Rename package to `skimage`.

.gitignore

@@ -11,6 +11,6 @@ doc/build
 source/api
 build
 dist
-scikits/image/version.py
+skimage/version.py
 *.swp
 .coverage

CONTRIBUTORS.txt

@@ -25,7 +25,7 @@
 
 - Tony Yu
   Reading of paletted images; build, bug and doc fixes.
-  Code to generate scikits-image logo.
+  Code to generate skimage logo.
 
 - Zachary Pincus
   Tracing of low cost paths, FreeImage I/O plugin
@@ -80,4 +80,7 @@
 
 - Neil Yager
   Skeletonization.
-  
+
+- Nelle Varoquaux
+  Renaming of the package to ``skimage``.
+

DEVELOPMENT.txt

@@ -2,7 +2,7 @@ Development process
 -------------------
 
 :doc:`Read this overview <gitwash/index>` of how to use Git with
-``scikits.image``.  Here's the long and short of it:
+``skimage``.  Here's the long and short of it:
 
  * Go to `https://github.com/scikits-image/scikits.image
    <http://github.com/scikits-image/scikits.image>`_ and follow the
@@ -52,13 +52,13 @@ i.e. statement coverage should be at 100%.
 
   $ make coverage
 
-This will print a report with one line for each file in `scikits.image`,
+This will print a report with one line for each file in `skimage`,
 detailing the test coverage::
 
   Name                                             Stmts   Exec  Cover   Missing
   ------------------------------------------------------------------------------
-  scikits/image/color/colorconv                       77     77   100%
-  scikits/image/filter/__init__                        1      1   100%
+  skimage/color/colorconv                             77     77   100%
+  skimage/filter/__init__                              1      1   100%
   ...
 
 Bugs

LICENSE.txt

@@ -1,12 +1,12 @@
 Unless otherwise specified by LICENSE.txt files in individual
 directories, all code is
 
-Copyright (C) 2011, the scikits-image team
+Copyright (C) 2011, the Image Scikit team
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
-met:
+met:	
 
  1. Redistributions of source code must retain the above copyright
     notice, this list of conditions and the following disclaimer.
@@ -14,9 +14,9 @@ met:
     notice, this list of conditions and the following disclaimer in
     the documentation and/or other materials provided with the
     distribution.
- 3. Neither the name of scikits.image nor the names of its
-    contributors may be used to endorse or promote products derived
-    from this software without specific prior written permission.
+ 3. Neither the name of skimage 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 AUTHOR ``AS IS'' AND ANY EXPRESS OR
 IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

MANIFEST.in

@@ -3,8 +3,8 @@ include setup*.py
 include MANIFEST.in
 include *.txt
 include Makefile
-recursive-include scikits *.pyx *.pxd *.pxi *.py *.c *.h *.ini
-recursive-include scikits/image/data *
+recursive-include skimage *.pyx *.pxd *.pxi *.py *.c *.h *.ini
+recursive-include skimage/data *
 
 include doc/Makefile
 recursive-include doc/source *.txt

Makefile

@@ -2,13 +2,13 @@
 
 all:
 	python setup.py build_ext --inplace
-	git update-index --assume-unchanged scikits/image/version.py
+	git update-index --assume-unchanged skimage/version.py
 
 clean:
 	find . -name "*.so" -o -name "*.pyc" | xargs rm -f
 
 test:
-	nosetests scikits/image
+	nosetests skimage
 
 coverage:
-	nosetests scikits/image --with-coverage --cover-package=scikits.image
+	nosetests skimage --with-coverage --cover-package=skimage

RELEASE.txt

@@ -1,5 +1,5 @@
-How to make a new release of ``scikits.image``
-==============================================
+How to make a new release of ``skimage``
+========================================
 
 - Update the version number in setup.py and commit
 - Update the docs and api, push upstream using "make gh-pages"

TASKS.txt

@@ -1,15 +1,15 @@
  ..  role:: strike
 
-How to contribute to ``scikits.image``
+How to contribute to ``skimage``
 ======================================
 
-Developing Open Source is great fun!  Join us on the `scikits-image mailing
+Developing Open Source is great fun!  Join us on the `skimage mailing
 list <http://groups.google.com/group/scikits-image>`_ and tell us which of the
 following challenges you'd like to solve.
 
