18 copying update (#565)

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Restores maintainer mode in the autotools (#200)

Maintainer mode should be enabled in development branches.

Also adds helpful commenting.

Add script bin/switch_maint_mode.

Add file changes generated by bin reconfigure in
    src/H5Edefin.h
    src/H5Einit.h
    src/H5Epubgen.h
    src/H5Eterm.h

* Update MANIFEST for switch_maint_mode.

* Update so numbers to match 1.8.22 release.

* Updated configure with reconfigure.

* Updates and corrections following HDF5 1.8.22 release.

* Commit Makefile.ins with so version numbers updated by bin/reconfigure.

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* 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>

* Remove non-existant file from MANIFEST.

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

18 files changed, 6 insertions, 224 deletions

diff --git a/COPYING b/COPYING
index 046424f..bd6f31f 100644
--- a/COPYING
+++ b/COPYING
@@ -60,6 +60,12 @@ 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 8c541f3..32b49e2 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -47,7 +47,6 @@
 ./.github/workflows/main.yml  _DO_NOT_DISTRIBUTE_
 ./.github/workflows/pr-check.yml  _DO_NOT_DISTRIBUTE_
 
-./bin/COPYING
 ./bin/bbrelease       _DO_NOT_DISTRIBUTE_
 ./bin/buildhdf5
 ./bin/pkgscrpts/build_and_package_hdf5_binaries.sh  _DO_NOT_DISTRIBUTE_
@@ -116,7 +115,6 @@
 ./bin/batch/ray_ctestS.lsf.in.cmake
 ./bin/batch/raybsub
 
-./config/COPYING
 ./config/BlankForm
 ./config/apple
 ./config/cce-fflags
@@ -246,7 +244,6 @@
 #
 #------------------------------------------------------------------------------
 
-./fortran/COPYING
 ./fortran/Makefile.am
 ./fortran/Makefile.in
 
@@ -405,7 +402,6 @@
 #
 #------------------------------------------------------------------------------
 
-./c++/COPYING
 ./c++/Makefile.am
 ./c++/Makefile.in
 
@@ -541,7 +537,6 @@
 #
 #------------------------------------------------------------------------------
 
-./release_docs/COPYING
 ./release_docs/HISTORY-1_0-1_8_0_rc3.txt
 ./release_docs/HISTORY-1_8.txt
 ./release_docs/INSTALL
@@ -560,7 +555,6 @@
 ./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
@@ -927,7 +921,6 @@
 ./src/libhdf5.settings.in
 ./src/H5win32defs.h
 
-./test/COPYING
 ./test/H5srcdir.h
 ./test/H5srcdir_str.h.in
 ./test/Makefile.am
@@ -1105,7 +1098,6 @@
 ./test/testfiles/error_test_2
 ./test/testfiles/links_env.out
 
-./testpar/COPYING
 ./testpar/Makefile.am
 ./testpar/Makefile.in
 ./testpar/t_cache.c
@@ -1130,7 +1122,6 @@
 ./testpar/testphdf5.c
 ./testpar/testphdf5.h
 
-./tools/COPYING
 ./tools/Makefile.am
 ./tools/Makefile.in
 
@@ -2276,7 +2267,6 @@
 ./tools/testfiles/h5mkgrp_single_p.ls
 ./tools/testfiles/h5mkgrp_single_l.ls
 
-./tools/perform/COPYING
 ./tools/perform/Makefile.am
 ./tools/perform/Makefile.in
 ./tools/perform/build_h5perf_alone.sh
@@ -2300,7 +2290,6 @@
 ./tools/perform/zip_perf.c
 
 # high level libraries
-./hl/COPYING
 ./hl/Makefile.am
 ./hl/Makefile.in
 ./hl/examples/Makefile.am
@@ -2329,7 +2318,6 @@
 ./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/Makefile.in
 ./hl/src/H5DO.c
@@ -2356,7 +2344,6 @@
 ./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/Makefile.in
@@ -2390,7 +2377,6 @@
 ./hl/test/usa.wri
 
 # tools
-./hl/tools/COPYING
 ./hl/tools/Makefile.am
 ./hl/tools/Makefile.in
 ./hl/tools/gif2h5/Makefile.am
@@ -2411,7 +2397,6 @@
 ./hl/tools/gif2h5/testfiles/h52giftst.h5
 
 # hl fortran
-./hl/fortran/COPYING
 ./hl/fortran/Makefile.am
 ./hl/fortran/Makefile.in
 ./hl/fortran/examples/Makefile.am
@@ -2440,7 +2425,6 @@
 ./hl/fortran/test/tsttable.f90
 
 # hl c++
-./hl/c++/COPYING
 ./hl/c++/Makefile.am
 ./hl/c++/Makefile.in
 ./hl/c++/examples/Makefile.am
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/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/perform/COPYING b/tools/perform/COPYING
deleted file mode 100644
index 97969da..0000000
--- a/tools/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. 
-