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* Fix release check version logic (#1438)Allen Byrne2022-02-241-1/+2
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* Fix issue with H5_now_usec() with 32 bit systems (#1416)Neil Fortner2022-02-101-3/+27
| | | | | | | | | | | | | | | | | | | | | | | * Implement H5ESget_requests() to retrieve request pointers and corresponding connector IDs from an event set. Add tests for this function. * Add "order" parameter to H5ESget_requests, to allow the user to specify the order in which requests are returned. * Fix bugs with H5ESinsert_request() * Change H5ESget_requests() API to have separate input and output parameters for the allocated array length(s) (in) and the number of events in the event set (out). * Fix issue with H5_now_usec() with 32 bit systems. Also improve event set test. * Committing clang-format changes * Add comments to H5_now_usec() explaining rationale for uint64_t casts. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implemented suggestion in #1381 for dtransform test (#1415)Allen Byrne2022-02-041-10/+7
| | | | | | | | | | | | | | | * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name
* Don't use a nonliteral format string in test/fheap.c:begin_test(). (#1401)David Young2022-02-031-87/+60
| | | | | | | | | * Avoid using a non-literal formatting string with sprintf in begin_test. Use snprintf. Don't duplicate a string on the heap unnecessarily. * Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format string any more. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Snprintf2 (#1399)Sean McBride2022-01-2820-266/+284
| | | | | | | | | | | | | * Replaced many uses of sprintf with safer snprintf Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable. * Removed unnecessary use of static on small buffers This improves thread safety. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove const from the argv tools/tests main sig. (#1390)Allen Byrne2022-01-2810-11/+11
| | | | | | | | | * Remove const from the argv tools/tests main sig. * also remove const from H5_get_option and parse_command_line. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Replaced several uses of sprintf with safer snprintf (#1383)Sean McBride2022-01-284-4/+4
| | | | | | | * Replaced several uses of sprintf with safer snprintf * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Used clang-tidy to change all floating point f suffixes to F (#1359)Sean McBride2022-01-281-1/+1
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* Open bsd fixes (#1195)Sean McBride2022-01-201-1/+3
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* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-201-4/+485
| | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix compilation issues with Mingw (#1342)Baljak2022-01-085-30/+30
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* Changed to correct return datatype for H5Lexists (#1330)Scot Breitenfeld2022-01-041-4/+5
| | | | | * changed to correct return datatype for H5Lexists Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix directory variable in shell scripts (#1273)Allen Byrne2021-12-107-146/+51
| | | | | | | | | | | | | | | | | | | | | * Fix testswmr scripts with utils/test variable * Change format of configure var assignment * quote the variable value in configure * Use sh.in expected var pattern * Only ref builddir in script * Create vars for utils/test and test as H5_<path>_BUILDDIR * Use abs_top_builddir in test scripts * Change script var to make it easier to read. * Use @abs_top_builddir@ directly in paths * Correct typos/comment
* OESS-168: Remove clang warnings. (#1269)H. Joe Lee2021-12-081-6/+10
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* Convert vds swmr test script to powershell (#1245)Allen Byrne2021-12-083-13/+769
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fixes const warnings in H5ES package (#1211) * Quiets a 'set but not used' warning in h5diff_array.c (#1210) * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Cleanup review issues * Fix variable assignment * Change the wait function to pass in the path * Disable actual test execution until programs fixed * Adjust copyright text * Fix spelling Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1263)H. Joe Lee2021-12-081-3/+3
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* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-0780-447/+447
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs (#1222)Dana Robinson2021-11-241-0/+99
| | | | | | | | | | | | * Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the library due to missing ID range checks in H5Pget_filter_by_id1/2. The library now returns a normal error code when filter IDs are out of range. Fixes HDFFV-11286. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Create 2D arrays on the heap in a different way (#1169)David Young2021-11-231-50/+9
| | | | | | | | | | | | * Create 2D arrays on the heap by malloc'ing `struct { TYPE arr[ROWS][COLS]; }`. This avoids the double-indirection through pointers and the additional memory of H5TEST_ALLOCATE_2D_ARRAY(). This change will safely quiet the cast warning that PR #1129 was intended to fix. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Make sure plugin interface is initialized before property list interface ↵jhendersonHDF2021-11-231-7/+58
| | | | phase 2 (#1216)
* Fixes unused parameter warnings in the null VFD (#1179)Dana Robinson2021-11-131-0/+31
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* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-084-133/+25
| | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1136)H. Joe Lee2021-11-051-2/+2
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @byrnHDF and @derobinson review.
