and add C flags (#3110) * Fix gh pages so that the doxygen files are uploaded (#3102) * Add workspace path * add debug * Make one job so workspace files are available * Put doxygen docs under docs folder in gh-pages * Fix a misc warning in test/vol.c (#3112) The compiler complains about using integers instead of size_t for some sizes. * Remove H5detect and H5make_libsettings (#3104) Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file * clang-tidy clang-analyzer-core issues addressed (#3113) src/H5system.c:1293:13: warning: Dereference of null pointer [clang-analyzer-core.NullDereference] src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains uninitialized data (e.g., via the field chain: 'initial.user') [clang-analyzer-core.CallAndMessage] * Add note for issue 3056 (#3117) * Use 1.14 toolchain (#3116) * Remove the checkposix script (#3122) This script was used to ensure that all non-HDF5 calls were prefixed with 'HD'. We are removing this scheme so this script is no longer needed. * Remove unused HD macros (#3120) * Remove unused HD macros The library prefixes most C and POSIX API calls with 'HD'. We are going to start removing these so the code looks like normal C. This PR removes most of the unused HD markup macros. * Replace ntohl/ntohs * Adds an optional version arg to bin/format_source (#3119) * Clean up mirror VFD code in utils dir (#3121) * Remove dead code * Replace mybzero with memset * Replace hbool_t/TRUE/FALSE with bool/true/false * Fix spelling issues flagged by codespell (#3130) * Make autogen.sh output message consistent (#3128) * Add Python for HDF-EOS zoo description (#3129) * Fix function name in comment in ros3 VFD (#3131) * Revert long double checks (#3133) * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit |
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Dana Robinson
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51ff48b887 | Fix several spelling/grammar issues (#3621) (#3632) | ||
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Allen Byrne
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cf6d3e0737 | Correct dimensions in java test (#3484) | ||
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Larry Knox
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3262891c6b |
Merges from develop Aug 2-4 (#3354)
* 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) * Windows runtime items go into the bin folder (#3320) |
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Larry Knox
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51715c1be6 | Set version to 1.14.3-1. (#3343) | ||
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Dana Robinson
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00f5d01c83 | Normalize java w/ develop (#3283) | ||
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Allen Byrne
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bfeb1b0dd5 |
Fix doxygen and actions - merge from develop (#3109)
* Update the workflows to changes in develop * Disable java for error only action * Fix Fortran doxygen * add fortran alias * Merge changes from develop to fix actions |
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Larry Knox
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722574e05c |
Update version (#2971)
* Update version Copy RELEASE.txt from 1.14.1-2 release into HISTORY-1_14.txt Clear out RELEASE.txt |
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Dana Robinson
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7707859279 | Merge with develop (#2790) | ||
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Dana Robinson
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69c720bffa |
Merge "Use additional CPUs" and related fixes (#2742)
* 2720 Fix java depends and pdb lib install * 2695 Use additional CPUs in GitHub actions |
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Allen Byrne
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2319d4a092 | Change name of test file to avoid conflict (#2703) | ||
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Allen Byrne
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097f65e7a6 | Update java logger version (#2644) | ||
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Allen Byrne
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d51c97e7f5 |
1.14 Merge doxygen plist tables changes #2470 from develop (#2503)
* Merge doxygen plist tables changes from develop * Doxy corrections |
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Allen ByrneandDana Robinson
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04bd873d77 |
1.14 Fix some doxygen warnings (#2323)
* Fix some doxygen warnings * Remove javadocs * Fix spelling * Fix section format * Correct doxygen function name * Remove duplicate Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> |
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Larry KnoxandAllen Byrne
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23be40ca4f |
Hdf5 1 14 (#2296)
* Update versions for hdf5_1_14 develop branch after creation of hdf5_1-14_0 branch for 1.14.0 release. * Update windows worker compilers (#2286) * Update windows worker compilers * Update bin and test issues * Update script and revert java test * Update scripts and versions in java files. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> |
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Larry Knox
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4e5bdb8c4e |
Update versions for hdf5_1_14 develop branch after creation of (#2294)
hdf5_1-14_0 branch for 1.14.0 release. |
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Allen Byrne
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2376723d4a |
Develop jni trans (#2266)
* Add compound and refactor out atomic types * Add Array String tests back * Convert Attribute version of compound example * Update transfer atom8ic read to return object |
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Allen Byrne
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719d800499 | Refactor JNI translate functions to a recursive switch on datatype (#2232) | ||
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Larry Knox
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11dfa25910 |
Update copyright headers (#2184)
* 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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Larry Knox
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0173706826 |
Update develop branch version to 1.13.4-1 (#2189)
* Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3 release. Added new version to exceptions in lines 74-5 of src/H5.c |
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Allen Byrne
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9c61f7b1e1 |
JNI: Improve varlen datatype handling in H5A/H5D read/write functions (#2156)
* Improve JNI VL datatype read/write to handle complex combinations * Implement VL of VL JNI writes and reads * Add Java VLofVL test for attributtes * Changes to address review issues * Fix H5Aread vl blocks |
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Allen Byrne
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ea902f9ace |
Implement option for using CMake GNUInstallDirs (#2175)
* Implement option for using CMake GNUInstallDirs * Add release notes |
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Allen Byrne
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c114bd64b0 | Fix mostly java warnings, and cpp cast (#2134) | ||
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Allen Byrne
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45178c87a3 | develop Merge doxygen from 1.12 branch (#2095) | ||
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Allen Byrne
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c8fdd92cd4 |
Update CMake code to 3.18 minimum version (#2080)
* Update CMake code to 3.18 minimum version * Updated release note |
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jhendersonHDF
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5719187a34 | Fix Java tests for Developer build modes (#2079) | ||
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jhendersonHDF
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281db5876e | Cleanup some warnings in Java JNI code (#2034) | ||
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Dana Robinson
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7f6261a677 |
Removes cmake_ext_mod (files moved to cmake) (#2041)
At one time this content was a git submodule shared between several projects but that time has long passed. |