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* Merge Fixes the last of the -Wextra-semi-stmt warnings #3326 (#3338)Allen Byrne2023-08-0347-1384/+1394
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* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312) (#3328)jhendersonHDF2023-08-021-3/+32
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* Fix loading plugin fails with missing directory GH issue #3248 (#3323)Allen Byrne2023-08-021-0/+6
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* Sync of src w/ develop (#3307)Dana Robinson2023-07-284-67/+46
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* Bring clang-format changes from develop (#3305)Dana Robinson2023-07-281-23/+21
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* Brings an enum fix from develop (#3304)Dana Robinson2023-07-281-488/+518
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* Sync test dir w/ develop (#3303)Dana Robinson2023-07-28109-2040/+1982
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* Sync testhdf5 files w/ develop (#3300)Dana Robinson2023-07-2821-532/+534
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* Sync ros3 VFD w/ develop (#3299)Dana Robinson2023-07-282-62/+61
| | | | | * Sync ros3 VFD w/ develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Convert H5F_addr calls to H5_addr (#3297)Dana Robinson2023-07-2711-156/+156
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* Misc missed things from previous merges (#3295)Dana Robinson2023-07-2726-25/+49
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* Remove "Programmer" lines (#3294)Dana Robinson2023-07-27153-3959/+24
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* Brings over most of the HD prefix removal (#3293)Dana Robinson2023-07-27175-17895/+17643
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* Misc warnings and cross-compile improvements (#3281)Dana Robinson2023-07-273-36/+10
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* Fix some warnings in developer builds (#3247) (#3291)jhendersonHDF2023-07-274-11/+4
| | | | | * Fix some warnings in developer builds * Switch approach to Winline flag
* API test updates (#3018) (#3287)jhendersonHDF2023-07-2724-3640/+3413
| | | | | | | | | | | | | | | | | | | | | | | | | * Remove macros from api tests (#2929) * Remove macros and undefined callbacks (#2959) * Remove remaining macros from H5_api_tests_disabled.h (#2968) * Put some vol capability checks in testpar tests and remove remaining warnings (#2995) * API tests datatype generation cleanup * Clean up API tests' random datatype generation and fix bug with enum datatype generation * Init parallel API tests with MPI_THREAD_MULTIPLE * HDF5 API tests - Check VOL connector registration * Determine whether a VOL connector failed to load before running API tests * Cleanup some usages of H5VL_CAP_FLAG_CREATION_ORDER in API tests * Remove some now-unused macros from H5_api_tests_disabled.h * Enable HDF5 API tests by default * Implement CMake option to install HDF5 API tests * Check for invalid AAPL from H5Acreate * Enable building of VOL connectors alongside HDF5 in CMake * Prepend CMake VOL URL option indices with 0s so they come in order * Don't turn on API tests by default yet * Document VOL connector FetchContent functionality * Add release note for API test updates * Only install testing library if API tests are installed * Fix grammar
* Add test for HDstrcasestr macro (#2115) (#3285)jhendersonHDF2023-07-271-3/+41
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* Fix warning in cache_common.c (#2952) (#3284)jhendersonHDF2023-07-271-65/+77
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* Brings over some H5F changes (#3278)Dana Robinson2023-07-271-325/+325
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* Some minor version text changes (#3134)Allen Byrne2023-06-151-1/+1
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* Add java options to build scripts (#3136)mattjala2023-06-153-3/+3
| | | | | | | | | | | | | | | | | Previously, cmakehdf5 turned on compiling of the java interface by default due to a value set in cacheinit.cmake. Now, consistent with how Fortran and CPP interfaces are handled, the script overwrites this default value to disable the libraries, fixing #2958. I also implemented the --enable-java/--disable java options for cmakehdf5, and -java for buildhdf5. Allen said these scripts should mention that compilers are to be specified in environment variables, but missing compilers causes errors at the CMake level, and CMake's error messages are already pretty informative (See the one in #2958 about JAVA_COMPILER).
