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Removed mentions of Wdeclaration-after-statement now that C99 is requ… #447

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merged 2 commits into from
May 3, 2021

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@seanm seanm commented Mar 8, 2021

…ired

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Sorry, I misunderstood this change - I don't think that allowing declarations in the middle of a block is helpful for understanding how the code is structured and operates.

@derobins
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MSVC has historically been poor about this. I'm skeptical that code readability would improve with variable declarations scattered around functions (I feel the real solution is to break long functions into smaller ones), but this would be handy for loop variable declarations and removing the need for block brackets when we declare variables in ifdef'd code.

@seanm
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seanm commented Mar 11, 2021

All I'm really proposing here is not to treat this warning as an error.

You can continue to put most variables at the beginning of a function by convention, but at least going forward cases like loop counters (as @derobins mentioned) can have reduced scope.

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qkoziol commented Mar 11, 2021

All I'm really proposing here is not to treat this warning as an error.

You can continue to put most variables at the beginning of a function by convention, but at least going forward cases like loop counters (as @derobins mentioned) can have reduced scope.

Yes, I understand, but I still think everything except loop variables should be an error, so they don't creep in.

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seanm commented Mar 11, 2021

but I still think everything except loop variables should be an error

I don't think there's any way to do that. (I also totally disagree :) but won't argue that point. :))

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byrnHDF commented Mar 11, 2021

Just a side comment about preferring declarations at the top based on experiences. Searching through a long function with declarations sprinkled about makes it harder to fully understand. Of course shorter functions help with both issues.
But logical groupings help too.
A second issue much more important to me is that we still have to support three other branches and merges are already difficult enough with worrying about features that need to be worked around.
Conclusion; requiring declarations at the top are a minor annoyance for not much improvement given the capability of todays compilers.

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gnuoyd commented Mar 11, 2021

Mid-block declarations are a tool that I use to clarify code, especially long functions, especially when I'm preparing to make those long functions shorter.

Sometimes I use mid-block declarations to enforce single assignment on a variable, either because that makes my intent crystal clear, or because I am refactoring and I want to poison subsequent assignments, using the errors spit by the compiler to find them.

@byrnHDF , are we supporting the three other branches (which are these? 1.8, 1.10, 1.12?) on different compilers than develop? It seems to me that we have already committed to C99. Please elaborate on your concern.

When you say functions with mid-block declarations are "hard to understand," I am skeptical. Hard to understand how? Why?

I don't see why this should not be left to a programmer's discretion. If functions come out hard to understand, then we'll catch that during review.

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byrnHDF commented Mar 11, 2021

The comments about mid-functions were in relation to other code bases, where there was probably not a rigorous review process.
The comment about merges to other branches are from many battles merging a innocuous change to the other branches because of changing code conventions. If you do it enough you are willing to sacrifice some freedom for simpler merges!

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derobins commented Mar 11, 2021

@byrnHDF , are we supporting the three other branches (which are these? 1.8, 1.10, 1.12?) on different compilers than develop? It seems to me that we have already committed to C99. Please elaborate on your concern.

Microsoft's support for C99 (or any C standard, really) has historically been atrocious. Even though we've agreed that we require C99, we still have to hedge that when it comes to Microsoft as we have a lot of users on that platform who build with that compiler. Heck, even the C standard library isn't fundamentally a Windows thing.

When using a C99 feature that is not already in use in the HDF5 codebase, you usually have to check to see if MSVC is going to have problems. Now that we've moved our earliest supported VS version to 2015, this should be less of an issue, but it's still something to be wary of. Ideally, we'd check for this via a github action, but the earliest version of VS they offer is 2017. We switched one of the actions to build against that, which will help, but 2015 checks are only done via our internal CI, which isn't as visible when it fails.

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derobins commented Mar 11, 2021

As for maintaining multiple branches, that's probably a lower-order concern here. If anything, not having a block of top-level declarations might make merges less annoying. Merge algorithms have problems figuring out what to do when two changes tail append to the same chunk of code, and that includes the variable declaration blocks.