* OESS-168: Remove clang warnings. (#1137)H. Joe Lee2021-11-051-68/+69
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @derobins review.
* OESS-168: Remove clang warnings. (#1146)H. Joe Lee2021-11-021-3/+3
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* OESS-168: Remove clang warnings. (#1135)H. Joe Lee2021-11-021-1/+1
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* Split dir create into separate macro (#1141)Allen Byrne2021-10-282-20/+23
| | | | | * Split dir create into separate macro * Correct VFD settings
* Consolidate VFD create list macro (#1132)Allen Byrne2021-10-261-2/+1
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* Removes the "try free" behavior from the skip lists (#1126)Dana Robinson2021-10-221-208/+0
| | | | | | | | | | | | | | * Removes the "try free" behavior from the skip lists This was only used in the ID code when iterating and a callback could delete IDs. It is not used anywhere else in the library and is now pointless overhead. Also quiets the const warnings when returning stored elements. They only need to be const with respect to the skip list code, which should never modify them. The library can do whatever it wants with the elements it stored. * Formatted source
* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-2010-147/+113
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* OESS-168: Remove clang warnings. (#1075)H. Joe Lee2021-10-201-12/+12
| | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * OESS-168: Fix CI failure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1072)H. Joe Lee2021-10-151-13/+13
| | | | | | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * Address review by @jehndersonHDF. * Address review by @jehndersonHDF. * OESS-168: Fix CI failure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1077)H. Joe Lee2021-10-081-1/+1
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* OESS-168: Remove clang warnings. (#1076)H. Joe Lee2021-10-081-1/+1
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* OESS-168: Remove clang warnings. (#1071)H. Joe Lee2021-10-061-3/+3
| | | | | * OESS-168: Remove clang warnings. * Address review by @jehndersonHDF.
* Move HDstrcmp operations inside casting block for PGI compilers (#1063)jhendersonHDF2021-09-301-6/+6
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* VFD plugins (#602)jhendersonHDF2021-09-2967-1181/+2356
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* VFD ctl feature (#981)jhendersonHDF2021-09-232-14/+531
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added "ctl" callback to the VFD interface, and the associated H5FDctl() and H5FD_ctl() calls. Modified the MPIO VFD accordingly -- specifically: Added ctl() call with op-code support to expose rank, size, and communicator. Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(), and H5FD_mpi_get_comm() to use the new ctl() callback. In passing removed the const qualifier from the file parameter of these functions, as the file parameter of the ctl callback is not const. Deleted the old H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and H5FD__mpio_communicator() calls from the MPIO VFD. Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the MPIO VFD accordingly. Note that all VFDs now use H5FD_class_t, with no special class for VFDs that that support MPI. Some minor touch ups to the Neil's selection I/O mods in passing. Tested serial and parallel, debug and production on charis and jelly. * Reserve a range of VFD "ctl" opcodes for library and experimental usage * Add "ctl" callbacks to passthrough VFDs * Add RELEASE.txt entry for "ctl" callback * Use H5FDopen with H5F_ACC_RDWR flag instead of H5F_ACC_TRUNC in vfd test * Remove handling of passthrough "ctl" flag from multi VFD * Move logic for testing H5FD_CTL__TEST_OPCODE into a testing VFD Revise description of "ctl" callback in RELEASE.txt Remove unused H5FD_CTL__NUM_OPCODES definition Fix some warnings in multi VFD Co-authored-by: mainzer <mainzer#hdfgroup.org>
* Modified gcc/clang warning suppression macros to account for some warnings ↵Sean McBride2021-09-166-16/+16
