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* Much normalization with develop (#701)Dana Robinson2021-05-281-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Brings optional filters from developDana Robinson2021-05-071-1/+0
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* Brings the rest of the header changes from developDana Robinson2021-04-061-3/+3
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* Updates license url and history docsDana Robinson2021-03-251-1/+1
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* Formats the source and updates the gcc warning pragmasDana Robinson2021-03-251-408/+389
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* Merge branch 'aug-develop' into aug-merge-attempt/feature/vfd_swmrDavid Young2020-08-041-1/+1
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| * Minor normalization with 1.10.Dana Robinson2020-07-201-1/+1
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| * Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2019-12-211-2/+2
| | | | | | | | generic fallback for VOL connectors that don't implement operation
| * Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-13/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * Implement support for using H5Dvlen_get_buf_size withNeil Fortner2019-12-051-0/+1
| | | | | | | | non-native VOL connectors.
| * Community-proposed fixChris Hogan2019-11-181-0/+1
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| * HDFFV-10677 and HDFFV-10661Binh-Minh Ribler2019-08-281-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Added functions to query chunk information: H5Dget_num_chunks(dset_id, fspace_id, *nchunks) Gets the number of written chunks that intersect with the given dataspace. However, in this version, the intersection is not yet completed. Thus, the number of all written chunks will be returned. H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size) Given a chunk's logical coordinates, returns the chunk's filter, address, and size. H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size) Given a chunk's index, returns the chunk's logical coordinates, filter, address, and size. The chunk belongs to a set of chunks that have nonempty intersection with the specified dataspace. However, in this version, the intersection is not yet completed, and the index is of all the written chunks. These functions comply with VOL. - Fixed some oversights found in the library for the tests in chunk_info.c to work correctly. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
| * Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to matchQuincey Koziol2019-08-221-1/+1
| | | | | | | | naming convention for shared structs in rest of library data structures.
| * Begin converting dataset code to use shared file pointer instead of top fileQuincey Koziol2019-08-201-0/+4
| | | | | | | | pointer.
| * Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-1/+1
| | | | | | | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
| * Merge remote-tracking branch 'origin/develop' into merge_hyperslab_update_01Quincey Koziol2019-03-171-2/+7
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| | * Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-061-2/+7
| | | | | | | | | | | | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
| * | Core changes to selection code from the hyperslab_updates branch.Quincey Koziol2019-03-161-4/+4
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| * Moved the native VOL connector's optional enums to theDana Robinson2018-12-151-9/+0
| | | | | | | | | | public headers and renamed to include native/NATIVE in the name.
| * Switch switch remainder of API routines to use VOL callbacks.Quincey Koziol2018-11-101-1/+1
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| * VOL FEATUREDana Robinson2018-10-101-1/+10
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* | Avoid leaving a v1 B-tree used as a chunk index in a bad stateDavid Young2020-06-121-2/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | that makes assertions fail. Add an optional `close` method to the `H5D_chunk_ops_t`, and use that to release "holds" on metadata cache (MDC) entries. For extensible arrays and v2 B-trees, use the existing `dest`(roy) method to implement `close`. For v1 B-trees and other chunk indices, don't provide `close`: we cannot safely close the v1 B-tree index, and the other indices don't have a meaningful presence in the MDC. Revert my first attempt at making v1 B-tree chunk indices closeable with `dest`. Put my comment about the stopgap fix for VFD SWMR at the right place in src/H5Dchunk.c.
* | Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-05-201-2/+2
| | | | | | | | generic fallback for VOL connectors that don't implement operation
* | Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-05-201-13/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | Implement support for using H5Dvlen_get_buf_size withNeil Fortner2020-05-201-0/+1
| | | | | | | | non-native VOL connectors.
* | Community-proposed fixChris Hogan2020-05-201-0/+1
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* | Merge all of my changes from merge-back-to-feature-vfd_swmr-attempt-1,David Young2019-12-091-8/+20
|/ | | | | | | | including the merge of `hdffv/hdf5/develop`, back to the branch that Vailin and I share. Now I need to put this branch on a fork with a less confusing name than vchoi_fork!
* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-12/+10
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* Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-09-181-3/+0
| | | | orginally intended to support the full SWMR feature.
* Finished move of H5DOread/write_chunk calls to H5D.Dana Robinson2018-04-301-2/+0
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-4/+7
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Fix for daily test failuresVailin Choi2018-02-141-0/+3
| | | | | | | | | | | | | | | | Move the declarations for the three arrays of versions from H5Opkg.h: (1) H5O_layout_vers_bounds to H5Dpkg.h (2) H5O_dtype_ver_bounds to H5Tpkg.h (3) H5O_sdspace_ver_bounds to H5Spkg.h This is to fix Windows' complaint for unresolved symbols.
| * HDFFV-9724 Corrected files and verified testsAllen Byrne2017-12-281-1/+2
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| * Revert "Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to ↵lrknox2017-12-221-2/+1
| | | | | | | | | | | | | | develop" This reverts commit b1223dd653e65e076af92b2dfe236f3704da81c8, reversing changes made to b25f123f5f5e25c1447a6a02861cb7c7265c12f2.
| * HDFFV-9724 Initial changes and testAllen Byrne2017-12-111-1/+2
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-103/+73
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* Normalization with VOL integration branch.Dana Robinson2017-11-301-0/+2
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* Remove tabsAllen Byrne2017-11-081-68/+68
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* Suggested changes from code reviewJordan Henderson2017-07-071-2/+1
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2017-07-051-6/+8
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits) Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting More minor whitespace cleanup Fixed a minor comment typo in H5R.c * Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c. Added missing free() call to test_misc19(). Purged the unused H5I_REFERENCE from the library. Added a test for VFD IDs to testhdf5. Revert "Partial removal of NDEBUG ifdefs from the library." Partial removal of NDEBUG ifdefs from the library. Removed compiler flag cleanup since Solaris chokes on it. Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file. Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true. Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely). Added awk processing to remove extraneous whitespace from H5_ flags in configure. Fixed a comment in configure.ac HDFFV-10219 another mode change HDFFV-10219 change subset to use BINARY mode for h5dump HDFFV-10219 default input binary to NATIVE Set default of var to NATIVE HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed ...
| * Fix for HDFFV-10051Vailin Choi2017-05-091-0/+1
| | | | | | | | | | Fix missing declaration for H5D__layout_compact_dirty_test(). Tested on mayll and osx1010test.
| * Incorporate patch from GE Healthcare (HDFFV-9934)Vailin Choi2017-04-251-0/+3
| | | | | | | | | | This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
| * 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.
* | Switch working branch from master to developJordan Henderson2017-01-131-0/+5
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* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-0/+1
| | | | and the tool and API wrappers will be coming in over the weekend.
* Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-0/+6
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* Added code to create the test file for all chunk index and layout types.Dana Robinson2016-09-301-0/+1
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* [svn-r30075] Description:Quincey Koziol2016-06-141-0/+10
| | | | | | | | | | Bring object/dataset/group/named datatype features from revise_chunks branch to trunk. Also CMake support for h5format_convert and a bunch of misc. cleanups. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29924] Description:Quincey Koziol2016-05-121-0/+4
| | | | | | | | Bring h5format_convert tool from revise_chunks branch to trunk. Tested on: MacoSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29850] Description:Quincey Koziol2016-05-011-0/+1
| | | | | | | | | | 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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