As an example, if I start with this:

int foo = 0;

And change it to this:

int foo = 0;
int bar = 0;

but somebody else merges a change to the parent branch that looks like this:

int foo = 0;
int baz = 0;

git will definitely complain when I pull in the upstream changes.

If that 'int baz = 0;' line were located near its use, the likelihood of a conflict would probably go down, particularly in longer functions. Again, the real solution is shorter functions, but in the meantime moving the declarations around could actually help when it comes to merging.

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It looks like VS2013 finally allowed declarations after statements as well as C99 Boolean variables. Now that VS2010/2012 are in the rearview mirror, we should probably think about allowing declarations mixed with code and change hbool_t/TRUE/FALSE to bool/true/false (at least internally, since hbool_t is in the public API).

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derobins commented Mar 11, 2021

A lot of the crap in H5public.h can also probably go away, now that C99 integer types are ubiquitous. I have a branch with some of that work done as it's needed to get the internal bits of H5pubconf.h out of the public API, which is a personal pet peeve of mine.

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seanm commented Mar 11, 2021

It looks like VS2013 finally allowed declarations after statements as well as C99 Boolean variables

Yes, and according to this "Visual Studio 2015 fully implements the C99 Standard Library, with the exception of any library features that depend on compiler features not yet supported by the Visual C++ compiler (for example, <tgmath.h> is not implemented)."

A lot of the crap in H5public.h can also probably go away, now that C99 integer types are ubiquitous

I was going to take a crack at that too, but trying not to make too many PRs at once. :)

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I was going to take a crack at that too, but trying not to make too many PRs at once. :)

Just keep in mind that removing symbols triggers binary compatibility report entries, which we try to avoid. It's okay to remove symbols from develop / 1.13, but we can't remove those symbols from 1.12 or 1.10 without angering people who consume our library.

If you are removing public symbols, try to split the changes into two PRs: one for internal things, where we effectively stop using the feature, and one for the public API changes. That helps us move the internal changes to the other supported branches.

As an example, check out what I did with the changes in #457, where I replace H5_HAVE_FORK with H5_HAVE_UNISTD_H but don't remove the CMake or Autotools checks. I'll do that in a future PR.

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byrnHDF commented Mar 12, 2021

I should have stated that, first, I am not arguing against the idea, just that changing the convention requires more thought and planning then just switching the flag off. What guidance will we provide devs so that we don't end up with spaghetti. We have a lot of configurations and platforms supported - have we checked known problem installations. What about support libraries, plugins, examples, vols, external tests, etc..

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qkoziol commented Mar 12, 2021

I should have stated that, first, I am not arguing against the idea, just that changing the convention requires more thought and planning then just switching the flag off. What guidance will we provide devs so that we don't end up with spaghetti. We have a lot of configurations and platforms supported - have we checked known problem installations. What about support libraries, plugins, examples, vols, external tests, etc..

Totally agree! I could see allowing variable declarations only for loop variable to start and building up guidance for other usage.

@@ -3,7 +3,6 @@
# circumstances, so ask the compiler to treat them as errors:
#
-Wbad-function-cast
-Wdeclaration-after-statement
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Should this warning also be taken out of error-general file or downgraded to just a warning in that file?
Also, line 2 and 3 of this file should be reworded. Maybe something like:

HDF5 code should not trigger the following warnings, they are identified
as candidates for the compiler to treat them as errors:

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There should not be a noerror-general file or any other noerror- file.

The error- and noerror- files are identical under a simple search and replace that is in config/gnu-flags: if PROMOTE_ERRORS is set to no then every occurrence of -Werror= is transformed to a warning (-W). Looks like the CMake files can do essentially the same thing.

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"Silence is golden." Declarations after statements are allowed, so let's just delete -Wdeclaration-after-statement everywhere it occurs.

