Hdf5 merge issue 486 v112 #489
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* 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.
* 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.
* Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function
… and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
Undefined Bahavior Sanitizer errored here about left shifting negative numbers.
* 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
#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <[email protected]>
Added H5_OVERRIDE macro for compatibility with both C++11 and older.
* Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <[email protected]>
After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <[email protected]>
* Stop using global variables to share parse context with the lexer. The lexer uses an unconventional strategy for parsing lexical categories NUMBER (decimal numbers) and STRING (double-quoted strings) that involves sharing the parse context with the lexer using global variables. There are a couple of problems with that. First, the lexer is too complicated for the simple tokenization it performs—it's hard to tell if it is correct. Second, as @seanm points out, the shared global variables spill into the namespace shared by other libraries and application programs—e.g., VTK. * Regenerate source files from *.[yl]. * Replace strndup, which isn't available on Windows, with a custom routine, `trim_quotes`, that produces a copy of its `const char *` argument with leading and trailing double quotes ('"') removed. While I am here, remove the unnecessary statement `BEGIN INITIAL;`, which I should have deleted in a previous commit. * Regenerate .c from .l. * You haven't programmed in C until you have programmed in High-Definition (HD) C. * \#include "H5private.h" for HD* definitions. * Regenerate *.[ch] from *.[yl].
Fixes -Wreserved-identifier warnings due to multiple underscores in H5_HAVE___INLINE.
* Replaces checks for fork, etc. with H5_HAVE_UNISTD_H Code previously checked for individual POSIX API calls using H5_HAVE_FORK, etc. The calls we use have been standardized for decades and available via unistd.h. Some test messages that were missing when tests are skipped due to a lack of unistd.h were also added. The configure checks for individual POSIX API calls will be removed in a later commit. * Stupid formatter
* OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
lrknox
requested review from
bmribler,
fortnern,
jhendersonHDF,
jrmainzer,
qkoziol,
soumagne and
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as code owners
lrknox
commented
Mar 21, 2021
| @@ -3388,6 +3388,7 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u) | |||
| H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - c:%ld b:%ld s:%ld", j, | |||
| curr_pos, curr_idx, cnt_idx, blk_idx, str_idx); | |||
| dim_size = opts->dims[j]; /* Current dimension size */ | |||
| /* elmnt_cnt *= dim_size; /* Total number of elements in dimension */ | |||
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@byrnHDF This came from develop - should it be deleted from both branches?
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Yes it is just a debug comment.
…5_merge_issue_486_v112
* Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee. * Revert extra commits to match canonical develop. * Added [] to H5LTanalyze.l line 126 to eliminate warning "rule could not be matched". Ran bin/genparser hl/src with flex v2.6.4 and Bison v3.0.4 on jelly. * Added HD to strdup in H5LTparse.y line 338. Ran bin/genparser hlsrc again. * Removed line 126 from H5LTanalyze.l - previous line matches. Added previously removed line 318 of H5LTparse.y to fix hl_test_lite failure. Ran bin/genparser. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
byrnHDF
approved these changes
Mar 24, 2021
| @@ -10,11 +10,11 @@ | |||
| #pragma GCC diagnostic ignored "-Wsign-conversion" | |||
| #pragma GCC diagnostic ignored "-Wstrict-overflow" | |||
| #pragma GCC diagnostic ignored "-Wstrict-prototypes" | |||
| #if !defined (__clang__) | |||
| #if !defined (__clang__) | |||
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Not sure why this is added. I would expect the format check to remove it.
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Format check doesn't remove it - I suppose because the line starts with '#'. Why the spaces are put in I don't know.
hl/src/H5LTanalyze.c
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| @@ -28,9 +28,9 @@ | |||
| #elif defined _MSC_VER | |||
| #pragma warning(push, 1) | |||
| #endif | |||
| #line 2 "hl/src/H5LTanalyze.c" | |||
| #line 2 "hl/src//H5LTanalyze.c" | |||
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Extra slash is gone.
hl/src/H5LTparse.c
Outdated
| @@ -28,23 +28,22 @@ | |||
| #elif defined _MSC_VER | |||
| #pragma warning(push, 1) | |||
| #endif | |||
| /* A Bison parser, made by GNU Bison 3.7.2. */ | |||
| /* A Bison parser, made by GNU Bison 2.7. */ | |||
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Was this a conscience revert to 2.7?
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Was this a conscience revert to 2.7?
What I committed says 3.0.4. I'll check it after the merge.
hl/src/H5LTparse.c
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| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
|
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Extra spaces must be a mistake in the file that generated this?
| @@ -3388,6 +3388,7 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u) | |||
| H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - c:%ld b:%ld s:%ld", j, | |||
| curr_pos, curr_idx, cnt_idx, blk_idx, str_idx); | |||
| dim_size = opts->dims[j]; /* Current dimension size */ | |||
| /* elmnt_cnt *= dim_size; /* Total number of elements in dimension */ | |||
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Yes it is just a debug comment.
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