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* Fixes an incorrect brief description for H5Dopen2() (#1920)Dana Robinson2022-07-211-1/+1
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* Fix for MSVC compile failures in h5dumpgentest due to VLA use (#1916)Dana Robinson2022-07-211-9/+9
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* Removes the ability to build h5perf and h5perf_serial in standalone mode (#1897)Dana Robinson2022-07-2014-1454/+36
| | | This feature has been broken for some time and lacks a clear use case.
* Fix bug in swmr.c introduced with recent merge (double_t) (#1913)Neil Fortner2022-07-191-3/+3
| | | | | | | | | | | | | | | * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes * Replace accidental use of double_t in swmr.c with double. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Marks H5Fformat_convert as internal in Doxygen (#1910)Dana Robinson2022-07-191-6/+5
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* Updates H5Zdevelop.h with better memory alloc/free advice (#1909)Dana Robinson2022-07-191-3/+30
| | | | | | | * Updates H5Zdevelop.h with better memory alloc/free advice Addresses GitHub #348 * Updates the filter memory calloc/free docs
* Persist dataset access properties when using H5Fstart_swmr_write (#1862)Neil Fortner2022-07-195-31/+495
| | | | | | | | | | | | | * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Greatly simplifies Autotools bits of autogen.sh (#1906)Dana Robinson2022-07-181-165/+6
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* Remove perf tool from CMakeTests file (#1907)jhendersonHDF2022-07-181-4/+0
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* Fix some hard-coded MPI I/O VFD checks (#1898)jhendersonHDF2022-07-182-4/+16
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* Removed compiler messages for language elements that are not standard in ↵Scot Breitenfeld2022-07-182-2/+2
| | | | Fortran 2003, #1344 (#1905)
* Updates comments in the gcc 4.8 warnings files (#1902)Dana Robinson2022-07-182-8/+0
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* Fixes a stack overflow in the h5dump test generator (#1903)Dana Robinson2022-07-183-30/+31
| | | | | | | | | | | | | * Fixes a stack overflow in the h5dump test generator The opaque type size was declared to be the size of the "buffer of two opaque elements", causing a memcpy call in H5Dwrite to read outside the buffer, dumping garbage into the file. Note that this only affected the test generator and not h5dump itself. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes warnings when the deflate filter is not built (#1904)Dana Robinson2022-07-183-6/+14
| | | | | | | * Fixes warnings when the deflate filter is not built * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds Autotools dependencies to CodeQL workflowDana Robinson2022-07-171-0/+5
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* Set up CodeQL analysis for developDana Robinson2022-07-171-0/+75
| | | This will be reverted if it causes problems
* Removes the small perf tool (#1896)Dana Robinson2022-07-174-832/+13
| | | | | | | | * Removes the small perf tool This tool doesn't really do anything special and installed, which conflicts with gnu's perf tool. * Adds suggestions from code review
* Updates branches-explained.md (#1900)Dana Robinson2022-07-151-16/+15
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* Create CODE_OF_CONDUCT.mdDana Robinson2022-07-141-0/+128
| | | Taken directly from GitHub's suggested CoC document. We may modify this in the future.
* Add utility JNI function for 1.10 style references (#1888)Allen Byrne2022-07-144-0/+98
| | | | | | | | | | | * Add utility JNI function for 1.10 style references * Clarify text * Correct signature * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove superfluous dot from hl doxygen. (#1891)vchoi-hdfgroup2022-07-147-17/+13
| | | Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
* Eliminate unnecessary error output (#1879)Allen Byrne2022-07-142-17/+20
| | | | | | | * Eliminate unnecessary error output * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for a tools compile issue when deprecated symbols are disabled (#1884)Dana Robinson2022-07-132-14/+30
| | | | | | | | | | | | | * Fix for a tools compile issue when deprecated symbols are disabled Introduced in #1811, also uses VOL token instead of addr * Fix for similar compile issues in java when deprecated symbols are disabled. * Committing clang-format changes Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Oflush fails for parallel (#1876)raylu-hdf2022-07-129-1/+142
| | | | | | | | | | * H5Oflush causes H5Fclose to trigger an assertion failure in metadata cache for parallel. This commit makes sure H5Oflush fails for parallel until this problem is solved in the future. * Committing clang-format changes * Changed the use of H5F_get_driver_id to H5F_HAS_FEATURE. Co-authored-by: songyulu <songyulu@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Moves -Wstrict-overflow=5 to the developer warnings (#1878)Dana Robinson2022-07-126-8/+18
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* Removes definitions for (U)LLONG_MAX and (S)SIZET_MAX (#1877)Dana Robinson2022-07-115-28/+21
| | | | | | | LLONG_MAX and ULLONG_MAX are defined in limits.h in C99. SIZET_MAX should be SIZE_MAX, which has been around forever. SSIZET_MAX should be SSIZE_MAX, which is defined whereever ssize_t is found. I've kept the definition for SSIZE_MAX (renamed from SSIZET_MAX) for platforms where ssize_T is not present (e.g., Windows).
