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* Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447)Sean McBride2021-05-033-4/+0
| | | | | | | * Removed mentions of Wdeclaration-after-statement now that C99 is required * Remove -Werror=declaration-after-statement from error-general file. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)Dana Robinson2021-04-304-13/+52
| | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Fixes incorrect size_hint handling in H5Gcreate1 * Updates the size hint type for group creation * Updates the RELEASE.txt note * Revert "Updates the RELEASE.txt note" This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff. * Reverts previous behavior to use a uint32_t struct field * Updates RELEASE.txt Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fortran target depends (#608)Allen Byrne2021-04-301-11/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a ↵Dana Robinson2021-04-293-8/+21
| | | | | | | | | | | | | | | | | | fapl (#601) * Committing clang-format changes * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times An internal string is incorrectly freed when the API call is invoked multiple times on a property list, which will usually cause a segfault to occur. On the first call the log location is NULL so the problem doesn't occur. Fixes HDFFV-11239 * Fixes typos Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)Dana Robinson2021-04-293-3/+30
| | | | | | | | | | | | | | | | | * Committing clang-format changes * Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid fapl ID This was due to a pointer-containing struct being memset after the first internal API call. If the first call failed, the error condition would check if the pointer was not NULL and then attempt to free it if not. This would lead to the freeing of a wild pointer if an invalid fapl ID were passed in. This was fixed by reordering the memset and adding a test to ensure the problem stays fixed. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Parallel builds need the mpi compiler for pkgconfig scripts. (#599)Allen Byrne2021-04-276-6/+44
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* fortran generated files depends (#598)Allen Byrne2021-04-262-4/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge doxygen2 into develop (#553)Gerd Heber2021-04-26110-1724/+61863
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed warnings and started H5Epublic.h. * Include H5FD* headers to correctly resolve references. * Doxygen2 (#330) * H5Eauto_is_v2. * Added a few more calls. * Added a few more H5E calls. * First cut of H5E v2. * Added the deprecated v1 calls. * Updated spacing. * Once more. * Taking some inspiration from Eigen3. * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352) * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2. * doxygen work. fixs format by using clang-format. * doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments. For Quincey's comments, since we are not supposed to change the source code. I leave this to future improvements. * added documentation for H5P APIs (#350) * add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios * format corrections * fixed grammer * fixed herr_t * Better name. * A fresh look. * add doxygen to H5Ppublic.h * use attention instead of warning * Add doxygen comments in H5Ppublic.h (#375) * Add doxygen comments in H5Ppublic.h * H5Pset_meta_block_size * H5Pset_metadata_read_attempts * H5Pset_multi_type * H5Pset_object_flush_cb * H5Pset_sieve_buf_size * H5Pset_small_data_block_size * H5Pset_all_coll_metadata_ops * H5Pget_all_coll_metadata_ops * Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt * Fix clang-format errors * Fix filenames in doxygen/examples * add doxygen to H5Ppublic.h (#378) * add doxygen to H5Ppublic.h * use attention instead of warning Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> * Revert "add doxygen to H5Ppublic.h (#378)" This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2. * Updated Doxygen variables. * I forgot to copy two images. * Enable desktop search by default. * Add my assigned Doxygen documentation. * Remove whitespace at EOL. Appease clang-format. * Addressed Chris' comments. * Added an alias for asynchronous functions. * One space is enough for all of us. * Slightly restructured RM page. * address some issues * reformatting * Style external links. * reformatting * reformatting * Added "Metadata Caching in HDF5" as a technical note example. * Revise this soon! * Added specification examples. * Fixed references. * Added H5AC cache image stuff and file format study. * Added older FMT versions. Where did 1.0 go? * Updated C/C++ note and replaced ambiguous labels. * Reformat source with clang v10.0.1. * Added the VFL technical note. * Added what I believe might be called version 1.0 