Merge pull request #1199 from blink1073/use-pypi-tifffile

Use PyPI tifffile or fall back on local version

.coveragerc

@@ -6,7 +6,7 @@ source = skimage
 include = */skimage/*
 omit =
     */setup.py
-    */skimage/io/_plugins/tifffile.py
+    */skimage/external/*
 
 [report]
 exclude_lines =

.travis.yml

@@ -15,13 +15,23 @@ python:
 - 3.4
 
 before_install:
-    - tools/travis_setup.sh
+    - export DISPLAY=:99.0
+    - export PYTHONWARNINGS="all"
+    - export WHEELHOUSE="--no-index --find-links=http://travis-wheels.scikit-image.org/"
+    - travis_retry tools/travis_setup.sh
 
 install:
     - python setup.py build_ext --inplace
     - python setup.py install
 
 script:
+    - tools/header.py "Run all tests with minimum dependencies"
+    - nosetests --exe -v skimage
+
+    - tools/header.py "Pep8 and Flake tests"
+    - flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
+
+    - travis_retry tools/travis_install_optional.sh
     - tools/travis_test.sh
 
 after_success:

bento.info

@@ -157,9 +157,9 @@ Library:
     Extension: skimage.graph._ncut_cy
         Sources:
             skimage/graph/_ncut_cy.pyx
-    Extension: skimage.io._plugins._tifffile
+    Extension: skimage.external.tifffile._tifffile
         Sources:
-            skimage/io/_plugins/tifffile.c
+            skimage/external/tifffile/_tifffile.c
 
 Executable: skivi
     Module: skimage.scripts.skivi

setup.py

@@ -141,12 +141,9 @@ if __name__ == "__main__":
         ],
 
         configuration=configuration,
-        install_requires=[
-            "six>=%s" % '.'.join(str(d) for d in DEPENDENCIES['six'])
-        ],
         packages=setuptools.find_packages(exclude=['doc']),
         include_package_data=True,
-        zip_safe=False, # the package can run out of an .egg file
+        zip_safe=False,  # the package can run out of an .egg file
 
         entry_points={
             'console_scripts': ['skivi = skimage.scripts.skivi:main'],

skimage/external/LICENSE.txt

@@ -1,5 +1,5 @@
 
-_plugins.tifffile.py
+tifffile
 
     Copyright (c) 2008-2014, Christoph Gohlke
     Copyright (c) 2008-2014, The Regents of the University of California

skimage/external/setup.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+
+import os.path
+
+base_path = os.path.abspath(os.path.dirname(__file__))
+
+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
+
+    config = Configuration('external', parent_package, top_path)
+
+    config.add_extension('tifffile._tifffile',
+                         sources=['tifffile/tifffile.c'],
+                         include_dirs=[get_numpy_include_dirs()])
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(maintainer='scikit-image Developers',
+          maintainer_email='scikit-image@googlegroups.com',
+          description='External Libaries',
+          url='https://github.com/scikit-image/scikit-image',
+          license='Modified BSD',
+          **(configuration(top_path='').todict())
+          )

skimage/external/tifffile/__init__.py

@@ -0,0 +1,4 @@
+try:
+    from tifffile import imread, imsave, TiffFile
+except ImportError:
+    from .tifffile_local import imread, imsave, TiffFile

skimage/external/tifffile/tifffile_local.py

@@ -151,15 +151,9 @@ from xml.etree import cElementTree as etree
 
 import numpy
 
-try:
-    from . import _tifffile
-except ImportError:
-    warnings.warn(
-        "failed to import the optional _tifffile C extension module.\n"
-        "Loading of some compressed images will be slow.\n"
-        "Tifffile.c can be obtained at http://www.lfd.uci.edu/~gohlke/")
+from . import _tifffile
 
-__version__ = '2014.08.24'
+__version__ = '0.3.3'
 __docformat__ = 'restructuredtext en'
 __all__ = ('imsave', 'imread', 'imshow', 'TiffFile', 'TiffWriter',
            'TiffSequence')
@@ -187,7 +181,7 @@ def imsave(filename, data, **kwargs):
     Examples
     --------
     >>> data = numpy.random.rand(2, 5, 3, 301, 219)
-    >>> description = u'{"shape": %s}' % str(list(data.shape))
+    >>> description = '{"shape": %s}' % str(list(data.shape))
     >>> imsave('temp.tif', data, compress=6,
     ...        extratags=[(270, 's', 0, description, True)])
 
@@ -669,12 +663,12 @@ def imread(files, **kwargs):
 
     Examples
     --------
-    >>> im = imread('test.tif', key=0)
+    >>> im = imread('temp.tif', key=0)
     >>> im.shape
-    (256, 256, 4)
-    >>> ims = imread(['test.tif', 'test.tif'])
+    (3, 301, 219)
+    >>> ims = imread(['temp.tif', 'temp.tif'])
     >>> ims.shape
-    (2, 256, 256, 4)
+    (2, 10, 3, 301, 219)
 
     """
     kwargs_file = {}
@@ -739,10 +733,10 @@ class TiffFile(object):
 
     Examples
     --------
-    >>> with TiffFile('test.tif') as tif:
+    >>> with TiffFile('temp.tif') as tif:
     ...     data = tif.asarray()
     ...     data.shape
-    (256, 256, 4)
+    (5, 301, 219)
 
     """
     def __init__(self, arg, name=None, offset=None, size=None,
@@ -2221,11 +2215,11 @@ class TiffSequence(object):
 
     Examples
     --------
-    >>> tifs = TiffSequence("test.oif.files/*.tif")
-    >>> tifs.shape, tifs.axes
+    >>> tifs = TiffSequence("test.oif.files/*.tif")  # doctest: +SKIP
+    >>> tifs.shape, tifs.axes  # doctest: +SKIP
     ((2, 100), 'CT')
-    >>> data = tifs.asarray()
-    >>> data.shape
+    >>> data = tifs.asarray()  # doctest: +SKIP
+    >>> data.shape  # doctest: +SKIP
     (2, 100, 256, 256)
 
     """
@@ -3454,7 +3448,7 @@ def stripnull(string):
 
     Clean NULL terminated C strings.
 
