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* Subfiling VFD - tidying up and fixing a few new testing failures (#1977)jhendersonHDF2022-08-091-1/+18
| | | | | | | | | | | | | | | | | | | * Rename Subfiling IOC "thread_pool_count" field to "thread_pool_size" * Add simple HDF5 example for Subfiling VFD * Subfiling VFD - never cache app topology as it may change * Subfiling VFD - cleanup unused funtionality and tidy up some TODOs * Subfiling VFD - tidy up subfiling error handling in H5subfiling_common.c * Subfiling VFD - show number of failed I/O requests on close * Subfiling VFD - Update file cmp callback after switching to MPI I/O VFD * Amend RELEASE.txt with info about h5fuse.sh and Subfiling limitations * Subfiling VFD - switch to using H5_basename and H5_dirname
* Subfiling updates for release (#1963)jhendersonHDF2022-08-041-1/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built * Switch to MPI I/O driver for Subfiling HDF5 stub file * Rough first implementation for Subfiling file deletion * Subfiling VFD - get file dirname for file deletion * Subfiling VFD - set lock callback to NULL for now to avoid performance issues * Committing clang-format changes * Minor tidying up of Subfiling testing * Fixups for Subfiling VFD support in tools * Tidy up Subfiling public interface and add Doxygen * Respect Subfiling configuration settings from application * Add release note for Subfiling VFD * Committing clang-format changes * Committing clang-format changes * Shorten some Subfiling environment variable names Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement improved CMake fortran module folder from GH#1411 (#1922)Allen Byrne2022-07-262-0/+28
| | | | | | | | | * Implement improved CMake fortran module folder from GH#1411 * Update docs * Fix whitespace * Fix name case
* Removes the ability to build h5perf and h5perf_serial in standalone mode (#1897)Dana Robinson2022-07-201-0/+15
| | | This feature has been broken for some time and lacks a clear use case.
* Removes the small perf tool (#1896)Dana Robinson2022-07-171-0/+7
| | | | | | | | * Removes the small perf tool This tool doesn't really do anything special and installed, which conflicts with gnu's perf tool. * Adds suggestions from code review
* Add utility JNI function for 1.10 style references (#1888)Allen Byrne2022-07-141-0/+7
| | | | | | | | | | | * Add utility JNI function for 1.10 style references * Clarify text * Correct signature * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop HDFFV-11310 (#1811)Allen Byrne2022-07-111-3/+38
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework java vl check in read/write. Handle old refs in h5dump * Committing clang-format changes * Java changes allow default VL reads * Fix JNI utility for old refs * HDFFV-11310 - implement vlen read/write for atomic types. * format check fix * Mostly format fixes * More format issues * Two format changes * Use JNI names for sizeof * format change * fix size typo * Change to older method to initialize list * remove unused var * format fix * switch writeVL functions to use datatype instead of java type * Add VL option to generic read/write check * Correct function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Add release note and format changes * Another format update * Fix unreleased allocations * Fix format * format correction Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Convert assertion on (possibly corrupt) file contents to normal error check ↵jhendersonHDF2022-07-081-1/+10
| | | | | | | | | (#1861) * Convert assertion on (possibly corrupt) file contents to normal error check * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Various warning fixes (#1812)Sean McBride2022-06-221-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed -Wreserved-id-macro warnings from header include guards * Removed all __int64 and LL suffix stuff now that C99 is minimum requirement * Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings Double underscore is reserved in C++ and this public header should be C++ compatible. * Never define __STDC_FORMAT_MACROS anymore Defining it causes a -Wreserved-id-macro. Happily, according to the C++11 standard: "The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++." https://cplusplus.github.io/LWG/issue984 So looks like it's not necessary to define it with reasonably new toolchains. * Fixed some -Wunused-macros warnings, removed dead code * Fixed all -Wdouble-promotion warnings in C++ files * Fixed remaining -Wsuggest-destructor-override warnings * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop sync (#1793)Allen Byrne2022-06-092-12/+17
| | | | | * Synch update * Branch sync changes
* Update windows VS2019 and fix comments (#1781)Allen Byrne2022-05-201-1/+1
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* Set default level to minimum time (#1722)Allen Byrne2022-05-172-2/+2
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* added HDFFV-11306 entry (#1662)Scot Breitenfeld2022-04-191-1/+6
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* Add missing release note for h5repack timing (#1572)Allen Byrne2022-04-051-0/+8
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* spelling fixes (#1561)Scot Breitenfeld2022-03-312-2/+2
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* Update release note (#1485)Allen Byrne2022-03-111-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Committing clang-format changes * Update main.yml * Update HISTORY-1_13.txt Missing release note added for changed location of CMake configuration files. * Update HISTORY-1_13.txt Fix typo * Update main.yml revert change Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update HISTORY-1_13.txt and clean RELEASE.txt (#1471)Larry Knox2022-03-072-139/+396
| | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Spelling of preceed was corrected to proceed, but should have been corrected to precede. * Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'. * Update version to 1.13.2-1 after 1.13.1 release. Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk. * Update VERS_RELEASE_EXCEPTIONS with new incompatible release version. * Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to HISTORY-1_13.txt. Clean entries from RELEASE.txt. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Disable memory alloc sanity checks by default for Autotools debug builds (#1468)jhendersonHDF2022-03-031-0/+19
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* Create HISTORY-1_13.txt and update release.txt (#1466)Larry Knox2022-03-012-1419/+1774
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* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-011-1/+1
| | | | | | to MANIFEST (#1460)
* Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463)jhendersonHDF2022-03-011-9/+17
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* Amend RELEASE.txt with note about parallel compression testing assertion ↵jhendersonHDF2022-02-251-0/+9
| | | | failure (#1458)
* Add release note for #1438 (#1457)Allen Byrne2022-02-251-0/+17
| | | | | * Add release note for #1438 * fix typos.
