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* Comment correctionAllen Byrne2019-11-212-2/+2
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-2012-40/+73
|\ | | | | | | | | | | | | | | * commit '13456df8a47fdcd8f96f170c9218e57a03066120': Minor correction Update list of tested platforms Add VS2019 support Fixed the H5_mpi_get_bigio_count function prototype
| * Merge pull request #2048 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:develop to ↵Allen Byrne2019-11-1911-39/+72
| |\ | | | | | | | | | | | | | | | | | | | | | | | | develop * commit 'efe234c832581d16d3da41fe71b50ef71fd44acc': Minor correction Update list of tested platforms Add VS2019 support
| | * Minor correctionAllen Byrne2019-11-181-1/+1
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| | * Update list of tested platformsAllen Byrne2019-11-181-23/+8
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| | * Add VS2019 supportAllen Byrne2019-11-1811-16/+64
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| * Merge pull request #2047 in HDFFV/hdf5 from h5_private_prototype_fix to developRichard Warren2019-11-181-1/+1
| |\ | | | | | | | | | | | | * commit 'c440e05de82b224a0a6b042ec8a27accdc1e48ae': Fixed the H5_mpi_get_bigio_count function prototype
| | * Fixed the H5_mpi_get_bigio_count function prototypeRichard Warren2019-11-181-1/+1
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-161-1/+1
|\ \ | |/ | | | | | | * commit '3593b3d201dd6eac4a71e67db02a54959d9a169e': Correct file extension
| * Merge pull request #2042 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:develop to ↵Allen Byrne2019-11-151-1/+1
| |\ | | | | | | | | | | | | | | | | | | develop * commit 'c2fd059704e9232a3d3221ddd0c84803256baec2': Correct file extension
| | * Correct file extensionAllen Byrne2019-11-141-1/+1
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-137-122/+308
|\ \ | |/ | | | | | | * commit '07b59c0b63041f1be964aee2a27f5c748c29d688': Implement public H5Sselect_project_intersection(). Updated internal algorithm to (optionally) avoid sharing selection data structures. Tested internal code (including with valgrind) by setting VDS code to avoid sharing selection, has since been changed to share selection for performance, so this code is not yet tested in regression tests. API has not been tested.
| * Merge pull request #2033 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:public_spi to ↵Neil Fortner2019-11-137-122/+308
| |\ | | | | | | | | | | | | | | | | | | develop * commit 'db6eab893e5f027f0b535316e0e7a9abe9ff8619': Implement public H5Sselect_project_intersection(). Updated internal algorithm to (optionally) avoid sharing selection data structures. Tested internal code (including with valgrind) by setting VDS code to avoid sharing selection, has since been changed to share selection for performance, so this code is not yet tested in regression tests. API has not been tested.
| | * Implement public H5Sselect_project_intersection(). Updated internalNeil Fortner2019-11-137-122/+308
| | | | | | | | | | | | | | | | | | | | | | | | algorithm to (optionally) avoid sharing selection data structures. Tested internal code (including with valgrind) by setting VDS code to avoid sharing selection, has since been changed to share selection for performance, so this code is not yet tested in regression tests. API has not been tested.
* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-1342-326/+792
|\ \ \ | |/ / | | | | | | | | | | | | | | | | | | | | | * commit 'e08b69d3d2e572de4707b1fbf908111d29f40a1b': Use HD prefix. Fix issue where H5R__reopen_file did not make the file "post open" callback. Apparently, + has no special meaning, and neither does \+, in so-called "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Implement H5VLget_file_type() to return a copy of a datatype with the 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. Fix HDFFV-10937: use a more reliable (and probably faster) scheme for visiting all elements of a matrix in an arbitrary order.
| * | Merge pull request #2027 in HDFFV/hdf5 from ~DYOUNG/hdf5:dsets-randomness to ↵David Young2019-11-121-32/+121
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit '4d834adba4aeb1a0174bddb83212b7073b64e269': Use HD prefix. Fix HDFFV-10937: use a more reliable (and probably faster) scheme for visiting all elements of a matrix in an arbitrary order.
| | * | Use HD prefix.David Young2019-11-121-8/+8
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| | * | Fix HDFFV-10937: use a more reliable (and probably faster) scheme forDavid Young2019-10-281-32/+121
| | | | | | | | | | | | | | | | visiting all elements of a matrix in an arbitrary order.
| * | | Merge pull request #2037 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to ↵Neil Fortner2019-11-122-1/+10
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit 'e5fc4889fa4f412056a4672435c96c17a6d1a936': Fix issue where H5R__reopen_file did not make the file "post open" callback.
| | * | | Fix issue where H5R__reopen_file did not make the file "post open"Neil Fortner2019-11-122-1/+10
| |/ / / | | | | | | | | | | | | callback.
