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* Remove HD from HDis* (e.g., isalpha) (#3212)Dana Robinson2023-06-295-23/+23
| | | | | | | | | | | | | * HDisalnum * HDisalpha * HDiscntrl * HDisdigit * HDisgraph * HDislower * HDisprint * HDispunct * HDisspace * HDisupper * HDisxdigit
* Remove HD from HDmem* calls (#3211)Dana Robinson2023-06-2935-296/+296
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* Remove programmer/date from comments (#3210)Dana Robinson2023-06-2946-561/+1
| | | | * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work
* Remove HD from C std lib file ops (#3206)Dana Robinson2023-06-2919-113/+113
| | | | | | | | | * HDfclose * HDferror * HDfeof * HDfflush * HDfopen * HDfread * HDfwrite
* Remove HD from strto* calls (#3204)Dana Robinson2023-06-2913-41/+41
| | | | | | | | * HDstrtod * HDstrtol * HDstrtoll * HDstrtoul * HDstrtoull * HDstrtoumax
* Rename HDexit() and related to exit(), etc. (#3202)Dana Robinson2023-06-2927-115/+115
| | | | | * HDatexit * HDexit * HD_exit
* Rename HDato*() to ato*() (#3201)Dana Robinson2023-06-2911-53/+53
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* Remove HD from protected POSIX calls (#3203)Dana Robinson2023-06-292-18/+18
| | | | | | | | | | | These calls are non-C99 but protected by ifdefs and have no Windows equivalents: * HDalarm * HDasprintf * HDclock_gettime * HDfcntl * HDgethostname * HDgetrusage * HDsymlink
* Remove HD from memory allocate/free calls (#3195)Dana Robinson2023-06-2850-889/+887
| | | | | | * HDcalloc * HDfree * HDmalloc * HDrealloc
* Rename HDsystem() to system() (#3197)Dana Robinson2023-06-281-2/+2
| | | | system() is only used in the iopipe test and the things it calls (which are POSIX-y) are protected by an ifdef.
* Add note about HDF5_VOL_CONNECTOR to tools usage (#3159)mattjala2023-06-2828-0/+99
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* Rename HD(f)printf() to (f)printf() (#3194)Dana Robinson2023-06-2856-2491/+2476
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* Rename HDassert() to assert() (#3191)Dana Robinson2023-06-2814-599/+599
| | | | | * Change HDassert to assert * Fix bin/make_err
* Remove HDva_(arg|copy|end|start) (#3184)Dana Robinson2023-06-284-14/+14
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* Many fixes to various compiler warnings (#3124)Sean McBride2023-06-1921-87/+98
| | | | | | | | | | | * Fixed various -Wmissing-variable-declarations by adding static keyword * In a few cases, renamed the variable suffix from _g to _s. * Fixed some -Wmissing-variable-declarations by using different declaration macros * Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero * Fixed various -Wcomma warnings * Fixed clang -Wstrict-prototypes warnings * Fixed various -Wunused-variable warnings * Updated some casts to fix the only 3 -Wcast-qual warnings * Fixed the only -Wsometimes-uninitialized warning
* Many clang -Wextra-semi-stmt fixes (#2537)Sean McBride2023-06-1633-114/+109
| | | | | * Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
* Add h5copy help test and verify consistency (#2902)Allen Byrne2023-05-1710-6/+178
| | | * Add autotools test for help
* Remove "the the" from comments and docs (#2865)Dana Robinson2023-05-011-1/+1
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* Fix ROS3 VFD anonymous credential usage with h5dump and h5ls (#2798)jhendersonHDF2023-04-242-4/+27
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* Add no subsets option to h5diff like h5dump #2688 (#2756)Allen Byrne2023-04-1815-268/+196
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* Comment cleanup (#2689)Quincey Koziol2023-04-1124-254/+2
| | | * Clean up content and redundant logging in comments.