of the format. * Added the remaining specs. * Added H5Z callback documentation and fixed a few mistakes. * Added dox for deprecated H5G calls and fixed a few snippet blockIDs. * clang-format happy? * Ok? * Bonus track: Deprecated H5D functions. * Carry over the more detailed group description. * Added documentation for the missing and deprecated H5R calls. * Life is easier and less repetitive w/ snippets. Use them! * Eliminate the snippet block ID artifacts in the HTML rendering. * Fixed snippet HTML artifacts and added a few missing calls. * Under 20 H5Ps to go! * Almost complete! * "This is a form of pedantry up with which I will not put." (Churchill) * Let's not waste as much space on bulleted lists! * First complete (?) draft of the Doxygen-based RM. * Completeness check and minor fixes along the way. * Pedantry. * Adding missing H5FD calls checkpoint. * Pedantry. * More pedantry. * Added H5Pset_fapl_log. * First draft of H5ES. * Fixed warnings. * Prep. for map module. * First cut of the map module. * Pedantry. * Possible H5F introduction. * Fix the indentation. * Pedantry. * Ditto. * Thanks to the reviewers for their comments. * Added missing images. * Line numbers are a distraction here. * More examples, references, and clean-up. Don't repeat yourself! * Clang pedantry. * Ditto. * More reviewer comments... * Templatized references and cleaned up \todos. * Committing clang-format changes * Fixed MANIFEST. * Addressed Quincey's comments. (OCPLs) * Fixed a few more \todo items. * Fixed more \todo items. * Added attribute life cycle. * Forgot the examples file. * Committing clang-format changes * Pedantry. * Live and learn! * Added a sample H5D life cycle. * Committing clang-format changes * Pedantry. Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com> Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake changes to byproducts - ninja warnings (#568)Allen Byrne2021-04-246-96/+98
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix set_tests_properties for parallel t_pflush tests (#569)jhendersonHDF2021-04-221-2/+2
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* Update top-level COPYING file and remove COPYING files from subdirectories ↵Larry Knox2021-04-2120-251/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#561) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Update top-level COPYING file and remove COPYING files from subdirectories. * Remove subdirectory COPYING files from MANIFEST. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added more C++11 override keywords (#485)Sean McBride2021-04-2123-71/+71
| | | | | | | | | | * Added more C++11 override keywords * Format updates in src/H5Tconv.c. * Committing clang-format changes Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake advanced options for clang needs an OPTION command #556 (#557)Allen Byrne2021-04-201-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake no longer builds the C++ library by default (#555)Dana Robinson2021-04-204-2/+11
| | | | | | | * Committing clang-format changes * CMake no longer builds C++ library by default Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes incorrect usage of H5I_BADID (#554)Dana Robinson2021-04-195-177/+177
| | | | | | | * Committing clang-format changes * Fixes incorrect use of H5I_BADID Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cleanup CMake code for doxygen and perl shell scripts (#552)Allen Byrne2021-04-195-22/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings the native implementation of H5Fdelete() from Bitbucket (#524)Dana Robinson2021-04-1627-208/+715
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Brings the native VFD H5Fdelete() implementation from Bitbucket Only brings the 'del' callbacks, not the 'open/close' scheme. * Formatter changes * Committing clang-format changes * Fixes direct VFD callback name * Removes UNUSED macro from family API call * Adds barrier and rank 0 check to MPI-I/O VFD delete * Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete" This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143. * Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"" This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702. * Adds a second barrier after the delete in MPI-I/O VFD * Only delete files in the core VFD when the backing store flag is set * Fixes string issues in multi VFD Also, h5test.c cleanup code now uses H5Fdelete(). * Formatted source * Rework fapl checks for MPI-I/O VFD delete callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Tools long double updates (#522)Allen Byrne2021-04-1525-75/+2356
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove unused #cmakedefine and autotools checks (#431)Sean McBride2021-04-133-34/+0
| | | With C99 as the minimum, there's no point checking for these standard things anymore.