| * | | Merge pull request #2036 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-126-5/+6
| |\ \ \ | | |_|/ | |/| | | | | | | | | | * commit 'f1b39ad80e2fc0d0f4f6ecae2a9fb0ea436c34cc': Apparently, + has no special meaning, and neither does \+, in so-called "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`.
| | * | Apparently, + has no special meaning, and neither does \+, in so-calledDavid Young2019-11-126-5/+6
| |/ / | | | | | | | | | | | | | | | | | | | | | "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Add config/netbsd to the MANIFEST.
| * | Merge pull request #2032 in HDFFV/hdf5 from ↵Neil Fortner2019-11-0834-289/+656
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | ~NFORTNE2/hdf5_naf:vlget_file_type to develop * commit '1dbec40d465072540f8507c524ae7b909a6b1cf0': Implement H5VLget_file_type() to return a copy of a datatype with the 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.
| | * | Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-0834-289/+656
| | |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | | HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-0763-3082/+5693
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* | Merge pull request #1984 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-0529-41/+275
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | * commit '0b721858e46a317c370a24115032d5be41688f67': Make these scripts relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Get the path to prefix right: needs a ../ to back out of subdirectory c/. Make this script relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Let us override the examples directory using --with-examplesdir=DIR. This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Follow longstanding execv convention for compatibility with NetBSD. Under the examples directories, always find the installed HDF5 executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Make the HDF5 configure script grok NetBSD. For portability, insulate the HDF5 library from some system macros. Not every system has perl installed in /usr/bin/, so change the shebang (#!) line to `/usr/bin/env perl` to locate perl on the PATH. For portability, use the POSIX sh(1) string-comparison operator `=` instead of `==`.
| * Make these scripts relocatable again: derive a relative path for theDavid Young2019-11-054-4/+97
| | | | | | | | | | | | | | original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived.
| * Get the path to prefix right: needs a ../ to back out of subdirectoryDavid Young2019-11-051-1/+1
| | | | | | | | c/.
| * Make this script relocatable again: derive a relative path for theDavid Young2019-11-051-2/+25
| | | | | | | | | | | | | | original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived.
| * Let us override the examples directory using --with-examplesdir=DIR.David Young2019-10-0313-18/+40
| | | | | | | | | | | | | | | | | | This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Place hdf5_examples/ under ${datarootdir} which on most systems will be ${prefix}/share/, anyway.
| * Follow longstanding execv convention for compatibility with NetBSD.David Young2019-10-031-1/+7
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| * Under the examples directories, always find the installed HDF5David Young2019-10-036-6/+6
| | | | | | | | | | | | | | | | | | | | executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Examples on NetBSD are installed at ${prefix}/share/examples/hdf5/ instead of at ${prefix}/share/hdf5_examples/, by convention. It may be the same on other BSDs, I'm not sure.
| * Make the HDF5 configure script grok NetBSD.David Young2019-10-032-0/+59
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| * For portability, insulate the HDF5 library from some system macros.David Young2019-10-031-1/+18
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| * Not every system has perl installed in /usr/bin/, so change the shebangDavid Young2019-10-0312-12/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#!) line to `/usr/bin/env perl` to locate perl on the PATH. Everything after the first pathname in the shebang line is treated as a single argument to the command interpreter (/usr/bin/env "perl -w"), and there is not ordinarily any such program as "perl -w". So if the old shebang line used an option such as `-w`, add a `use warnings;` statement to the script---note that the semantics change slightly. `bin/destdep` uses a trick to pass `-p` to `/usr/bin/env perl`. It couldn't hurt to use the same trick to pass `-w`. With these changes, `sh autogen.sh` runs on NetBSD. It ought to still work on every other system HDF5 supports, too.
| * For portability, use the POSIX sh(1) string-comparison operator `=`David Young2019-10-031-2/+2
| | | | | | | | instead of `==`.
* | Merge pull request #2015 in HDFFV/hdf5 from HDFFV-10943 to developRichard Warren2019-10-254-14/+13
|\ \ | | | | | | | | | | | | | | | * commit '299c9ed5fe19edac37cab27bc04d587fa67568c2': Removed set_bigio_count prototype since it has been added to H5private.h Change API names for get/set bitio_count. Also added H5_mpi_set_bigio_count to H5private.h.
| * | Removed set_bigio_count prototype since it has been added to H5private.hRichard Warren2019-10-251-2/+0
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| * | Change API names for get/set bitio_count. Also added H5_mpi_set_bigio_count ↵Richard Warren2019-10-234-13/+14
| | | | | | | | | | | | to H5private.h.
* | | Merge pull request #2016 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-234-8/+15
|\ \ \ | |/ / |/| | | | | | | | * commit '9affb7f12ec6084ccaadec9fcdc8d94bccf4dd4f': Fix MPI test depends
| * | Fix MPI test dependsAllen Byrne2019-10-234-8/+15
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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.
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