* Fix mirror VFD test timeouts (#2915)Quincey Koziol2023-05-051-2/+17
| | | | | | | | | * Close & re-open socket when looping for timeouts * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix CMake generator expression syntax (#2910)Allen Byrne2023-05-052-23/+23
| | | | | * Fix CMake generator expression syntax * Add missing quotes
* Minor tidying of API tests files (#2878)jhendersonHDF2023-05-032-7/+9
| | | | | | * Minor tidying of API tests files * Remove old API test configuration setting
* Changes to isolate API Test option files and use fetchcontent (#2880)Allen Byrne2023-05-03109-36581/+52
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* Add initial version of HDF5 API tests (#2877)jhendersonHDF2023-05-03159-31/+176005
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* Sync with develop (#2871)Dana Robinson2023-05-0214-4/+3296
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* Sync with develop (#2849)Dana Robinson2023-04-283-85/+176
| | | | | | | | | Cherry pick of ea7dfcd (Change Powershell to PowerShell in docs) to 4497feb (Update H5Dget_space_status bug note to reference 1.14.0)
* Merge with develop (#2790)Dana Robinson2023-04-2269-1498/+1166
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2545)Allen Byrne2023-04-042-3/+3
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* 1.14 Correct VERS compatible (#2460)Allen Byrne2023-02-171-1/+0
| | | | | | | | | * Correct VERS compatible * Remove FAIL check in CMake test * Remove unnecessary value in vers array * revert empty list
* Fix up the H5Pencode2 test for virtual layout. (#2325) (#2335)Dana Robinson2022-12-211-91/+87
| | | | | | | | | | | | | * Fix up the H5Pencode2 test for virtual layout. * Committing clang-format changes * Remove VERIFY and use TEST_ERROR. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings the following changesets over from develop: (#2328)Dana Robinson2022-12-214-9/+57
| | | | | | | | | | | | b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) 70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320) 8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319) 784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321) 6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315) 10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html 0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303) a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295) 502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293) a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* Bug Fix: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called ↵raylu-hdf2022-11-171-0/+76
| | | | | | | | | | | | | | | | from an application (#2248) * Jira HDFFV-10881: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application. A quick and simple fix to make it fail with a relevant error message. * Format changes. * Committing clang-format changes * Minor change: split one condition check into two for clarity. * Adding doxygen comment for H5VLwrap_register. * Minor change: adding a little more detail to the Doxygen comment for H5VLwrap_register.
* Bug fix: the previous checkin only supported the native connector (#2211)raylu-hdf2022-11-051-5/+21
| | | | | | | * Bug fix: make sure the test case supports the pass_through connector. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the memory allocation sanity checks feature (#2218)Dana Robinson2022-11-031-46/+11
| | | | | | | | | | | | | | | * Removes the memory allocation sanity checks feature * Committing clang-format changes * Removes zero size checks for H5MM_(c|m)alloc() * Explicitly return NULL when size == 0 in H5allocate_memory() * Committing clang-format changes * Format fix Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update copyright headers (#2184)Larry Knox2022-11-01171-183/+22
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Added a test case for H5VLget_connector_name (#2195)raylu-hdf2022-10-281-0/+58
| | | | | | | * Added a test case for H5VLget_connector_name. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added a test case to verify the VOL capacity flags work correctly. (#2178)raylu-hdf2022-10-251-10/+112
| | | | | | | * Added a test case to verify the VOL capacity flags work correctly. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-10-251-1/+78
| | | | | | | | | | | file handles (#2181) * Fix bug with variable length attributes being accessed through multiple file handles. * Committing clang-format changes Co-authored-by: Neil Fortner <nfortne2@localhost.localdomain> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Multi Dataset (#2120)Neil Fortner2022-10-194-3/+718
