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* Cleanup some warnings in Java JNI code (#2034)jhendersonHDF2022-08-194-162/+278
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* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-1951-726/+702
| | | | At one time this content was a git submodule shared between several projects but that time has long passed.
* Removes bin/deploy, which just calls h5redeploy under the hood (#2027)Dana Robinson2022-08-192-59/+0
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* Updates the warnist script to report gfortran generic warnings (#2040)Dana Robinson2022-08-191-0/+12
| | | | These are not associated with a file and line number, like specifying a non-existant include directory on the compile line.
* Release updates (#2033)Larry Knox2022-08-182-189/+611
| | | * Update HISTORy-1_13.txt and clean RELEASE.txt entries after 1.13.2 release.
* Add note to RELEASE.txt for GitHub #2016 (#2030)Neil Fortner2022-08-181-0/+9
| | | | | | | | | | | | | | | | | * 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. * Add RELEASE.txt note for PR #2016 * Add GitHub number to release note Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes codespell issues (#2032)Dana Robinson2022-08-1713-24/+24
| | | | | * Fixes codespell issues * Fixed another typo
* Add note to RELEASE.txt for HDFFV-11308 (#2029)Neil Fortner2022-08-171-0/+10
| | | | | * Add note to RELEASE.txt for HDFFV-11308 * Fix formatting error in RELEASE.txt
* Remove unused dependency files (#2025)Dana Robinson2022-08-172-78/+0
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* Update bin/README.mdDana Robinson2022-08-171-2/+2
| | | Correct missing space after # and ##
* Adds a TODO section to bin/README.md (#2028)Dana Robinson2022-08-171-0/+5
| | | Mainly to address the semi-broken state of chkcopyright
* Adjustments to t_bigio.c for >2GiB I/O test (#1992)jhendersonHDF2022-08-171-23/+34
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* Adds a README.md file to bin that indicates script usage (#2024)Dana Robinson2022-08-171-0/+27
| | | | | * Adds a README.md file to bin that indicates script usage * Forgot header row
* Removes bin/chkconfigure (#2023)Dana Robinson2022-08-171-82/+0
| | | | We check autoconf in configure.ac and can check for anything else in autogen.sh
* Removes bin/format_source_patch (#2022)Dana Robinson2022-08-171-34/+0
| | | This differs only trivially from bin/format_source
* Removes the bin/gcov_script file (#2021)Dana Robinson2022-08-171-51/+0
| | | We don't need fragile scripts to run basic profiling programs
* Replaces bin/newer with -nt comparison in Makefiles (#2020)Dana Robinson2022-08-172-45/+2
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* Removes the bin/yodconfigure script which appears unused (#2019)Dana Robinson2022-08-171-76/+0
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* Replaced bin/mkdirs w/ `mkdir -p -m 755`, which is POSIX (#2018)Dana Robinson2022-08-172-35/+2
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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>
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