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* Fix a few issues noted by LGTM (#1421)jhendersonHDF2022-02-0410-32/+38
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* Don't use a nonliteral format string in test/fheap.c:begin_test(). (#1401)David Young2022-02-031-87/+60
| | | | | | | | | * Avoid using a non-literal formatting string with sprintf in begin_test. Use snprintf. Don't duplicate a string on the heap unnecessarily. * Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format string any more. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update doc with HDF5_ROOT usage. (#1414)Allen Byrne2022-02-023-14/+16
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* Unify handling of collective metadata reads status (#1206)jhendersonHDF2022-01-2911-136/+357
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* Added another missing override keyword on a dtor (#1384)Sean McBride2022-01-291-1/+1
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* Fix some spelling. (#1402)David Young2022-01-281-3/+3
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* Snprintf2 (#1399)Sean McBride2022-01-2841-425/+467
| | | | | | | | | | | | | * 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 Byrne2022-01-2838-78/+82
| | | | | | | | | * 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 McBride2022-01-2824-46/+43
| | | | | | | * 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 McBride2022-01-286-8/+8
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* Revert 61464d7e (#1396)Larry Knox2022-01-261-10/+22
| | | | | | | | Commit 61464d7e was a fix for a compiler error on OpenBSD where int_fast8_t is in fact larger than 1 byte. However, the changes broke H5detect.c generation of H5Tinit.c on Power8 big-endian, and probably on all big-endian machines. Switching DETECT_BYTE to DETECT_I for 8 byte types doesn't work on our big-endian Power8 machine because switching the last parameter of DETECT_I_BYTE_CORE from "int" to the 8 byte type incorrectly sets dt->shared->u.atomic.order = H5T_ORDER_LE on a big-endian machine. A different fix to accomodate both big-endian and OpenBSD is needed. See commit 61464d7e for OpenBSD info. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update code owners file with more names (#1386)Allen Byrne2022-01-261-15/+15
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* Fix cmake dynamic analysis on windows (#1373)Allen Byrne2022-01-242-5/+21
| | | | | * Fix sanitizer flag form on windows * Add search paths to windows code-coverage
* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-229-71/+180
| | | | | | | * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Open bsd fixes (#1195)Sean McBride2022-01-203-82/+70
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* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-207-18/+659
| | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix documentation for H5D_space_status_t enum values (#1372)jhendersonHDF2022-01-191-3/+3
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* Do not set CMAKE_INSTALL_PREFIX when built externally (#1380)Matt McCormick2022-01-191-1/+1
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* various cleanup java test, test files, comments (#1363)Allen Byrne2022-01-185-12/+17
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* Develop java newrefs fixes for obj ref datasets (#1354)Allen Byrne2022-01-183-249/+207
| | | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update the java slf4j logging jars to latest 1.7.33 (#1369)Allen Byrne2022-01-1821-32/+32
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* Updated README.txt to README.md (#1375)Scot Breitenfeld2022-01-1410-36/+42
| | | | | | | | | | | * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * Converted README.txt to README.md and updated files referring to README.txt to README.md. * removed references to README.txt * updated MANIFEST
* Documentation fixes right in time for the holidays (#1321)Gerd Heber2022-01-1413-164/+759
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Sketch of the H5S life cycle. * Committing clang-format changes * Fix H5S_UNLIMITED snafu. * Updated RM template and RM page. * Added H5S life cycle. * Committing clang-format changes * Added H5T life cycle. * Committing clang-format changes * Cleaner layout (?) * Cleaned the H5F life cycle. Called out unfinished biz. * Committing clang-format changes * Remaining life cycle skeletons. * Committing clang-format changes * Committing clang-format changes * Added H5Z life cycle. * Committing clang-format changes * Added H5G life cycle. * Committing clang-format changes * H5 and H5I life cycle updates. * Committing clang-format changes * Added H5PL life cycle. * Committing clang-format changes * Added H5L life cycle. * Committing clang-format changes * Fix for Chris' comment. * Add a variable for Doxygen pre-processor definitions. * Forgot to add the H5M API. * Clarify