* Remove dead code hidden behind #ifdef LATER (#2686)Dana Robinson2023-04-102-36/+0
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* Fix #2598 sanitize leak (#2660)Allen Byrne2023-04-071-4/+4
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2544)Allen Byrne2023-03-1323-58/+48
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* GH issue #1142, print must have verbose on first (#2540)Allen Byrne2023-03-131-4/+6
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* Check for overflow when calculating on-disk attribute data size (#2459)Egbert Eich2023-03-023-0/+10
| | | | | | | | | | | | | | | | | * Remove duplicate code Signed-off-by: Egbert Eich <eich@suse.com> * Add test case for CVE-2021-37501 Bogus sizes in this test case causes the on-disk data size calculation in H5O__attr_decode() to overflow so that the calculated size becomes 0. This causes the read to overflow and h5dump to segfault. This test case was crafted, the test file was not directly generated by HDF5. Test case from: https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md
* Fix uninitialized variable in pio_engine.c (#2463)Dana Robinson2023-02-131-11/+11
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* Fix a possible uninitialized variable in pio_perf (#2461)Dana Robinson2023-02-131-1/+1
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* Determine if native connector is terminal (#2397)Quincey Koziol2023-01-092-8/+12
| | | | | | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths * Use API routine to determine if native connector is terminal. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Play nice with existing plugin paths (#2394)Quincey Koziol2023-01-064-4/+4
| | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-213-9/+11
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)vchoi-hdfgroup2022-12-131-2/+6
| | | | | | | | | | | | | | | | | | | | | | * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Output should only be printed if verbose. (#2273)Allen Byrne2022-12-021-26/+36
| | | | | * Output should only be printed if verbose. * Add note
* Add aarch64 toolchain and change dump test to long opt (#2271)Allen Byrne2022-12-011-1/+1
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* Correct the CMake link for MPI (#2198)Allen Byrne2022-11-013-6/+6
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* Update copyright headers (#2184)Larry Knox2022-11-01149-150/+12
| | | | | * 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.
* Update develop branch version to 1.13.4-1 (#2189)Larry Knox2022-10-261-7/+7
| | | | | | * Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3 release. Added new version to exceptions in lines 74-5 of src/H5.c
* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-0330-37/+32
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-1916-89/+89
| | | | At one time this content was a git submodule shared between several projects but that time has long passed.
* Fixes codespell issues (#2032)Dana Robinson2022-08-171-1/+1
| | | | | * Fixes codespell issues * Fixed another typo
* Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)Larry Knox2022-08-121-7/+7
| | | | release. Added new version to exceptions in line 75 of src/H5.c.
* Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for ↵Larry Knox2022-08-121-7/+7
| | | | | | | | release" This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95. H5TEST-tcheck_version-release failed.
* Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for releaseLarry Knox2022-08-121-7/+7
| | | | of HDF5 1.13.2.
* Only use Subfiling VFD in tools if MPI was initialized previously (#1998)jhendersonHDF2022-08-111-3/+11
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* Fix typos found in the rest of the hdf5 code-base (#1985)luzpaz2022-08-109-11/+11
| | | | | | | | | | | * Fix typos found in the rest of the hdf5 code-base * Typo in tool.cmake * Revert "Typo in tool.cmake" This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b. * Fix clang-format styling
* Fix CMake macro code commands (#1989)Allen Byrne2022-08-101-3/+0
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* Revert for older cmake versions (#1974)Allen Byrne2022-08-086-157/+0
| | | | | * Revert for older cmake versions * Remove unneeded clear/clean tests because of changes to test macro
* Develop cmake clean (#1971)Allen Byrne2022-08-0742-1080/+1058
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* Fix issues in tools code after Subfiling VFD updates (#1973)jhendersonHDF2022-08-061-2/+13
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* Subfiling updates for release (#1963)jhendersonHDF2022-08-042-9/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built * Switch to MPI I/O driver for Subfiling HDF5 stub file * Rough first implementation for Subfiling file deletion * Subfiling VFD - get file dirname for file deletion * Subfiling VFD - set lock callback to NULL for now to avoid performance issues * Committing clang-format changes * Minor tidying up of Subfiling testing * Fixups for Subfiling VFD support in tools * Tidy up Subfiling public interface and add Doxygen * Respect Subfiling configuration settings from application * Add release note for Subfiling VFD * Committing clang-format changes * Committing clang-format changes * Shorten some Subfiling environment variable names Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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