* Parallel Compression improvements (#1302)jhendersonHDF2022-02-241-1/+39
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* Enable creation of RPM/DEB binaries GH#1394 (#1398)Allen Byrne2022-02-221-0/+9
| | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Revert "Fix metadata cache bug when resizing a pinned/protected entry ↵Larry Knox2022-02-121-17/+0
| | | | | (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
* Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)Allen Byrne2022-02-111-0/+7
| | | | | * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note
* Fix metadata cache bug when resizing a pinned/protected entry (#1358)jhendersonHDF2022-02-081-0/+17
| | | | | | | | | | | | | | When resizing a pinned/protected cache entry, the metadata cache code previously would wait until after resizing the entry to attempt to log the newly-dirtied entry. This would cause H5C_resize_entry to mark the entry as dirty and make H5AC_resize_entry think that it doesn't need to add the newly-dirtied entry to the dirty entries skiplist. Thus, a subsequent H5AC__log_moved_entry would think it needs to allocate a new entry for insertion into the dirty entry skip list, since the entry doesn't exist on that list. This causes an assertion failure, as the code to allocate a new entry assumes that the entry is not dirty.
* Update doc with HDF5_ROOT usage. (#1414)Allen Byrne2022-02-022-12/+14
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* Unify handling of collective metadata reads status (#1206)jhendersonHDF2022-01-291-0/+21
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* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-221-0/+12
| | | | | | | * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-201-0/+7
| | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Convert vds swmr test script to powershell (#1245)Allen Byrne2021-12-081-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fixes const warnings in H5ES package (#1211) * Quiets a 'set but not used' warning in h5diff_array.c (#1210) * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Cleanup review issues * Fix variable assignment * Change the wait function to pass in the path * Disable actual test execution until programs fixed * Adjust copyright text * Fix spelling Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-077-102/+102
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236)Larry Knox2021-11-301-1/+1
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* Fix indentation in RELEASE.txt to be consistent. (#1232)Larry Knox2021-11-301-519/+519
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* Add support for parallel tools based on the 3rd party library mpiFileUtils ↵rawarren2021-11-291-0/+19
| | | | | | | | | | (libMFU) … (#1177) Adds tool h5dwalk and configure options to enable building it. Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs (#1222)Dana Robinson2021-11-241-0/+8
| | | | | | | | | | | | * Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the library due to missing ID range checks in H5Pget_filter_by_id1/2. The library now returns a normal error code when filter IDs are out of range. Fixes HDFFV-11286. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-enable collective metadata reads after disabling for chunk lookup (#1173)jhendersonHDF2021-11-091-0/+7
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* New references for Dimension Scale APIs (#1139)jhendersonHDF2021-11-051-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org>
* H5repack tests should fail if a corrupted file causes h5repack to (#1138)Larry Knox2021-10-261-0/+11
| | | | | | * H5repack tests should fail if a corrupted file causes h5repack to segfault/core dump. * Add release note for HDFV-10590, CVE-2018-17432.
* Add release note for HDFFV-11150 fix. (#1106)Larry Knox2021-10-211-1/+23
| | | | | * Add release note for HDFFV-11150 fix. * Add note about gif tool CVEs.
* Fixed HL_test_packet, incorrect length assignment (#1100)Allen Byrne2021-10-201-1/+5
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-201-2/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* To reduce maintenance effort, delete the `noerror-` variants of the compiler ↵David Young2021-10-061-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | flags files (#1033) * Avoid maintenance headaches: delete the `noerror-` variants of the compiler flags files, since they essentially duplicate the `error-` files modulo the replacement of `-Werror=` with `-W` and any changes in comments. (I verified the duplication with a script.) For autoconf, reinstate the use of the `demote_errors` shell function to derive the `noerror-` content from the `error-` content. `demote_errors` replaces `-Werror=` with `-W` when `WARNINGS_AS_ERRORS` is `no`. Slightly reorder `configure.ac` so that the setting of `WARNINGS_AS_ERRORS` takes effect before the `error-` files are sourced. * Take a stab at updating the CMake files to match the changes I made to the autoconf files to remove `noerror-` files. I'm not much of a CMake user so these changes are quite rough. Looks like the duplication can be reduced with the introduction of a new macro. * Delete `noerror-` files from the MANIFEST. * Reduce duplication in the CMake files: perform the HDF5_ENABLE_WARNINGS_AS_ERRORS test once in the ADD_H5_FLAGS macro. * Add a release note.
* Fix bug with cross platform compatibility of references within vlens. (#1064)Neil Fortner2021-10-011-0/+9
| | | No testing yet.
* Update compact dataset I/O routines to handle driver-level memory copy (#1054)jhendersonHDF2021-09-301-0/+42
| | | | | | | | | | * Update compact dataset I/O routines to handle driver-level memory copy * Combine compact I/O read/write struct into single I/O struct Rename CTL memory copy flag and H5Fquery routine to get file driver structure * Add RELEASE.txt entry for new "ctl" memory copy operation
* Update version to 1.13.0-7 after snapshot release 1.13.0-6. (#1048)Larry Knox2021-09-291-1/+1
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* Update Platforms Tested in RELEASE.txt. (#1045)hdf5-1_13_0-rc6Larry Knox2021-09-281-143/+97
| | | | | | * Update Platforms Tested in RELEASE.txt. Remove Tested Configuration Features Summary for updated replacement. * Set version to 1.13.0-6 for rc6 snapshot.
* Develop cmake install dir (#1041)Allen Byrne2021-09-281-0/+9
| | | | | | | * Corrected path searched by CMake find_package command * Correct path for depend libs * Adjust examples script for install path
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