| | | | | | | | | | | | | | | | | flags being supported by one compiler but not the other (#379) * Committing clang-format changes * Fixed GCC warning suppression pragmas to also work with clang H5_GCC_DIAG_ON remains gcc-only. Added a new H5_CLANG_DIAG_ON that's clang-only, but it's not used anywhere currently. Added a new H5_GCC_CLANG_DIAG_ON that works with both compilers, which afterall support mostly the same warnings. Changed almost all uses of H5_GCC_DIAG_ON to use H5_GCC_CLANG_DIAG_ON, with the exception of a couple, where they really were suppressing gcc-only warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix several warnings (#720)jhendersonHDF2021-09-141-1/+1
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* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() … (#933)Jan-Willem Blokland2021-09-131-0/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() function - Made a small improvement for H5Z_xform_noop() function. Now, the function will also return TRUE if the data transform function expression = "x". For this case, the HDF5 library behaves in a similar fashion as the case when no data transform function has been specified. - Improved the inline documentation of the function H5Z_xform_create() such it is more inline with the rest of the code. * Committing clang-format changes * H5Ztrans: (feature) Added 3 tests for improved H5Z_xform_noop() function - Added serial test with data transform expression = "x" to verify the improved H5Z_xform_noop() function behaves as expected. - Added 2 parallel tests with data transform expression = "x" in combination with a filter. Before, these tests will fail but with the improved H5Z_xform_noop() function they work and result in the expected behavior. - Small bug fix for one of parallel filter tests. * Committing clang-format changes * H5Ztrans: (feature) Added release note about detection of the simple data transform function "x". - Added a brief explanation about the implemented improvement of the detection of the simple data transform function "x" to the RELEASE.txt file. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* More various warnings (#958)Sean McBride2021-08-259-29/+28
| | | | | | | | | | | | | * Committing clang-format changes * Fixed various -Wdouble-promotion warnings * Fixed -Wshadow warning for `optopt` conflict On macOS at least, there is a global various named `optopt` in unistd.h. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* More clang tidy (#908)Sean McBride2021-08-2316-70/+71
| | | | | | | | | | | | | | | | | | | * Pacify clang-analyzer-unix.cstring.NullArg * Apply some bugprone-suspicious-string-compare * Apply some readability-simplify-boolean-expr * Apply some readability-make-member-function-const * Apple some bugprone-macro-parentheses * Changed an f suffix to L for `long double` * Applied some readability-uppercase-literal-suffix automatically * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake should use the output dir programs for shell scripts (#928)Allen Byrne2021-08-194-144/+52
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* Fixes a bad memory read and unfreed memory in fsinfo code (#893)Dana Robinson2021-08-122-0/+56
| | | | | | | | | | | | | | * Fixes a bad memory read and unfreed memory in fsinfo code The segfaul from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove version-check for relnum in H5check. (#812)Allen Byrne2021-07-272-54/+54
| | | | | | | | | | | | | | | | | | | | | | | | | * Remove version-check for relnum in H5check. * Add in release exception code check * Fix typos * Fix more typos * Rework comments * format change * format whitespace * Library version must be less than or equal to headers * Need the NOT version of the compare * Enable release+1 check for PASS * Add release note * Update note
* Fixes a couple of warnings: (#849)Dana Robinson2021-07-221-0/+1
| | | | | | | - warn_unused_result warnings from h5jamgentest and j5stat_gentest that were triggered by write(2) calls where we didn't check the return value - A missing callback in the NULL VOL connector - A possibly uninitialized property list pointer
* OESS-168:Remove implicit conversion warnings. (#829)H. Joe Lee2021-07-121-559/+559
| | | | | * OESS-168:Remove implicit conversion increases floating-point precision warnings. * OESS-168:Remove clang warnings.
* Removes develop header cruft (#828)Dana Robinson2021-07-092-2/+2
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* Fixes parallel issues from recent C99 changes (#809)Dana Robinson2021-06-303-3/+3
| | | | | | | * Fixes parallel issues from recent C99 changes * Adds MPE FUNC --> __func__ changes missed in earlier PRs * Even more missed FUNC --> __func__ macros
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