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* Hdf5 1 12 parallel compression merge (#1529)jhendersonHDF2022-03-281-4/+8
| | | | | | | | | | | | | | | | * Fix the function cast error in H5Dchunk.c and activate (#1170) `-Werror=cast-function-type`. Again. * Parallel Compression improvements (#1302) * Fix for parallel compression examples on Windows (#1459) * Parallel compression adjustments for HDF5 1.12 * Committing clang-format changes Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 12 Merge SZ plugin changes from develop (#1455)Allen Byrne2022-02-241-2/+2
| | | | | | | * Merge SZ plugin changes from develop * Update examples version * Update examples version
* Merge Update the java slf4j logging jars to latest 1.7.33 (#1370)Allen Byrne2022-01-241-3/+3
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* 1.12 Merge Consolidate VFD create list macro #1132 (#1133)Allen Byrne2021-10-311-0/+3
| | | | | | | * Merge Consolidate VFD create list macro #1132 * Split dir create into separate macro * fix VFD settings
* 1.12 Merge Move test utilities to utils/test folder #1109 (#1110)Allen Byrne2021-10-211-4/+1
| | | | | | | * Merge Move test utilities to utils/test folder #1109 * Merge Correct shell tests and c++ flag warning * Fix typo
* Merge Fix various warnings and issues in doxygen doc generation #994 (#996)Allen Byrne2021-09-101-14/+15
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* Hdf5 1 12 merge changes (#604)Allen Byrne2021-04-281-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * Some Javadoc warning fixes * Committing clang-format changes * Updated javadoc fixes * HDFFV-11228/9 merges from develop * remove obsolete debug comment * Fix conflict * HDFFV-11229 merge changes from develop * HDFFV-11229 merge second compare from develop * HDFFV-11229 fix reference file * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update with changes from develop * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 12 CMake advanced options for clang needs an OPTION command #556 (#558)Allen Byrne2021-04-201-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * Some Javadoc warning fixes * Committing clang-format changes * Updated javadoc fixes * HDFFV-11228/9 merges from develop * remove obsolete debug comment * Fix conflict * HDFFV-11229 merge changes from develop * HDFFV-11229 merge second compare from develop * HDFFV-11229 fix reference file * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update with changes from develop * Add "option" command for clang options Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 12 merge CMake flag groups and tools long double changes from develop (#523)Allen Byrne2021-04-191-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * Some Javadoc warning fixes * Committing clang-format changes * Updated javadoc fixes * HDFFV-11228/9 merges from develop * remove obsolete debug comment * Fix conflict * HDFFV-11229 merge changes from develop * HDFFV-11229 merge second compare from develop * HDFFV-11229 fix reference file * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update with changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add cmake variable HDF5_LIB_INFIX (#7)Raphael Grimm2021-03-221-14/+21
| | | | | | | | | | | | | | | | * Add cmake variable HDF5_LIB_INFIX This infix is added to all library names after 'hdf5'. e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' This name is used in packages on debian based systems. (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) This option is useful when testing projects on debian based systems with custom builds of hdf5 while trying to minimize differences between the custom setup and the environment created by installing system packages. * Added RELEASE.txt entry for HDF5_LIB_INFIX. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Hdf5 merge issue #458 to hdf5_1_12 (#463)Larry Knox2021-03-121-3/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* 1 12 merge recent changes from develop (#344)Allen Byrne2021-02-171-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo
* 1 12 merge of changes from dev (#271)Allen Byrne2021-01-191-35/+54
| | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix
* OESS-98 fix tools test for plugins - HDF5 1 12 (#178)Allen Byrne2020-12-151-0/+15
| | | | | | | | | | | | | | | | | * merge updates from develop * remove extension on command * Run autogen before chkmanifest * Update release text files and whitespace cleanup * Update list * OESS-98 Update plugin build option * OESS-98 fix tools test for plugins * Fix conflict
* OESS-98 Update plugin build option - HDF5 1 12 (#173)Allen Byrne2020-12-151-16/+15
| | | | | | | | | | | | | * merge updates from develop * remove extension on command * Run autogen before chkmanifest * Update release text files and whitespace cleanup * Update list * OESS-98 Update plugin build option
* hdf5 1 12 add missing files and use chkmanifest (#103)Allen Byrne2020-11-201-1/+1
