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* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Jan ws changes (#282)Allen Byrne2021-01-271-1/+1
| | | | | | | | | | | | | | | | | | | | | * 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 * Whitespace fixes except for H5Tprivate.h typo fix
* Fix problems with vlens and refs inside compound using H5VLget_file_type() ↵hdf5-1_13_0-rc5Neil Fortner2021-01-221-1/+12
| | | | | | | | | | | | (#274) * Fixed problems with vlens and refs inside compound using H5VLget_file_type() * Fix date in RELEASE.txt * Add assertions * Move some manipulation of H5VL_object_t struct fields into the H5VL package.
* Reformat source (#244)Quincey Koziol2021-01-071-4/+4
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* Avoid aligned access for references by decoding into temporary buffer and ↵Quincey Koziol2020-12-191-6/+11
| | | | then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* Replaces C std library calls with H5MM equivalentsDana Robinson2020-10-301-2/+2
| | | | Mostly H5MM_memcpy in newer VFDs
* Removes -Wimplicit-fallthrough=5 from the gcc warningsDana Robinson2020-10-221-0/+1
| | | | | | | | | | | | -Wimplicit-fallthrough=3 is added by -Wextra, which we already set. Bumping the warning level only changes how fall-through comments are parsed, with level 5 turning off fall-through comments entirely. This is unnecessary and results in having to do extra work to squash warnings when included external code uses fall-through. This change also adds /* FALLTHROUGH */ comments where H5_ATTR_FALLTHROUGH is used so compilers that don't use attributes but do respect fall-through comments don't raise spurious warnings.
* Clang-format of source filesAllen Byrne2020-09-301-302/+302
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-4/+4
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* H5R: fix encoding of references that are part of compound typesJerome Soumagne2020-07-281-0/+31
| | | | Add corresponding test and some debug information
* H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-161-23/+40
| | | | Update trefer.c with vlen test case
* Replaced a few calls to HDmemcpy with H5MM_memcpy, which does overlapDana Robinson2020-05-151-2/+2
| | | | checking.
* merge and fixkmu2020-01-211-3/+3
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| * Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-3/+3
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* | merge and fix conflictkmu2020-01-191-3/+4
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| * H5R: set app ref when incrementing ref_count on location held by referenceJerome Soumagne2020-01-101-2/+3
| | | | | | | | (fix HDFFV-10992)
* | merge and fix conflictskmu2020-01-141-84/+185
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| * Cleanups from PR reviewsQuincey Koziol2019-12-201-77/+77
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| * Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-90/+191
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | fix unused related warningskmu2020-01-131-1/+7
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* Merge pull request #2063 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:vol_file_cmp ↵Neil Fortner2019-12-011-30/+71
|\ | | | | | | | | | | | | | | | | to develop * commit '40b2658b4b266b4dc65ec3db2897e0aaf54f8e42': Fix missing free in H5T__ref_mem_read() Fix bugs in H5VL file comparison code. Add short circuit success to H5VL_cmp_connector_cls(). Implement file comparison VOL callback. Other changes to allow references to work with non-native connectors. There is a bug somewhere.
| * Fix missing free in H5T__ref_mem_read()Neil Fortner2019-11-291-0/+2
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| * Fix bugs in H5VL file comparison code. Add short circuit success toNeil Fortner2019-11-281-6/+6
| | | | | | | | H5VL_cmp_connector_cls().
| * Implement file comparison VOL callback. Other changes to allowNeil Fortner2019-11-271-30/+69
| | | | | | | | | | references to work with non-native connectors. There is a bug somewhere.
* | Merge pull request #2059 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:topic_nullref to ↵Jerome Soumagne2019-11-281-12/+252
|\ \ | |/ |/| | | | | | | | | develop * commit '6b68cc352ffabb5fe997db1eb52216b3ee80e669': H5R: fix H5Tconv to check for null references
| * H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-11-261-12/+252
| | | | | | | | | | | | Valid for both deprecated and non-deprecated references Update test
* | Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILEJerome Soumagne2019-11-271-1/+1
|/ | | | Remove H5F__get_file_id() and use only private routine instead
* Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-87/+148
| | | | | | | | | | | location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
* Merge pull request #2000 in HDFFV/hdf5 from ↵Jerome Soumagne2019-10-111-14/+21
|\ | | | | | | | | | | | | ~JSOUMAGNE/hdf5:fix_endian_develop to develop * commit '294e4faab724c26985867fe8ede684967da8a698': Fix encode and decode of tokens in H5VLnative
| * Fix encode and decode of tokens in H5VLnativeJerome Soumagne2019-10-111-14/+21
| | | | | | | | | | | | | | | | Fix encode and decode of deprecated object reference addresses Make H5Rdeprec.c use tokens instead of haddr_t Fix H5Oopen_by_addr() to serialize addr to token
* | Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-0/+761
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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