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* Update READMERE.md and RELEASE.txt with release date.hdf5-1_13_2hdf5_1_13_2Larry Knox2022-08-162-2/+2
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* Update release.txt (#2015)Larry Knox2022-08-152-20/+51
| | | | * Update Platforms tested in RELEASE.txt. Remove incorrect comment from c++/src/H5File.cpp
* Adds release notes for Onion VFD & H5Dchunk_iter changes (#2014)Dana Robinson2022-08-151-1/+24
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* Merge C++ fix to 1.3.2 (#2009)Larry Knox2022-08-134-49/+128
| | | | | | | 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)
* HDF5 1.13.2 released August 12, 2022 (#2006)Larry Knox2022-08-12105-27/+194051
| | | | | | | | | | | | * HDF5 1.13.2 released August 12, 2022 Updated so numbers for release Set version to 1.13.2 Switch default build mode to production for release in configure.ac, lines 435 and 442. Switch AM_MAINTAINER_MODE to disabled with bin/switch_maint_mode Set HDF5_GENERATE_HEADERS to OFF in src/CMakeLists.txt Commit Makefile.ins and other generated files for release except 2 ...~ files and autom4te.cache. * Add generated files with misspellings to excluded list in codespell.yml.
* 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
* Updates uthash and makes some tweaks (#1928)Dana Robinson2022-07-253-68/+38
| | | | | | | | | | | * Updates uthash from 2.1.0 to 2.3.0 * Moves uthash include and related to H5private.h * Defines HASH_NONFATAL_OOM so that out-of-memory doesn't abort() * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Switches the tagged metadata list from a skip list to a hash table (#1925)Dana Robinson2022-07-255-130/+98
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