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* Merge pull request #2008 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:develop to ↵Allen Byrne2019-10-231-185/+112
|\ | | | | | | | | | | | | develop * commit '685956cd4c088d38862b36b8138e643b114b2929': Update format and fix missing prefix
| * Update format and fix missing prefixAllen Byrne2019-10-211-185/+112
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* Merge pull request #2000 in HDFFV/hdf5 from ↵Jerome Soumagne2019-10-118-158/+226
|\ | | | | | | | | | | | | ~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 Soumagne2019-10-118-158/+226
| | | | | | | | | | | | | | | | 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
* | Merge pull request #1998 in HDFFV/hdf5 from ↵Jordan Henderson2019-10-1011-27/+131
|\ \ | | | | | | | | | | | | | | | | | | ~JHENDERSON/hdf5:bugfix/H5Dvlen_reclaim_ref_fix to develop * commit '93f509a2f2d5143450a0e6753325557b2bb8b707': Fix various Java issues when deprecated symbols are disabled
| * | Fix various Java issues when deprecated symbols are disabledJordan Henderson2019-10-1011-27/+131
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* | | Merge pull request #1996 in HDFFV/hdf5 from ↵Jordan Henderson2019-10-102-9/+14
|\ \ \ | |/ / |/| | | | | | | | | | | | | | ~JHENDERSON/hdf5:feature/unify_H5Lcopy_H5Lmove to develop * commit '54d149061f36eaadf5308839a3627f9158d24458': Unify code between H5Lcopy and H5Lmove
| * | Unify code between H5Lcopy and H5LmoveJordan Henderson2019-10-102-9/+14
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* | Merge pull request #1993 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-10-091-9/+15
|\ \ | | | | | | | | | | | | | | | | | | * commit '78268762bcf9cb949f711fa0e5290f96957cb60a': Improvements in response to Allen's suggestions. Corrections and improvements to testh5dump.sh.in changes. Fix errors in testh5dump.sh tests that grep for reference error messages.
| * | Improvements in response to Allen's suggestions.Larry Knox2019-10-091-12/+12
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| * | Corrections and improvements to testh5dump.sh.in changes.Larry Knox2019-10-091-34/+10
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| * | Fix errors in testh5dump.sh tests that grep for reference error messages.Larry Knox2019-10-091-3/+33
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* | Merge pull request #1994 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:ref_fix to developJerome Soumagne2019-10-091-1/+1
|\ \ | |/ |/| | | | | * commit 'cc1546ea92304e3b8d24ad32aa7252af367d5762': Fix func enter macro in H5T_ref_reclaim()
| * Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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* Merge pull request #1991 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developLarry Knox2019-10-081-3/+3
|\ | | | | | | | | * commit 'd42203b1d44686a0e5309f061c996b959023ce57': Change reference test to grep for specific error
| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-10-08111-3048/+12295
| |\ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '4c558700ab33934e7358483c5d20fea4823baf9e': Update RELEASE.txt for reference changes Fix reference type comparison in h5dump Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() Add new H5R API that abstracts object, region and attribute reference types Remove ability to loc by ref from H5VL layer Add support for retrieving object name by token Add H5VL_OBJECT_GET_TYPE to get object type Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info. Fix H5VL_blob_get to return size of blob Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs. Remove debugging logic from the new t_bigio test Expanded t_bigio.c to include Jordan's test from HDFFV-10539 Another cleanup pass as suggested by the reviewers. Fix some typos and remove an unused prototype from H5Sprivate.h At the suggestion of the PR reviewers, moved the mpio_create_large_type to H5mpi.c and renamed the function appropriately. Also moved some support functions to set and get the vvalue where we transistion to using derived datatypes. Made code review edit suggested by Jerome, plus various code updates to files that I touched to eliminate compile warnings (on my Linux box). No functional changes, just removed some tab characters Make the initial bug fixes to allow >2GB writes with Independent IO
* | Merge pull request #1931 in HDFFV/hdf5 from feature/references to developJerome Soumagne2019-10-08104-2854/+11989
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '9ed9762889fcd05dc230d6652b92fddc5ec880a4': Update RELEASE.txt for reference changes Fix reference type comparison in h5dump Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() Add new H5R API that abstracts object, region and attribute reference types Remove ability to loc by ref from H5VL layer Add support for retrieving object name by token Add H5VL_OBJECT_GET_TYPE to get object type Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info. Fix H5VL_blob_get to return size of blob Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
| * | Update RELEASE.txt for reference changesJerome Soumagne2019-10-081-0/+10
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| * | Fix reference type comparison in h5dumpJerome Soumagne2019-10-081-1/+5
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| * | Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-0831-274/+276
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| * | Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-0854-1953/+10097
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * | Remove ability to loc by ref from H5VL layerJerome Soumagne2019-10-083-113/+2
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| * | Add support for retrieving object name by tokenJerome Soumagne2019-10-081-0/+12
