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* Develop gh doxy (#3041)Allen Byrne2023-06-053-6/+36
| | | | | * Add doxygen generation to daily-build and main * Add doxygen option to matrix
* Print out the VOL connector being used in the ASYNC test (#3016)Scot Breitenfeld2023-06-059-97/+389
| | | | | * Print out the VOL connector being used in the ASYNC test * Add h5pget_vol_cap_flags_f with test
* CMake: (fix) Szip / libaec filter (#3035)Jan-Willem Blokland2023-06-051-23/+11
| | | | | | | | | | | * CMake: (fix) Szip / libaec filter - Fixed the cmake configuration for the filter Szip / libaec. Now, the decoding of this filter is properly configured and included in the HDF5 library. * CMake: (fix) Zlib filter - Improved the cmake configuration for the filter zlib.
* Convert H5F haddr_t macros to H5 (#3039)Dana Robinson2023-06-05135-1104/+1101
| | | | | | | | | | | | | | | | | | | | | | Several macros for handling haddr_t values exist in H5Fprivate.h and have H5F prefixes, even though they have nothing to do with a particular file (e.g., H5F_addr_lt()). These macros have been moved to H5private.h and renamed to have an H5 prefix. Affected macros: H5F_addr_overflow H5F_addr_defined H5F_addr_eq H5F_addr_ne H5F_addr_lt H5F_addr_le H5F_addr_gt H5F_addr_ge H5F_addr_cmp H5F_addr_overlap H5F_addr_pow2 was unused and removed instead of converted.
* Add casts to type conversion to fix long dbl bug (#3038)Dana Robinson2023-06-031-2/+22
| | | | | | If a user buffer is misaligned in the type conversion code, memcpy could fail if the call is SSE-optimized by the compiler. This change adds uint8_t * casts so the compiler won't make optimistic assumptions about buffer alignment.
* Only pass efc pointer to H5F__efc_open (#3026)Dana Robinson2023-05-304-347/+346
| | | | The H5F__efc_open() API call only needs the efc pointer, so there is no need to pass the entire file struct in.
* Remove unused H5F_EN|DECODE_OFFSET macros (#3027)Dana Robinson2023-05-301-26/+0
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* Cleans up Java JNI warnings and add java to -Werror checks (#2383)Dana Robinson2023-05-278-127/+94
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* API test updates (#3018)jhendersonHDF2023-05-2637-3692/+4248
| | | | | | | | | | | | | | | | | | | | | | | | | * 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
* correct warning ignore match for zlib (#3021)Allen Byrne2023-05-261-0/+2
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* Fix release version for some H5Pfapl routines (#3023)jhendersonHDF2023-05-261-3/+3
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* Correct name of fetch content variable name (#3020)Allen Byrne2023-05-261-1/+1
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* Remove most unused options which are defaulted #2998 (#3019)Allen Byrne2023-05-264-899/+3
| | | | | * Remove most unused options which are defaulted #2998 * Fix property list references
* Fixed Fortran Doxygen warnings (#3017)Scot Breitenfeld2023-05-269-94/+106
| | | | Fixes Fortran doxygen warnings, #2998
* Bump GitHub Autotools actions to gcc-12 (#3015)Dana Robinson2023-05-251-4/+4
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* Suppress vfd.c test warning (#3014)Dana Robinson2023-05-251-8/+13
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* Fix multiConfig variable usage and remove unused CMake vars (#3013)Allen Byrne2023-05-254-31/+1
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* Fix assert in Debug Windows Java JNI (#3012)Dana Robinson2023-05-252-6/+5
| | | | | | | | | Use of an uninitialized H5L_info2_t struct caused some JNI tests to raise asserts, causing a dialog box to be emitted, which would hang automated tests. Initializing the struct fixes the problem. This change also re-enables tests in the Windows Debug GitHub actions.
* Develop release workflow (#3002)Allen Byrne2023-05-253-3/+130
| | | Implement (pre)release workflow for daily build
* Remove src/.indent.pro (#3008)Dana Robinson2023-05-251-150/+0
| | | | | There is no need for this since we use clang-format Fixes #3004
* Add release note for #2999 (#3009)Dana Robinson2023-05-251-0/+8
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* Only run ttsafe in thread-safe GitHub actions (#2777)Dana Robinson2023-05-251-8/+24
| | | Also fixes broken thread-safety testing (due to a typo in the GitHub action checks)
* Update GitHub macOS actions to v13 (#2999)Dana Robinson2023-05-245-3/+14
| | | | | * Update macOS to 13 * Fix the DYLD_LIBRARY_PATH issue on macOS 12 & 13 + CMake that caused the accum test to fail
* Fix missing/misplaced h5_reset calls (#3001)Dana Robinson2023-05-233-23/+17
| | | | | | Fixes failures when running tests after building with thread-safety w/ code stacks on. Fixes #2990
* Fix FUNC_ENTER macro mismatch in H5VL_object_inc_rc() (#2991)bazimo2023-05-231-1/+1
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* fixed GNU 4.8.5 compilation issue with C_LOC and strings (#2996)Scot Breitenfeld2023-05-231-2/+2
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* Updated H5Ovisit_f and H5Ovisit_by_name_f wrappers internals. (#2987)Scot Breitenfeld2023-05-227-171/+72
| | | | | | | | | * * Removed C wrappers for H5Ovisit_f and H5Ovist_by_name_f, modifying the Fortran source accordingly. * The intent for op_data was declared INOUT, even though the pointer address INTENT is, in actuality, IN. gfortran was optimizing out op_data in tests where the values were repeatedly reset to the same value. The values were reset in the test because the data the pointer targeted was updated in the callback. * Made use of the 'verify' function to check value correctness. * changed to useing INTEGER(C_INT) instead of C_BOOL, updated the documentation
* Fix plugin cache variable name (#2988)Allen Byrne2023-05-225-22/+34
| | | | * Fix plugin cache variable name * Prefix plugin project local variables
* Fix 'datatype' misspellings ('dataype') (#2984)Dana Robinson2023-05-1913-38/+38
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* Add test for HDstrcasestr macro (#2115)jhendersonHDF2023-05-193-4/+65
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* ci: set minimal permissions on GitHub Workflows (#2980)Diogo Teles Sant'Anna2023-05-188-0/+23
| | | Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>
* Fixes failures with gfortran 4.8 (#2979)Scot Breitenfeld2023-05-183-19/+25
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* Change defaults of standard filters. (#2927)Allen Byrne2023-05-188-48/+56
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* Remove version specific examples from README_HPC. (#2613) (#2975)Larry Knox2023-05-171-14/+12
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* Add h5copy help test and verify consistency (#2902)Allen Byrne2023-05-1710-6/+178
| | | * Add autotools test for help
* Updated INTENT to IN for C_PTR types dummy args. (#2961)Scot Breitenfeld2023-05-178-133/+133
| | | | * Changed to INTENT(IN) for C_PTR dummy args since it refers to whether C_PTR can be changed and does not relate to the INTENT state of the target.