 * Mentoring is available for those new to scientific programming in Python.
 * The technical detail of the `development process`_ is given below.
-* :doc:`How to use GitHub <gitwash/index>` when developing scikits.image
+* :doc:`How to use GitHub <gitwash/index>` when developing skimage
 
 .. contents::
    :local:

doc/examples/plot_hough_transform.py

@@ -59,9 +59,9 @@ References
 
 '''
 
-from scikits.image.transform import hough, probabilistic_hough
-from scikits.image.filter import canny
-from scikits.image import data
+from skimage.transform import hough, probabilistic_hough
+from skimage.filter import canny
+from skimage import data
 
 import numpy as np
 import matplotlib.pyplot as plt

doc/examples/plot_lena_tv_denoise.py

@@ -19,8 +19,8 @@ the tradeoff between denoising and faithfulness to the original image.
 import numpy as np
 import matplotlib.pyplot as plt
 
-from scikits.image import data, color, img_as_ubyte
-from scikits.image.filter import tv_denoise
+from skimage import data, color, img_as_ubyte
+from skimage.filter import tv_denoise
 
 l = img_as_ubyte(color.rgb2gray(data.lena()))
 l = l[230:290, 220:320]

doc/examples/plot_radon_transform.py

@@ -20,9 +20,9 @@ input image based on the resulting sinogram.
 
 import matplotlib.pyplot as plt
 
-from scikits.image.io import imread
-from scikits.image import data_dir
-from scikits.image.transform import radon, iradon
+from skimage.io import imread
+from skimage import data_dir
+from skimage.transform import radon, iradon
 from scipy.ndimage import zoom
 
 image = imread(data_dir + "/phantom.png", as_grey=True)

doc/examples/plot_watershed.py

@@ -27,7 +27,7 @@ more details on the algorithm.
 import numpy as np
 from scipy import ndimage
 import matplotlib.pyplot as plt
-from scikits.image.morphology import watershed, is_local_maximum
+from skimage.morphology import watershed, is_local_maximum
 
 # Generate an initial image with two overlapping circles
 x, y = np.indices((80, 80))

doc/logo/scikits_image_logo.py

@@ -1,5 +1,5 @@
 """
-Script to draw scikits.image logo using Scipy logo as stencil. The easiest
+Script to draw skimage logo using Scipy logo as stencil. The easiest
 starting point is the `plot_colorized_logo`; the "if-main" demonstrates its use.
 
 Original snake image from pixabay [1]_
@@ -10,8 +10,8 @@ import numpy as np
 import matplotlib.pyplot as plt
 import scipy.misc
 
-import scikits.image.io as sio
-import scikits.image.filter as imfilt
+import skimage.io as sio
+import skimage.filter as imfilt
 
 import scipy_logo
 

doc/logo/scipy_logo.py

@@ -3,7 +3,7 @@ Code used to trace Scipy logo.
 """
 import numpy as np
 import matplotlib.pyplot as plt
-import scikits.image.io as imgio
+import skimage.io as imgio
 from scipy.misc import lena
 import matplotlib.nxutils as nx
 

doc/logo/shrink_logo.py

@@ -1,4 +1,4 @@
-from scikits.image import io, transform
+from skimage import io, transform
 
 s = 0.7
 

doc/source/conf.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# scikits.image documentation build configuration file, created by
+# skimage documentation build configuration file, created by
 # sphinx-quickstart on Sat Aug 22 13:00:30 2009.
 #
 # This file is execfile()d with the current directory set to its containing dir.
@@ -48,8 +48,8 @@ source_suffix = '.txt'
 master_doc = 'index'
 
 # General information about the project.
-project = u'scikits.image'
-copyright = u'2011, scikits-image team'
+project = u'skimage'
+copyright = u'2011, the Image Scikit team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -122,7 +122,7 @@ html_theme_path = ['themes']
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = 'scikits.image v%s docs' % version
+html_title = 'skimage v%s docs' % version
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #html_short_title = None
@@ -197,7 +197,7 @@ htmlhelp_basename = 'scikitsimagedoc'
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('contents', 'scikitsimage.tex', u'scikits.image Documentation',
+  ('contents', 'scikitsimage.tex', u'The Image Scikit Documentation',
    u'SciPy Developers', 'manual'),
 ]
 

doc/source/index.txt

@@ -1,5 +1,5 @@
 ****************************
-scikits.image |version| docs
+skimage |version| docs
 ****************************
 
 This SciKit_ is an image processing toolbox for SciPy_.
@@ -16,15 +16,15 @@ Sections
 
    * - `Overview <overview.html>`_
 
-       Introduction to scikits.image.
+       Introduction to skimage.
 
