Change license to GPL. Resolves #3.

ljosa · ljosa · commit 79e86aa93c39 · 2014-03-10T12:40:57.000-04:00
The license of python-bioformats as a whole has to be GPL because
loci_tools.jar is GPL licensed. The python files remain under the more
permissive BSD license.
diff --git a/COPYING b/COPYING
diff --git a/README.rst b/README.rst
@@ -15,7 +15,8 @@ GitHub repository: https://github.com/CellProfiler/python-bioformats
 
 Report bugs here: https://github.com/CellProfiler/python-bioformats/issues
 
-python-bioformats is licensed under the BSD license.  See the
-accompanying file LICENSE for details.
+python-bioformats is licensed under the GNU General Public License
+(GPL).  Many files are licensed under the more permissive BSD license.
+See the accompanying files COPYING and LICENSE for details.
 
 Copyright (c) 2009-2014 Broad Institute. All rights reserved.
diff --git a/bioformats/__init__.py b/bioformats/__init__.py
@@ -1,16 +1,12 @@
-'''Bioformats package - wrapper for loci.bioformats java code
-
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
 
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2013 Broad Institute
-All rights reserved.
-
-Please see the AUTHORS file for credits.
+'''Bioformats package - wrapper for loci.bioformats java code
 
-Website: http://www.cellprofiler.org
 '''
 __version__ = "$Revision$"
 
diff --git a/bioformats/formatreader.py b/bioformats/formatreader.py
@@ -1,3 +1,10 @@
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
+
 '''formatreader.py - mechanism to wrap a bioformats ReaderWrapper and ImageReader
 
 Example:
@@ -13,17 +20,6 @@
     my_red_image, my_green_image, my_blue_image = \
         [cs.open_bytes(cs.getIndex(0,i,0)) for i in range(3)]
 
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
-
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2014 Broad Institute
-All rights reserved.
-
-Please see the AUTHORS file for credits.
-
-Website: http://www.cellprofiler.org'
 '''
     
 __version__ = "$Revision$"
diff --git a/bioformats/formatwriter.py b/bioformats/formatwriter.py
@@ -1,3 +1,10 @@
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
+
 '''formatwriter.py - mechanism to wrap a bioformats WriterWrapper and ImageWriter
 
 The following file formats can be written using Bio-Formats:
@@ -21,17 +28,6 @@
 and is especially useful for formats that do not support multiple images per
 file.
 
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
-
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2014 Broad Institute
-All rights reserved.
-
-Please see the AUTHORS file for credits.
-
-Website: http://www.cellprofiler.org
 '''
 
 __version__ = "$Revision$"
diff --git a/bioformats/log4j.py b/bioformats/log4j.py
@@ -1,3 +1,10 @@
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
+
 import unittest
 import javabridge
 
diff --git a/bioformats/metadatatools.py b/bioformats/metadatatools.py
@@ -1,16 +1,12 @@
-''' metadatatools.py - mechanism to wrap some bioformats metadata classes
-
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
 
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2014 Broad Institute
-All rights reserved.
-
-Please see the AUTHORS file for credits.
+''' metadatatools.py - mechanism to wrap some bioformats metadata classes
 
-Website: http://www.cellprofiler.org
 '''
 
 __version__ = "$Revision$"
diff --git a/bioformats/noseplugin.py b/bioformats/noseplugin.py
@@ -1,12 +1,9 @@
-# CellProfiler is distributed under the GNU General Public License.
-# See the accompanying file LICENSE for details.
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
 # 
-# Copyright (c) 2003-2009 Massachusetts Institute of Technology
-# Copyright (c) 2009-2013 Broad Institute
-# 
-# Please see the AUTHORS file for credits.
-# 
-# Website: http://www.cellprofiler.org
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
 
 import logging
 from nose.plugins import Plugin
diff --git a/bioformats/omexml.py b/bioformats/omexml.py
@@ -1,19 +1,14 @@
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
+
 """omexml.py read and write OME xml
 
