112 copying update (#563)

* 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.

* Update top-level COPYING file and remove COPYING files from
subdirectories.

* Update top-level COPYING file and remove COPYING files from subdirectories (#561)

* 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 e4a9cee441efa75b16a8ee030c86189e186dd266.

* Revert extra commits to match canonical develop.

* Update top-level COPYING file and remove COPYING files from
subdirectories.

* Remove subdirectory COPYING files from MANIFEST.

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

1 files changed, 0 insertions, 18 deletions

diff --git a/MANIFEST b/MANIFEST
index faf703f..ae9f696 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -63,7 +63,6 @@
 ./m4/ax_try_compile_java.m4
 ./m4/ax_try_run_java.m4
 
-./bin/COPYING
 ./bin/bbrelease         _DO_NOT_DISTRIBUTE_
 ./bin/buildhdf5
 ./bin/checkapi        _DO_NOT_DISTRIBUTE_
@@ -122,7 +121,6 @@
 ./bin/pkgscrpts/makeInternalREADME.pl      _DO_NOT_DISTRIBUTE_
 ./bin/pkgscrpts/makeOuterREADME.pl         _DO_NOT_DISTRIBUTE_
 
-./config/COPYING
 ./config/BlankForm
 ./config/apple
 ./config/cce-fflags
@@ -283,7 +281,6 @@
 #
 #------------------------------------------------------------------------------
 
-./fortran/COPYING
 ./fortran/Makefile.am
 ./fortran/robodoc.rc
 
@@ -415,7 +412,6 @@
 #
 #------------------------------------------------------------------------------
 
-./c++/COPYING
 ./c++/Makefile.am
 
 ./c++/examples/chunks.cpp
@@ -546,7 +542,6 @@
 #
 #------------------------------------------------------------------------------
 
-./release_docs/COPYING
 ./release_docs/HISTORY-1_0-1_8_0_rc3.txt
 ./release_docs/HISTORY-1_8_0-1_10_0.txt
 ./release_docs/HISTORY-1_10_0-1_12_0.txt
@@ -569,7 +564,6 @@
 ./src/hdf5.lnt        _DO_NOT_DISTRIBUTE_
 ./src/hdf5-win.lnt      _DO_NOT_DISTRIBUTE_
 ./src/hdf5-lin.lnt      _DO_NOT_DISTRIBUTE_
-./src/COPYING
 ./src/H5.c
 ./src/H5checksum.c
 ./src/H5dbg.c
@@ -1069,7 +1063,6 @@
 ./src/H5win32defs.h
 
 ./test/AtomicWriterReader.txt
-./test/COPYING
 ./test/H5srcdir.h
 ./test/H5srcdir_str.h.in
 ./test/Makefile.am
@@ -1429,7 +1422,6 @@
 ./test/testfiles/plist_files/strcpl_64be
 ./test/testfiles/plist_files/strcpl_64le
 
-./testpar/COPYING
 ./testpar/Makefile.am
 ./testpar/t_bigio.c
 ./testpar/t_cache.c
@@ -1461,7 +1453,6 @@
 ./testpar/testphdf5.c
 ./testpar/testphdf5.h
 
-./tools/COPYING
 ./tools/Makefile.am
 ./tools/src/Makefile.am
 ./tools/test/Makefile.am
@@ -2884,7 +2875,6 @@
 ./tools/testfiles/h5mkgrp_single_p.ls
 ./tools/testfiles/h5mkgrp_single_l.ls
 
-./tools/test/perform/COPYING
 ./tools/test/perform/Makefile.am
 ./tools/test/perform/build_h5perf_alone.sh
 ./tools/test/perform/build_h5perf_serial_alone.sh
@@ -2909,7 +2899,6 @@
 ./tools/test/perform/zip_perf.c
 
 # Utils directory
-./utils/COPYING
 ./utils/Makefile.am
 
 # Mirror VFD utilities
@@ -2921,7 +2910,6 @@
 ./utils/mirror_vfd/mirror_writer.c
 
 # high level libraries
-./hl/COPYING
 ./hl/Makefile.am
 ./hl/examples/Makefile.am
 ./hl/examples/ex_ds1.c
@@ -2948,7 +2936,6 @@
 ./hl/examples/ptExampleFL.c
 ./hl/examples/run-hl-ex.sh
 ./hl/examples/run-hlc-ex.sh.in
-./hl/src/COPYING
 ./hl/src/Makefile.am
 ./hl/src/H5DO.c
 ./hl/src/H5DOpublic.h
@@ -2977,7 +2964,6 @@
 ./hl/src/H5TBprivate.h
 ./hl/src/H5TBpublic.h
 ./hl/src/hdf5_hl.h
-./hl/test/COPYING
 ./hl/test/H5srcdir_str.h.in
 ./hl/test/Makefile.am
 ./hl/test/dsdata.txt
@@ -3013,7 +2999,6 @@
 ./hl/test/usa.wri
 
 # tools
-./hl/tools/COPYING
 ./hl/tools/Makefile.am
 ./hl/tools/gif2h5/Makefile.am
 ./hl/tools/gif2h5/decompress.c
@@ -3078,7 +3063,6 @@
 ./hl/tools/testfiles/w-help1.ddl
 
 # hl fortran
-./hl/fortran/COPYING
 ./hl/fortran/Makefile.am
 ./hl/fortran/examples/Makefile.am
 ./hl/fortran/examples/run-hlfortran-ex.sh.in
@@ -3103,7 +3087,6 @@
 ./hl/fortran/test/tsttable.F90
 
 # hl c++
-./hl/c++/COPYING
 ./hl/c++/Makefile.am
 ./hl/c++/examples/Makefile.am
 ./hl/c++/examples/ptExampleFL.cpp
@@ -3116,7 +3099,6 @@
 ./hl/c++/test/Makefile.am
 
 # java
-./java/COPYING
 ./java/Makefile.am
 ./java/CMakeLists.txt