* Fixes for warnings identified by MSVC (#1874)Dana Robinson2022-07-112-13/+10
| | | | | | | | | * Fixes for warnings identified by MSVC * Committing clang-format changes * Moves the casts in H5Binternal.c to the other side Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop HDFFV-11310 (#1811)Allen Byrne2022-07-1120-568/+2706
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework java vl check in read/write. Handle old refs in h5dump * Committing clang-format changes * Java changes allow default VL reads * Fix JNI utility for old refs * HDFFV-11310 - implement vlen read/write for atomic types. * format check fix * Mostly format fixes * More format issues * Two format changes * Use JNI names for sizeof * format change * fix size typo * Change to older method to initialize list * remove unused var * format fix * switch writeVL functions to use datatype instead of java type * Add VL option to generic read/write check * Correct function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Add release note and format changes * Another format update * Fix unreleased allocations * Fix format * format correction Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Support for UnifyFS with MPI_File_sync (#1801)Houjun Tang2022-07-1110-11/+172
| | | | | | | | | | | | | | | | | | | | | | | | | * Initial implementation for supporting UnifyFS in HDF5 with MPI_File_sync after write * Committing clang-format changes * Fix format * Fix env variable and return value check * Fix flag retrieve * Fix issues with getting/setting the flag * Fix merge conflicts * Update * Committing clang-format changes * Update based on suggestions * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Reduce -Wstrict-overflow= from 5 to 2 (#1872)Dana Robinson2022-07-112-2/+2
| | | | The signal-to-noise ratio of the higher warning level is very low and the noise obscures things we should fix
* Misc clang warning fixes (#1869)Dana Robinson2022-07-1119-904/+741
| | | | | | | | | | | | | | | | | * Minor clang warning fixes in src and test * Fixes clang warnings in high-level library * clang format-nonliteral warning fixes * Committing clang-format changes * Fixed int -> float clang cast warnings in h5diff * Quiets some warnings in flex/bison generated code * Suppress overlong string warning for libinfo on clang Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for production mode gcc warnings (#1873)Dana Robinson2022-07-118-38/+75
| | | | | | | | | | | | * Fixes for production mode gcc warnings With the strict-overflow changes, this brings the number of warnings in the C library w/ gcc 12 to zero. * Fix typo * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes C++ sign-conversion warnings w/ clang 14 (#1870)Dana Robinson2022-07-1115-59/+108
| | | | | | | * Fixes sign-conversion warnings w/ clang 14 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds the mirror and direct VFDs to GitHub actions (#1871)Dana Robinson2022-07-112-6/+54
| | | Both Autotools and CMake
* Adds format attribute to additional functions (#1868)Dana Robinson2022-07-114-9/+9
| | | | | | | | | * Adds format attribute to (s|p)io_perf code * Added gcc format attribute to additional test code * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds explicit indices to drivernames array in the tools (#1867)Dana Robinson2022-07-111-1/+4
| | | Will help keep the drivernames and driver_idx enum in sync.
* Adds the malloc attribute to appropriate functions (gcc only) (#1866)Dana Robinson2022-07-113-55/+71
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* Updates the patterns in Doxyfile.in to accept H5*develop.h (#1865)Dana Robinson2022-07-111-3/+1
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* Merge pull request #1857 from gheber/fix-doxy-warnings-and-cosmeticsGerd Heber2022-07-094-91/+82
|\ | | | | Fix Doxygen warnings and cosmetics
| * Resolve Allen's comment.Gerd Heber2022-07-081-1/+1
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| * Fix Doxygen warningsGerd Heber2022-07-083-84/+75
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| * Cosmetic changes to RM frontGerd Heber2022-07-081-7/+7
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* | Convert assertion on (possibly corrupt) file contents to normal error check ↵jhendersonHDF2022-07-082-2/+13
| | | | | | | | | | | | | | | | | | (#1861) * Convert assertion on (possibly corrupt) file contents to normal error check * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* | Fix for memory allocation issue identified by fuzzer (#732) (#1860)Dana Robinson2022-07-081-1/+1
| | | | | | | | | | | | | | GitHub issue #732 claims that mallocing a particular buffer can trigger undefined behavior and that callocing the buffer fixes the issue. I did not confirm this, but the fix is trivial and better anyway.
* | Updated vfd swmr and reference rfcs (#1854)Gerd Heber2022-07-072-2/+4
|/ | | | | * Add PDFs * Update RFC table
* Suppress the "obsolete" category of Autoconf warnings (#1853)Dana Robinson2022-07-061-1/+4
| | | | | Very new versions of Autoconf complain about our Java macros. Since they work well enough and there is no obvious upgrade path, we're suppressing the category for now.
* Updates messages in cache sanity checks (#1851)Dana Robinson2022-07-061-23/+23
| | | | Previous messages were numbered, which was a maintenance burden, and non-specific
* Minor tweaks to the test_swmr.sh script (#1852)Dana Robinson2022-07-061-10/+7
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* Update Doxyfile.in (#1849)Gerd Heber2022-07-061-0/+1
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* Fix invalid comment about character encoding in H5Fint.c (#1845)jhendersonHDF2022-07-011-2/+5
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