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix bug with cross platform compatibility of references within vlens. No testing yet. * Merge from multi_rd_wd_coll_io to a more recent branch from develop. Untested, probably does not work yet. * Committing clang-format changes * Committing clang-format changes * Fix many bugs in multi dataset branch. Mostly works, some issues in SWMR tests. * Committing clang-format changes * Disable test in swmr.c that was failing due to bug in HDF5 unrelated to multi dataset. * Committing clang-format changes * Fixed fortran multi-dataset tests * Fixed xlf errors * Added benchmark code for multi-datasets * loops over datasets * added missing error arg. * Added gnuplot formatting * Jonathan Kim original MD benchmarking code * updated MD benchmarking code * code clean-up * Only make files in feature test mode * misc clean-up * removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option * Committing clang-format changes * Change multi dataset API to use arrays of individual parameters instead of the parameter struct. * Committing clang-format changes * Update to new multi dataset Fortran API and tests. (#1724) * Update to new multi dataset Fortran API and tests. * Sync Fortran with develop. * skipping h5pget_mpio_actual_io_mode_f for now * Fixed issue with dxpl_id, changed to variable size dim. (#1770) * Remove "is_coll_broken" field from H5D_io_info_t struct * Committing clang-format changes * Minor cleanup in multi dataset code. * Committing clang-format changes * Clean up in multi dataset code. * Committing clang-format changes * Committing clang-format changes * Fix speeling * Fix bug in parallel compression. Switch base_maddr in io_info to be a union. * Committing clang-format changes * Implement selection I/O support with multi dataset. Will be broken in parallel until PR 1803 is merged to develop then the MDS branch. * Committing clang-format changes * Spelling * Fix bug in multi dataset that could cause errors when only some of the datasets in the multi dataset I/O used type conversion. * Committing clang-format changes * Integrate multi dataset APIs with VOL layer. Add async versions of multi dataset APIs. * Committing clang-format changes * Spelling fixes * Fix bug in non-parallel HDF5 compilation. * Committing clang-format changes * Fix potential memory/free list error. Minor performance fix. Other minor changes. * Committing clang-format changes * Fix memory leak with memory dataspace for I/O. * Committing clang-format changes * Fix stack variables too large. Rename H5D_dset_info_t to H5D_dset_io_info_t. * Committing clang-format changes * Remove mem_space_alloc field from H5D_dset_io_info_t. Each function is now responsible for freeing any spaces it adds to dset_info. * Committing clang-format changes * fixed _multi Fortran declaration * Refactor various things in (mostly) the serial I/O code path to make things more maintainable. * Committing clang-format changes * updated to array based, doxygen, and examples * Reinstate H5D_chunk_map_t, stored (via pointer) inside H5D_dset_io_info_t. * Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t. Switch temporary dset_infos to be local stack variables. * Committing clang-format changes * format cleanup * format cleanup * added coll and ind * Modify all parallel I/O paths to take dset_info instead of assuming dset_info[0]. * Committing clang-format changes * fixed output * Rework parallel I/O code to work properly with multi dataset in more cases. Fix bug in parallel compression. * Committing clang-format changes * Prevent H5D__multi_chunk_collective_io() from messing up collective opt property for other datasets in I/O. Other minor cleanup. Add new test case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now due to failures apparently unrelated to multi dataset code. * Fix spelling * Committing clang-format changes * Replace N log N algorithm for finding chunk in H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of io_info->sel_pieces in that function. * Committing clang-format changes * Replace sel_pieces skiplist in io_info with flat array of pointers, use qsort in I/O routine only when necessary. * Committing clang-format changes * Add new test case to mdset.c * Committing clang-format changes * Fix spelling * Very minor fix in H5VL__native_dataset_read() * Fix bug that could affect filtered parallel multi-dataset I/O. * Add RM entries for H5Dread_multi(), H5Dread_multi_async(), H5Dwrite_multi(), and H5Dwrite_multi_async() * Unskip test in swmr.c * Committing clang-format changes * Eliminate H5D__pre_read and H5D__pre_write * Remove examples/ph5mdsettest.c. Will fix and re-add as a test. * Enable hyperslab combinations in mdset test * Committing clang-format changes * Clarify H5Dread/write_multi documentation. * Fix bugs in multi-dataset I/O. Expand serial multi dataset test. Update macro in parallel multi dataset test. * Committing clang-format changes * Spelling * Remove obsolete entry in bin/trace * Rework type conversion buffer allocation. Only one buffer is shared between datasets in mdset mode, and it is malloced instead of calloced. * Committing clang-format changes * Fix bug in error handling in H5D__read/write * added multi-dataset fortran check with optional dataset creation id (#2150) * removed dup. dll entry * Address comments from code review. * Remove spurious changes in H5Fmpi.c * Fix issue with reading unallocated datasets in multi-dataset mode. Address other comments from code review. * Committing clang-format changes * Delay chunk index lookup from io_init to mdio_init so it doesn't add overhead to single dataset I/O. * Committing clang-format changes * Fix inappropriate use of piece_count * updated copyright on new file, removed benchmark from testing dir. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fix mostly java warnings, and cpp cast (#2134)Allen Byrne2022-10-031-1/+1
