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* Moves the lists of VOL connectors and VFDs in Autotools builds (#162)Dana Robinson2020-12-1210-50/+16
| | | | | The VOL_LIST variable used in the Autotools was duplicated in many subdirectories. It's been moved to config/conclude.am to avoid duplication. VFD_LIST was also moved to conclude.am.
* Minor normalization with the async branch (#159)Dana Robinson2020-12-1217-41/+52
| | | | | * Minor normalization with the async branch * Update CMake and the Autotools to use the new pass-through VOL ID
* Add Makefile.ins in utils directory to MANIFEST. (#152)Larry Knox2020-12-101-0/+2
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* Enforce VOL framework version compatibility when registering connectors. ↵Quincey Koziol2020-12-1012-42/+132
| | | | Also add a version for the connector itself, some refactoring on the register calls, and move the logic for matching / rejecting a VOL connector class from the plugin module to the VOL module. (#151)
* Fixes a minor memory leak in the SWMR use cases tests (#147)Dana Robinson2020-12-031-1/+3
| | | * Due to a missing free(3) call
* (fix) Segmentation fault when using a compound type. (#143)Jan-Willem Blokland2020-12-025-12/+153
| | | | | | | | | | | | | | | | | | | | | | | * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Fix autotools clang debug optimization level w/ older clang and Xcode ↵Dana Robinson2020-12-021-2/+12
| | | | | | | | | | | | | | versions (#146) * Fixes clang debug optimization level w/ Autotools NOTE: This was only released in HDF5 1.10.7, so only the 1.10 branch needs a note in RELEASE.txt. * Updates the clang -Og setting with a version check w/ autotools * Sets -Og when clang >= 4.0 or Xcode >= 9.0 * Older versions get -O1 * Autotools only
* (fix) H5Z_xform_create function and scientific notation (#144)jwsblokland2020-12-022-16/+50
| | | | | | | | | | | | | | * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Add H5atclose and H5is_library_terminating routines. (#139)Quincey Koziol2020-12-013-8/+279
| | | | | | | | | | | * Add H5atclose and H5is_library_terminating routines. * Add brief Doxygen comment for H5_atclose_func_t typedef. * Added /*out*/ flag to parameter list, for the tracing script. * Update doxygen comment for H5atclose with additional detail. * Return FAIL for H5is_library_threadsafe and H5is_library_terminating when their parameters are NULL.
* Break single loop with interleaved sends and receives into two separate ↵Quincey Koziol2020-12-011-12/+20
| | | | loops, to avoid deadlocks. Also avoid copying chunk entries when determining ownership. (#138)
* Expand ID dec_ref and close callbacks to allow for asynchronous close ↵Quincey Koziol2020-12-0120-81/+313
| | | | | | | | | | | operations (#135) * Expand ID dec_ref and close callbacks to allow for asynchronous close operations. * Fix typo * Rename token -> request, remove programmer name * H5E_ATOM to H5E_ID
* Add flag to H5CX_pop that allow setting the properties to return to ↵Quincey Koziol2020-12-0129-78/+80
| | | | application to be skipped. (#134)
* Expand 'opt_query' VOL callback to return a bitfield instead of a flag (#136)Quincey Koziol2020-11-3017-84/+295
| | | | | * Expand 'opt_query' VOL callback to return a bitfield instead of a flag * Correct pastos
* Move API routines for VOL objects to main source file. (#133)Quincey Koziol2020-11-3012-996/+1000
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* Replace H5E_ATOM major error category with H5E_ID (#121)Dana Robinson2020-11-3089-485/+503
| | | | | | | | | | * Renames H5I_ATOM to H5I_ID, among other related changes * Java has been updated. * Fortran is failing on my VM, even though I don't touch that. * Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes * Fixes typos in comments
* FreeBSD autotools changes (#142)Dana Robinson2020-11-302-4/+38
| | | | | | | | | | | | | | | | * Updates to allow autotools builds on recent FreeBSD * Switches the default C compiler to cc from gcc (this may need a version string check if we want to support FreeBSD 9 and earlier. FreeBSD 10 was released in 2014) * Makes the default C++ compiler c++ (no previous setting) * Both of these resolve to Clang on FreeBSD 10+ * Added a note about flang being unsuitable on FreeBSD (the port uses an ancient build of flang that lacks Fortran 2003 support) * Autotools only - CMake appears to use different CPP flags which cause compilation errors * Adds a RELEASE.txt note for new FreeBSD autotools changes
* Fixes clang debug optimization level w/ Autotools (#141)Dana Robinson2020-11-301-1/+1
| | | | NOTE: This was only released in HDF5 1.10.7, so only the 1.10 branch needs a note in RELEASE.txt.
