Hdf5 merge issue 488 v112 (#534)

* 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.

* Purge the buffer used in type conversion. (#263)

Some of the uniniitialized bits in the buffer may get carried through
all the way to disk, creating a risk for leaks.

We observed an msan error during the floating point output conversion.
Due to the encoding certain bits could remain untouched during the conversion.

In this draft we zero initialize the dbuf used by every convertor.

* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#405)

* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033)
Description
    Checked against buffer size to prevent segfault, in case of data corruption.

    + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
    + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode
Platforms tested:
    Linux/64 (jelly)

* Accidentally left in another occurrence of the previous patch from user
   after a more correct fix was applied, that is the check now accounted
   for the previous advance of the buffer pointer.  Removed it.

* Typo

* Fixed format issues.

* Added test.

* Changed arguments to ADD_H5_TEST

* Fixing arguments to ADD_H5_TEST again.

* Fixing arguments again.

* Took out the CMake changes until Allen can help.

* Added files:

tCVE_2018_11206_fill_old.h5
tCVE_2018_11206_fill_new.h5

* Revert "Took out the CMake changes until Allen can help."

This reverts commit c21324d6e0044994c5cd24b0671e7d1dd41096cc.

* Revert "Fixing arguments again."

This reverts commit 5832a70674339e4b524749adde5a181f8c3a446a.

* Revert "Fixing arguments to ADD_H5_TEST again."

This reverts commit b45de823c22ce83a388d46466ef7c04b66ff05ed.

* Revert "Changed arguments to ADD_H5_TEST"

This reverts commit 16719824f57e52158451ddd261788c0dcaa3ec55.

* Added first argument to ADD_H5_TEST for HDFFV-10480 fix.

* Changed argument 0 to 1

* Revert "Changed argument 0 to 1"

This reverts commit b343d6613ba681b43248dd5820e96389984ebcf7.

* Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix."

This reverts commit b8a0f9a9e8ec8e6c6ff38d33195d63edff76a563.

* Added first argument and corrected the second.

* Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049

* Improved error messages.

* Added description of the current HDF5 branches; added a draft of contribution policy. (#445)

* Added description of the current HDF5 branches.

* Removed capitalization in from Develop, Release, Feature to reflect the real naming schema

* Added a draft of contributions guidance document.

* Fixed typos.

* Fixed section title.

* Fixed typo.

* Fixed typos and formatting.

* Fixed many typos and simplified the text (e.g., removed testing instructions and left pointers to where to find them, etc.)

* Fixed a typo.
 Please enter the commit message for your changes. Lines starting

* Added contributing.md file and rearranged doc entries in alphabetical order.

* ddressed Gerd's review comments; found and fixed more typos.

* Addressed comments from Larry and Scot.

* Fix CMake error message location. (#478)

Print error message if Perl is not found.

* 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: Yu Feng <rainwoodman@gmail.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: epourmal <epourmal@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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