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* Fixed an issue that could occur when combining hyperslab selections (#2122)Neil Fortner2022-09-271-0/+52
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* Use case-insensitive comparison for headers fix #2100 (#2101)Frank Berghaus2022-09-211-0/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use case-inseneitive comparison for headers HTTP headers should be case-insensitive. Use case-insensitive string comparisons when working with HTTP header responses to ensure compatibility. * Revert "Use case-inseneitive comparison for headers" This reverts commit a02f591723506b62b7208449be6eef7122120398 * Ignore case when searching HTTP header responses Looking up the Content-Length in the header returned by S3 storage endpoints should ignore case. To guarantee portability implement a function for case-insensitive string search, because it is non-standard. * Add an _ after H5 for the strcasestr implementation It is a private function and should sport that underscore. * Remove author comment from the doc comment * Use search function defined by system if available Check whether the system provides a function implementing case insensitive string searches. Only use the custom implementation if the system does not provide the functionality. * Add tests for case-insensitive search Basic tests: - Search for empty string - Search with exact match - Search with case-insensitive match - search with no match * Enforce clang-format style Some variable definitions in the th5_system tests did not conform to clang-format's expectations. Updated the offending lines. * Correct comment describing test case * Added some spaces to please clang-format * Ignore discarding const Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
* Updates VOL capabilities flags (#2105)Dana Robinson2022-09-172-23/+23
| | | | | | | | | | | | | | | * Added feature/vol_cap_flags branch to GitHub actions * Convert unsigned cap flag field to uint64_t and add flags * Committing clang-format changes * Convert unsigned cap flag field to uint64_t and add flags * Committing clang-format changes * Updates the VOL struct version number Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-031-1/+1
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Address review comments from downstream merge of #2016 (#2073)Neil Fortner2022-08-311-1/+1
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* GitHub workflow cleanup (#2047)Dana Robinson2022-08-221-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up main GitHub workflow(s) * Combines main.yml and pr-check.yml, which differed trivially * Reduces config redundancy via proper use of the matrix scheme * Adds build-only configs for: - Version 1.6 default API - No deprecated symbols - Parallel HDF5 * The -Werror config was converted to build-only * Makes the naming scheme more uniform * Spaces out the code and adds comments * Typo fix * Fix mirror VFD CMake configure typo * Debugging hack * Undo debug hack and fix CMake build mode * Set CC=mpicc for parallel builds * Another attempt to fix parallel builds * Updates comments in main.yml * Fixes a v16 API bug in the mirror VFD test code * Committing clang-format changes * Added checks for v1.8 - 1.12 APIs * Manually specify Windows configs Java debug builds time out when running tests on Windows. We'll disable them in debub mode while we investigate. * Revert "Manually specify Windows configs" This reverts commit d710d8d21990a57084841e82bd9f7e7d9f53a244. * Skip Debug Windows configs while we investigate Java H5L timeouts Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* [WIP] Add Developer build mode to CMake (#1659)jhendersonHDF2022-08-203-7/+64
| | | | | | | | | | | | | | | | * Add Developer build mode to CMake * Set a few CMake variables for Developer build modes * Refactor enabling of debug and developer-level compile definitions * Convert cache debugging macros to normal ifdef style Normal ifdef-style instead of if-style allows build system to define macros without warning about redefining macros with different values (0 vs. 1) * Add HDF5 Developer compile definitions to testing files * Temporarily disable -fanalyzer flag for GCC 12+ Developer builds
* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-191-11/+11
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