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There should not be a noerror-general file or any other noerror- file.

The error- and noerror- files are identical under a simple search and replace that is in config/gnu-flags: if PROMOTE_ERRORS is set to no then every occurrence of -Werror= is transformed to a warning (-W). Looks like the CMake files can do essentially the same thing.

But wouldn't that promote ALL warnings? I thought the error-general file was intended to only promote those that should pass?

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"Silence is golden." Declarations after statements are allowed, so let's just delete -Wdeclaration-after-statement everywhere it occurs.

I didn't think we came to a conclusion on this. We would need a way to identify (maybe a ./bin/check_declaration script?) what was valid vs not wanted behavior.

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I don't know what you mean, "promote ALL warnings." Not all warnings are in the error- files. The error- files are supposed to contain those warnings that should ordinarily stop the library compilation cold.

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If there is an objectionable declaration after statement, then the place to flag that is during PR review.

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If there is an objectionable declaration after statement, then the place to flag that is during PR review.

I'd rather avoid many "noisy" PRs and just keep the error

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From a quick review of the platforms being reported in DT, it looks like no configuration is complaining about for loop declarations. This is looking at code that I know have these for loop declarations (blosc filter). Therefore I don't think we need to remove this warning at this time and still allow for loop declarations.
Let's start by implementing for loop declarations and then in a few months take the next step if we all agree?

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It was decided after engineering discussion to remove the warnings/errors for declaration-after-statement, and to allow them at the beginning of for loops and ifdef blocks. They are to be avoided otherwise and we will depend on code reviews to enforce that.

@lrknox lrknox merged commit 44db310 into HDFGroup:develop May 3, 2021
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qkoziol commented May 3, 2021

It was decided after engineering discussion to remove the warnings/errors for declaration-after-statement, and to allow them at the beginning of for loops and ifdef blocks. They are to be avoided otherwise and we will depend on code reviews to enforce that.

Where is this written down?

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lrknox commented May 3, 2021

I wrote it down here because there didn't seem to be anywhere else to put it.
2 questions:
Do you disagree with the statement?
Do you have a suggestion as to where to post?

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qkoziol commented May 4, 2021

I wrote it down here because there didn't seem to be anywhere else to put it.
2 questions:
Do you disagree with the statement?
Do you have a suggestion as to where to post?

I'm OK with the decision, but current+future people reviewing PRs for conforming to this decision aren't going to be consulting closed PRs for coding style guidelines. ;-)

Is there a coding style guide where it makes sense?

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epourmal commented May 4, 2021

I don't think it belongs to the "coding style"-type of document. Guidance should be added to the source file.

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lrknox commented May 5, 2021

The source files in this PR are two Warning list files, error or noerror, and INSTALL_warnings.txt in release_docs, but the notice to code reviewers and code writers applies to hundreds or possibly a thousand source files. Allen and I brainstormed a bit in this morning's engineering standup and we suggest adding a paragraph similar to the one at the start of this discussion to the bottom of the doc/code-conventions.md file.

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qkoziol commented May 5, 2021

The source files in this PR are two Warning list files, error or noerror, and INSTALL_warnings.txt in release_docs, but the notice to code reviewers and code writers applies to hundreds or possibly a thousand source files. Allen and I brainstormed a bit in this morning's engineering standup and we suggest adding a paragraph similar to the one at the start of this discussion to the bottom of the doc/code-conventions.md file.

That sounds like a good place for it. :-)

lrknox added a commit that referenced this pull request May 6, 2021
* 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 <lrknox@hdfgroup.org>

* 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 <lrknox@hdfgroup.org>

* 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 <lrknox@hdfgroup.org>

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

* Minor parallel improvements (#519)

* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Clean up MPI-IO VFD tracing support (#520)

* Clean up tracing support

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Brings the native implementation of H5Fdelete() from Bitbucket (#524)

* Committing clang-format changes

* Brings the native VFD H5Fdelete() implementation from Bitbucket

Only brings the 'del' callbacks, not the 'open/close' scheme.

