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* VFD SWMR: normalization with develop (#1472)Dana Robinson2022-03-061-3/+13
| | | Much normalization with develop. Still needs tools changes wrt VFD plugins.
* Much normalization with develop (#701)Dana Robinson2021-05-281-40/+342
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings CMake updates from develop * Brings reduction in pedantic casts from develop * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Formatted source * Bring over some VOL registration changes * VOL cleanup * H5VL_request_status_t substitutions * H5F.c cleanup * Minor API tweaks from develop * Moves H5G package init/teardown to H5Gint.c * H5G cleanup * H5M cleanup * H5SM cleanup * H5T cleanup * H5R cleanup * H5Lpublic.h cleanup * H5L cleanup * H5O cleanup * H5A, H5CS, and H5AC cleanup * Moved H5A init/teardown code to H5Aint.c * Moves H5D I/O functions to H5D.c * H5D cleanup * Misc minor cleanup * H5P close cleanup * H5Tpublic.h cleanup * Fixes err_compat test * H5PLpublic.h cleanup * Updates H5Ppublic.h * H5Fpublic.h updates * H5A.c cleanup * Brings over H5Aexists and related changes * Brings CMake shell testing changes from develop * Close callback changes * H5R and H5Tcommit normalization * err_compat test works now * H5O tweaks * Updates VOL registration code * Brings over H5VL_create_object * H5Tconv.c reformatting * H5T.c tweaks * Brings datatype and reference updates from develop * Brings VOL plugin loading changes from develop * Brings event sets from develop * Brings async functions over * Tools changes * Brings over many tools changes from develop * Brings VOL flags from develop * Fixes h5dump double/float tests * Updates h5repack tests * Brings h5diff test changes from develop * Last h5dump changes * Brings test changes from develop * Committing clang-format changes * Tidied h5_testing() * Brings chunk iteration code + misc from develop * Updates vds test * Enables external link parallel test * Brings updated property lists from develop * H5G changes from develop * H5MF cleanup * Brings vfd_swmr test back into CMake * Updates threadsafe test * Updates plist test * Brings recent changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updates license url and history docsDana Robinson2021-03-251-1/+1
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* Formats the source and updates the gcc warning pragmasDana Robinson2021-03-251-432/+460
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* Minor normalizations with hdf5_1_10Dana Robinson2020-07-311-4/+4
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* H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-161-0/+270
| | | | Update trefer.c with vlen test case
* Minor tweaks to testhdf5 code after normalization with 1.10.Dana Robinson2020-05-281-6/+6
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* Trim trailing whitespaceQuincey Koziol2020-04-201-6/+6
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* A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-03-231-348/+388
| | | | | | | | | | H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
* Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required.David Young2020-01-291-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c.
* squash cast warning fixkmu2020-01-231-3/+3
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-7/+7
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* Small changes from the token_refactoring branch, to reduce the delta to developQuincey Koziol2020-01-041-1/+1
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* Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-12/+24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Added a new VOL sub-class called "introspect" where callbacks that report information about the connector or container can be placed. Added an 'opt_query' callback to this sub-class, for a connector to report back to the library whether a particular optional callback operation is supported. Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or the terminal connector, H5VL_GET_CONN_LVL_TERM). Moved the "post open" operation from a file 'specific' operation to a file 'optional' operation, now that it's possible to detect (with the 'opt_query' introspection callback) whether a VOL connector implements an optional operation, without just returning an error. Added new internal VOL helper routines: H5VL_object_is_native, to determine if an object is in (or is a) native file, and H5VL_file_is_same, to determine if two objects are in (or are) the same terminal VOL connector's container. (And moved the special handling for FILE_IS_EQUAL operation out of internal VOL callback routine into H5VL_file_is_same) Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better with other 'get' operations in API. Fixed several issues with pass-through connectors, which are now passing the 'make check-passthrough-vol' tests again. A bunch of warning and style cleanups as well.
* More fixes for previous committed PR #2079 dated Dec 5 2019.Vailin Choi2019-12-061-1/+1
| | | | | (1) H5O_dtype_ver_bounds[] for V112 should be H5O_DTYPE_VRESION_4 (2) The tests for the new reference types should work for V112 and beyond
* Merge pull request #2076 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:type_fixes to ↵Jerome Soumagne2019-12-051-133/+138
|\ | | | | | | | | | | | | | | develop * commit '7b03a1c03633d695b487642e54f897c715f8622e': Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc.
| * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char toDavid Young2019-12-051-133/+138
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. An interesting side-effect that we probably should *not* rely on is that the struct-encapsulation changes the alignment so that some GCC warnings about casts that increase the alignment requirement of the operand go away. Warnings like that have to be taken seriously: I will add -Werror=cast-align to the default compiler flags so that they stop the build quickly. GCC warnings led me to some surprising casts in test/trefer.c. I found that it was possible to make many simplifications after introducing the struct-encapsulation that I described, above. In test objcopy_ref `same_file` is assigned but never used. Delete it.