the H5Z life cycle. * Committing clang-format changes * Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle. * Committing clang-format changes * Clarified introduction and fixed missing label declaration. * Added H5O life cycle. * Committing clang-format changes * H5O cleanup, part 1. * Committing clang-format changes * Cleaned up some of the endless repetition in H5O. * Committing clang-format changes * Cookbook & RFC draft layouts. * Updated manifest. * Updated the manifest, the example paths, and sketched the 1st recipe. * Committing clang-format changes * Outlined two more recipes. * Committing clang-format changes * More recipes and RFCs. * Committing clang-format changes * Draft of templatized RFC references. * Another batch of RFC changes. * Another batch of RFCs. * Fixed reference. * RFCs in reverse chronological order. * First cut of RFCs. * Fixed reference. * Updated recipes. * Updated recipes. * More RFCs. * Updated D*PL comments. * Added H5P descriptions. * Committing clang-format changes * H5R life-cycle snapshot. * Committing clang-format changes * H5R life-cycle. Added line numbers to life-cycle examples. * Committing clang-format changes * Fixed formatting for H5Dchunk_iter(). * Added comment on collective mode requirement w/ compression. * Simplified API compat. macro dox. * More API vers. updates. * Hide the async macro entrails. * Latest VFD SWMR RFC. * Create a tag file for permalinks. * Added TODOs for metadoc. * Removed duplication. * Revised RM landing page. * Trimmed more duplication. * Committing clang-format changes * Revised H5D. * Committing clang-format changes * Updated survey link. * Added Doxygen RM entry template link. * Added the "Multi-Thread HDF5" RFC. * Added DOXYGEN_TAG_FILE. * Added selection I/O RFC. * Added the VFD Sub-filing RFC. * Updated meta-documentation and added two old presentations. * Added a few more RFCs (4). * Fixed MANIFEST. * Updated meta-documentation. * Added Filters technical note. * Fixed MANIFEST. * Restore the path stripper. * Experimental full-text search via Google. * Better full-text search integration. * Whoops. Forgot this one. * Oh boy. * Make CMake happy. * Added "Debugging HDF5 Applications" technical note. * Another batch of RFCs. * Fixes for #1221. * Updated overview. * Fixed image dependencies. * CMake updates. * Fixed SET. * Better? * Update doxygen/dox/Overview.dox * Fixed documentation errors. Added missing version info. * Callback documentation updates. * Fixed indexing errors in the outline. * Doxygen-ized the HDF5 glossary. * Fix a few minor typos . Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fix H5ACmpio dirty bytes creation debugging (#1357)jhendersonHDF2022-01-121-5/+5
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* cmake custom command fix (#1356)Allen Byrne2022-01-121-32/+36
| | | | | | | | | | | | | * From gitlab.kitware.com/third-party/hdf5 rework custom commands commit/757aa42ebff8c9819c054f5e00559143c60f653d * Correct stamp file generation * Needs to support pregenerated H5Tinit.c file * Adjust custom command for all build systems types * Custom target only depends on OUTPUT of custom command
* Corrected H5Oget_info parameter description (#1349)Scot Breitenfeld2022-01-111-3/+3
| | | | | * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group
* Use appropriate printf format specifiers for haddr_t and hsize_t types ↵jhendersonHDF2022-01-1111-173/+129
| | | | directly (#1340)
* fixed off-by-one error in h5fget_name_f, HDFFV-11290 (#1345)Scot Breitenfeld2022-01-112-5/+37
| | | | | * fixed off-by-one error in h5fget_name_f, HDFFV-11290 * fixed typo
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x ↵Scot Breitenfeld2022-01-111-3/+3
| | | | releases, HDFFV-11289 (#1335)
* sort out/ref files for line compare (#1337)Allen Byrne2022-01-081-3/+7
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* Add tests for H5Ocopy of new object refs (#1338)Allen Byrne2022-01-0810-251/+700
| | | | | | | | | | | * Add tests for H5Ocopy of new object refs * Correct class name * Skip test because of issue with debug assertions * Update reference file * Fix object examples for new refs
* Fix compilation issues with Mingw (#1342)Baljak2022-01-086-31/+33
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* OESS-168: Remove clang warnings. (#1308)H. Joe Lee2022-01-071-1/+4
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* OESS-168: Remove clang warnings. (#1305)H. Joe Lee2022-01-071-2/+4
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* OESS-168: Remove clang warnings. (#1304)H. Joe Lee2022-01-071-1/+5
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* Fix usage of several HDfprintf format specifiers after HDfprintf removal (#1324)jhendersonHDF2022-01-0410-147/+231
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* Fix typo. (#1303)H. Joe Lee2022-01-041-1/+1
| | | chksum -> checksum
* Fix typo. (#1301)H. Joe Lee2022-01-041-1/+1
