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* | Committing clang-format changesgithub-actions2022-01-281-62/+60
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* | Replace H5detect's build-time detection of C99 integer properties with aDavid Young2022-01-284-535/+312
|/ | | | | | | | | | | | | table-driven routine, `H5T__init_native_int()`, that is run at library initialization time. Always respect the alignment used by the compiler for integers. The library invites trouble by using different alignment than the compiler expects. Here and there update a comment about alignment. Retire the H5detect code that tries to find the least permissible integer alignment by running experiments and catching any signals thrown or unexpected results.
* Replaced several uses of sprintf with safer snprintf (#1383)Sean McBride2022-01-2811-25/+22
| | | | | | | * 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 McBride2022-01-281-1/+1
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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>
* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-228-71/+168
| | | | | | | * 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 McBride2022-01-201-22/+10
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* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-205-14/+167
| | | | | | (#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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* various cleanup java test, test files, comments (#1363)Allen Byrne2022-01-181-1/+1
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* Documentation fixes right in time for the holidays (#1321)Gerd Heber2022-01-146-142/+174
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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)
* 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)
* Fix compilation issues with Mingw (#1342)Baljak2022-01-081-1/+3
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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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* OESS-168: Remove clang warnings. (#1297)H. Joe Lee2021-12-151-1/+1
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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
* 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
* Remove duplicate memcpy in chunk_file_cb (#1285)jhendersonHDF2021-12-111-1/+0
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* Initialize filter mask and chunk nbytes for 'Single' chunk index (#1261)jhendersonHDF2021-12-091-1/+7
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* Correct spelling correction of preceed incorrectly to proceed. Should (#1268)Larry Knox2021-12-071-2/+2
| | | * Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'.
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-07140-344/+346
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236)Larry Knox2021-11-301-3/+3
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* Only check HDF5_DRIVER in MPI I/O VFD if VFD isn't initialized (#1213)jhendersonHDF2021-11-253-15/+14
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* Fix a few H5CX warnings from recent init changes (#1224)jhendersonHDF2021-11-241-8/+4
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* Fix a few warnings after recent H5S const-related changes (#1225)jhendersonHDF2021-11-242-16/+16
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* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs (#1222)Dana Robinson2021-11-241-0/+4
| | | | | | | | | | | | * Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the library due to missing ID range checks in H5Pget_filter_by_id1/2. The library now returns a normal error code when filter IDs are out of range. Fixes HDFFV-11286. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Closes #1221 (#1223)Gerd Heber2021-11-241-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Make sure plugin interface is initialized before property list interface ↵jhendersonHDF2021-11-232-1/+2
| | | | phase 2 (#1216)
* Stop lying about H5S_t const-ness (#1209)Dana Robinson2021-11-2018-239/+289
| | | | | | Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate.
* Fixes const warnings in H5ES package (#1211)Dana Robinson2021-11-181-5/+5
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* Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201)jhendersonHDF2021-11-181-4/+2
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* Quiets most const warnings in the fractal heap code (#1188)Dana Robinson2021-11-133-9/+32
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* Fix MPI Comm and Info leak in H5FD__mpio_delete (#1189)jhendersonHDF2021-11-121-0/+6
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* Cleans up pointer and ID reset code in H5Pint.c (#1182)Dana Robinson2021-11-101-74/+112
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* Quiets const warning in H5RS code (#1181)Dana Robinson2021-11-101-2/+10
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* Fix H5DS warnings related to new H5DSwith_new_ref and H5VLobject_is_native ↵jhendersonHDF2021-11-102-11/+15
| | | | APIs (#1184)
* Fixes FUNC_ENTER warnings in VFDs due to recent init changes (#1178)Dana Robinson2021-11-106-15/+9
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* Fixes const issues in the version 2 B-trees (#1172)Dana Robinson2021-11-092-24/+21
| | | | The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use.
* Re-enable collective metadata reads after disabling for chunk lookup (#1173)jhendersonHDF2021-11-091-7/+21
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