-    >>> stripnull(b'string\\x00')
+    >>> stripnull(b'string\\x00')  # doctest: +SKIP
     b'string'
 
     """
@@ -3467,9 +3461,9 @@ def stripascii(string):
 
     Clean NULL separated and terminated TIFF strings.
 
-    >>> stripascii(b'string\\x00string\\n\\x01\\x00')
+    >>> stripascii(b'string\\x00string\\n\\x01\\x00')  # doctest: +SKIP
     b'string\\x00string\\n'
-    >>> stripascii(b'\\x00')
+    >>> stripascii(b'\\x00')  # doctest: +SKIP
     b''
 
     """

skimage/io/_plugins/pil_plugin.py

@@ -14,7 +14,7 @@ except ImportError:
 from skimage.util import img_as_ubyte, img_as_uint
 
 from six import string_types
-from .tifffile import imread as tif_imread, imsave as tif_imsave
+from skimage.external.tifffile import imread as tif_imread, imsave as tif_imsave
 
 
 def imread(fname, dtype=None):

skimage/io/_plugins/tifffile_plugin.py

@@ -1,6 +1 @@
-try:
-    from .tifffile import imread, imsave
-except ImportError:
-    raise ImportError("The tifffile module could not be found.\n"
-        "It can be obtained at "
-        "<http://www.lfd.uci.edu/~gohlke/code/tifffile.py>\n")
+from skimage.external.tifffile import imread, imsave

skimage/io/setup.py

@@ -27,10 +27,6 @@ def configuration(parent_package='', top_path=None):
                          sources=['_plugins/_histograms.c'],
                          include_dirs=[get_numpy_include_dirs()])
 
-    config.add_extension('_plugins._tifffile',
-                         sources=['_plugins/tifffile.c'],
-                         include_dirs=[get_numpy_include_dirs()])
-
     return config
 
 if __name__ == '__main__':

skimage/setup.py

@@ -21,6 +21,7 @@ def configuration(parent_package='', top_path=None):
     config.add_subpackage('transform')
     config.add_subpackage('util')
     config.add_subpackage('segmentation')
+    config.add_subpackage('external')
 
     def add_test_directories(arg, dirname, fnames):
         if dirname.split(os.path.sep)[-1] == 'tests':

tools/travis_install_optional.sh

@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+set -ex
+
+tools/header.py "Install optional dependencies"
+
+# Install Qt and then update the Matplotlib settings
+if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+    sudo apt-get install -q python-qt4
+
+else
+    sudo apt-get install -q libqt4-dev
+    pip install PySide $WHEELHOUSE
+    python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
+fi
+
+# imread does NOT support py3.2
+if [[ $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
+    sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
+    pip install imread
+fi
+
+# TODO: update when SimpleITK become available on py34 or hopefully pip
+if [[ $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
+    easy_install SimpleITK
+fi
+
+sudo apt-get install libfreeimage3
+pip install astropy
+
+if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
+    pip install pyamg
+fi
+
+pip install tifffile

tools/travis_setup.sh

@@ -4,8 +4,6 @@ set -ex
 sh -e /etc/init.d/xvfb start
 sudo apt-get update
 
-WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
-
 pip install wheel flake8 coveralls nose
 pip uninstall -y numpy
 

tools/travis_test.sh

@@ -1,52 +1,17 @@
 #!/usr/bin/env bash
 set -ex
 
-export DISPLAY=:99.0
-export PYTHONWARNINGS="all"
-WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
-
-tools/header.py "Run all tests with minimum dependencies"
-nosetests --exe -v skimage
-
-tools/header.py "Pep8 and Flake tests"
-flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
-
-tools/header.py "Install optional dependencies"
-
-# Install Qt and then update the Matplotlib settings
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
-    sudo apt-get install -q python-qt4
     MPL_QT_API=PyQt4
     MPL_DIR=$HOME/.matplotlib
     export QT_API=pyqt
 
 else
-    sudo apt-get install -q libqt4-dev
-    pip install PySide $WHEELHOUSE
-    python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
     MPL_QT_API=PySide
     MPL_DIR=$HOME/.config/matplotlib
     export QT_API=pyside
 fi
 
-# imread does NOT support py3.2
-if [[ $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
-    sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
-    pip install imread
-fi
-
-# TODO: update when SimpleITK become available on py34 or hopefully pip
-if [[ $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
-    easy_install SimpleITK
-fi
-
-sudo apt-get install libfreeimage3
-pip install astropy
-
-if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
-    pip install pyamg
-fi
-
 # Matplotlib settings - do not show figures during doc examples
 mkdir -p $MPL_DIR
 touch $MPL_DIR/matplotlibrc
@@ -75,10 +40,9 @@ echo 'backend.qt4 : '$MPL_QT_API >> $MPL_DIR/matplotlibrc
 
 tools/header.py "Run tests with all dependencies"
 # run tests again with optional dependencies to get more coverage
+TEST_ARGS='--exe -v --with-doctest'
 if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
-    export TEST_ARGS="--with-cov --cover-package skimage"
-else
-    export TEST_ARGS=""
+    TEST_ARGS="$TEST_ARGS --with-cov --cover-package skimage"
 fi
-nosetests --exe -v --with-doctest $TEST_ARGS
+nosetests $TEST_ARGS