Simplified hl parsing #399

gnuoyd · 2021-02-26T22:31:33Z

Fixes #398 .

@seanm

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.

lrknox · 2021-02-26T23:06:35Z

There were 5 variations of this error in the Windows Latest MSVC test:
Building Custom Rule D:/a/hdf5/hdf5/hl/tools/gif2h5/CMakeLists.txt
decompress.c
gif2hdf.c
gif2mem.c
gifread.c
writehdf.c
Generating Code...
libhdf5_hl.lib(H5LTanalyze.obj) : error LNK2019: unresolved external symbol strndup referenced in function H5LTyylex [D:\a\hdf5\build\hl\tools\gif2h5\gif2h5.vcxproj]
D:\a\hdf5\build\bin\Release\gif2h5.exe : fatal error LNK1120: 1 unresolved externals [D:\a\hdf5\build\hl\tools\gif2h5\gif2h5.vcxproj]
Building Custom Rule D:/a/hdf5/hdf5/hl/src/CMakeLists.txt

seanm · 2021-02-27T18:50:34Z

lgtm. Once ready, can you please bring this to 1.10 branch too?

seanm · 2021-03-02T02:47:12Z

@gnuoyd seems strndup wasn't in HDF5 before this patch. It's a POSIX function, so not in Windows I guess, and only officially added to ISO C in C2x.

I guess you can replace with malloc+strcpy.

byrnHDF · 2021-03-02T12:37:36Z

@gnuoyd seems strndup wasn't in HDF5 before this patch. It's a POSIX function, so not in Windows I guess, and only officially added to ISO C in C2x.

I guess you can replace with malloc+strcpy.

However strdup is used in the library.

qkoziol · 2021-03-02T16:26:52Z

hl/src/H5LTanalyze.l

-                            return NUMBER;
-                        } else
-                            REJECT;
+                        H5LTyylval.ival = atoi(yytext);


Please use the HD* portability macros for all standard / system calls. (atoi, strdup, etc)

seanm · 2021-03-05T16:15:07Z

@gnuoyd any chance you might be able to update this soon? It seems to be the last thing blocking me from updating VTK's HDF (specifically the is_enum vs std::is_enum conflict).

gnuoyd · 2021-03-05T18:38:10Z

On Fri, Mar 05, 2021 at 08:15:24AM -0800, Sean McBride wrote: @gnuoyd any chance you might be able to update this soon? It seems to be the last thing blocking me from updating VTK's HDF (specifically the `is_enum` vs `std::is_enum` conflict).

I can probably get us over the Windows hump, today. Dave

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.

derobins

Please follow THG coding conventions. In particular, using the HD prefix on standard library calls.

seanm · 2021-03-07T07:03:58Z

hl/src/H5LTanalyze.l

+
+    assert(quoted[0] == '"' && quoted[len - 1] == '"');
+
+    trimmed = strdup(quoted + 1);


Even MSVC 2015 supports enough C99 to do the declaration & initialization at once, as in: char *trimmed = strdup(quoted + 1); Is there a reason you do this C89 style? (I've noticed most of HDF5 is the same.)

gnuoyd · 2021-03-08T03:11:03Z

On Sat, Mar 06, 2021 at 11:04:09PM -0800, Sean McBride wrote: +/* Allocate a copy of `quoted` with the double quote character at + * the beginning and the one at the end both removed. The caller is + * responsible for free()ing the copy. + */ +static char * +trim_quotes(const char *quoted) +{ + size_t len = strlen(quoted); + char *trimmed; + + assert(quoted[0] == '"' && quoted[len - 1] == '"'); + + trimmed = strdup(quoted + 1); Even MSVC 2015 supports enough C99 to do the declaration & initialization at once, as in: `char *trimmed = strdup(quoted + 1);` Is there a reason you do this C89 style? (I've noticed most of HDF5 is the same.)

It's only in the last year that THG dropped support for older versions of MSVC. So it has not been long that declarations that appeared elsewhere than the beginning of a block would compile on every supported platform. Looks like -Wdeclaration-after-statement is still enabled. Probably just inertia? Sometimes I use a mid-block declaration, combined with a liberal dose of `const`, to get the compiler's help to enforce properties on my code---for example, the property that a variable is assigned only once. Dave

seanm · 2021-03-08T15:02:49Z

@gnuoyd I see, thanks. So I guess it's only in develop that mid-block declarations are allowed, since you presumably don't want old branches to stop working with old toolchains. And since I need this change of your in 1.10.x, I retract my suggestion/comment. :) But for develop, I made this quickie: #447

(HD) C.

epourmal · 2021-03-10T23:05:08Z

@gnuoyd I see, thanks. So I guess it's only in develop that mid-block declarations are allowed, since you presumably don't want old branches to stop working with old toolchains. And since I need this change of your in 1.10.x, I retract my suggestion/comment. :) But for develop, I made this quickie: #447

Sorry, maybe I missing some context :-) 1_10 is not old and should comply with C99. I don't see why the change that is in develop would not be in 1_10 branch for upcoming 1.10.8 release.

seanm · 2021-03-15T20:24:24Z

@gnuoyd so I'm just integrating this into VTK and it looks like it will fix the is_enum issue. Thanks!

There are still a small number of public symbols that don't have any H5 (or similar) prefix, namely:

In hl:

indent
input_len
my_yyinput -> looks like this could be static
myinput

in main library:

Nflock
Pflock
use_locks_env_g

Would be cool if they could be either prefixed or marked as non-exported. Thoughts?

