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* ci: add h5py action (#2986) (#3028)H. Joe Lee2023-06-081-0/+36
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* Don't use -fstdarg-opt with clang-tidy (#3079)Dana Robinson2023-06-071-1/+3
| | | | | | | | | | | * HDFCompilerFlags: mask -fstdarg-opt with clang-tidy `clang-tidy` doesn't understand this `-f` flag and errors out. * Add helpful comment --------- Co-authored-by: Sean McBride <sean@rogue-research.com>
* Removes old header/library checks (#3078)Dana Robinson2023-06-073-22/+2
| | | | | | | | | | | | | In both CMake and the Autotools, remove checks for: * lstat * srandom In CMake, remove checks for: * string.h * strings.h * stdlib.h We assume these exist. Configure will always check for them (we don't add any special code to do this), but there's no reason to duplicate that nonsense in CMake.
* Remove ref to format_source_patch (#3072)Dana Robinson2023-06-071-2/+0
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* Remove Win32 POSIX redefinitions (#3068)Dana Robinson2023-06-071-35/+15
| | | | | | Microsoft has redefined most POSIX API calls with a leading underscore in order to strictly comply with C99. Nobody else cares about this and we define _CRT_NONSTDC_NO_WARNINGS in CMake Windows builds to suppress their warnings.
* Fix MSVC 32/64 bit shift conversion warnings (#3067)Dana Robinson2023-06-071-5/+5
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* Fix paths for doxygen and add step to upload to gh-pages (#3061)Allen Byrne2023-06-072-5/+15
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* Update README.md (#3069)Dana Robinson2023-06-071-3/+2
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* Update the release schedule for 1.12.3 (#3066)Dana Robinson2023-06-072-2/+2
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* Add netCDF and HDF-EOS5 badges to README.md (#3065)Dana Robinson2023-06-072-1/+3
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* ci: add netcdf action (#2934) (#2981)H. Joe Lee2023-06-061-0/+53
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* Correct path for doxygen files (#3055)Allen Byrne2023-06-061-1/+1
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* Fix doxygen comments in structure and enable FAIL_ON_WARNINGS (#3059)Allen Byrne2023-06-062-1/+7
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* HDF5Array arrayify is missing break statement #3056 (#3060)Allen Byrne2023-06-061-0/+2
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* CMake build is missing H5FDsubfiling.h #3037 (#3053)Allen Byrne2023-06-061-2/+2
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* Move encode/decode macros to a new header (#3040)Dana Robinson2023-06-0634-456/+492
| | | | | | | | | | | Moves the file-independent encode and decode macros to a new H5encode.h header that is itself included in H5private.h. Removes UINT64ENCODE_VARLEN and UINT64DECODE_VARLEN, which were unused. Fixes include statements in files where H5VMprivate.h and H5MMprivate.h were included via H5Fprivate.h.
* 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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