* | Two fixes:Vailin Choi2019-12-051-1/+1
|/ | | | | (1) Set the version for reference datatype messge to H5O_DTYPE_VERSION_4. (2) Verify the decoded version for hyperslab selection.
* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-041-2/+2
| | | | the Autotools and CMake.
* Add OAPL parameter to H5Rcreate_ APIsJordan Henderson2019-12-021-36/+36
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* H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-11-261-4/+4
| | | | | | Valid for both deprecated and non-deprecated references Update test
* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-577/+1611
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* OESS-29 Update HD prefix mostlyAllen Byrne2019-08-241-2/+2
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* Fixed a memory issue in trefer.c.Dana Robinson2019-06-251-4/+4
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* HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.Vailin Choi2019-04-061-24/+34
| | | | This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* Set V112 as the latest format and extend the arrays of version bounds.Vailin Choi2019-04-041-91/+135
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* Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-132/+46
| | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-06-041-1/+1
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| * Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-1/+1
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| * Fix for HDFFV-10180 Performance issues with H5Oget_info.Vailin Choi2018-04-241-1/+1
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| * More includes cleanupAllen Byrne2018-02-141-90/+88
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| * Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | | | | | | | | | | | 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.
* | Needs to sync with lib version and Sencode.M. Scot Breitenfeld2018-03-071-92/+83
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* | HDFFV-10384 and includes cleanup merged from devlopAllen Byrne2018-02-161-2/+0
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* | Fix for HDFFV-9947 H5SencodeVailin Choi2017-11-281-70/+165
| | | | | | | | Modifications to fix H5Sencode bug when num points selected is > 2^32.
* | Change copyright headers to replace url referring to file to be removedlrknox2017-04-141-6/+4
|/ | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* [svn-r30285] Description:Quincey Koziol2016-08-131-13/+15
| | | | | | | | | More warning cleanups, bringing the build down to 25 unique types of warnings, with 550 warnings in 122 files (down from 28, 770, and 134). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27593] Merge revisions 27453 through 27592 from trunk to vds branch.Neil Fortner2015-08-271-3/+3
|\ | | | | | | Tested: ummon
| * [svn-r27460] Minor code cleanup in test/trefer.cDana Robinson2015-08-041-3/+3
| | | | | | | | | | | | | | | | - Fixed an out-of-range char assignment. - Added a couple of malloc() casts. Tested on: jam (minor change, tests only)
* | [svn-r27546] Add tests for H5O__dset_bh_info (H5Oget_info) and unlimited ↵Neil Fortner2015-08-211-0/+45
|/ | | | | | | | selections in a region reference. Tested: ummon
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-1/+1
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r26389] Revision 26387 failed with configure option ↵Larry Knox2015-03-081-1/+1
| | | | | | | | --with-default-api-version=v16. Changed H5Dcreate() to H5Dcreate2 in test/trefer.c line 633. Tested with h5committest and with --with-default-api-version=v16 on platypus.
* [svn-r26373] Fix for HDFFV-7959:Scot Breitenfeld2015-03-051-0/+75
| | | | | | H5Rdereference should check for default (HADDR_UNDEF) value and not continue processing and return so that ret value can be checked and handled properly Tested: jam (gnu)
* [svn-r25531] remove use of C99 PRI that failed on windows in dtypes.cMohamad Chaarawi2014-08-111-6/+7
| | | | fix bugs where hid_t were assumed to be 32 bit ints or herr_t.
* [svn-r25496] Description:Quincey Koziol2014-07-301-22/+22
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r24681] Description:Scot Breitenfeld2014-02-041-2/+2
| | | | | | | | | Fix for HDF5/HDFFV-8620 H5Rget_name with NULL name parameter fails. The name parameter now excepts NULL, in which case the length of then name is returned. Tested: jam (intel and gnu)
* [svn-r24376] Updated all code to use HDmalloc, HDcalloc, and HDfree.Dana Robinson2013-10-311-20/+20
| | | | | | | | | | | | | Prep work for adding a memory free function, part of HDFFV-8551. Tested on: 32-bit LE linux (jam) * with C++, Fortran * with thread safety on These are minor changes (almost entirely renaming foo functions to HDfoo) that don't change functionality. This should not require a full commit test.
* [svn-r24020] Description:Quincey Koziol2013-08-171-1/+1
| | | | | | | | Clean up compiler warnings Tested on: Mac OSX/64 10.8.4 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r22750] Removed check-in r22746 because it causes an error in objcopy ↵Scot Breitenfeld2012-09-101-5/+0
| | | | | | on Linew 64 byte. Will check-in again after the issue is resolved.
* [svn-r22746] Description:Scot Breitenfeld2012-09-091-0/+5
| | | | | | | | Fix for HDFFV-7959 H5Rdereference should check for default (HADDR_UNDEF) value and not continue processing and return so that ret value can be checked and handled properly. Added fix and test, reviewed: Tested: jam (gnu, intel)
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