@seanm

* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * 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. * Full set of current H5F documentation. (#105) * 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 (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * 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 * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#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 C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * 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]> * Removed checks/workarounds for pre-C++89 compatibility (#449) 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 (#451) * 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]> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * Simplified hl parsing (#399) * 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]. * Removed workarounds for pre-standard inline keyword (#423) Fixes -Wreserved-identifier warnings due to multiple underscores in H5_HAVE___INLINE. * Replaces checks for fork, etc. with checks for unistd.h (#457) * 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 * develop JNI export references and java updates (#467) * 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> * Update h5LT files with latest flex and Bison available on jelly (#502) * 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> Co-authored-by: Gerd Heber <[email protected]> Co-authored-by: bljhdf <[email protected]> Co-authored-by: H. Joe Lee <[email protected]> Co-authored-by: Quincey Koziol <[email protected]> Co-authored-by: Sean McBride <[email protected]> Co-authored-by: Dana Robinson <[email protected]> Co-authored-by: David Young <[email protected]> Co-authored-by: Allen Byrne <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

@seanm

* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * 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. * Full set of current H5F documentation. (#105) * 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 (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * 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 * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#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 C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * 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]> * Removed checks/workarounds for pre-C++89 compatibility (#449) 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 (#451) * 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]> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * Simplified hl parsing (#399) * 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]. * Removed workarounds for pre-standard inline keyword (#423) Fixes -Wreserved-identifier warnings due to multiple underscores in H5_HAVE___INLINE. * Replaces checks for fork, etc. with checks for unistd.h (#457) * 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 * develop JNI export references and java updates (#467) * 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> * Fix display of long double in tools (#469) * 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 * HDFFV-11113 long double in tools * HDFFV-11113 add note Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Update clang config (#473) * 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> * Correct syntax error. (#474) a Fortran compile -> a Fortran compiler * Cleans up a couple of MSVC warnings in testhdf5 (#475) * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix typos and grammar errors. (#476) * Suppresses the tcheck_version test's abort dialog on Windows (#477) * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Rerun genparser. * Fix merge issues and rerun genparser. Co-authored-by: Gerd Heber <[email protected]> Co-authored-by: bljhdf <[email protected]> Co-authored-by: H. Joe Lee <[email protected]> Co-authored-by: Quincey Koziol <[email protected]> Co-authored-by: Sean McBride <[email protected]> Co-authored-by: Dana Robinson <[email protected]> Co-authored-by: David Young <[email protected]> Co-authored-by: Allen Byrne <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <[email protected]>

@seanm

* close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * 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. * Simplified hl parsing (#399) * 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]. * Removed workarounds for pre-standard inline keyword (#423) Fixes -Wreserved-identifier warnings due to multiple underscores in H5_HAVE___INLINE. * Replaces checks for fork, etc. with checks for unistd.h (#457) * 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 * Update h5LT files with latest flex and Bison available on jelly (#502) * 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> * Add cmake variable HDF5_LIB_INFIX (#7) * Add cmake variable HDF5_LIB_INFIX This infix is added to all library names after 'hdf5'. e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' This name is used in packages on debian based systems. (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) This option is useful when testing projects on debian based systems with custom builds of hdf5 while trying to minimize differences between the custom setup and the environment created by installing system packages. * Added RELEASE.txt entry for HDF5_LIB_INFIX. Co-authored-by: Larry Knox <[email protected]> * Update test/accum.c to correct merge for replacing checks for fork, etc. with checks for unistd.h (#457) * Committing clang-format changes Co-authored-by: H. Joe Lee <[email protected]> Co-authored-by: Sean McBride <[email protected]> Co-authored-by: David Young <[email protected]> Co-authored-by: Dana Robinson <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Raphael Grimm <[email protected]>

gnuoyd added 2 commits February 26, 2021 16:14

Regenerate source files from *.[yl].

4b810db

gnuoyd requested review from derobins and raylu-hdf February 26, 2021 22:31

gnuoyd self-assigned this Feb 26, 2021

gnuoyd requested review from bmribler and byrnHDF as code owners February 26, 2021 22:31

gnuoyd mentioned this pull request Feb 26, 2021

Made some publicly exported symbols static, prefixed others with H5_ #347

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qkoziol requested changes Mar 2, 2021

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gnuoyd added 2 commits March 5, 2021 14:53

Regenerate .c from .l.

4d880b3

derobins requested changes Mar 7, 2021

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seanm reviewed Mar 7, 2021

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You haven't programmed in C until you have programmed in High-Definition

7f8aa01

(HD) C.

qkoziol approved these changes Mar 10, 2021

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seanm approved these changes Mar 10, 2021

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derobins approved these changes Mar 13, 2021

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gnuoyd added 2 commits March 13, 2021 16:42

\#include "H5private.h" for HD* definitions.

319f2c4

Regenerate *.[ch] from *.[yl].

c86960f

seanm approved these changes Mar 15, 2021

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lrknox merged commit f6d919a into HDFGroup:develop Mar 15, 2021

lrknox mentioned this pull request Mar 21, 2021

Merge changes from PRs #399, 423, 453, 457, 467, #502 to support branches. #486

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Simplified hl parsing #399

Simplified hl parsing #399

gnuoyd commented Feb 26, 2021

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byrnHDF commented Mar 2, 2021

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epourmal commented Mar 10, 2021

seanm commented Mar 15, 2021


		assert(quoted[0] == '"' && quoted[len - 1] == '"');

		trimmed = strdup(quoted + 1);

Simplified hl parsing #399

Simplified hl parsing #399

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gnuoyd commented Feb 26, 2021

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