Update top-level COPYING file and remove COPYING files from subdirect…

…ories (HDFGroup#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 e4a9cee.

* 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>

COPYING

@@ -67,6 +67,12 @@ under Prime Contract No. DE-AC02-05CH11231.
 
 -----------------------------------------------------------------------------
 
+Portions of HDF5 were developed with support from Lawrence Livermore 
+National Laboratory and the United States Department of Energy under 
+Prime Contract No. DE-AC52-07NA27344.
+
+-----------------------------------------------------------------------------
+
 Portions of HDF5 were developed with support from the University of 
 California, Lawrence Livermore National Laboratory (UC LLNL).  
 The following statement applies to those portions of the product and must 

MANIFEST

@@ -58,7 +58,6 @@
 ./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_
@@ -117,7 +116,6 @@
 ./bin/pkgscrpts/makeInternalREADME.pl      _DO_NOT_DISTRIBUTE_
 ./bin/pkgscrpts/makeOuterREADME.pl         _DO_NOT_DISTRIBUTE_
 
-./config/COPYING
 ./config/BlankForm
 ./config/apple
 ./config/cce-fflags
@@ -263,7 +261,6 @@
 #
 #------------------------------------------------------------------------------
 
-./fortran/COPYING
 ./fortran/Makefile.am
 ./fortran/robodoc.rc
 
@@ -395,7 +392,6 @@
 #
 #------------------------------------------------------------------------------
 
-./c++/COPYING
 ./c++/Makefile.am
 
 ./c++/examples/chunks.cpp
@@ -526,7 +522,6 @@
 #
 #------------------------------------------------------------------------------
 
-./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
@@ -549,7 +544,6 @@
 ./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
@@ -1061,7 +1055,6 @@
 ./src/libhdf5.settings.in
 
 ./test/AtomicWriterReader.txt
-./test/COPYING
 ./test/H5srcdir.h
 ./test/H5srcdir_str.h.in
 ./test/Makefile.am
@@ -1319,11 +1312,12 @@
 ./test/vds_swmr_reader.c
 ./test/vds_swmr_writer.c
 ./test/vfd_swmr.c
+./test/vfd_swmr_addrem_writer.c
+./test/vfd_swmr_attrdset_writer.c
+./test/vfd_swmr_bigset_writer.c
 ./test/vfd_swmr_common.c
 ./test/vfd_swmr_common.h
 ./test/vfd_swmr_generator.c
-./test/vfd_swmr_addrem_writer.c
-./test/vfd_swmr_bigset_writer.c
 ./test/vfd_swmr_group_writer.c
 ./test/vfd_swmr_reader.c
 ./test/vfd_swmr_remove_reader.c
@@ -1440,7 +1434,6 @@
 ./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
@@ -1472,7 +1465,6 @@
 ./testpar/testphdf5.c
 ./testpar/testphdf5.h
 
-./tools/COPYING
 ./tools/Makefile.am
 ./tools/src/Makefile.am
 ./tools/test/Makefile.am
@@ -2859,7 +2851,6 @@
 ./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
@@ -2884,7 +2875,6 @@
 ./tools/test/perform/zip_perf.c
 
 # Utils directory
-./utils/COPYING
 ./utils/Makefile.am
 
 # Mirror VFD utilities
@@ -2896,7 +2886,6 @@
 ./utils/mirror_vfd/mirror_writer.c
 
 # high level libraries
-./hl/COPYING
 ./hl/Makefile.am
 ./hl/examples/Makefile.am
 ./hl/examples/ex_ds1.c
@@ -2923,7 +2912,6 @@
 ./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
@@ -2952,7 +2940,6 @@
 ./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
@@ -2988,7 +2975,6 @@
 ./hl/test/usa.wri
 
 # tools
-./hl/tools/COPYING
 ./hl/tools/Makefile.am
 ./hl/tools/gif2h5/Makefile.am
 ./hl/tools/gif2h5/decompress.c
@@ -3053,7 +3039,6 @@
 ./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
@@ -3078,7 +3063,6 @@
 ./hl/fortran/test/tsttable.F90
 
 # hl c++
-./hl/c++/COPYING
 ./hl/c++/Makefile.am
 ./hl/c++/examples/Makefile.am
 ./hl/c++/examples/ptExampleFL.cpp
@@ -3091,7 +3075,6 @@
 ./hl/c++/test/Makefile.am
 
 # java
-./java/COPYING
 ./java/Makefile.am
 ./java/CMakeLists.txt