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* Adds generated filesDana Robinson2022-05-161-0/+1890
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* VFD SWMR: Merges from develop (#1670)Dana Robinson2022-04-212-6/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up SWMR test scripts (both legacy and VFD) * Brings over format source changes for Java * Normalization of HL, Fortran, C++, Java w/ develop * Removes the STATIC flavor of FUNC_ENTER macros (#1622) * Removes the STATIC flavor of FUNC_ENTER macros * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes unused definitions from module headers (#1624) * Misc stuff from develop (includes some parallel things) * Brings over SWMR test quiet mode changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD SWMR: normalization with develop (#1472)Dana Robinson2022-03-0620-100/+96
| | | Much normalization with develop. Still needs tools changes wrt VFD plugins.
* VFD SWMR: Normalization with develop (#1270)Dana Robinson2021-12-081-8/+0
| | | Brings many October-November changes from develop
* VFD SWMR: Normalization with develop (#1078)Dana Robinson2021-10-062-2/+15
| | | Brings many changes from develop, particularly VOL changes for async
* VFD SWMR: Sync with develop (#711)Dana Robinson2021-06-011-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Require a C++11 compiler to build the C++ wrappers (#693) * Committing clang-format changes * Requires a C++11 compiler to build the C++ wrappers Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (#699) * Removes pre-C99 build and header cruft (#700) * Assumes ANSI C headers exist * Assumes stdbool.h, stdint.h, and inttypes.h are present * Assumes the C++ compiler can handle stdint.h * Removes all work-arounds for missing functionality, especially stdbool.h Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Updates release documents * Brings parallel changes from develop * Adds a VFD/parallel check program for the VFD SWMR shell test * Updates MANIFEST * Disable building VFD SWMR acceptance tests on CMake * Removes err.h from genall5.c * Partial cleanup of H5Cpkg.h * Fixes printf specifiers in H5Cdbg.c * Java and fortran cmake changes (#694) * 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 * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Split H5L.c internal code to H5Lint.c (#691) * Committing clang-format changes * Splits internal parts of H5L.c to H5Lint.c Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up type size checks in configure.ac (#702) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Much normalization with develop (#701)Dana Robinson2021-05-281-16/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Many small changes from develop. Should allows running VFD SWMRDana Robinson2021-05-031-31/+47
| | | | tests from CMake.
* Brings many CMake changes from developDana Robinson2021-04-081-9/+30
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* Normalized Fortran with developDana Robinson2021-04-058-52/+163
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* Updates license url and history docsDana Robinson2021-03-2544-47/+47
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* Formats the source and updates the gcc warning pragmasDana Robinson2021-03-2519-6713/+7133
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* HDFFV-11116 Add option for install location of Fortran MOD filesAllen Byrne2020-07-091-0/+20
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* Removed trailing space from Fortran files.Dana Robinson2020-05-2618-1666/+1666
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* Trim trailing whitespaceQuincey Koziol2020-04-2013-71/+71
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-04-069-40/+34
|\ | | | | | | | | * commit 'a09f810e8d372d1e85661c52a7ef735a164904ad': Narrowed the scope of ISO_C_BINDING with ONLY additions
| * Narrowed the scope of ISO_C_BINDING with ONLY additionsScot Breitenfeld2020-04-069-40/+34
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* | Flag construction must be after compiler detectionAllen Byrne2020-04-051-45/+19
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* | TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-051-3/+3
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* Copy generated files instead creating twiceAllen Byrne2020-02-251-8/+32
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* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-211-1/+1
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* Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size ↵M. Scot Breitenfeld2020-02-181-1/+1
| | | | | | inh5fget_file_image_f. HDFFV-11029
* HDFFV-11018 Add Fortran H5F_LIBVER_V*_F definitionsM. Scot Breitenfeld2020-02-107-63/+104
| | | | | | | | | | | | | | | | | | | Added ------ New Definitions: INTEGER :: H5F_LIBVER_ERROR_F INTEGER :: H5F_LIBVER_NBOUNDS_F INTEGER :: H5F_LIBVER_V18_F INTEGER :: H5F_LIBVER_V110_F INTEGER :: H5F_LIBVER_V112_F INTEGER :: H5F_LIBVER_V114_F New API: h5pget_libver_bounds_f(fapl_id, low, high, hdferr) Removed: call to C wrapper h5pset_libver_bounds_c in h5pset_libver_bounds_f
* HDFFV-11012 - add correct fortran include path propertiesAllen Byrne2020-02-041-2/+2
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* Merge pull request #2321 in HDFFV/hdf5 from ↵David Young2020-01-292-14/+21
|\ | | | | | | | | | | | | ~DYOUNG/werror:reduce-werror-diffs-3 to develop * commit 'f19e06b59ee53f17465a7b5974c25c3245a40d9a': testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2].