      - `API Reference <api/api.html>`_ (`changes <api_changes.html>`_)
 
-       Documentation for the functions included in scikits.image.
+       Documentation for the functions included in skimage.
 
    * - `Installation Steps <install.html>`_
 
-       How to install scikits.image.
+       How to install skimage.
 
      - `User Guide <user_guide.html>`_
 

doc/source/plots/hough_tf.py

@@ -1,7 +1,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from scikits.image.transform import hough
+from skimage.transform import hough
 
 img = np.zeros((100, 150), dtype=bool)
 img[30, :] = 1

doc/source/plots/show_collection.py

@@ -3,8 +3,8 @@ import os
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid import AxesGrid
 
-from scikits.image.io import MultiImage
-from scikits.image import data_dir
+from skimage.io import MultiImage
+from skimage import data_dir
 
 # Load the multi-layer image
 fname = os.path.join(data_dir, 'multipage.tif')

doc/source/user_guide/data_types.txt

@@ -5,7 +5,7 @@ Image data types and what they mean
 
    This is a preliminary design document.
 
-In ``scikits.image``, we assume the following dtype ranges:
+In ``skimage``, we assume the following dtype ranges:
 
 =========== ================
 Data type   Range 

doc/source/user_guide/plugins.txt

@@ -4,8 +4,8 @@ A plugin consists of two files, the source and the descriptor ``.ini``.  Let's
 say we'd like to provide a plugin for ``imshow`` using ``matplotlib``.  We'll
 call our plugin ``mpl``::
 
-  scikits/image/io/_plugins/mpl.py
-  scikits/image/io/_plugins/mpl.ini
+  skimage/io/_plugins/mpl.py
+  skimage/io/_plugins/mpl.ini
 
 The name of the ``.py`` and ``.ini`` files must correspond.  Inside the
 ``.ini`` file, we give the plugin meta-data::
@@ -45,10 +45,10 @@ provide it as follows::
       plt.show()
 
 Any plugin in the ``_plugins`` directory is automatically examined by
-``scikits.image.io`` upon import.  You may list all the plugins on your
+``skimage.io`` upon import.  You may list all the plugins on your
 system::
 
-  >>> import scikits.image.io as io
+  >>> import skimage.io as io
   >>> io.plugins()
   {'gtk': ['imshow'],
    'matplotlib': ['imshow', 'imsave'],
@@ -63,7 +63,7 @@ or only those already loaded::
 
 A plugin is loaded using the ``use_plugin`` command::
 
-  >>> import scikits.image.io as io
+  >>> import skimage.io as io
   >>> io.use_plugin('pil') # Use all capabilities provided by PIL
 
 or

doc/tools/apigen.py

@@ -13,7 +13,7 @@ Previously functions and classes were found by parsing the text of .py files.
 Extension modules should be discovered and included as well.
 
 This is a modified version of a script originally shipped with the PyMVPA
-project, then adapted for use first in NIPY and then in scikits.image. PyMVPA
+project, then adapted for use first in NIPY and then in skimage. PyMVPA
 is an MIT-licensed project.
 """
 

doc/tools/build_modref_templates.py

@@ -17,7 +17,7 @@ def abort(error):
     exit()
 
 if __name__ == '__main__':
-    package = 'scikits.image'
+    package = 'skimage'
 
     # Check that the 'image' package is available. If not, the API
     # documentation is not (re)generated and existing API documentation
@@ -26,7 +26,7 @@ if __name__ == '__main__':
     try:
         __import__(package)
     except ImportError, e:
-        abort("Can not import scikits.image")
+        abort("Can not import skimage")
 
     module = sys.modules[package]
 

scikits/__init__.py

@@ -1 +0,0 @@
-__import__('pkg_resources').declare_namespace(__name__)

scikits/image/version.py

@@ -1 +0,0 @@
-version='unbuilt-dev'

setup.py

@@ -9,7 +9,7 @@ Please refer to the online documentation at
 http://scikits-image.org/
 """
 
