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* Cleans up POSIX/C bits in H5private.h (#804)Dana Robinson2021-06-291-13/+13
| | | | | | | | | | | | | | | | | | * Cleans up POSIX/C bits in H5private.h * Assume difftime exists (C89) * Reorg AC_CHECK_HEADERS so headers are in alphabetical order * Split off networking-related AC_CHECK_HEADERS * Remove unused UNAME_CYGWIN from configure.ac * Remove checks for unused sys/timeb.h * Tidying pass over H5private.h HD prefix macros * Tidy H5win32defs.h * Add HD prefix to various scanf calls * Committing clang-format changes * Fixes to the alarm(2) code used in the tests to make Windows happy Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update clang config (#473)Quincey Koziol2021-03-171-2/+8
| | | | | | | * 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>
* develop JNI export references and java updates (#467)Allen Byrne2021-03-121-174/+369
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Primary change is HDFFV-11212 - new refs and JNI (#372)Allen Byrne2021-02-251-359/+394
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Update license url part2 (#333)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - files not in src or test.
* Clang-format of source filesAllen Byrne2020-09-301-687/+664
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* Fix jni with %Lg instead of %LfAllen Byrne2020-09-291-3/+1
| | | Fix warnings due to improper formed define tag in h5diff
* Pre-format fixes for warnings as errorsAllen Byrne2020-09-291-0/+2
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* testpar/t_2Gio.c: Fix a typo that I think was introduced by aDavid Young2020-01-291-2/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings.
* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-127/+136
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* HDFFV-10976,-10980 Init obj_type before calling H5Rget_obj_type3Allen Byrne2019-12-201-1/+1
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* Address compile warningsAllen Byrne2019-12-061-2/+4
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* Fix compile errors - mostly in jniAllen Byrne2019-12-061-26/+67
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* HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-071-111/+170
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* Fix various Java issues when deprecated symbols are disabledJordan Henderson2019-10-101-1/+1
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* Java formatting of argsAllen Byrne2019-05-301-3/+3
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* Minor fix in h5str_sprintf for NULL region referencesJordan Henderson2019-02-221-1/+1
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* Fixes for JNI updatesJordan Henderson2019-02-121-7/+11
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* Re-write of Java JNI error handlingJordan Henderson2019-02-111-2140/+2564
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* HD prefix and whitespaceAllen Byrne2018-08-281-5/+5
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* HDFFV-10536 callback crash fixed by using stack structureAllen Byrne2018-08-171-1/+0
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* Fix ptr arithAllen Byrne2018-06-291-47/+38
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* Correct function callAllen Byrne2018-06-281-1/+1
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* Correct cast formattingAllen Byrne2018-06-281-2/+2
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* Correct var nameAllen Byrne2018-06-281-2/+2
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* Need to cast from void ptrAllen Byrne2018-06-281-2/+2
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* Update Java util lib, Refactor H5D write VL to match readAllen Byrne2018-06-271-0/+422
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* Fix attribute ReadAllen Byrne2018-06-251-110/+0
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* Correct "," handlingAllen Byrne2018-06-251-4/+4
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* Remove debug statementsAllen Byrne2018-06-211-12/+0
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* Split/fix utility for vl typesAllen Byrne2018-06-211-45/+150
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* H5O_info fixes for java and examplesAllen Byrne2018-05-311-3/+3
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* HDFFV-10412 add error on function for JavaAllen Byrne2018-03-131-0/+3
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* HDFFV-10186 Add endianess to bitfield and fix testsAllen Byrne2017-05-101-4/+28
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Fix URL nameAllen Byrne2017-04-111-1/+1
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* Eliminate unreferenced local variable warningAllen Byrne2016-09-191-17/+1
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* [svn-r30313] HDFFV-9972: unsatisfied link error under debug on Windows.Allen Byrne2016-08-221-30/+31
| | | | | | | | | | Added windows name suffix for debug to CMake cmd_arg for examples and test. Fix issues discovered under debug testing; Create a version of H5Iget_name that correctly returns the name. Rework PIN_JAVA_STRING macro and usage to eliminate possible memory leaks by using if-else instead of mid-routine return. Update example to use new H5Iget_name API. Tested: windows under debug
* [svn-r30213] Add H5Aread_complex for reading arrays and compounds that are ↵Allen Byrne2016-07-201-0/+54
| | | | not VL strings.
* [svn-r29873] Java add missing APIs.Allen Byrne2016-05-041-41/+80
| | | | | Adjust whitespace in H5.java for exception indentation. Adjust whitespace in JNI for function signature formatting.
* [svn-r29226] HDFFV-9552: merge in java code.Allen Byrne2016-02-291-0/+2592
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