* Removes implementation of my_strdup() from the multi VFD (#527)Dana Robinson2021-03-313-47/+27
| | | | | | | | | * Committing clang-format changes * Removes my_strdup() from the multi VFD * Use strdup directly when memory sanity checks are off Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Minor warning fixes in develop (#526)Dana Robinson2021-03-315-138/+145
| | | | | | | * Committing clang-format changes * Minor warning fixes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix HDFFV-11232 (#530)Scot Breitenfeld2021-03-311-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * 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 * added H5fortkit dependency for H5VLff.F90, HDFFV-11232 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes dead H5ST package from the library (#528)Dana Robinson2021-03-3011-1255/+4
| | | | | | | * Committing clang-format changes * Removes the unused H5ST package from the library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updates that allow accum SWMR tests to work on Windows (#493)Dana Robinson2021-03-271-60/+102
| | | | | | | | | | | | | | | * Committing clang-format changes * Updates the accum test to work on Windows Uses CreateProcess() on Windows * Source formatting * Fix for Unix child result * Fixes process return code bug on Windows Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Clean up MPI-IO VFD tracing support (#520)Quincey Koziol2021-03-261-128/+196
| | | | | | | * Clean up tracing support * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Minor parallel improvements (#519)Quincey Koziol2021-03-265-51/+46
| | | | | | | * Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge pr7 (#516)Larry Knox2021-03-252-14/+30
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Add cmake variable HDF5_LIB_INFIX (#7) * 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> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
* develop - Javadoc warning fixes (#506)Allen Byrne2021-03-2412-54/+386
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Align with "parallel fence" changes (#479)Quincey Koziol2021-03-2413-393/+148
| | | | | | | | | * Small code updates and simplifications * Committing clang-format changes * Fix 'make installcheck' for parallel builds Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes c99_(v)snprintf() calls from the standalone test code (#509)Dana Robinson2021-03-242-56/+32
| | | | | | | | | | | | * Committing clang-format changes * Removes c99_(v)snprintf from standalone code These internal API calls were removed in a previous commit but were missed in the sio/pio_standalone code. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Misc warning fixes (#495)Dana Robinson2021-03-249-61/+73
| | | | | | | | | | | | | * Committing clang-format changes * Misc warning fixes from Visual Studio * Committing clang-format changes * Fixes warnings in swmr.c test * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update h5LT files with latest flex and Bison available on jelly (#502)Larry Knox2021-03-245-1369/+1436
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Added [] to H5LTanalyze.l line 126 to eliminate warning "rule could not be matched". Ran bin/genparser hl/src with flex v2.6.4 and Bison v3.0.4 on jelly. * Added HD to strdup in H5LTparse.y line 338. Ran bin/genparser hlsrc again. * Removed line 126 from H5LTanalyze.l - previous line matches. Added previously removed line 318 of H5LTparse.y to fix hl_test_lite failure. Ran bin/genparser. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes support for pre-2015 Visual Studio (#496)Dana Robinson2021-03-243-180/+21
| | | | | | | | | | | | | | | | * Committing clang-format changes * Removes work-around code for pre-2015 Visual Studio HDF5 no longer provides an implementation for: * <inttypes.h> * snprintf and vsnprintf * llround(f), lround(f), round(f) * strtoll and strtoull * va_copy * struct timespec Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492)Dana Robinson2021-03-232-1/+57
| | | | | | | | | | | * Committing clang-format changes * Updates H5SYS_GOTO_ERROR to emit Win32's GetLastError() * Committing clang-format changes * Format source changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Disable long double tests and remove CMake flag groups (#494)Allen Byrne2021-03-225-218/+99
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* small edits (#481)Scot Breitenfeld2021-03-221-20/+19
| | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Applied clang-tidy readability-delete-null-pointer fixes (#430)Sean McBride2021-03-2216-70/+38
| | | | | delete nullptr is well-defined, does not need check. Manually fixed indentation after automatic changes.
* File locks now work on Windows (#480)Dana Robinson2021-03-225-54/+140
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * File locks now work on Windows Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial). * Committing clang-format changes * Committing clang-format changes * Fixes commenting in h5repack * Reworks H5Fis_accessible() H5Fis_accessible() created a new file handle and attempted to read through it, which will fail when a file has been opened with an exclusive lock on operating systems that have mandatory locks. This change uses the same scheme we use in H5Fopen() to check if the file is already open and only tries to read the file signature if the file has not already been opened. Also adds a test for this behavior. * Committing clang-format changes * Trivial change to force github to run actions Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds an implementation for nanosleep on Windows (#483)Dana Robinson2021-03-223-30/+24
| | | | | | | | | * Adds an implementation for nanosleep on Windows * Committing clang-format changes * Fix insane formatter issue Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix CMake error message location. (#478)H. Joe Lee2021-03-201-2/+2
| | | Print error message if Perl is not found.
* Purge the buffer used in type conversion. (#263)Yu Feng2021-03-191-6/+6
| | | | | | | | | Some of the uniniitialized bits in the buffer may get carried through all the way to disk, creating a risk for leaks. We observed an msan error during the floating point output conversion. Due to the encoding certain bits could remain untouched during the conversion. In this draft we zero initialize the dbuf used by every convertor.
