Make initial authorship of Bio.NeuralNetwork explicit

Cross reference discussion on
#1518 (comment)

Bio/NeuralNetwork/BackPropagation/Layer.py

@@ -1,14 +1,15 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Model a single layer in a nueral network.
 
 These classes deal with a layers in the neural network (ie. the input layer,
 hidden layers and the output layer).
 """
-# standard library
+
 import math
 import random
 

Bio/NeuralNetwork/BackPropagation/Network.py

@@ -1,7 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Represent Neural Networks.
 
@@ -16,7 +17,7 @@
 My sincerest thanks to him for making this available for me to work from,
 and my apologies for anything I mangled.
 """
-# standard library
+
 import math
 
 

Bio/NeuralNetwork/BackPropagation/__init__.py

@@ -1,2 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
 """Back-propagation for neural networks."""
 # TODO: Remove empty __init__.py once we drop Python 2 support

Bio/NeuralNetwork/Gene/Motif.py

@@ -1,7 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Find and deal with motifs in biological sequence data.
 

Bio/NeuralNetwork/Gene/Pattern.py

@@ -1,7 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Generic functionality useful for all gene representations.
 
@@ -10,10 +11,9 @@
 signatures and schemas). These are the general classes which should be
 handle any of the different specific patterns.
 """
-# standard library
+
 import random
 
-# biopython
 from Bio.Alphabet import _verify_alphabet
 from Bio.Seq import Seq, MutableSeq
 

Bio/NeuralNetwork/Gene/Schema.py

@@ -1,7 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Deal with Motifs or Signatures allowing ambiguity in the sequences.
 
@@ -15,7 +16,7 @@
 character can be anything. This helps us condense a whole ton of
 motifs or signatures.
 """
-# standard modules
+
 from __future__ import print_function
 
 import random

Bio/NeuralNetwork/Gene/Signature.py

@@ -1,7 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Find and deal with signatures in biological sequence data.
 

Bio/NeuralNetwork/Gene/__init__.py

@@ -1,2 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
 """Module for using neural networks to model genetic data."""
 # TODO: Remove empty __init__.py once we drop Python 2 support

Bio/NeuralNetwork/StopTraining.py

@@ -1,7 +1,8 @@
+# Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
 
 """Classes to help deal with stopping training a neural network.
 

Bio/NeuralNetwork/Training.py

@@ -1,7 +1,9 @@
+# Copyright 2001 Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-#
+
 
 """Provide classes for dealing with Training Neural Networks."""
 

Bio/NeuralNetwork/__init__.py

@@ -1,4 +1,5 @@
 # Copyright 2001 by Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.

Tests/test_NNExclusiveOr.py

@@ -1,11 +1,17 @@
-#!/usr/bin/env python
+# Copyright 2001 Brad Chapman.  All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
 """Test function to teach the neural network an XOR function.
 
 This is a very basic test of Neural Network functionality.
 """
 from __future__ import print_function
 
 import warnings
+
 from Bio import BiopythonDeprecationWarning
 with warnings.catch_warnings():
     warnings.simplefilter('ignore', BiopythonDeprecationWarning)

Tests/test_NNGene.py

@@ -1,5 +1,5 @@
-#!/usr/bin/env python
-
+# Copyright 2001 Brad Chapman.  All rights reserved.
+#
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
@@ -9,19 +9,18 @@
 This exercises the Motif, Schema and Signature methods of representing
 genes, as well as generic Pattern methods.
 """
-# standard library
+
 from __future__ import print_function
 
 import os
 import unittest
+import warnings
 
-# Biopython
 from Bio import SeqIO
 from Bio.Seq import Seq
 from Bio.Alphabet import IUPAC
 from Bio.SeqRecord import SeqRecord
 
-import warnings
 from Bio import BiopythonDeprecationWarning
 with warnings.catch_warnings():
     warnings.simplefilter('ignore', BiopythonDeprecationWarning)

Tests/test_NNGeneral.py

@@ -1,10 +1,15 @@
-#!/usr/bin/env python
+# Copyright 2001 Brad Chapman.  All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
 """General test for the NeuralNetwork libraries.
 
 This exercises various elements of the BackPropagation NeuralNetwork
 libraries.
 """
-# standard library
+
 import random
 import unittest