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BSD dual license Bio.Pathway and most of Bio.KEGG #2248

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merged 14 commits into from
Nov 4, 2019
Merged

BSD dual license Bio.Pathway and most of Bio.KEGG #2248

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e001987
Dual license Bio/KEGG/__init__.py
peterjc Sep 1, 2019
4ea24d5
Dual license Bio/KEGG/REST.py
peterjc Sep 1, 2019
d0bdd1f
Update Leighton's contact information
peterjc Sep 1, 2019
b959eef
Dual license Bio/KEGG/Map/__init__.py
peterjc Sep 2, 2019
9b8d5ca
Update Tarjei's contact details in CONTRIB.rst
peterjc Sep 2, 2019
b12fafa
Dual license Bio/KEGG/KGML/__init__.py
peterjc Sep 2, 2019
031f28f
Dual license Bio/KEGG/KGML/KGML_pathway.py
peterjc Sep 2, 2019
dff41c2
Dual license Bio/KEGG/KGML/KGML_parser.py
peterjc Sep 2, 2019
366bbe1
Dual license Bio/KEGG/Gene/__init__.py
peterjc Sep 2, 2019
5645349
Dual license Bio/KEGG/Compound/__init__.py
peterjc Sep 2, 2019
c340d18
Dual license Bio/Pathway/__init__.py
peterjc Sep 2, 2019
06ac9c9
Dual license Bio/Pathway/Rep/__init__.py
peterjc Sep 2, 2019
0b8670d
Dual license Bio/Pathway/Rep/MultiGraph.py
peterjc Sep 2, 2019
78839a0
Dual license Bio/Pathway/Rep/Graph.py
peterjc Sep 2, 2019
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8 changes: 5 additions & 3 deletions Bio/KEGG/Compound/__init__.py
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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Code to work with the KEGG Ligand/Compound database.

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8 changes: 5 additions & 3 deletions Bio/KEGG/Gene/__init__.py
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# Copyright 2017 by Kozo Nishida. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Code to work with the KEGG Gene database.

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8 changes: 5 additions & 3 deletions Bio/KEGG/KGML/KGML_parser.py
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# Copyright 2013 by Leighton Pritchard. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Classes and functions to parse a KGML pathway map.

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8 changes: 5 additions & 3 deletions Bio/KEGG/KGML/KGML_pathway.py
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# Copyright 2013 by Leighton Pritchard. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Classes to represent a KGML Pathway Map.

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8 changes: 5 additions & 3 deletions Bio/KEGG/KGML/__init__.py
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# Copyright 2013 by Leighton Pritchard. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Code to work with data from the KEGG database.

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8 changes: 5 additions & 3 deletions Bio/KEGG/Map/__init__.py
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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Load KEGG Pathway maps for use with the Biopython Pathway module.

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8 changes: 5 additions & 3 deletions Bio/KEGG/REST.py
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# Copyright 2014 by Kevin Wu.
# Revisions copyright 2014 by Peter Cock.
# 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Provides code to access the REST-style KEGG online API.

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8 changes: 5 additions & 3 deletions Bio/KEGG/__init__.py
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# Copyright 2001 by Tarjei Mikkelsen. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Code to work with data from the KEGG database.

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8 changes: 5 additions & 3 deletions Bio/Pathway/Rep/Graph.py
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# Copyright 2002 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 by Maximilian Greil. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""get/set abstraction for graph representation."""

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8 changes: 5 additions & 3 deletions Bio/Pathway/Rep/MultiGraph.py
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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 by Maximilian Greil. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""get/set abstraction for multi-graph representation."""

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8 changes: 5 additions & 3 deletions Bio/Pathway/Rep/__init__.py
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# Copyright 2001 by Tarjei Mikkelsen. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""BioPython Pathway support module.

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8 changes: 5 additions & 3 deletions Bio/Pathway/__init__.py
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# Copyright 2001 by Tarjei Mikkelsen. 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.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""BioPython Pathway module.

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4 changes: 2 additions & 2 deletions CONTRIB.rst
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Expand Up @@ -166,7 +166,7 @@ please open an issue on GitHub or mention it on the mailing list.
- Kuan-Yi Li <https://github.com/kuanyili>
- Kurt Graff <https://github.com/graph1994>
- Kyle Ellrott <https://github.com/kellrott>
- Leighton Pritchard <lpritc at domain scri.sari.ac.uk>
- Leighton Pritchard <https://github.com/widdowquinn>
- Lenna Peterson <ark first-name at gmail dot com>
- Leonhard Heizinger <https://github.com/he-leon>
- Leszek Pryszcz <https://github.com/lpryszcz>
Expand Down Expand Up @@ -241,7 +241,7 @@ please open an issue on GitHub or mention it on the mailing list.
- Stuart Nelis <https://github.com/biostu24>
- Sunhwan Jo <https://github.com/sunhwan>
- Tarcisio Fedrizzi <https://github.com/hcraT>
- Tarjei Mikkelsen <tarjei at domain genome.wi.mit.edu>
- Tarjei Mikkelsen <https://github.com/tmikkelsen>
- Ted Cybulski <https://github.com/tcyb>
- Terry Jones <https://github.com/terrycojones>
- Thomas Hamelryck <thamelry at domain binf.ku.dk>
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