| | | If the are -> If they are
* OESS-168: Remove clang warnings. (#1300)H. Joe Lee2022-01-041-1/+1
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* Changed to correct return datatype for H5Lexists (#1330)Scot Breitenfeld2022-01-041-4/+5
| | | | | * changed to correct return datatype for H5Lexists Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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. (#1297)H. Joe Lee2021-12-151-1/+1
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* OESS-168: Remove clang warnings. (#1280)H. Joe Lee2021-12-131-8/+8
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* OESS-168: Remove clang warnings. (#1283)H. Joe Lee2021-12-131-2/+2
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* OESS-168: Remove clang warnings. (#1284)H. Joe Lee2021-12-131-8/+8
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* Call FUNC_ENTER immediately in H5_init_library (#1287)jhendersonHDF2021-12-131-2/+2
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* Fix free list tracking and cleanup cast alignment warnings (#1288)jhendersonHDF2021-12-131-27/+120
| | | | | * Fix free list tracking and cleanup cast alignment warnings * Add free list tracking code to H5FL 'arr' routines
* Make it easier to find version specific docs. (#1260)Gerd Heber2021-12-133-12/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Sketch of the H5S life cycle. * Committing clang-format changes * Fix H5S_UNLIMITED snafu. * Updated RM template and RM page. * Added H5S life cycle. * Committing clang-format changes * Added H5T life cycle. * Committing clang-format changes * Cleaner layout (?) * Cleaned the H5F life cycle. Called out unfinished biz. * Committing clang-format changes * Remaining life cycle skeletons. * Committing clang-format changes * Committing clang-format changes * Added H5Z life cycle. * Committing clang-format changes * Added H5G life cycle. * Committing clang-format changes * H5 and H5I life cycle updates. * Committing clang-format changes * Added H5PL life cycle. * Committing clang-format changes * Added H5L life cycle. * Committing clang-format changes * Fix for Chris' comment. * Add a variable for Doxygen pre-processor definitions. * Forgot to add the H5M API. * Clarify the H5Z life cycle. * Committing clang-format changes * Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle. * Committing clang-format changes * Clarified introduction and fixed missing label declaration. * Added H5O life cycle. * Committing clang-format changes * H5O cleanup, part 1. * Committing clang-format changes * Cleaned up some of the endless repetition in H5O. * Committing clang-format changes * Cookbook & RFC draft layouts. * Updated manifest. * Updated the manifest, the example paths, and sketched the 1st recipe. * Committing clang-format changes * Outlined two more recipes. * Committing clang-format changes * More recipes and RFCs. * Committing clang-format changes * Draft of templatized RFC references. * Another batch of RFC changes. * Another batch of RFCs. * Fixed reference. * RFCs in reverse chronological order. * First cut of RFCs. * Fixed reference. * Updated recipes. * Updated recipes. * More RFCs. * Updated D*PL comments. * Added H5P descriptions. * Committing clang-format changes * H5R life-cycle snapshot. * Committing clang-format changes * H5R life-cycle. Added line numbers to life-cycle examples. * Committing clang-format changes * Fixed formatting for H5Dchunk_iter(). * Added comment on collective mode requirement w/ compression. * Simplified API compat. macro dox. * More API vers. updates. * Hide the async macro entrails. * Latest VFD SWMR RFC. * Create a tag file for permalinks. * Added TODOs for metadoc. * Removed duplication. * Revised RM landing page. * Trimmed more duplication. * Committing clang-format changes * Revised H5D. * Committing clang-format changes * Updated survey link. * Added Doxygen RM entry template link. * Added the "Multi-Thread HDF5" RFC. * Added DOXYGEN_TAG_FILE. * Added selection I/O RFC. * Added the VFD Sub-filing RFC. * Updated meta-documentation and added two old presentations. * Added a few more RFCs (4). * Fixed MANIFEST. * Updated meta-documentation. * Added Filters technical note. * Fixed MANIFEST. * Restore the path stripper. * Experimental full-text search via Google. * Better full-text search integration. * Whoops. Forgot this one. * Oh boy. * Make CMake happy. * Added "Debugging HDF5 Applications" technical note. * Another batch of RFCs. * Fixes for #1221. * Updated overview. * Fixed image dependencies. * CMake updates. * Fixed SET. * Better? * Update doxygen/dox/Overview.dox Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes for async operations (#1272)jhendersonHDF2021-12-112-6/+68
| | | | | Setup VOL wrapping context for each "request" callback Set H5ES_event_t "next" pointer to NULL when appending to event list
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