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* sprintf to snprintf (#1815)Sean McBride2022-06-229-66/+66
| | | | | | | | | | | * Straightforward conversion of sprintf to the safer snprintf * Trickier conversion of sprintf to safer snprintf This involved minor changes to private function signatures to take the size of the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Various warning fixes (#1812)Sean McBride2022-06-226-45/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed -Wreserved-id-macro warnings from header include guards * Removed all __int64 and LL suffix stuff now that C99 is minimum requirement * Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings Double underscore is reserved in C++ and this public header should be C++ compatible. * Never define __STDC_FORMAT_MACROS anymore Defining it causes a -Wreserved-id-macro. Happily, according to the C++11 standard: "The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++." https://cplusplus.github.io/LWG/issue984 So looks like it's not necessary to define it with reasonably new toolchains. * Fixed some -Wunused-macros warnings, removed dead code * Fixed all -Wdouble-promotion warnings in C++ files * Fixed remaining -Wsuggest-destructor-override warnings * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for S3 and HDFS VFDs with tools (#1740)jhendersonHDF2022-05-065-59/+38
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* Fixes unused/unset variable warnings from aocc (#1712)Dana Robinson2022-05-031-4/+1
| | | | | | | * Fixes unused/unset variable warnings from aocc * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Clean stack size warnings in sio_engine (#1687)Dana Robinson2022-04-251-20/+35
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* Warnings fixes (#1680)jhendersonHDF2022-04-251-1/+1
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* OESS-168: Remove clang warnings. (#1376)H. Joe Lee2022-04-151-1/+2
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* Move error-stack text to top of usage display (#1564)Allen Byrne2022-04-0128-68/+122
| | | | | | | | | * Move error-stack text to top of usage display * Add optional tag ti list * format changes * Revert incorrect change
* spelling fixes (#1561)Scot Breitenfeld2022-03-313-3/+3
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* Fixes for format string warnings raised by -Wformat=2/-Wformat-security (#1489)Dana Robinson2022-03-112-4/+4
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* Removes remaining register keywords (#1481)Dana Robinson2022-03-1010-70/+68
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* Remove addition of non-standalone use of H5_ATTR_FORMAT (#1470)Allen Byrne2022-03-071-1/+1
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* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-011-7/+7
| | | | | | to MANIFEST (#1460)
* Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix ↵David Young2022-02-2113-146/+139
| | | | | | | | | | | | | | | | issues (#1423) * Correct some conversion specifications. * Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few instances where PRIdHSIZE was appropriate. Remove a couple of casts and use correct format strings, instead. * Copy values from a possibly unaligned buffer to aligned local variables instead of casting and dereferencing pointers into the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Make a buffer bigger: GCC 8.3.0 warned that a `snprintf` may be (#1403)David Young2022-02-111-1/+1
| | | | | truncated because the recipient buffer was too small, and the warning is one that we promote to an error. Now there is a warning that the buffer is too big (-Wlarger-than=), but we don't promote those to errors, yet.
* Fix a few issues noted by LGTM (#1421)jhendersonHDF2022-02-047-14/+19
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* Snprintf2 (#1399)Sean McBride2022-01-286-20/+20
| | | | | | | | | | | | | * 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 Byrne2022-01-2823-57/+60
| | | | | | | | | * 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 McBride2022-01-281-1/+1
| | | | | | | * 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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* OESS-168: Remove clang warnings. (#1295)H. Joe Lee2021-12-151-1/+1
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* OESS-168: Remove clang warnings. (#1294)H. Joe Lee2021-12-151-4/+4
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* OESS-168: Remove clang warnings. (#1277)H. Joe Lee2021-12-101-1/+1
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* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-0772-185/+185
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Fix windows test with floating point rounding issues (#1237)Allen Byrne2021-11-301-1/+1
| | | | | | | * Check windows sdk version for test * Correct variable reference form * Use VERSION_LESS in IF check
* Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236)Larry Knox2021-11-301-7/+7
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* Create 2D arrays on the heap in a different way (#1169)David Young2021-11-234-387/+520
| | | | | | | | | | | | * 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>
* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171)David Young2021-11-231-4/+10
| | | | | | | | | | | | | | | | * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Quiets a 'set but not used' warning in h5diff_array.c (#1210)Dana Robinson2021-11-181-0/+3
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* Add option for h5repack timing (#1142)Allen Byrne2021-11-086-51/+168
| | | | | | | | | | | | | | | | | * Add timing option to h5repack * Adjust help text * fix format * fix typos * Correct spacing * Change timing to use H5Timer * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-086-88/+24
| | | | | | | | | | | | | * 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>
* Split dir create into separate macro (#1141)Allen Byrne2021-10-282-0/+2
| | | | | * Split dir create into separate macro * Correct VFD settings
* H5repack tests should fail if a corrupted file causes h5repack to (#1138)Larry Knox2021-10-262-6/+17
| | | | | | * H5repack tests should fail if a corrupted file causes h5repack to segfault/core dump. * Add release note for HDFV-10590, CVE-2018-17432.
* Consolidate VFD create list macro (#1132)Allen Byrne2021-10-262-4/+0
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-202-47/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. (#1074)H. Joe Lee2021-10-061-2/+2
| | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix ASAN issue in h5dump error path (#1051)Allen Byrne2021-10-032-3/+1
| | | | | * Fix ASAN issue in h5dump error path * Rework error allocation free.
* OESS-168: Remove clang warnings. (#1057)H. Joe Lee2021-09-301-56/+56
| | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1056)H. Joe Lee2021-09-301-20/+20
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* VFD plugins (#602)jhendersonHDF2021-09-2947-586/+1101
| | | | | | | | | | | | | | | | | * 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
* OESS-168: Remove clang warnings. (#1050)H. Joe Lee2021-09-291-1/+1
| | | This patch will remove clang double-promotion warning.
* OESS-168: Remove clang warnings (#1049)H. Joe Lee2021-09-291-1/+1
| | | This patch will remove clang double-promotion warning.
* OESS-168: Remove clang warnings. (#1047)H. Joe Lee2021-09-291-1/+1
| | | | | This patch will remove clang warnings on Mac: 'float' to 'double' [-Wdouble-promotion]
* OESS-168: Remove clang warnings. (#1046)H. Joe Lee2021-09-291-9/+9
| | | | | | | This patch will remove clang warnings on Mac: ``` warning: implicit conversion increases floating-point precision: 'float' to 'double' [-Wdouble-promotion] ```
* Modified gcc/clang warning suppression macros to account for some warnings ↵Sean McBride2021-09-161-2/+2
| | | | | | | | | | | | | | | | | 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)jhendersonHDF2021-09-143-9/+21
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* Update copyright headers with reproduction notice in 5 files (#993)Larry Knox2021-09-081-9/+9
| | | | | | | | | * Update copyright headers with reproduction notice in 5 files that did not match terms in COPYING file . * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* More clang tidy (#908)Sean McBride2021-08-238-15/+15
| | | | | | | | | | | | | | | | | | | * 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>
* Remove non-published short arg names (#917)Allen Byrne2021-08-183-303/+0
| | | | | | | * Remove non-published short arg names * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix link issue with perf/h5perf in parallel library (#889)jhendersonHDF2021-08-111-4/+4
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