* Formatter changes

* Committing clang-format changes

* Fixes direct VFD callback name

* Removes UNUSED macro from family API call

* Adds barrier and rank 0 check to MPI-I/O VFD delete

* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"

This reverts commit 909765f.

* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""

This reverts commit 9b04bef.

* Adds a second barrier after the delete in MPI-I/O VFD

* Only delete files in the core VFD when the backing store flag is set

* Fixes string issues in multi VFD

Also, h5test.c cleanup code now uses H5Fdelete().

* Formatted source

* Rework fapl checks for MPI-I/O VFD delete callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Minor warning fixes in develop (#526)

* Committing clang-format changes

* Minor warning fixes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes implementation of my_strdup() from the multi VFD (#527)

* Committing clang-format changes

* Removes my_strdup() from the multi VFD

* Use strdup directly when memory sanity checks are off

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes dead H5ST package from the library (#528)

* Committing clang-format changes

* Removes the unused H5ST package from the library

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix HDFFV-11232 (#530)

* 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

* added H5fortkit dependency for H5VLff.F90, HDFFV-11232

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes incorrect usage of H5I_BADID (#554)

* Committing clang-format changes

* Fixes incorrect use of H5I_BADID

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386a.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)"

This reverts commit 38d1b12.

* Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447)

* Removed mentions of Wdeclaration-after-statement now that C99 is required

* Remove -Werror=declaration-after-statement from error-general file.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Made private my_yyinput function static (#618)

This prevents it being exported as a public symbol.

* Adds const to a few global variables (#623)

* Committing clang-format changes

* Adds consts to a few global variables

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
lrknox added a commit that referenced this pull request May 6, 2021
* 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 <lrknox@hdfgroup.org>

* 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 <lrknox@hdfgroup.org>

* 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 <lrknox@hdfgroup.org>

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

* Minor parallel improvements (#519)

* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Clean up MPI-IO VFD tracing support (#520)

* Clean up tracing support

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Brings the native implementation of H5Fdelete() from Bitbucket (#524)

* Committing clang-format changes

* Brings the native VFD H5Fdelete() implementation from Bitbucket

Only brings the 'del' callbacks, not the 'open/close' scheme.

* Formatter changes

* Committing clang-format changes

* Fixes direct VFD callback name

* Removes UNUSED macro from family API call

* Adds barrier and rank 0 check to MPI-I/O VFD delete

* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"

This reverts commit 909765f.

* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""

This reverts commit 9b04bef.

* Adds a second barrier after the delete in MPI-I/O VFD

* Only delete files in the core VFD when the backing store flag is set

* Fixes string issues in multi VFD

Also, h5test.c cleanup code now uses H5Fdelete().

* Formatted source

* Rework fapl checks for MPI-I/O VFD delete callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Minor warning fixes in develop (#526)

* Committing clang-format changes

* Minor warning fixes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes implementation of my_strdup() from the multi VFD (#527)

* Committing clang-format changes

* Removes my_strdup() from the multi VFD

* Use strdup directly when memory sanity checks are off

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes dead H5ST package from the library (#528)

* Committing clang-format changes

* Removes the unused H5ST package from the library

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix HDFFV-11232 (#530)

* 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

* added H5fortkit dependency for H5VLff.F90, HDFFV-11232

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes incorrect usage of H5I_BADID (#554)

* Committing clang-format changes

* Fixes incorrect use of H5I_BADID

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386a.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)"

This reverts commit 38d1b12.

* Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447)

* Removed mentions of Wdeclaration-after-statement now that C99 is required

* Remove -Werror=declaration-after-statement from error-general file.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Made private my_yyinput function static (#618)

This prevents it being exported as a public symbol.