-DISTNAME            = 'scikits.image'
+DISTNAME            = 'skimage'
 DESCRIPTION         = 'Image processing routines for SciPy'
 LONG_DESCRIPTION    = descr
 MAINTAINER          = 'Stefan van der Walt'
@@ -31,8 +31,7 @@ def configuration(parent_package='', top_path=None):
     if os.path.exists('MANIFEST'): os.remove('MANIFEST')
 
     from numpy.distutils.misc_util import Configuration
-    config = Configuration(None, parent_package, top_path,
-                           namespace_packages=['scikits'])
+    config = Configuration(None, parent_package, top_path)
 
     config.set_options(
             ignore_setup_xxx_py=True,
@@ -40,15 +39,13 @@ def configuration(parent_package='', top_path=None):
             delegate_options_to_subpackages=True,
             quiet=True)
 
-    config.add_subpackage('scikits')
     config.add_subpackage(DISTNAME)
-    config.add_data_files('scikits/__init__.py')
-    config.add_data_dir('scikits/image/data')
+    config.add_data_dir('skimage/data')
 
     return config
 
-def write_version_py(filename='scikits/image/version.py'):
-    template = """# THIS FILE IS GENERATED FROM THE SCIKITS.IMAGE SETUP.PY
+def write_version_py(filename='skimage/version.py'):
+    template = """# THIS FILE IS GENERATED FROM THE SKIMAGE SETUP.PY
 version='%s'
 """
 
@@ -92,14 +89,13 @@ if __name__ == "__main__":
 
         configuration=configuration,
         install_requires=[],
-        namespace_packages=['scikits'],
         packages=setuptools.find_packages(),
         include_package_data=True,
         zip_safe=False, # the package can run out of an .egg file
 
         entry_points={
             'console_scripts': [
-                'scivi = scikits.image.scripts.scivi:main']
+                'scivi = skimage.scripts.scivi:main']
             },
 
         cmdclass={'build_py': build_py},

skimage/__init__.py

@@ -20,7 +20,7 @@ def _setup_test():
         print("Could not load nose.  Unit tests not available.")
         return None
     else:
-        return functools.partial(_nose.run, 'scikits.image', argv=args)
+        return functools.partial(_nose.run, 'skimage', argv=args)
 
 test = _setup_test()
 if test is None:

skimage/_build.py

@@ -53,7 +53,10 @@ def cython(pyx_files, working_path=''):
                 # if the generated .c file differs from the one provided,
                 # use that one instead
                 shutil.copy(c_file_new, c_file)
-            os.remove(c_file_new)
+            try:
+                os.remove(c_file_new)
+            except OSError:
+                pass
 
 
 def same_cython(f0, f1):

skimage/color/colorconv.py

@@ -82,8 +82,8 @@ def convert_colorspace(arr, fromspace, tospace):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_hsv = convert_colorspace(lena, 'RGB', 'HSV')
@@ -147,8 +147,8 @@ def rgb2hsv(rgb):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_hsv = color.rgb2hsv(lena)
@@ -222,8 +222,8 @@ def hsv2rgb(hsv):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_hsv = rgb2hsv(lena)
@@ -345,9 +345,9 @@ def xyz2rgb(xyz):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
-    >>> from scikits.image.color import rgb2xyz, xyz2rgb
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
+    >>> from skimage.color import rgb2xyz, xyz2rgb
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_xyz = rgb2xyz(lena)
@@ -386,8 +386,8 @@ def rgb2xyz(rgb):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_xyz = rgb2xyz(lena)
@@ -420,9 +420,9 @@ def rgb2rgbcie(rgb):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
-    >>> from scikits.image.color import rgb2rgbcie
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
+    >>> from skimage.color import rgb2rgbcie
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_rgbcie = rgb2rgbcie(lena)
@@ -455,9 +455,9 @@ def rgbcie2rgb(rgbcie):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
-    >>> from scikits.image.color import rgb2rgbcie, rgbcie2rgb
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
+    >>> from skimage.color import rgb2rgbcie, rgbcie2rgb
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_rgbcie = rgb2rgbcie(lena)
@@ -498,9 +498,9 @@ def rgb2grey(rgb):
     Examples
     --------
     >>> import os
-    >>> from scikits.image import data_dir
-    >>> from scikits.image.io import imread
-    >>> from scikits.image.color import rgb2grey
+    >>> from skimage import data_dir
+    >>> from skimage.io import imread
+    >>> from skimage.color import rgb2grey
 
     >>> lena = imread(os.path.join(data_dir, 'lena.png'))
     >>> lena_grey = rgb2grey(lena)

skimage/color/tests/test_colorconv.py

@@ -16,8 +16,8 @@ import os.path
 import numpy as np
 from numpy.testing import *
 