| * testpar/t_2Gio.c: Fix a typo that I think was introduced by aDavid Young2020-01-292-14/+21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings.
* | Introduce new H5VL _by_value routinesJordan Henderson2020-01-292-9/+93
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-1615-327/+462
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* Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-081-8/+8
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* Reverts the removal of config/conclude_fc.am while keepingDana Robinson2019-08-011-1/+1
| | | | the changes to config/gnu-fflags.
* Merge pull request #1808 in HDFFV/hdf5 from ↵Dana Robinson2019-07-291-1/+1
|\ | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:gnu-flags-work to develop * commit '7d291d059da6287f769951c4854c566da0b93ce8': Parallel Fortran tests now use the MPI module instead of including mpif.h. First stab at gfortran versions. Tested on gfortran 7-9 so far. Moved the -std=f2008 option to gfortran 9 for now. Updated gfortran options. * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| * Updated gfortran options.Dana Robinson2019-07-171-1/+1
| | | | | | | | | | | | | | | | * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
* | HDFFV-10845 add_custom_command requires emulatorAllen Byrne2019-07-171-4/+4
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* | Correct install syntaxAllen Byrne2019-07-171-7/+21
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* | HDFFV-10845 fix configure check and PATHsAllen Byrne2019-07-171-1/+1
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* Fix packaging issueAllen Byrne2019-07-111-2/+7
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* HDFFV-10581 fix locations for static pdb filesAllen Byrne2019-07-081-2/+2
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-282-8/+7
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-212-2/+0
| | | | clean up warnings.
* Add missing fortran modsAllen Byrne2019-06-191-0/+2
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* HDFFV-10616 add h5fc scriptAllen Byrne2019-06-191-0/+50
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-06-183-0/+466
|\ | | | | | | | | | | | | | | * commit '712a2a13d8add828d053135a172abb2e819d59ad': Fixed a warning in H5CX.c concerning incorrect use of freeing VOL connector info. Add H5S_SEL_ITER_SHARE_WITH_DATASPACE selection iterator creation flag, to share dataspace's selection with iterator (and with caution about not modifying or closing the dataspace while the iterator is open). Fix misc. typos, etc. from code review New hyperslab selection routines and new public selection iterator routines.
| * New hyperslab selection routines and new public selection iterator routines.Quincey Koziol2019-06-163-0/+466
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* | HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-181-116/+132
|/ | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
* fixed invalid pointerM. Scot Breitenfeld2019-06-131-1/+2
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* move the vol_info to an optional parameterM. Scot Breitenfeld2019-06-111-7/+14
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* added H5Pset_volM. Scot Breitenfeld2019-05-222-0/+87
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* removed H5VL constantsM. Scot Breitenfeld2019-05-164-293/+3
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* removed VOLL NULL connector and replaced it with native VOLM. Scot Breitenfeld2019-05-162-52/+10
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* added connector_name testM. Scot Breitenfeld2019-04-241-1/+1
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