| | | | | | | * merge updates from develop * remove extension on command * Run autogen before chkmanifest
* Add doxygen framework for CMake and autotoolsAllen Byrne2020-11-131-0/+15
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* Correct TARGET variable and CMake config file locationAllen Byrne2020-11-121-5/+8
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* OESS-98 add CMake option to build plugins project within hdf5Allen Byrne2020-10-161-1/+18
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* Add clang-format changes from develop.Allen Byrne2020-09-281-0/+3
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* The version string has a second use for packagingAllen Byrne2020-08-261-1/+3
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* Revert H5_VERS_SUBRELEASE checkAllen Byrne2020-08-241-5/+1
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* Add special case when H5_VERS_SUBRELEASE is 0Allen Byrne2020-08-241-3/+7
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* Condition if (H5_VERS_SUBRELEASE) is incorrectly false whenLarry Knox2020-08-241-3/+3
| | | | | | H5_VERS_SUBRELEASE is 0, a valid value for H5_VERS_SUBRELEASE. Updated to if (${H5_VERS_SUBRELEASE} STREQUAL "") with corresponding reversal of action statements to avoid NOT.
* Add hypen to subrelease regexAllen Byrne2020-08-231-1/+1
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* Sync with developDana Robinson2020-08-011-0/+15
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* CMake updates:Allen Byrne2020-07-151-0/+11
| | | | | | Add build folder as Include for generated files Add install option for copying Fortran mod files to include folder Add PRI defines to win32defs file Exclude mingw from extra flags
* OESS-65 replace szip with aec libraryAllen Byrne2020-04-271-5/+5
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* TRILAB-192 - merge changes from developAllen Byrne2020-04-071-0/+2
| | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* Correct usage of add_compile_definitionsAllen Byrne2020-02-231-3/+1
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* Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-231-13/+16
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* Merge changes from develop for CMake and JavaAllen Byrne2020-02-211-3/+0
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* Merge changes from develop to fix various issuesAllen Byrne2020-01-301-8/+15
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* Improved CMake options for testsAllen Byrne2020-01-191-6/+42
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* TRILABS-135 add clang sanitizer supportAllen Byrne2019-12-131-6/+21
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* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-091-14/+3
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-061-3/+14
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* Add policy to use <package>_ROOTAllen Byrne2019-09-051-0/+4
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-08-131-0/+9
|\ | | | | | | | | | | | | | | | | * commit 'aeb145428f5e6bc51742fff031b0cf8cf6fbefbb': Updated h5trav.c to emit output that doesn't require ddl changes for map support. Fixed Map API CMake option Renamed H5Mdelete_key to H5Mdelete and H5Mset to H5Mput. Added ifdef for intel compilers, __GNUC__ has to be defined for header files which use it to work with intel compilers. This gives a warning for intel compiler about fallthrough, so added a check not to include fallthrough if using intel compilers. Added the map (H5M) API
| * Fixed Map API CMake optionDana Robinson2019-08-131-0/+3
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| * Added the map (H5M) APIDana Robinson2019-08-131-0/+6
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* | HDFFV-10879 set default API versionAllen Byrne2019-08-131-1/+2
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* HDFFV-10879 correct API version set commandAllen Byrne2019-08-121-1/+1
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* Use a STRING option for API versionAllen Byrne2019-08-121-15/+8
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* Fix API version optionAllen Byrne2019-08-121-1/+4
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* Squashed commit of the following:Larry Knox2019-07-251-0/+21
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* HDFFV-10845 skip test if CMake command doesn't support ignore EOLAllen Byrne2019-07-171-0/+6
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* HDFFV-10845 fix configure check and PATHsAllen Byrne2019-07-171-2/+2
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* HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-181-4/+13
| | | | | 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
* HDFFV-10741 - remove SKIP_ERRSTK_TESTS optionAllen Byrne2019-04-151-1/+0
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