* Removed H5_ECXXFLAGS from libhdf5.settings (#140)Dana Robinson2020-11-301-1/+1
| | | This variable is unused and was missed in the -Werror changes.
* Minor cleanups (#132)Quincey Koziol2020-11-263-27/+27
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* Minor refactoring in tid.c (#127)Dana Robinson2020-11-261-137/+239
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* Enhance API tracing (#120)Quincey Koziol2020-11-2661-2735/+3524
| | | Enhance API tracing to handle more types, and to put tracing info in a string, allowing it to be used when reporting errors. Also refactor ref-counted strings (H5RS) module to add capabilities needed for the tracing. Refactored H5Gname.c routines to use new H5RS routines also. Added /*out*/ tags to API routines that are returning information to the application. Updated H5TRACE macros from running updated trace script over library code. Added tests for new H5RS routines.
* Refactor to avoid using fork to create initial file (#122)Quincey Koziol2020-11-251-331/+19
| | | | | * Refactor to avoid using fork to create initial file * Use correct exit value on failure
* Update H5TS code to reflect library's coding style (#123)Quincey Koziol2020-11-252-42/+178
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* Move package initialization code for H5A and H5G to internal source file. (#125)Quincey Koziol2020-11-255-353/+343
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* Add else choice to error flags option (#128)Allen Byrne2020-11-2514-0/+279
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* Minor/solaris gcc fix (#126)Dana Robinson2020-11-252-4/+21
| | | | | | | * Adds gnu99 as the standard when building with gcc on Solaris * Adds a note to RELEASE.txt and improves comments For Solaris + gcc fix (HDFFV-11191)
* Adds a configure/CMake option to control -Werror behavior (#119)Dana Robinson2020-11-256-19/+95
| | | | | * Works in both Autotools and CMake * OFF by default * Reverts "always on" -Werror behavior released in 1.10.7
* Doxygen - added (mostly) beginner functions (#112)bljhdf2020-11-236-27/+1551
| | | | | * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function
* Update release text files (#109)Allen Byrne2020-11-238-2449/+7659
| | | | | | | * Update release text files * spelling correction * Update list
* Basic alignment with async branch (#115)Quincey Koziol2020-11-23170-1452/+1443
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Full set of current H5F documentation. (#105)Gerd Heber2020-11-215-44/+1311
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Minor/id code cleanup (#114)Dana Robinson2020-11-2111-1692/+1854
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Switch ID code to use a hash table instead of a skip list (#52)" This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4. * H5I_id_type_t and H5I_class_t are no longer managed via free lists * Fixed commenting issues * Naming and commenting cleanup in H5I.c * H5I cleanup * Header cleanup * Commenting * More uniform naming * Renames H5I_id_type_t and related in H5I.c * Adds gcc pragmas to ignore H5I const casting * Split H5I code into multiple files * Rename id_type to simply type in H5I code * Minor typo in H5Itest.c
* Corrects use of unitialized bytes in the chunk_info test (#106)Dana Robinson2020-11-201-2/+2
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* chkmanifest will run autogen (#102)Allen Byrne2020-11-202-0/+2
| | | | | | | * chkmanifest will run autogen * remove extension on command * run autogen first
* Revert "Switch ID code to use a hash table instead of a skip list (#52)" (#104)Dana Robinson2020-11-207-1367/+30
| | | This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4.
