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* Replaces HDgetenv with getenv (#3599)Scot Breitenfeld2023-09-261-1/+1
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* Strip HD prefix from string/char C API calls (#3540)Dana Robinson2023-09-151-4/+4
| | | | | | | | | | | | | | | | | | | | | * Strip HD prefix from string/char C API calls * HD(f)(put|get)(s|c) * HDstr* * HDv*printf * HD(s)(print|scan)f * HDperror But NOT: * HDstrcase* * HDvasprintf * HDstrtok_r * HDstrndup As those are not C99 and have portability work-around implementations. They will be handled later. * Fix th5_system.c screwup
* Consistent initialization of hid_t in the tests (#3521)Scot Breitenfeld2023-09-081-11/+11
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* Convert hbool_t --> bool in test (#3494)Dana Robinson2023-09-051-3/+3
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* Fixes the last of the -Wextra-semi-stmt warnings (#3326)Sean McBride2023-08-021-27/+27
| | | | | | | | | | | | | | | | | | | | | | | * Fixed extra semi warning by adjusting alternative macro definitions * Find-replace H5E_END_TRY; -> H5E_END_TRY * Made H5Epush_goto a do-while loop, fixed indentation * Made GOTOERROR and ERRMSG do-while loops * Made Hgoto_error and Hgoto_done do-while loops * Made vrfy_cint_type and vrfy_ctype do-while loops * Made TEST_TYPE_CONTIG and others do-while loops * Removed extraneous semi-colons * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove HD from HDmem* calls (#3211)Dana Robinson2023-06-291-1/+1
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* Remove programmer/date from comments (#3210)Dana Robinson2023-06-291-3/+0
| | | | * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work
* Remove HD from memory allocate/free calls (#3195)Dana Robinson2023-06-281-81/+81
| | | | | | * HDcalloc * HDfree * HDmalloc * HDrealloc
* Rename HD(f)printf() to (f)printf() (#3194)Dana Robinson2023-06-281-12/+12
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* Many clang -Wextra-semi-stmt fixes (#2537)Sean McBride2023-06-161-5/+5
| | | | | * Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
* Comment cleanup (#2689)Quincey Koziol2023-04-111-2/+0
| | | * Clean up content and redundant logging in comments.
* Synchronize HDF5 tests with VOL tests (#2628)jhendersonHDF2023-04-031-38/+148
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* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * 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.
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-16/+16
| | | | | * Update format source to clang 13 * More format changes
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* VFD plugins (#602)jhendersonHDF2021-09-291-2/+12
| | | | | | | | | | | | | | | | | * 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
* Update clang config (#473)Quincey Koziol2021-03-171-3/+12
| | | | | | | * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes various warnings noticed on Windows (#425)Dana Robinson2021-03-051-1/+1
| | | | | | | | | | | | * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Avoid aligned access for references by decoding into temporary buffer and ↵Quincey Koziol2020-12-191-35/+32
| | | | then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* Clang-format of source filesAllen Byrne2020-09-301-465/+484
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* Fixes a size mismatch when copying old-style to new-style referencesDana Robinson2020-08-121-4/+4
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* Fixes memory leads in trefer.cDana Robinson2020-08-121-20/+22
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* Merge pull request #2715 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_vlen_ref to ↵Jerome Soumagne2020-08-061-0/+303
|\ | | | | | | | | | | | | develop * commit 'ef6db167a86e6c065d46963dbd75cd325fe83813': H5R: fix encoding of references that are part of compound types
| * H5R: fix encoding of references that are part of compound typesJerome Soumagne2020-07-281-0/+303
| | | | | | | | Add corresponding test and some debug information
* | Minor normalizations with hdf5_1_10Dana Robinson2020-07-311-4/+4
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* H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-161-0/+270
| | | | Update trefer.c with vlen test case
* Minor tweaks to testhdf5 code after normalization with 1.10.Dana Robinson2020-05-281-6/+6
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* Trim trailing whitespaceQuincey Koziol2020-04-201-6/+6
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* A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-03-231-348/+388
| | | | | | | | | | H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
* Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required.David Young2020-01-291-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c.
* squash cast warning fixkmu2020-01-231-3/+3
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-7/+7
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* Small changes from the token_refactoring branch, to reduce the delta to developQuincey Koziol2020-01-041-1/+1
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* Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-12/+24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Added a new VOL sub-class called "introspect" where callbacks that report information about the connector or container can be placed. Added an 'opt_query' callback to this sub-class, for a connector to report back to the library whether a particular optional callback operation is supported. Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or the terminal connector, H5VL_GET_CONN_LVL_TERM). Moved the "post open" operation from a file 'specific' operation to a file 'optional' operation, now that it's possible to detect (with the 'opt_query' introspection callback) whether a VOL connector implements an optional operation, without just returning an error. Added new internal VOL helper routines: H5VL_object_is_native, to determine if an object is in (or is a) native file, and H5VL_file_is_same, to determine if two objects are in (or are) the same terminal VOL connector's container. (And moved the special handling for FILE_IS_EQUAL operation out of internal VOL callback routine into H5VL_file_is_same) Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better with other 'get' operations in API. Fixed several issues with pass-through connectors, which are now passing the 'make check-passthrough-vol' tests again. A bunch of warning and style cleanups as well.
* More fixes for previous committed PR #2079 dated Dec 5 2019.Vailin Choi2019-12-061-1/+1
| | | | | (1) H5O_dtype_ver_bounds[] for V112 should be H5O_DTYPE_VRESION_4 (2) The tests for the new reference types should work for V112 and beyond
* Merge pull request #2076 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:type_fixes to ↵Jerome Soumagne2019-12-051-133/+138
|\ | | | | | | | | | | | | | | develop * commit '7b03a1c03633d695b487642e54f897c715f8622e': Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc.
| * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char toDavid Young2019-12-051-133/+138
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. An interesting side-effect that we probably should *not* rely on is that the struct-encapsulation changes the alignment so that some GCC warnings about casts that increase the alignment requirement of the operand go away. Warnings like that have to be taken seriously: I will add -Werror=cast-align to the default compiler flags so that they stop the build quickly. GCC warnings led me to some surprising casts in test/trefer.c. I found that it was possible to make many simplifications after introducing the struct-encapsulation that I described, above. In test objcopy_ref `same_file` is assigned but never used. Delete it.
* | Two fixes:Vailin Choi2019-12-051-1/+1
|/ | | | | (1) Set the version for reference datatype messge to H5O_DTYPE_VERSION_4. (2) Verify the decoded version for hyperslab selection.
* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-041-2/+2
| | | | the Autotools and CMake.
* Add OAPL parameter to H5Rcreate_ APIsJordan Henderson2019-12-021-36/+36
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* H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-11-261-4/+4
| | | | | | Valid for both deprecated and non-deprecated references Update test
* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-577/+1611
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
* OESS-29 Update HD prefix mostlyAllen Byrne2019-08-241-2/+2
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* Fixed a memory issue in trefer.c.Dana Robinson2019-06-251-4/+4
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* HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.Vailin Choi2019-04-061-24/+34
| | | | This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* Set V112 as the latest format and extend the arrays of version bounds.Vailin Choi2019-04-041-91/+135
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* Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-132/+46
| | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-06-041-1/+1
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| * Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-1/+1
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