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| * | Add H5VL_OBJECT_GET_TYPE to get object typeJerome Soumagne2019-10-083-1/+63
| | | | | | | | | | | | Add H5VL_OBJECT_LOOKUP to lookup objects
| * | Add H5VL_MAX_TOKEN_SIZE and H5VL_token_tJerome Soumagne2019-10-081-0/+7
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| * | Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.Quincey Koziol2019-10-088-81/+135
| | | | | | | | | | | | Remove "by address" location for VOL operations. (Switching to "by token")
| * | Fix H5VL_blob_get to return size of blobJerome Soumagne2019-10-0814-104/+490
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix const in blob API Add H5HG_HEAP_ID_SIZE macro to return native blob size Add maximum size for blobs Fix blob API callbacks to pass VOL file object Add public wrappers for blob VOL API Implement passthrough blob callbacks Update H5Tvlen after callback changes Update trace information for H5VL blob routines Fix public header inclusion in native and passthru headers
| * | Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-0822-468/+1033
| | | | | | | | | | | | | | | | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
* | | Merge pull request #1987 in HDFFV/hdf5 from ↵Richard Warren2019-10-087-194/+306
|\ \ \ | |/ / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-10539-2GB-Write-Independent to develop * commit 'abb43d3d3ac2e802d0efbe21e028381ed99722f9': Remove debugging logic from the new t_bigio test Expanded t_bigio.c to include Jordan's test from HDFFV-10539 Another cleanup pass as suggested by the reviewers. Fix some typos and remove an unused prototype from H5Sprivate.h At the suggestion of the PR reviewers, moved the mpio_create_large_type to H5mpi.c and renamed the function appropriately. Also moved some support functions to set and get the vvalue where we transistion to using derived datatypes. Made code review edit suggested by Jerome, plus various code updates to files that I touched to eliminate compile warnings (on my Linux box). No functional changes, just removed some tab characters Make the initial bug fixes to allow >2GB writes with Independent IO
| * | Remove debugging logic from the new t_bigio testRichard Warren2019-10-081-18/+0
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| * | Expanded t_bigio.c to include Jordan's test from HDFFV-10539Richard Warren2019-10-081-3/+82
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| * | Another cleanup pass as suggested by the reviewers.Richard Warren2019-10-073-8/+5
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| * | Fix some typos and remove an unused prototype from H5Sprivate.hRichard Warren2019-10-072-2/+1
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| * | At the suggestion of the PR reviewers, moved the mpio_create_large_type to ↵Richard Warren2019-10-076-177/+211
| | | | | | | | | | | | H5mpi.c and renamed the function appropriately. Also moved some support functions to set and get the vvalue where we transistion to using derived datatypes.
| * | Made code review edit suggested by Jerome, plus various code updates to ↵Richard Warren2019-10-072-9/+9
| | | | | | | | | | | | files that I touched to eliminate compile warnings (on my Linux box).
| * | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Richard Warren2019-10-072-80/+88
| |\ \ | |/ / |/| | | | | HDFFV-10539-2GB-Write-Independent
| * | No functional changes, just removed some tab charactersRichard Warren2019-10-051-4/+4
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| * | Make the initial bug fixes to allow >2GB writes with Independent IORichard Warren2019-10-054-26/+47
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| | * Change reference test to grep for specific errorAllen Byrne2019-10-071-3/+3
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* | Merge pull request #1985 in HDFFV/hdf5 from ↵Dana Robinson2019-10-042-80/+88
|\ \ | |/ |/| | | | | | | | | ~DEROBINS/hdf5_der:H5Gget_object_behavior_change to develop * commit 'ff3278f1a0d57663d73caa6aaa7f209864e9a9bd': Fixed a bug (HDFFV-10899) where the behavior of the deprecated H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before.
| * Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-042-80/+88
|/ | | | | | | | H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before.
* Merge pull request #1983 in HDFFV/hdf5 from ↵Dana Robinson2019-10-031-3/+4
|\ | | | | | | | | | | | | ~DEROBINS/hdf5_der:small_develop_tweaks to develop * commit '638d31a78a9ea5db438d30e78f8cbaa1146b7f87': Fixed the java assert issue with H5O cache corking calls.
| * Fixed the java assert issue with H5O cache corking calls.Dana Robinson2019-10-031-3/+4
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* Merge pull request #1980 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-033-370/+214
|\ | | | | | | | | | | * commit '4394f0776b3e695b9ab383421824e4533da821a8': More whitespace changes Whitespace cleanup
| * More whitespace changesAllen Byrne2019-10-032-211/+57
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| * Whitespace cleanupAllen Byrne2019-10-031-159/+157
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* Merge pull request #1973 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-029-302/+198
|\ | | | | | | | | | | * commit 'bc6115931877c6f6d63977f2c03c5e2dbffe3e56': HDFFV-10919 merge synching HDFFV-10408,10918 Add note
| * HDFFV-10919 merge synchingAllen Byrne2019-10-028-301/+189
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| * HDFFV-10408,10918 Add noteAllen Byrne2019-10-021-1/+9
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* Merge pull request #1968 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-022-1/+121
|\ | | | | | | | | * commit '643d298823255a684862f4c6eb85ac5afde4b796': HDFFV-10918 add tests for h5repack ext storage
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