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* Add API support for Fortran MPI_F08 module definitions. (#3959)Scot Breitenfeld2024-01-2914-24/+649
| | | | | * revert to using c-stub for _F08 MPI APIs * use mpi compiler wrappers for cmake and nvhpc
* Fix doxygen errors (#3962)Allen Byrne2024-01-2937-72/+209
| | | | | | | | | | | * 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
* Document that fileno is same for all handles (#3963)mattjala2024-01-262-10/+19
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* Add RELEASE.txt note for the fix for issue #1256 (#3955)jhendersonHDF2024-01-261-0/+28
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* RF: move codespell configuration into .codespellrc so could be used locally ↵Yaroslav Halchenko2024-01-262-3/+6
| | | | | | | | as well (#3958) ATM configuration was embedded within the CI workflow but that makes impossible to use codespell locally since the tool would not find those settings. I moved them into .codespellrc but then also removed codespell.yml workflow from skips, added .git and in general makde it look for .dotfiles too
* Change 'extensible' to 'fixed' in H5FA code (#3964)Dana Robinson2024-01-262-2/+2
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* Fix potential infinite loop in API test (#3960)mattjala2024-01-251-1/+1
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* fixed BIND name (#3957)Scot Breitenfeld2024-01-242-8/+3
| | | * update H5Ssel_iter_reset_f test
* Remove cached datatype conversion path table entries on file close (#3942)jhendersonHDF2024-01-235-12/+307
| | | | | | | | | | | | | | | | | | | | Remove cached datatype conversion path table entries on file close When performing datatype conversions during I/O, the library checks to see whether it can re-use a cached datatype conversion pathway by performing comparisons between the source and destination datatypes of the current operation and the source and destination datatypes associated with each cached datatype conversion pathway. For variable-length and reference datatypes, a comparison is made between the VOL object for the file associated with these datatypes, which may change as a file is closed and reopened. In workflows involving a loop that opens a file, performs I/O on an object with a variable-length or reference datatype and then closes the file, this can lead to constant memory usage growth as the library compares the file VOL objects between the datatypes as different and adds a new cached conversion pathway entry on each iteration during I/O. This is now fixed by clearing out any cached conversion pathway entries for variable-length or reference datatypes associated with a particular file when that file is closed.
* Add the user test program in HDFFV-9174 for committed types. (#3937)vchoi-hdfgroup2024-01-231-0/+169
| | | Add the user test program for committed types in HDFFV-9174
* Fortran API work. (#3941)Scot Breitenfeld2024-01-2312-172/+441
| | | | | | | | | | | | * - Added Fortran APIs: H5FGET_INTENT_F, H5SSELECT_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F, H5SSELECT_ITER_CLOSE_F, H5S_mp_H5SSELECT_ITER_RESET_F - Added Fortran Parameters: H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F - Added tests for new APIs - Removed H5F C wrapper stubs - Documentation misc. cleanup.
* Update H5Fget_obj_count/ids docs to reflect dtype behavior (#3932)mattjala2024-01-202-3/+4
| | | | | * Update H5Fget_obj_count/ids to reflect dtype behavior * Clarify comments on H5Fget_obj_ids
* Fix chid_t to hid_t (#3948)Glenn Song2024-01-201-1/+1
| | | Co-authored-by: Glenn Song <gsong@hdfgroup.org>
* Replace off_t with HDoff_t internally (#3944)Dana Robinson2024-01-186-15/+19
| | | | | | off_t is a 32-bit signed value on Windows, so we should use HDoff_t (which is __int64 on Windows) internally instead. Also defines HDftell on Windows to be _ftelli64().
* Clean up Doxygen for szip functions and constants (#3943)Dana Robinson2024-01-182-14/+46
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* autogen.sh: check directly for libtoolize instead of libtool [as libtool is ↵Satish Balay2024-01-131-28/+8
| | | | | | | not used here] (#3886) * autogen.sh: check directly for libtoolize instead of libtool [as libtool is not used here] * autogen.sh: simplify (g)libtoolize check - look for glibtoolize first - and then libtoolize
* Remove incorrect include of sz header (#3939)Allen Byrne2024-01-101-4/+0
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* Add binary build for linux S3 (#3936)Allen Byrne2024-01-097-4/+122
| | | | | | | | | | | | | * 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
* Reorg and update options for doc and cmake config (#3934)Allen Byrne2024-01-093-27/+42
| | | | * Reorg and update options for doc and cmake config * Correct subfiling depends
* Remove check for MPI initialization in tools library when using parallel VFDsH. Joe Lee2024-01-091-13/+16
| | | The tools library no longer checks for whether MPI is initialized when attempting to use a parallel VFD, such as the MPI I/O VFD or Subfiling VFD. This requires that parallel VFDs check for this situation and initialize MPI on their own if need be, but also allows parallel VFDs to be used with non-parallel HDF5 tools, such as h5dump.
* Update upload- artifact to match download version (#3929)Allen Byrne2024-01-084-16/+16
| | | | | * Update upload- artifact to match download version * Correct form of action call
* Add H5Dread/write_multi to API tests (#3919)mattjala2024-01-062-0/+1541
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* renamed defined H5_VERS* to avoid conflicts (#3926)Scot Breitenfeld2024-01-052-15/+15
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* Use props for includes and remove global includes (#3921)Allen Byrne2024-01-0416-52/+27
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* Fix building VOLs under library with CMake <3.24 (#3920)mattjala2024-01-041-11/+7
| | | | | * Fix building VOLs under library with CMake <3.24 * Handle CMake version through override variable
* Remove examples that have been moved to HDF5Examples folder (#3917)Allen Byrne2024-01-0317-3489/+22
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* New Fortran Examples added (#3916)Scot Breitenfeld2024-01-0321-41/+964
| | | | | * added subfiling example * Added filtered writes with no selection example
* Bump the github-actions group with 3 updates (#3913)dependabot[bot]2024-01-023-16/+16
| | | | (https://github.com/ilammy/msvc-dev-cmd), [actions/download-artifact](https://github.com/actions/download-artifact) and [github/codeql-action](https://github.com/github/codeql-action).
