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* Removes the broken bin/errors script (#2017)Dana Robinson2022-08-161-139/+0
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* Fix cpp comment (#2011)bmribler2022-08-161-2/+1
| | | | | | | | | | | | | | | | | | * Fix test failure Description: - Added two H5File constructors to open file with non-default fapl - Added non-default fapl to test functions - Commented certain renaming attribute tests because of the unexpected behavior in renaming an attribute (HDFFV-11327) Platform tested: Linux/64 (jelly) * Committing clang-format changes * Update H5File.cpp Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix bug in attribute type conversion wiith compound types (#2016)Neil Fortner2022-08-162-9/+175
| | | | | | | | | | | | | * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix c++ test failure (#2005)bmribler2022-08-124-49/+128
| | | | | | | | | | | | | | | | * Fix test failure Description: - Added two H5File constructors to open file with non-default fapl - Added non-default fapl to test functions - Commented certain renaming attribute tests because of the unexpected behavior in renaming an attribute (HDFFV-11327) Platform tested: Linux/64 (jelly) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)Larry Knox2022-08-1210-18/+18
| | | | release. Added new version to exceptions in line 75 of src/H5.c.
* Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for ↵Larry Knox2022-08-129-16/+16
| | | | | | | | release" This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95. H5TEST-tcheck_version-release failed.
* Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for releaseLarry Knox2022-08-129-16/+16
| | | | of HDF5 1.13.2.
* Correct target name for szaec lib (#2000)Allen Byrne2022-08-112-4/+5
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* Only use Subfiling VFD in tools if MPI was initialized previously (#1998)jhendersonHDF2022-08-111-3/+11
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* Fix Cmake depends prop (#1995)Allen Byrne2022-08-111-1/+1
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* Remove misnamed java vol clear test (#1990)Allen Byrne2022-08-101-10/+0
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* Only include and run Subfiling example when Subfiling is enabled (#1991)jhendersonHDF2022-08-102-2/+10
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* Fix typos found in the rest of the hdf5 code-base (#1985)luzpaz2022-08-1068-150/+149
| | | | | | | | | | | * Fix typos found in the rest of the hdf5 code-base * Typo in tool.cmake * Revert "Typo in tool.cmake" This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b. * Fix clang-format styling
* Fix CMake macro code commands (#1989)Allen Byrne2022-08-101-3/+0
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* Fix bug in cppcheck in tool.cmake (#1988)luzpaz2022-08-101-1/+1
| | | Ref: https://github.com/HDFGroup/hdf5/pull/1985#issuecomment-1211046328
* Fix4 readme (#1986)Gerd Heber2022-08-101-9/+8
| | | | | * Update README.md * Update README.md
* Move VFD SWMR release version to 1.13.3 in README.md (#1987)Dana Robinson2022-08-101-2/+2
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* Fix typos found in src/ subdirectory (#1983)luzpaz2022-08-1050-73/+73
| | | Found via `codespell -q 3 -S ./release_docs,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c -L isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn\'t,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ake,gord,numer,ro,oce`
* Remove usage of libgen.h (#1984)jhendersonHDF2022-08-106-9/+0
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* Add documentation for parallel compression feature (#1981)jhendersonHDF2022-08-091-0/+313
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* Subfiling VFD - tidying up and fixing a few new testing failures (#1977)jhendersonHDF2022-08-0913-1491/+916
| | | | | | | | | | | | | | | | | | | * Rename Subfiling IOC "thread_pool_count" field to "thread_pool_size" * Add simple HDF5 example for Subfiling VFD * Subfiling VFD - never cache app topology as it may change * Subfiling VFD - cleanup unused funtionality and tidy up some TODOs * Subfiling VFD - tidy up subfiling error handling in H5subfiling_common.c * Subfiling VFD - show number of failed I/O requests on close * Subfiling VFD - Update file cmp callback after switching to MPI I/O VFD * Amend RELEASE.txt with info about h5fuse.sh and Subfiling limitations * Subfiling VFD - switch to using H5_basename and H5_dirname
* Remove stray files, incorrect vds and mpi clean files (#1979)Allen Byrne2022-08-093-283/+0
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* Revert for older cmake versions (#1974)Allen Byrne2022-08-089-181/+8
| | | | | * Revert for older cmake versions * Remove unneeded clear/clean tests because of changes to test macro
* Turns off clang optimizations on a couple of onion VFD functions (#1976)Dana Robinson2022-08-083-2/+15
| | | Ancient clang (7.7.3 on OS X) emits problematic code with -O2 or -O3
* Fixes some badness in the onion VFD revision comment code (#1975)Dana Robinson2022-08-082-13/+20
| | | | | | | * Fixes some badness in the revision comment code * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop cmake clean (#1971)Allen Byrne2022-08-0774-1418/+2017
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* H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969)Mark Kittisopikul2022-08-073-16/+25
| | | | | | | | | | | * H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419 * Update docs for H5Dchunk_iter, H5Dget_chunk_info* Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following * offset Logical position of the chunk’s first element in units of dataset elements * filter_mask Bitmask indicating the filters used when the chunk was written * size Chunk size in bytes, 0 if the chunk does not exist