 """
-# CellProfiler is distributed under the GNU General Public License.
-# See the accompanying file LICENSE for details.
-# 
-# Developed by the Broad Institute
-#
-# Copyright (c) 2003-2009 Massachusetts Institute of Technology
-# Copyright (c) 2003-2013 Broad Institute
-# All rights reserved.
-# 
-# Please see the AUTHORS file for credits.
-# 
-# Website: http://www.cellprofiler.org
-#
+
 import xml.etree.ElementTree
 from xml.etree import cElementTree as ElementTree
 from cStringIO import StringIO
diff --git a/bioformats/tests/__init__.py b/bioformats/tests/__init__.py
@@ -1,14 +0,0 @@
-'''
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
-
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2013 Broad Institute
-All rights reserved.
-
-Please see the AUTHORS file for credits.
-
-Website: http://www.cellprofiler.org
-'''
-
diff --git a/bioformats/tests/test_formatreader.py b/bioformats/tests/test_formatreader.py
@@ -1,16 +1,12 @@
-'''test_formatreader.py - test the Bioformats format reader wrapper
-
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
 
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2014 Broad Institute
-All rights reserved.
-
-Please see the AUTHORS file for credits.
+'''test_formatreader.py - test the Bioformats format reader wrapper
 
-Website: http://www.cellprofiler.org
 '''
 
 import numpy as np
diff --git a/bioformats/tests/test_formatwriter.py b/bioformats/tests/test_formatwriter.py
@@ -1,16 +1,12 @@
-'''test_formatwriter.py - test the Bioformats format reader wrapper
-
-CellProfiler is distributed under the GNU General Public License,
-but this file is licensed under the more permissive BSD license.
-See the accompanying file LICENSE for details.
-
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2014 Broad Institute
-All rights reserved.
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
 
-Please see the AUTHORS file for credits.
+'''test_formatwriter.py - test the Bioformats format reader wrapper
 
-Website: http://www.cellprofiler.org
 '''
 
 import numpy as np
@@ -75,4 +71,4 @@ def test_02_01_write_movie(self):
         for i in range(img.shape[0]):
             result = load_using_bioformats(path, t=i, rescale = False)
             np.testing.assert_array_equal(img[i], result)
-        
+        
diff --git a/bioformats/tests/test_load_using_bioformats.py b/bioformats/tests/test_load_using_bioformats.py
@@ -1,4 +1,9 @@
-#!/usr/bin/env python
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
 
 import os
 import unittest
diff --git a/bioformats/tests/test_omexml.py b/bioformats/tests/test_omexml.py
@@ -1,19 +1,14 @@
+# Python-bioformats is distributed under the GNU General Public
+# License, but this file is licensed under the more permissive BSD
+# license.  See the accompanying file LICENSE for details.
+# 
+# Copyright (c) 2009-2014 Broad Institute
+# All rights reserved.
+
 """test_omexml.py read and write OME xml
 
 """
-# CellProfiler is distributed under the GNU General Public License.
-# See the accompanying file LICENSE for details.
-# 
-# Developed by the Broad Institute
-#
-# Copyright (c) 2003-2009 Massachusetts Institute of Technology
-# Copyright (c) 2003-2013 Broad Institute
-# All rights reserved.
-# 
-# Please see the AUTHORS file for credits.
-# 
-# Website: http://www.cellprofiler.org
-#
+
 import datetime
 import os
 import unittest
@@ -924,4 +919,4 @@ def test_14_17_set_position_z(self):
 			</Value>
 		</XMLAnnotation>
 	</StructuredAnnotations>
-</OME>"""
+</OME>"""
diff --git a/docs/index.rst b/docs/index.rst
@@ -13,6 +13,9 @@ Python-bioformats and python-javabridge were developed for and are
 used by the cell image analysis software CellProfiler
 (cellprofiler.org).
 
+python-bioformats is licensed under the GNU General Public License
+(GPL).  Many files are licensed under the more permissive BSD license.
+
 
 Installation and testing
 ========================
diff --git a/setup.py b/setup.py
@@ -15,12 +15,12 @@
     url="http://github.com/CellProfiler/python-bioformats/",
     packages=['bioformats'],
     classifiers=['Development Status :: 5 - Production/Stable',
-                 'License :: OSI Approved :: BSD License',
+                 'License :: OSI Approved :: GPL License',
                  'Programming Language :: Java',
                  'Topic :: Scientific/Engineering :: Bio-Informatics',
                  'Topic :: Multimedia :: Graphics :: Graphics Conversion'
              ],
-    license='BSD License',
+    license='GPL License',
     package_data={'bioformats': ['jars/*.jar']},
     install_requires=['javabridge>=1.0']
 )