* added missing H5ES function DLLs (#2969)Scot Breitenfeld2023-05-172-0/+21
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* Change UBSAN for undefined instaed of address (#2964)Allen Byrne2023-05-171-2/+2
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* Remove unnecessary fields from cache structs (#2951)Quincey Koziol2023-05-1532-597/+41
| | | | | | | | | | | | * Remove unnecessary 'magic' field from cache structs Signed-off-by: Quincey Koziol <quincey@koziol.cc> * Committing clang-format changes --------- Signed-off-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* addresses gfortran issue https://gcc.gnu.org/bugzilla/show_bug.cgi?id=109861 ↵Scot Breitenfeld2023-05-152-9/+9
| | | | (#2957)
* Fix warning in cache_common.c (#2952)jhendersonHDF2023-05-151-65/+77
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* Warn about changing collections during iteration (#2950)mattjala2023-05-157-15/+37
| | | Resolves #92
* Prevent buffer overrun in H5S_select_deserialize (#2931)mattjala2023-05-1212-104/+233
| | | | | | | | | | | | | | | | | | | | | * Prevent buffer overrun in H5S_select_deserialize The call to H5S_select_deserialize from H5S_decode doesn't have the buffer size available to it, so to allow decoding there I set it to assume a max size buffer for now. Making the buffer size known in H5S_decode could be done by modifying the external API's H5Sdecode, or splitting H5Sdecode into two functions using a macro (similar to H5Sencode), with the macro taking one argument and assuming a max buffer size. * Conditional buffer check in H5S_select_deserialize Moved and renamed a macro for only checking buffer overflow when buffer size is known from H5Odtype.c to H5private.h, so it can be used throughout the library. Also silenced some build warnings about types.
* Move functions into more focused source code modules (#2936)Quincey Koziol2023-05-1218-7446/+7512
| | | | | | | | | | | | | | * Move functions into more focused source code modules, along with a small # of directly secondary effects. No actual changes to the contents of any moved routines. Signed-off-by: Quincey Koziol <quincey@koziol.cc> * Committing clang-format changes --------- Signed-off-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Bump Autoconf version to 2.71 (#2944)Dana Robinson2023-05-121-1/+1
| | | Required for building with Intel's oneAPI
* Update action uses version (#2937)Allen Byrne2023-05-111-1/+1
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* More code duplication reduction (#2930)Quincey Koziol2023-05-095-2247/+1536
| | | | | | | | | | | | | | | | | | | | | | | | * Add failure value where it's missing from 1+ macros. Clean up whitespace / continuation characters ('\'). Made hash-table macros generic for use in both the package header and test header. Remove duplicated copy & pasted macros (by hoisting difference into #ifdef'd macro). Updated and re-flowed comments to read better. Also clean up a few compiler warnings in production builds. Signed-off-by: Quincey Koziol <quincey@koziol.cc> * Committing clang-format changes * Remove unused variable warning in H5C.c (#2844) * Remove trailing /* NDEBUG */ comment from #endif's * Committing clang-format changes --------- Signed-off-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove unused variable warning in H5C.c (#2844)H. Joe Lee2023-05-091-2/+2
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* Reduce code duplication in macros (#2914)Quincey Koziol2023-05-081-539/+126
| | | | | | | | | | | | | | | | | | * Reduce code duplication in macros Signed-off-by: Quincey Koziol <quincey@koziol.cc> * "insert" -> "remove" in error string Signed-off-by: Quincey Koziol <koziol@lbl.gov> * Remove unused macro also Signed-off-by: Quincey Koziol <quincey@koziol.cc> --------- Signed-off-by: Quincey Koziol <quincey@koziol.cc> Signed-off-by: Quincey Koziol <quincey@koziol.cc>
* Public header cleanup (#2923)Dana Robinson2023-05-0721-93/+59
| | | | | | Removes unnecessary headers and adds missing headers, ensuring that headers can be included independently and in any order. Fixes #2789
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