* Add new files to CMake and MANIFEST (#100)Allen Byrne2020-11-192-0/+3
| | | | | * Add new header file * Add missing file
* First cut of the H5 public API documentation. (#80)Gerd Heber2020-11-1825-562/+6930
| | | | | | | | | | | | | | | | | | | | | * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch.
* Switch ID code to use a hash table instead of a skip list (#52)Dana Robinson2020-11-177-30/+1367
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings hash table ID code over from Bitbucket branch * Includes reformatting via clang. * Excludes uthash.h from reformatting. * Still has the failing test issue in tid.c. This should only be a problem if a custom ID type is used and its free function deletes other IDs. * Fixes munged H5_GCC_DIAG_ON/OFF macros in H5I.c The H5_GCC_DIAG_ON/OFF macros used to turn off fallthrough warnings in uthash.h (external code) were munged when formatting with clang due to their lack of quotes. e.g.; H5_GCC_DIAG_OFF(implicit-fallthrough) was munged to: H5_GCC_DIAG_OFF(implicit - fallthrough) which compiles, but is useless. So, with quotes, this is now: H5_GCC_DIAG_OFF("implicit-fallthrough") which survives reformatting with clang. * Fixes issues with user callbacks in the ID hash tables The skip lists (previously) used to handle IDs use a mark-and-sweep scheme to deal with user-defined ID delete callbacks which themselves delete other IDs in the list. The uthash hash table implementation used to manage the IDs in this feature branch does not have this ability. This commit restores the skip lists for non-library ID types in lieu of significantly modifying the uthash code. The hash tables are used to manage the library IDs as those do not delete other IDs when they are closed. * Adds uthash.h to MANIFEST * Removes implicit-fallthrough diagnostic disable Removing -Wimplicit-fallthrough=5 means that the uthash code no longer raises warnings so the H5_GCC_DIAG_OFF/ON macros that disabled those warnings have been removed from H5I.c. * Adds a test to ensure you can delete IDs in the H5Iiterate() callback
* obsolete CMAKE_BUILD_TOOL => CMAKE_MAKE_PROGRAM (#97)Michael Hirsch2020-11-171-1/+1
| | | CMAKE_BUILD_TOOL has been [replaced](https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TOOL.html) by CMAKE_MAKE_PROGRAM
* Merge pull request #91 from ksunden/patch-1Larry Knox2020-11-131-1/+1
|\ | | | | Fix spelling of metadata
| * Fix spelling of metadataKyle Sunden2020-11-131-1/+1
|/ | | was spelled "metadatda"
* Merge pull request #82 from derobins/minor/skip_list_errorLarry Knox2020-11-131-1/+1
|\ | | | | H5SL_release() returns SUCCEED on errors
| * H5SL_release() returns SUCCEED on errorsDana Robinson2020-11-121-1/+1
| | | | | | | | | | H5SL_release() erroneously returned SUCCEED on errors. It now correctly returns ret_value.
* | Merge pull request #84 from byrnHDF/developLarry Knox2020-11-135-57/+62
|\ \ | | | | | | Downgrade m4 doxygen macros.
| * | Correction for location of doxygen folderAllen Byrne2020-11-121-1/+1
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| * | downgrade doxygen.m4 macro file to previous version.Allen Byrne2020-11-121-43/+43
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| * | Add missing entries, remove m4 referenceAllen Byrne2020-11-125-15/+20
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* | | Merge pull request #60 from bmribler/developLarry Knox2020-11-125-7/+53
|\ \ \ | | | | | | | | Fix HDFFV-10590
| * | | Fixed typo!!Binh-Minh Ribler2020-11-121-1/+1
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| * | | Fixed typo!Binh-Minh Ribler2020-11-121-1/+1
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