Merge branch 'master' of github.com:CellProfiler/python-bioformats

Lee Kamentsky · Lee Kamentsky · commit d26c99f8ba64 · 2014-03-12T08:49:22.000-04:00
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@
 /docs/_build
 /python_bioformats.egg-info
 /dist
+/bioformats/_version.py
diff --git a/COPYING b/COPYING
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,3 @@
+recursive-include bioformats/tests *.py
+recursive-include bioformats/tests *.tif
+recursive-include bioformats/tests *.xml
diff --git a/README.rst b/README.rst
@@ -15,9 +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) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2013 Broad Institute
-All rights reserved.
+Copyright (c) 2009-2014 Broad Institute. All rights reserved.
diff --git a/bioformats/__init__.py b/bioformats/__init__.py
@@ -1,27 +1,31 @@
-'''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.
-
-Copyright (c) 2003-2009 Massachusetts Institute of Technology
-Copyright (c) 2009-2013 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.
+'''Bioformats package - wrapper for loci.bioformats java code
 
-Website: http://www.cellprofiler.org
 '''
-__version__ = "$Revision$"
+
+try:
+    from _version import __version__
+except ImportError:
+    # We're running in a tree that doesn't have a _version.py, so we don't know what our version is.
+    __version__ = "0.0.0"
 
 import os.path
 import javabridge
 from . import formatreader as _formatreader
 from . import formatwriter as _formatwriter
 
 _jars_dir = os.path.join(os.path.dirname(__file__), 'jars')
+
 JARS = javabridge.JARS + [os.path.realpath(os.path.join(_jars_dir, name + '.jar'))
                           for name in ['loci_tools']]
+"""List of directories, jar files, and zip files that should be added
+to the Java virtual machine's class path."""
 
 # See http://www.loci.wisc.edu/software/bio-formats
 READABLE_FORMATS = ('al3d', 'am', 'amiramesh', 'apl', 'arf', 'avi', 'bmp', 
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/demo/demo.py b/demo/demo.py
@@ -5,15 +5,14 @@
 import bioformats
 from bioformats import log4j
 
-class_path = os.pathsep.join(bioformats.JARS + javabridge.JARS)
-javabridge.start_vm(['-Djava.class.path=' + class_path], 
+javabridge.start_vm(class_path=bioformats.JARS,
                     run_headless=True)
 try:
     log4j.basic_config()
     image_path = os.path.join(os.path.dirname(bioformats.__file__), 'tests', 
                               'Channel1-01-A-01.tif')
-    image, scale = bioformats.load_using_bioformats(image_path, rescale=False,
-                                                    wants_max_intensity=True)
+    image, scale = bioformats.load_image(image_path, rescale=False,
+                                         wants_max_intensity=True)
     print image.shape
 finally:
     javabridge.kill_vm()
diff --git a/docs/conf.py b/docs/conf.py
@@ -43,14 +43,31 @@
 project = u'python-bioformats'
 copyright = u'2014, Broad Institute of MIT and Harvard'
 
+def get_version():
+    version_file = os.path.join(os.path.dirname(__file__), '..', 'bioformats',
+                                '_version.py')
+    if os.path.exists(version_file):
+        with open(version_file) as f:
+            cached_version_line = f.read().strip()
+        try:
+            import re
+            # From http://stackoverflow.com/a/3619714/17498
+            cached_version = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", 
+                                       cached_version_line, re.M).group(1)
+        except:
+            raise RuntimeError("Unable to find version in %s" % version_file)
+        split_version = cached_version.split('.')
+        return '.'.join(split_version[:2]), cached_version
+    else:
+        return '0.0', '0.0.0'
+
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-version = '1.0'
-# The full version, including alpha/beta/rc tags.
-release = '1.0.0pr1'
+# version: The short X.Y version.
+# release: The full version, including alpha/beta/rc tags.
+version, release = get_version()
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -249,4 +266,4 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {'javabridge': ('http://pythonhosted.org/javabridge/', None)}
diff --git a/docs/index.rst b/docs/index.rst
diff --git a/nosetests.py b/nosetests.py
diff --git a/setup.py b/setup.py

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+recursive-include bioformats/tests *.py`
	`2`	`+recursive-include bioformats/tests *.tif`
	`3`	`+recursive-include bioformats/tests *.xml`