* Adds const to a few global variables (#623)

* Committing clang-format changes

* Adds consts to a few global variables

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* (fix) Segmentation fault when using a compound type. (#143)

* (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) H5Z_xform_create function and scientific notation (#144)

* (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>

* Committing clang-format changes

Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Jan-Willem Blokland <J.W.S.Blokland@XS4All.nl>
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
lrknox added a commit that referenced this pull request May 15, 2021
* 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 <lrknox@hdfgroup.org>

* 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 <lrknox@hdfgroup.org>

* 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 <lrknox@hdfgroup.org>

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

* Minor parallel improvements (#519)

* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Clean up MPI-IO VFD tracing support (#520)

* Clean up tracing support

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Brings the native implementation of H5Fdelete() from Bitbucket (#524)

* Committing clang-format changes

* Brings the native VFD H5Fdelete() implementation from Bitbucket

Only brings the 'del' callbacks, not the 'open/close' scheme.

* Formatter changes

* Committing clang-format changes

* Fixes direct VFD callback name

* Removes UNUSED macro from family API call

* Adds barrier and rank 0 check to MPI-I/O VFD delete

* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"

This reverts commit 909765f.

* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""

This reverts commit 9b04bef.

* Adds a second barrier after the delete in MPI-I/O VFD

* Only delete files in the core VFD when the backing store flag is set

* Fixes string issues in multi VFD

Also, h5test.c cleanup code now uses H5Fdelete().

* Formatted source

* Rework fapl checks for MPI-I/O VFD delete callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Minor warning fixes in develop (#526)

* Committing clang-format changes

* Minor warning fixes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes implementation of my_strdup() from the multi VFD (#527)

* Committing clang-format changes

* Removes my_strdup() from the multi VFD

* Use strdup directly when memory sanity checks are off

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes dead H5ST package from the library (#528)

* Committing clang-format changes

* Removes the unused H5ST package from the library

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix HDFFV-11232 (#530)

* 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

* added H5fortkit dependency for H5VLff.F90, HDFFV-11232

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes incorrect usage of H5I_BADID (#554)

* Committing clang-format changes

* Fixes incorrect use of H5I_BADID

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386a.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)"

This reverts commit 38d1b12.

* Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447)

* Removed mentions of Wdeclaration-after-statement now that C99 is required

* Remove -Werror=declaration-after-statement from error-general file.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Made private my_yyinput function static (#618)

This prevents it being exported as a public symbol.

* Adds const to a few global variables (#623)

* Committing clang-format changes

* Adds consts to a few global variables

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* (fix) Segmentation fault when using a compound type. (#143)

* (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) H5Z_xform_create function and scientific notation (#144)

* (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>

* Committing clang-format changes

* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)

* Cleanup tools debug build warnings (#627)

* 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

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

* Cleanup warnings for tools debug builds

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* h5diff subset indexing (#628)

* 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

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

* Cleanup warnings for tools debug builds

* TRILAB-227 - fix indexing for h5diff selections

* Correct location of pos to index function call

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes gratuitous (double)x.yF casts (#632)

* Committing clang-format changes

* Removes gratuitous (double)x.yF casts

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Cleans up a const warning left over from previous constification (#633)

* Committing clang-format changes

* Adds consts to a few global variables

* Cleans up a const warning left over from previous constification

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Purges UFAIL from the library (#637)

* Committing clang-format changes

* Purges UFAIL from the library

* H5HL_insert change requested in PR

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Bmr dev hdffv 11223 (#640)

* Fixed HDFFV-11223 (CVE-2018-14460)

Description
    - Added checks against buffer size to prevent segfault, in case of data
      corruption, for sdim->size and sdim->max.
    - Renamed data files in an existing test to shorten their length
      as agreed with other developers previously.
Platforms tested:
    Linux/64 (jelly)

* Committing clang-format changes

* Updated for test files

* Updated for HDFFV-11223

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)"

This reverts commit 7a68286.

Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Jan-Willem Blokland <J.W.S.Blokland@XS4All.nl>
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
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7 participants