Normalize licenses. Closes khmer#864.

benchmarks/faGen.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 
 import sys, os
 import random

benchmarks/fqGen.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 
 import sys, os
 import random

benchmarks/fqToFaConvert.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 import sys
 import os
 

benchmarks/screedCreateTimeit.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 
 import sys
 import timeit

benchmarks/screedTimeit.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 
 import timeit
 import sys

benchmarks/screedTimeit1M.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 
 import timeit
 import sys

bigtests/__init__.py

@@ -1,3 +1,5 @@
+# Copyright (c) 2016, The Regents of the University of California.
+
 import gc
 import os
 import sys

doc/LICENSE.rst

@@ -2,13 +2,29 @@
 License
 =======
 
-Copyright (c) 2008-2015, Michigan State University
+Copyright (c) 2008, Michigan State University.
+Copyright (c) 2015, The Regents of the University of California.
 All rights reserved.
 
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
 
-    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-    * Neither the name of the author nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+    * Redistributions of source code must retain the above copyright notice,
+      this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    * Neither the name of the author nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

doc/index.rst

@@ -6,7 +6,8 @@
 screed - short read sequence utils
 ==================================
 
-:Copyright: 2008-2012 Michigan State University
+:Copyright: 2008, Michigan State University.
+:Copyright: 2015, The Regents of the University of California.
 :Authors: Alex Nolley, C. Titus Brown
 :Contact: ctb@msu.edu
 :License: BSD
@@ -18,18 +19,17 @@ Contents:
 
    screed
    example
-   
+
    dev/index
    release-notes/index
    user/known-issues
-   
+
    CODE_OF_CONDUCT
    LICENSE
-   
+
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-

get_version.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 """ Extracts the version of screed """
 
 import sys

screed/DBConstants.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2008-2010, Michigan State University
+# Copyright (c) 2008, Michigan State University.
 
 """
 Defines some constant strings identifications used in multiple

screed/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2008-2010, Michigan State University
+# Copyright (c) 2008, Michigan State University.
 
 """
 screed is a database tool useful for retrieving arbitrary kinds of sequence

screed/__main__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (C) 2016, The Regents of the University of California.
+# Copyright (c) 2016, The Regents of the University of California.
 
 from __future__ import absolute_import, print_function
 

screed/conversion.py

@@ -1,6 +1,6 @@
-from __future__ import absolute_import
-# Copyright (c) 2008-2010, Michigan State University
+# Copyright (c) 2008-2010, Michigan State University.
 
+from __future__ import absolute_import
 from .openscreed import ScreedDB
 
 _MAXLINELEN = 80

screed/createscreed.py

@@ -1,3 +1,5 @@
+# Copyright (c) 2016, The Regents of the University of California.
+
 from __future__ import absolute_import
 
 import argparse

screed/dna.py

@@ -1,3 +1,5 @@
+# Copyright (c) 2016, The Regents of the University of California.
+
 import array
 import string
 

screed/dump_fasta.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-# Copyright (C) 2008-2010, Michigan State University
-# Copyright (C) 2016, The Regents of the University of California.
+# Copyright (c) 2008, Michigan State University.
+# Copyright (c) 2016, The Regents of the University of California.
 
 from __future__ import print_function
 

screed/dump_fastq.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2010, Michigan State University
-# Copyright (C) 2016, The Regents of the University of California.
+# Copyright (c) 2008, Michigan State University.
+# Copyright (c) 2016, The Regents of the University of California.
 
 from __future__ import print_function
 from screed import ToFastq

screed/fasta.py

@@ -1,5 +1,6 @@
-from __future__ import absolute_import
+# Copyright (c) 2016, The Regents of the University of California.
 
+from __future__ import absolute_import
 from . import DBConstants
 from .screedRecord import Record
 from .utils import to_str

screed/fastq.py

@@ -1,5 +1,6 @@
-from __future__ import absolute_import
+# Copyright (c) 2016, The Regents of the University of California.
 
+from __future__ import absolute_import
 from . import DBConstants
 from .screedRecord import Record
 from .utils import to_str

screed/hava.py

@@ -1,5 +1,6 @@
-from __future__ import absolute_import
+# Copyright (c) 2016, The Regents of the University of California.
 
+from __future__ import absolute_import
 from . import DBConstants
 from .utils import to_str
 

screed/openscreed.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2008-2015, Michigan State University
+# Copyright (c) 2008, Michigan State University.
 """Reader and writer for screed."""
 
 from __future__ import absolute_import

screed/pygr_api.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2008-2010, Michigan State University
+# Copyright (c) 2008, Michigan State University.
 
 """
 A simple wrapper implementing a pygr-compatible SequenceDB based on screed.

screed/screedRecord.py

@@ -1,3 +1,5 @@
+# Copyright (c) 2016, The Regents of the University of California.
+
 from __future__ import absolute_import
 from functools import total_ordering
 import types

screed/seqparse.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2008-2010, Michigan State University
+# Copyright (c) 2008, Michigan State University.
 
 """
 seqparse contains custom sequence parsers for extending screed's

screed/utils.py

@@ -1,3 +1,5 @@
+# Copyright (c) 2016, The Regents of the University of California.
+
 def to_str(line):
     try:
         line = line.decode('utf-8')

setup.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# Copyright (c) 2016, The Regents of the University of California.
 from __future__ import print_function
 try:
     from setuptools import setup