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* Onion VFD: Sync with develop (#1685)Dana Robinson2022-04-2520-690/+788
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * First stab at a Github status bar * Adds a .tokeignore file for counting lines of code accurately * Yanks lines of code calculation since it wildly overcounts * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651) * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t * Committing clang-format changes * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Mirror vfd test fixes (#1629) * Use the FAPL that was created earlier in the test (and delete an unused variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd. * Check for testing directory before creating, to avoid warning from bash. Clean out .libs directory before re-using it (after a failed test), to remove any files generated by libtool. * Committing clang-format changes * Increment error count on failed file open and skip tests for VFDs that need modified filenames. * Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking configuration parameters and can't be provided for an automated test that is configured with an environment variable. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes HDF Group paths, adds shellcheck fixes (#1656) For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le... * HDFFV-11306 Fixed (#1657) * HDFFV-11306, * Fixed it so both h5open_f and h5close_f can be called multiple times. * Fixed an issue with open objects remaining after h5close_f was called. * Added additional tests. * comments clean-up * Develop clang format java (#1653) * added HDFFV-11306 entry (#1662) * Adds the -q flag to all swmr test programs, quieting noisy output (#1665) * Adds paths-ignore to the Github pull request workflow (#1663) * Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666) So the PR action name is not the same as the one in main.yml * Replace H5detect's build-time detection of C99 integer properties with a (#1400) * Replace H5detect's build-time detection of C99 integer properties with a table-driven routine, `H5T__init_native_int()`, that is run at library initialization time. * Improve handling of copying of dynamic libraries and clean them up after (#1681) test finishes. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Develop java newrefs fixes for obj ref datasets (#1354)Allen Byrne2022-01-182-210/+149
| | | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update the java slf4j logging jars to latest 1.7.33 (#1369)Allen Byrne2022-01-182-4/+4
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* Add tests for H5Ocopy of new object refs (#1338)Allen Byrne2022-01-082-152/+121
| | | | | | | | | | | * Add tests for H5Ocopy of new object refs * Correct class name * Skip test because of issue with debug assertions * Update reference file * Fix object examples for new refs
* #386 copyright corrections for java folder (#389)Allen Byrne2021-02-2620-20/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Primary change is HDFFV-11212 - new refs and JNI (#372)Allen Byrne2021-02-2518-173/+173
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2021-02-1720-20/+20
| | | | | | * 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.
* Modify temporary rpath for testing in java example scripts. (#230)Larry Knox2020-12-291-1/+9
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* CMake: MINGW implies WIN32Michel Zou2020-10-301-1/+1
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* Trim trailing whitespaceQuincey Koziol2020-04-201-1/+1
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* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-211-1/+1
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* HDFFV-11001 need to qualify all by parallel or serial typesAllen Byrne2020-01-151-1/+1
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* HDFFV-11001 Add fine control over testingAllen Byrne2020-01-151-1/+1
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* HDFFV-10995 - add missing importAllen Byrne2020-01-082-0/+2
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* HDFFV-10995 - need to add importAllen Byrne2020-01-082-0/+2
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* HDFFV-10995 adjust testing to tolerate non-US localeAllen Byrne2020-01-082-2/+2
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* small syntax changesAllen Byrne2019-09-191-1/+3
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* Use generator expr to get correct nameAllen Byrne2019-07-221-33/+20
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* Correct java load library name accessAllen Byrne2019-07-181-2/+3
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* HDFFV-10845 fix configure check and PATHsAllen Byrne2019-07-171-1/+1
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* Change how name is retrievedAllen Byrne2019-07-081-1/+2
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* HDFFV-10581 remove special name checkingAllen Byrne2019-07-081-1/+1
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* HDFFV-10703 Update CMake commands to latest standardAllen Byrne2019-02-151-2/+2
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* Same changes needed for examples as testAllen Byrne2018-08-231-9/+34
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* Update Java util lib, Refactor H5D write VL to match readAllen Byrne2018-06-272-5/+5
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* TRILABS-20 set a compiler name on all project commandsAllen Byrne2018-04-201-1/+1
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* TRILABS-19 Initial conversion of include_directories to targetsAllen Byrne2018-04-171-5/+0
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* Change CMake min to 3.10Allen Byrne2018-03-091-1/+1
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* Inc CMake min, Add new tests, rework test CMake filesAllen Byrne2018-02-271-1/+1
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* HDFFV-10385 rework java namesAllen Byrne2018-01-171-2/+1
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* HDFFV-10385 Use OUTPUT_NAME property instead of CMAKE_BUILD_TYPEAllen Byrne2018-01-161-7/+2
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* Revert CMAKE_BUILD_TYPE for matches - need to redesignAllen Byrne2018-01-121-1/+1
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* HDFFV-10385 refactor CMAKE_BUILD_TYPE usageAllen Byrne2018-01-091-1/+1
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* Change name for test results tableAllen Byrne2017-09-202-2/+2
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* Add chekexe and chklog generation to testsAllen Byrne2017-09-201-18/+36
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-2520-120/+80
| | | | | | | | | | 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.
* Update CMake files and formattingAllen Byrne2017-03-011-3/+3
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-01-131-0/+1
|\ | | | | | | | | * commit 'bd85e57904f1f943774bb99ea5e8b0d074db0edb': tools/test/h5diff/testh5diff.sh.in: Add code to delete copies of test .h5 files copied from tools/testfiles/vds to tools/test/h5diff/testfiles when running "make check" for an in-source build.
| * tools/test/h5diff/testh5diff.sh.in:lrknox2017-01-131-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add code to delete copies of test .h5 files copied from tools/testfiles/vds to tools/test/h5diff/testfiles when running "make check" for an in-source build. tools/test/misc/testh5repart.sh.in: Change the name of the temporary test directory from "testfiles" which is also used for 2 h5mkgrp test files under source control to "testrepart" to avoid deleting source controlled files when running "make check" in the source directory. Fix test scripts that remove source-controlled files during "make check" when run in-source. Fix test scripts that don't remove test files because they add files to test directories but don't remove them if the build directories are the same as the source directory. Fix any test source file or Makefile.am files for tests that leave data files are removed by neither "make check" nor "make distclean".
* | Update cmake min version and cmake command conventionAllen Byrne2017-01-101-12/+12
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* Change examples to match junit testAllen Byrne2016-12-011-1/+1
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* Merge test output file clearing into runTest.cmakeAllen Byrne2016-10-031-2/+0
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* [svn-r30313] HDFFV-9972: unsatisfied link error under debug on Windows.Allen Byrne2016-08-223-11/+11
| | | | | | | | | | 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-r29871] HDFFV-9743: Fix java examples Debug build commands.Allen Byrne2016-05-041-4/+7
| | | | rename examples clear-objects test names.
* [svn-r29513] Only delete the copied and generated test files.Allen Byrne2016-03-221-10/+2
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* [svn-r29507] Add actual file name to delete functions to prevent accidental ↵Allen Byrne2016-03-221-2/+2
| | | | | | deletion of source files. (HDFFV-9730 created for tools scripts, which is the basis for the java scripts)
* [svn-r29480] Correct copy functions to test the directoryAllen Byrne2016-03-211-4/+4
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* [svn-r29465] Fix issue with .classes dir not getting created for java by ↵Allen Byrne2016-03-171-3/+3
| | | | adding mkdir .classes to configure.
* [svn-r29463] qualify .classes with $(top_builddir)Allen Byrne2016-03-171-1/+1
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* [svn-r29226] HDFFV-9552: merge in java code.Allen Byrne2016-02-2921-0/+5979
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