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>

20 files changed, 6 insertions, 251 deletions

diff --git a/COPYING b/COPYING
index da64ef8..9d32232 100644
--- a/COPYING
+++ b/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 
diff --git a/MANIFEST b/MANIFEST
index fb43579..9b0ce1c 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
@@ -1076,7 +1070,6 @@
 ./src/H5win32defs.h
 
 ./test/AtomicWriterReader.txt
-./test/COPYING
 ./test/H5srcdir.h
 ./test/H5srcdir_str.h.in
 ./test/Makefile.am
@@ -1437,7 +1430,6 @@
 ./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
@@ -1469,7 +1461,6 @@
 ./testpar/testphdf5.c
 ./testpar/testphdf5.h
 
-./tools/COPYING
 ./tools/Makefile.am
 ./tools/src/Makefile.am
 ./tools/test/Makefile.am
@@ -2893,7 +2884,6 @@
 ./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
@@ -2918,7 +2908,6 @@
 ./tools/test/perform/zip_perf.c
 
 # Utils directory
-./utils/COPYING
 ./utils/Makefile.am
 
 # Mirror VFD utilities
@@ -2930,7 +2919,6 @@
 ./utils/mirror_vfd/mirror_writer.c
 
 # high level libraries
-./hl/COPYING
 ./hl/Makefile.am
 ./hl/examples/Makefile.am
 ./hl/examples/ex_ds1.c
@@ -2957,7 +2945,6 @@
 ./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
@@ -2986,7 +2973,6 @@
 ./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
@@ -3022,7 +3008,6 @@
 ./hl/test/usa.wri
 
 # tools
-./hl/tools/COPYING
 ./hl/tools/Makefile.am
 ./hl/tools/gif2h5/Makefile.am
 ./hl/tools/gif2h5/decompress.c
@@ -3087,7 +3072,6 @@
 ./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
@@ -3112,7 +3096,6 @@
 ./hl/fortran/test/tsttable.F90
 
 # hl c++
-./hl/c++/COPYING
 ./hl/c++/Makefile.am
 ./hl/c++/examples/Makefile.am
 ./hl/c++/examples/ptExampleFL.cpp
@@ -3125,7 +3108,6 @@
 ./hl/c++/test/Makefile.am
 
 # java
-./java/COPYING
 ./java/Makefile.am
 ./java/CMakeLists.txt
 
diff --git a/bin/COPYING b/bin/COPYING
deleted file mode 100755
index 97969da..0000000
--- a/bin/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/c++/COPYING b/c++/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/c++/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/config/COPYING b/config/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/config/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/fortran/COPYING b/fortran/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/fortran/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/COPYING b/hl/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/hl/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/c++/COPYING b/hl/c++/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/hl/c++/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/fortran/COPYING b/hl/fortran/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/hl/fortran/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/src/COPYING b/hl/src/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/hl/src/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/test/COPYING b/hl/test/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/hl/test/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/tools/COPYING b/hl/tools/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/hl/tools/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/java/COPYING b/java/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/java/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/release_docs/COPYING b/release_docs/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/release_docs/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/src/COPYING b/src/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/src/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/test/COPYING b/test/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/test/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/testpar/COPYING b/testpar/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/testpar/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/tools/COPYING b/tools/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/tools/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/tools/test/perform/COPYING b/tools/test/perform/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/tools/test/perform/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/utils/COPYING b/utils/COPYING
deleted file mode 100644
index 9cec22f..0000000
--- a/utils/COPYING
+++ /dev/null
@@ -1,12 +0,0 @@
-
-  Copyright by The HDF Group.
-  All rights reserved.
-
-  The files and subdirectories in this directory are part of HDF5.
-  The full HDF5 copyright notice, including terms governing use,
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://www.hdfgroup.org/licenses.  If you do
-  not have access to either file, you may request a copy from
-  help@hdfgroup.org.
-