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* Initial preparation of hdf5-1_11_3 release branch for HDF5 1.12.3 ↵Larry Knox2023-10-231-0/+1575
| | | | release:\nUpdated configure.ac for release: switched configure default to production mode and disabled maintainer mode.\nSet HDF5_GENERATE_HEADERS to OFF in src/CMakeLists.txt.\n Generated release files including Makefile.ins with autogen.sh, autoconf 2.71 and automake 1.16.2.\nIncremented version to 1.12.3-2. (#3756)
* Fix spelling (#3633)Dana Robinson2023-10-042-2/+2
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* Merge/update CMake, presets,java and tools (#3393)Allen Byrne2023-08-213-16/+7
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* Move config/cmake_ext_mod content to config/cmake (#3062)Dana Robinson2023-06-071-2/+2
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* Add h5copy help test and verify consistency (#2903)Allen Byrne2023-05-183-3/+3
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2546)Allen Byrne2023-03-141-1/+1
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* Update Copyright headers. (#2534)Larry Knox2023-03-133-3/+0
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* Commit codespell spelling corrections.Larry Knox2022-04-071-1/+1
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* 1.12 Move error-stack text to top of usage display #1564 (#1566)Allen Byrne2022-04-013-3/+9
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* 1.12 Tools merges from develop (#949)Allen Byrne2021-08-233-36/+113
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Tools merges from develop Brings the tools getopt(3) replacement into the main library (#803) Perform option arg variables (#834) Removes unused commented-out code from h5jamgentest.c (#851) Reorg tools perform to provide h5perf for installation (#884) * Fix missing files * Remove empty files * Remove empty file * Resync defines * Fix endif typo * Add Makfile to list * Fix typo * Remove H5_GCC_DIAG_ON line to match removal of H5_GCC_DIAG_OFF line in sio_engine.c/ Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Merge1 issue 839 PRs to hdf5 1 12 (#904)Larry Knox2021-08-121-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixes for a couple of trivial warnings (#676) * Committing clang-format changes * Trivial warning fixes: * Removes an unused done target in H5Tbit.c * Add (void) to quiet "ignored return value" warnings in the generators (which generally ignore errors) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Various CMake changes (#679) * Committing clang-format changes * Several CMake updates: * Removes unused HDF5_ENABLE_HSIZET * Switches TEST_SHELL_SCRIPTS to ON * Sets SH_PROGRAM to bash instead of sh * Set default build type back to RelWithDebInfo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * err_compat test cleanup (#681) * Committing clang-format changes * Cleans up err_compat test and output * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * CMake fix for sporadic flush2 failures (#692) * Committing clang-format changes * Runs the flush1/flush2 tests in their own directory Avoids file deletions by other tests. * Revert "Runs the flush1/flush2 tests in their own directory" This reverts commit 746c04882434cb502e4231de8f7dd5acb4949f54. Also pulls the flush files from the clean list, which is a simpler fix. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Ubsan fixes (#498) * Fixed use of null pointer identified by UBSan UBSan warned: runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t') with these two tests: H5REPACK-committed_dt_DFF H5REPACK-committed_dt Reformulated per @gnuoyd suggestion. * Fixed undefined float -> unsigned char conversion in HL_test_image * Removed dead skip_overflow_tests_g global The global `skip_overflow_tests_g` was being set but never read. * Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5` * Committing clang-format changes * Remove extra ']' in line 730. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * BUG: DataSet assignment operator is missing (#503) * BUG: DataSet assignment operator is missing * Some compilers complain if the copy constructor is given explicitly but the assignment operator is implicitly set to default. * Explicitly defining the assignment operator allows us to properly handle reference counters for shared resources. * BUG: DataSet assignment operator is missing. * Mimicking code of H5DataType::operator() as suggested by @bmribler. * Added test Description: Added test for DataSet::operator= that Leengit added Platform tested: Linux/64 (jelly) * Removed Author field. * Commit clang format changes. * Entry for Leengit's github PR #503 * Removed lines left by mistake Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Hdf5 merge pr7 (#516) * 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> * Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a 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) * 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> * Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611) * 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> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Lee Newberg <35611400+Leengit@users.noreply.github.com> Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org> Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-204-4/+4
| | | | file - files not in src or test.