* Added H5Fdelete_f with test (#3912)Scot Breitenfeld2023-12-304-13/+85
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* Add 'warning density' computation to the warnhist script (#3910)Quincey Koziol2023-12-2918-136/+414
| | | | | | | | | * Add 'warning density' computation to the warnhist script, along with several cleanups to it. Add "--enable-show-all-warnings" configure (and CMake) option to disable compiler diagnostic suppression (and therefore show all the otherwise suppressed compiler diagnostics), disabled by default. Clean up a buncn of misc. warnings. Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
* Implement optimized support for vector I/O in Subfiling VFD (#3896)jhendersonHDF2023-12-278-1060/+2190
| | | | | | | | | | | | Vector I/O requests are now processed within a single set of I/O call batches, rather than each I/O vector entry (tuple constructed from the types, addrs, sizes and bufs arrays) being processed individually. This allows I/O to be more efficiently parallelized among the I/O concentrator processes during large I/O requests. * Fixed some calculations and add test cases for issues spotted from review * Removed a variable that was compensating for previous miscalculations
* Added new H5G Fortran HDF5examples (#3908)Scot Breitenfeld2023-12-2227-94/+768
| | | | | | | * updated traverse example * added H5PAR success statement * skipping H5_f90_h5ex_g_traverse
* Add CMake api checks to test the new Examples folder. (#3907)Allen Byrne2023-12-2222-99/+449
| | | | | | | | | * Fix missing build-mode value * Use 110 version file only for the 1.10 library * Fix H5_LIBVER_DIR variable * Disable 1.6 API tests for now.
* Change Trouble Shooting to Troubleshooting (#3905)H. Joe Lee2023-12-221-1/+1
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* Doc versions (#3903)Gerd Heber2023-12-2112-60/+315
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added missing \since tags to H5D. * Committing clang-format changes * Fixed H5T version info. * Committing clang-format changes * Added missing version info to H5E. * Committing clang-format changes * Added version info to H5F public APIs. * Committing clang-format changes * Added missing H5Z public API version info. * Added missing version info to H5G public APIs * Added missing version info to H5I public API. * Added missing version info to H5 public APIs * Committing clang-format changes * Added missing version info to H5P public APIs * Added missing version info to H5R public APIs * Fix comment error. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move Glossary to the end of docs navigation menu (#3902)H. Joe Lee2023-12-211-1/+1
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* Add VDS examples and fix non-standalone build (#3898)Allen Byrne2023-12-2160-473/+6433
| | | | | | | | * Choose a size for rdata dimension * Fix platform naming conflicts * Fix doxygen references to point within library repo
* Disable doxygen as errors for netcdf (#3900)Allen Byrne2023-12-201-1/+1
| | | * disable building doxygen for netcdf test
* Remove redundant backslash character from comment. (#3899)H. Joe Lee2023-12-201-1/+1
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* Add period(.) at the end of the sentence for consistency. (#3897)H. Joe Lee2023-12-191-1/+1
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* Add intel binaries to daily-build/release workflows (#3895)Allen Byrne2023-12-184-25/+242
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* Add variable option syncing for examples (#3885)Allen Byrne2023-12-14163-16406/+509
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* Bump the github-actions group with 4 updates (#3894)dependabot[bot]2023-12-1324-46/+46
| | | | | | Bumps the github-actions group with 4 updates: [actions/checkout](https://github.com/actions/checkout), [ossf/scorecard-action](https://github.com/ossf/scorecard-action), [github/codeql-action](https://github.com/github/codeql-action) and [actions/setup-python](https://github.com/actions/setup-python). Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Some changes to portal links when they could be found on docs.hdfgroup.org, ↵Lori Cooper2023-12-133-7/+7
| | | | | | | and changed the helpdesk link to help.hdfgroup.org (#3893) * Updated some portal links to go directly to docs.hdfgroup. * Fixed some portal and help desk links
* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot ↵Diogo Teles Sant'Anna2023-12-133-14/+24
| | | | | | | | | | | | | | | to update them monthly (#3892) * feat: hashpin sensitive dependencies on GHAs Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> * feat: enable dependabot for monthly updates on GHA Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> --------- Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>
* Correct urls and handling of external git repos (#3890)Allen Byrne2023-12-134-11/+31
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* Correct CMake command and example packaging (#3888)Allen Byrne2023-12-082-3/+3
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* Fix build error on freebsd (#3883)Satish Balay2023-12-071-1/+1
| | | | | | | | | Fixes: checking for config freebsd12.1... no checking for config freebsd... found compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0 compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0 stdout: .: cannot open ./config/classic-fflags: No such file or directory
* Updated URL in funding.yml (#3882)Lori Cooper2023-12-041-1/+1
| | | Using new shortened URL, might look better.
* Update examples with 1.6 api and static libs (#3874)Allen Byrne2023-11-298-38/+98
| | | | | | | * Update examples with 1.6 api and static libs * Only check for STATIC only builds * Do not calculate version as library has already.
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