-from scikits.image.io import imread
-from scikits.image.color import (
+from skimage.io import imread
+from skimage.color import (
     rgb2hsv, hsv2rgb,
     rgb2xyz, xyz2rgb,
     rgb2rgbcie, rgbcie2rgb,
@@ -25,7 +25,7 @@ from scikits.image.color import (
     rgb2grey
     )
 
-from scikits.image import data_dir
+from skimage import data_dir
 
 import colorsys
 

skimage/data/__init__.py

@@ -5,7 +5,7 @@
 import os as _os
 
 from ..io import imread
-from ...image import data_dir
+from skimage import data_dir
 
 def load(f):
     """Load an image file located in the data directory.
@@ -18,7 +18,7 @@ def load(f):
     Returns
     -------
     img : ndarray
-        Image loaded from scikits.image.data_dir.
+        Image loaded from skimage.data_dir.
     """
     return imread(_os.path.join(data_dir, f))
 

skimage/data/tests/test_data.py

@@ -1,4 +1,4 @@
-import scikits.image.data as data
+import skimage.data as data
 from numpy.testing import assert_equal, assert_array_equal
 import numpy as np
 

skimage/draw/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 import os
-from scikits.image._build import cython
+from skimage._build import cython
 
 base_path = os.path.abspath(os.path.dirname(__file__))
 

skimage/draw/tests/test_draw.py

@@ -1,7 +1,7 @@
 from numpy.testing import assert_array_equal
 import numpy as np
 
-from scikits.image.draw import bresenham
+from skimage.draw import bresenham
 
 def test_bresenham_horizontal():
     img = np.zeros((10, 10))

skimage/feature/hog.py

@@ -129,7 +129,7 @@ def hog(image, orientations=9, pixels_per_cell=(8, 8),
         hog_image = np.zeros((sy, sx), dtype=float)
 
     if visualise:
-        from scikits.image import draw
+        from skimage import draw
         
         for x in range(n_cellsx):
             for y in range(n_cellsy):

skimage/feature/tests/test_hog.py

@@ -1,10 +1,10 @@
 import numpy as np
 import scipy
 
-from scikits.image.feature import hog 
+from skimage.feature import hog 
 
 def test_histogram_of_oriented_gradients():
-    # Replace with scikits.image.data.lena() after merge
+    # Replace with skimage.data.lena() after merge
     img = scipy.misc.lena().astype(np.int8) 
     
     fd = hog(img, orientations=9, pixels_per_cell=(8, 8), 

skimage/filter/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 import os
-from scikits.image._build import cython
+from skimage._build import cython
 
 base_path = os.path.abspath(os.path.dirname(__file__))
 

skimage/filter/tests/test_canny.py

@@ -1,7 +1,7 @@
 import unittest
 import numpy as np
 from scipy.ndimage import binary_dilation, binary_erosion
-import scikits.image.filter as F
+import skimage.filter as F
 
 
 class TestCanny(unittest.TestCase):

skimage/filter/tests/test_ctmf.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from scikits.image.filter import median_filter
+from skimage.filter import median_filter
 
 
 def test_00_00_zeros():

skimage/filter/tests/test_edges.py

@@ -4,8 +4,8 @@ from numpy.testing import *
 import numpy as np
 from scipy.ndimage import binary_dilation, binary_erosion
 
-import scikits.image.filter as F
-from scikits.image import data_dir
+import skimage.filter as F
+from skimage import data_dir
 
 class TestSobel():
     def test_00_00_zeros(self):

skimage/filter/tests/test_lpi_filter.py

@@ -3,9 +3,9 @@ import os.path
 import numpy as np
 from numpy.testing import *
 
-from scikits.image import data_dir
-from scikits.image.io import *
-from scikits.image.filter import *
+from skimage import data_dir
+from skimage.io import *
+from skimage.filter import *
 
 class TestLPIFilter2D():
     img = imread(os.path.join(data_dir, 'camera.png'),

skimage/filter/tests/test_tv_denoise.py

@@ -1,8 +1,8 @@
 import numpy as np
 from numpy.testing import run_module_suite
 
-from scikits.image import filter, data, color
-from scikits.image import img_as_uint
+from skimage import filter, data, color
+from skimage import img_as_uint
 
 class TestTvDenoise():
 

skimage/graph/setup.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from scikits.image._build import cython
+from skimage._build import cython
 import os.path
 
 base_path = os.path.abspath(os.path.dirname(__file__))