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#405)bmribler2021-03-198-20/+99
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) Description Checked against buffer size to prevent segfault, in case of data corruption. + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode Platforms tested: Linux/64 (jelly) * Accidentally left in another occurrence of the previous patch from user after a more correct fix was applied, that is the check now accounted for the previous advance of the buffer pointer. Removed it. * Typo * Fixed format issues. * Added test. * Changed arguments to ADD_H5_TEST * Fixing arguments to ADD_H5_TEST again. * Fixing arguments again. * Took out the CMake changes until Allen can help. * Added files: tCVE_2018_11206_fill_old.h5 tCVE_2018_11206_fill_new.h5 * Revert "Took out the CMake changes until Allen can help." This reverts commit c21324d6e0044994c5cd24b0671e7d1dd41096cc. * Revert "Fixing arguments again." This reverts commit 5832a70674339e4b524749adde5a181f8c3a446a. * Revert "Fixing arguments to ADD_H5_TEST again." This reverts commit b45de823c22ce83a388d46466ef7c04b66ff05ed. * Revert "Changed arguments to ADD_H5_TEST" This reverts commit 16719824f57e52158451ddd261788c0dcaa3ec55. * Added first argument to ADD_H5_TEST for HDFFV-10480 fix. * Changed argument 0 to 1 * Revert "Changed argument 0 to 1" This reverts commit b343d6613ba681b43248dd5820e96389984ebcf7. * Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix." This reverts commit b8a0f9a9e8ec8e6c6ff38d33195d63edff76a563. * Added first argument and corrected the second. * Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049 * Improved error messages.
* Added description of the current HDF5 branches; added a draft of ↵epourmal2021-03-193-0/+130
| | | | | | | | | | | | | | | | | | | | | | | | | | | | contribution policy. (#445) * Added description of the current HDF5 branches. * Removed capitalization in from Develop, Release, Feature to reflect the real naming schema * Added a draft of contributions guidance document. * Fixed typos. * Fixed section title. * Fixed typo. * Fixed typos and formatting. * Fixed many typos and simplified the text (e.g., removed testing instructions and left pointers to where to find them, etc.) * Fixed a typo. Please enter the commit message for your changes. Lines starting * Added contributing.md file and rearranged doc entries in alphabetical order. * ddressed Gerd's review comments; found and fixed more typos. * Addressed comments from Larry and Scot.
* Suppresses the tcheck_version test's abort dialog on Windows (#477)Dana Robinson2021-03-171-0/+23
| | | | | | | | | | | | | | * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix typos and grammar errors. (#476)H. Joe Lee2021-03-171-23/+16
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* Cleans up a couple of MSVC warnings in testhdf5 (#475)Dana Robinson2021-03-172-5/+7
| | | | | | | | | | * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix display of long double in tools (#469)Allen Byrne2021-03-1712-7/+93
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct syntax error. (#474)H. Joe Lee2021-03-171-1/+1
| | | a Fortran compile -> a Fortran compiler
* Update clang config (#473)Quincey Koziol2021-03-17126-913/+3346
| | | | | | | * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Simplified hl parsing (#399)David Young2021-03-155-1889/+1879
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Stop using global variables to share parse context with the lexer. The lexer uses an unconventional strategy for parsing lexical categories NUMBER (decimal numbers) and STRING (double-quoted strings) that involves sharing the parse context with the lexer using global variables. There are a couple of problems with that. First, the lexer is too complicated for the simple tokenization it performs—it's hard to tell if it is correct. Second, as @seanm points out, the shared global variables spill into the namespace shared by other libraries and application programs—e.g., VTK. * Regenerate source files from *.[yl]. * Replace strndup, which isn't available on Windows, with a custom routine, `trim_quotes`, that produces a copy of its `const char *` argument with leading and trailing double quotes ('"') removed. While I am here, remove the unnecessary statement `BEGIN INITIAL;`, which I should have deleted in a previous commit. * Regenerate .c from .l. * You haven't programmed in C until you have programmed in High-Definition (HD) C. * \#include "H5private.h" for HD* definitions. * Regenerate *.[ch] from *.[yl].
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