| Commit message (Collapse) | Author | Age | Files | Lines |
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* Merge doxygen plist tables changes #2470 from develop
* Add new/moved files
* More add new/moved files
* Doxy corrections
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* Merge UG from 1.10 and add prelim vol section
* Spelling fixes
* Merge format and autotools javadoc from 1.10
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* Merge A batch of life-cycle examples for different modules #654
* Remove generated file
* Change doxygen generated file location
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* Use internal version of H5Eprint2 to avoid possible stack overflow (#661)
* Reduces overly-pedantic casting in the public headers (#644)
* Committing clang-format changes
* Fixes overly pedantic casting in public headers
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (#699)
* fixed missed closing of a dataset
* fixed missed closing of a dataset
* fixed typo in error return
* Committing clang-format changes
* minor edits
* code format
* Committing clang-format changes
* code format
* minor edit
* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging
* Committing clang-format changes
* changed size_i in printf to reflect the I/O.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes pre-C99 build and header cruft (#700)
* Committing clang-format changes
* Removes pre-C99 build and header cruft
* Assumes ANSI C headers exist
* Assumes stdbool.h, stdint.h, and inttypes.h are present
* Assumes the C++ compiler can handle stdint.h
* Removes all work-arounds for missing functionality, especially stdbool.h
* Formats source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Clean up type size checks in configure.ac (#702)
* Removes some DEC Alpha cruft from H5detect and H5private.h (#708)
* Updates bin/trace script to correctly wrap H5TRACE macros near clang-format column limit (#719)
* Removes clang-format comments from H5O.c call
* Fixes bin/trace to correctly wrap lines near the clang-format limit
* Removed unused variable from bin/trace
* Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ (#726)
* Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++
Allows C++ library to be built on older versions of gcc.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Moves H5PacketTable default ctor inside source file (#731)
* Remove private H5_GCC_DIAG_OFF/ON from standalone program (#734)
* Organize and align compiler flags (#741)
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fixes C++ warnings when passing hsize_t values to printf in test code (#745)
* Normalization of H5_nanosleep() with VFD SWMR branch (#746)
* Normalization of H5_nanosleep() with VFD SWMR branch
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct missing variable declaration.
* Fixes some H5SL include statements (#758)
* Fixes non-C99 format strings in tarray test code (#766)
* Cleans up some POSIX header bits in H5private.h (#783)
* Further simplifies Autotools type size checks (#789)
Also fixes an issue where clock_gettime and difftime are not detected
due to earlier simplifications of this code.
* Normalization of CMake H5pubconf.h with Autotools (#791)
Mostly just moving things around and changing the comments to keep the
delta small. The only symbol change is that for curl/curl.h which I
changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol
is not used in the library and is just an artifact of the checks.
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
* Merge workflow and minor changes from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge serval small changes from dev
* fix typo
* Minor non-space formatting changes
* GH #386 copyright corrections for java folder
* revert because logic requires false return
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Remove case statement for H5I_EVENTSET
* Correct call with versioning
* Remove tabs
* Double underscore change
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards
* Merge #380 from develop
* Correct date entry
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* Some Javadoc warning fixes
* Committing clang-format changes
* Updated javadoc fixes
* HDFFV-11228/9 merges from develop
* remove obsolete debug comment
* Fix conflict
* HDFFV-11229 merge changes from develop
* HDFFV-11229 merge second compare from develop
* HDFFV-11229 fix reference file
* HDFFV-11229 update autotools test script for two ref files
* HDFFV-11229 merge dev changes for long double display in tools
* Committing clang-format changes
* Update with changes from develop
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.
* Whitespace changes
* Rework CMake add_custom to use the BYPRODUCTS argument
* Revert CMake configure checks for round defines
* With VS 2015 minimum strdup is supported
* Doxygen comments merged from develop
* doxygen build updates
* Correct version string for map functions
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
* Merge workflow and minor changes from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge serval small changes from dev
* fix typo
* Minor non-space formatting changes
* GH #386 copyright corrections for java folder
* revert because logic requires false return
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Remove case statement for H5I_EVENTSET
* Correct call with versioning
* Remove tabs
* Double underscore change
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file - src and test directories.
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
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* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4.
* First cut of the H5 public API documentation. (#80)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Full set of current H5F documentation. (#105)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Migrated documentation for SWMR functions.
* Catching up on MDC functions.
* Integrated the H5F MDC function documentation.
* Added MDC and parallel H5F functions.
* Slightly updated main page.
* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Doxygen - added (mostly) beginner functions (#112)
* Doxygen - added (mostly) beginner functions
* Removed duplicate H5Pset_szip function
* Add src/H5module.h to MANIFEST.
Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
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Brings all features from develop. Note that RELEASE.txt has not been
updated (will be done in a future PR).
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Also support references to external files
Add new H5T_REF type and type conversion routines
Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF
Add H5Treclaim() API to reclaim memory of vlen/reference types
Deprecate H5Dvlen_reclaim()
Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback
Add H5T_ref_reclaim()
Move previous H5R APIs to H5Rdeprec.c
Clean up H5Ocopy
Separate H5O_copy_expand_ref() to H5Ocopy_ref()
Add support for copying new reference types
Clean up deprecated routines to go through VOL and same code path
Fix return codes in existing trefer.c test
Rename trefer.c to trefer_deprec.c
trefer.c is for new references
Add performance test for trefer
Add additional obj_copy_ref test
Make use of tokens and blobs to store references
Skip blob encoding for object references
Start adding new reference examples
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VFD info in H5FDmpio.c.
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This also addresses HDFFV-10255: H5Sencode/decode performance issue.
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collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
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modified: test/dsets.c
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CMake stuff is not verified.
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Add line to libhdf5settings file for status of Parallel writes to
filtered datasets status
Surround Parallel Compression code in MPI_VERSION >= 3 checks
Add disabled message for Parallel Compression built w/ MPI-2
Modify Parallel Compression tests to only run the parallel filtered read
tests when parallel filtered writes are disabled
Update big I/O code to handle being built with MPI-2
Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
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Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
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~HDFTEST/hdf5_hft:hdf5_1_10 to develop"
This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing
changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
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develop"
This reverts commit b1223dd653e65e076af92b2dfe236f3704da81c8, reversing
changes made to b25f123f5f5e25c1447a6a02861cb7c7265c12f2.
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Modifications to fix H5Sencode bug when num points selected is > 2^32.
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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supporting metadata cache callback changes, etc.
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const void *. Fixes HDFFV-10017.
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The features is controlled via H5Pset/get_evict_on_close()
and is currently enabled by default (it will be disabled
by default in the final implementation).
There is a bug in the code where the eviction of tagged
metadata fails due to some of the metadata being dirty,
resulting in error return values and test failures.
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Bring H5DOappend(), H5P[s|g]et_object_flush_cb, and H5P[s|g]et_append_flush
from revise_chunks branch to trunk. Brings along updated metadata cache
entry tagging, and the internal object flush routine.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Change 'value' pointer to H5Pset() from 'void *' to 'const void *'.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial
(h5committest forthcoming)
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Bring "don't filter partial edge chunks" capability from revise_chunks
to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/debug, production & parallel
(h5committest forthcoming)
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external dataset storage path behavior.
This check-in fixes a bug in the original check-in where the
external path stored in the file struct was not copied on reopen
causing subsequent dataset operations to fail.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial w/ fortran and C++
autotools parallel (MPICH 3.1.4) w/ fortran
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