* Set entry pointer mem type for vector I/O in collective metadata writes (#1961)jhendersonHDF2022-08-071-7/+5
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* Fix issues in tools code after Subfiling VFD updates (#1973)jhendersonHDF2022-08-063-19/+45
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* Adds platform-independent basename and dirname (#1951)Dana Robinson2022-08-0510-1/+831
| | | | | | | | | | | | | | | | | | | | * Adds platform-independent basename and dirname * Tidy up H5_dirname and H5_basename implementations and add tests * Committing clang-format changes * Fix misspelling * Several fixes for H5_dirname/H5_basename from review * Committing clang-format changes * Add reason to VERIFY_STR macros in th5_system.c * Use H5MM_free instead of HDfree in H5_dirname/H5_basename tests Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Sanity checks for H5Xcreate_anon functions to make sure the IDs passed in ↵raylu-hdf2022-08-053-1/+16
| | | | | | | | | are valid (#1967) * Sanity checks for H5Xcreate_anon functions to make sure the IDs passed in are valid. * Removed unnecessary sanity checks. Co-authored-by: songyulu <songyulu@jelly.ad.hdfgroup.org>
* Subfiling updates for release (#1963)jhendersonHDF2022-08-0416-574/+1004
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built * Switch to MPI I/O driver for Subfiling HDF5 stub file * Rough first implementation for Subfiling file deletion * Subfiling VFD - get file dirname for file deletion * Subfiling VFD - set lock callback to NULL for now to avoid performance issues * Committing clang-format changes * Minor tidying up of Subfiling testing * Fixups for Subfiling VFD support in tools * Tidy up Subfiling public interface and add Doxygen * Respect Subfiling configuration settings from application * Add release note for Subfiling VFD * Committing clang-format changes * Committing clang-format changes * Shorten some Subfiling environment variable names Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Corrects some bad format strings in the tools (#1964)Dana Robinson2022-08-032-8/+11
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* Onion VFD (#1953)Dana Robinson2022-08-0255-39/+10632
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Onion VFD feature * Fixes onion VFD errors with non-sec2 backing store VFDs * Disables the onion VFD tests w/ ph5diff * Disables non-sec2 VFDs as onion VFD backing stores * Committing clang-format changes * Formatted source * Typo * Adds onion VFD tools tests to CMake * Fixes for v16 API compatibility * Memset structs to avoid bad frees on errors * H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE * Properly decodes checksums on BE machines * Be more careful about uint64_t to haddr_t/hsize_t conversions * Another fix for BE data comparison * Removed double underscores from onion constants * Replace hard-coded onion header string w/ constant * Fixes cleanup paths in H5FD__onion_ingest_history() * Fixed use of size_t revision numbers * Fix h5dump revision count format string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the Win32 macro for strdup (#1960)Dana Robinson2022-08-011-1/+0
| | | | Windows has strdup() so there's no need for this. We already ignore all the other "underscore" string functions.
* Removes Windows getlogin() equivalents (#1958)Dana Robinson2022-08-014-22/+1
| | | This function is no longer used in the library
* Removes (void *) cast from memset on Windows (#1957)Dana Robinson2022-08-011-1/+0
| | | | The comments claim this fixes an MSVC warning. Let's see if that's still true.
* Fixes clang warnings in H5Tconv.c (long) double macros (#1956)Dana Robinson2022-07-311-4/+4
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* Fixes format string warnings in tselect w/ clang 14 (#1955)Dana Robinson2022-07-311-11/+11
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* Reverts the autogen.sh changes from e3800e1 (#1906) (#1954)Dana Robinson2022-07-301-6/+165
| | | | | This is causing issues with the NAG Fortran compiler in our daily testing due to -shared getting inappropriately added. Reverting while we investigate.
* Cleanup of mirror VFD test code (#1949)Dana Robinson2022-07-304-1568/+1319
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* Created a pull request templateDana Robinson2022-07-291-0/+8
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* Update issue templatesDana Robinson2022-07-292-0/+45
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* Fixes #1946 (#1947)Gerd Heber2022-07-291-3/+12
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* H5Tconv: fix H5T_CONV_INTERNAL_ checks (#1936)Dana Robinson2022-07-271-1/+1
| | | | Other locations check if it is defined and in cases where it is not available, it is undefined, not 0.
* Misc clang production warning fixes (#1932)Dana Robinson2022-07-277-57/+79
| | | | | | | * Misc clang production warning fixes * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop clang 13 format (#1933)Allen Byrne2022-07-26685-6967/+6992
| | | | | * Update format source to clang 13 * More format changes
* Subfiling VFD misc fixes (#1938)jhendersonHDF2022-07-263-91/+15
| | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built
* Removes padding-right from Doxygen href tags (#1934)Dana Robinson2022-07-261-1/+0
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* Implement improved CMake fortran module folder from GH#1411 (#1922)Allen Byrne2022-07-2610-20/+77
| | | | | | | | | * Implement improved CMake fortran module folder from GH#1411 * Update docs * Fix whitespace * Fix name case
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