* OESS-98 add CMake option to build plugins project within hdf5Allen Byrne2020-10-161-1/+1
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* Source formattedAllen Byrne2020-10-011-163/+174
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* Add clang-format changes from develop.Allen Byrne2020-09-281-0/+7
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* Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-231-1/+1
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* Merge changes from develop to fix various issuesAllen Byrne2020-01-301-10/+4
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* Improved CMake options for testsAllen Byrne2020-01-191-1/+3
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* Merge tools changes from developAllen Byrne2020-01-131-28/+28
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* Add HD prefix to testsAllen Byrne2019-08-151-7/+7
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-07-293-0/+30
|\ | | | | | | | | | | | | | | * commit 'f97e11e7635a0cd8728d4604ca5dceb3925ba44c': Update comment and check for strtoumax. Modify CMakeLists.txt file for renamed h5tools_test_utils files. Add HD to string functions. Switched strtoul to strtoumax in H5FDs3comms.c. Removed unused functions and variables in s3 and hdfs TestH5Pfapl*.java. Update Copyright headers. Squashed commit of the following:
| * Squashed commit of the following:Larry Knox2019-07-253-0/+30
| | | | | | | | | | | | | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* | HDFFV-10529 Update CMake tests to use test fixturesAllen Byrne2019-07-231-34/+1
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* HDFFV-10845 use of TARGETFILE disables auto emulatorAllen Byrne2019-07-172-3/+5
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* HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-182-6/+12
| | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
* HDFFV-10741 - remove SKIP_ERRSTK_TESTS optionAllen Byrne2019-04-151-20/+12
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* HDFFV-10741 - add option to skip tool error stack testsAllen Byrne2019-03-261-12/+20
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* HDFFV-10703 Update CMake commands to latest standardAllen Byrne2019-02-151-7/+7
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* HDFFV-10632 update autotools test scripts to match cmakeAllen Byrne2018-12-061-12/+24
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* Need nonexistent file to skip stdout compareAllen Byrne2018-12-051-0/+1
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* HDFFV-10632 - split stderr and stdout in cmakeAllen Byrne2018-12-0315-13/+60
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* TRILAB-81 coverity fixesAllen Byrne2018-10-171-178/+134
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* Develop normalization with vol_integration.Dana Robinson2018-09-191-1/+0
| | | | | Mostly peripheral things like the tools and wrappers, with just enough core library code to support that.
* Changes based on feedback from pull request.Vailin Choi2018-07-121-1/+0
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* Modifications made based on feedback from pull request.Vailin Choi2018-07-112-9/+23
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* Fix for HDFFV-10333:Vailin Choi2018-07-1111-1/+165
| | | | | | | | | 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
* Fix MPI on Windows by adding MPI include folderAllen Byrne2018-05-091-1/+1
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* TRILABS-19 remove add_defintions and use generator expressionsAllen Byrne2018-04-261-3/+3
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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 Byrne2018-04-171-16/+12
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* Add missing test fileAllen Byrne2018-03-281-0/+2
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* Add missing test which is in autotoolsAllen Byrne2018-03-271-0/+4
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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 Byrne2018-01-171-1/+0
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* Cleanup cmake clean macrosAllen Byrne2017-10-031-95/+47
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* Fix STREQUAL if commands.Allen Byrne2017-10-021-1/+1
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* Make test scripts fail if result files are createdAllen Byrne2017-05-021-29/+31
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-254-18/+23
| | | | | | | | | | 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.
* Final merge of page buffering branch to developQuincey Koziol2017-03-1411-17/+26
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