Merge pull request #811 from ahojnnes/doctests

Fix doctests and let TravisCI run doctests

.travis.yml

@@ -1,42 +1,68 @@
 # vim ft=yaml
-# travis-ci.org definition for skimage build
-#
-# We pretend to be erlang because we can't use the python support in
-# travis-ci; it uses virtualenvs, they do not have numpy, scipy, matplotlib,
-# and it is impractical to build them
-
-language: erlang
-env:
-    - PYTHON=python PYSUF='' PYVER=2.7
-    - PYTHON=python3 PYSUF='3' PYVER=3.2
-install:
-    - sudo apt-get update  # needed for python3-numpy
-    - sudo apt-get install $PYTHON-dev
+
+# After changing this file, check it on:
+#   http://lint.travis-ci.org/
+
+
+language: python
+
+python:
+    - 2.6
+
+matrix:
+    include:
+        - python: 2.7
+          env:
+            - PYTHON=python
+            - PYVER=2.x
+        - python: 3.2
+          env:
+            - PYTHON=python3
+            - PYVER=3.x
+    exclude:
+        - python: 2.6
+
+virtualenv:
+    system_site_packages: true
+
+before_install:
+    - export DISPLAY=:99.0
+    - sh -e /etc/init.d/xvfb start
+
+    - sudo apt-get update
     - sudo apt-get install $PYTHON-numpy
     - sudo apt-get install $PYTHON-scipy
-    - sudo apt-get install $PYTHON-setuptools
-    - sudo apt-get install $PYTHON-nose
-    - sudo easy_install$PYSUF pip
-    - sudo pip-$PYVER install cython
     - sudo apt-get install libfreeimage3
-    - if [[ $PYVER == '2.7' ]]; then sudo apt-get install $PYTHON-matplotlib; fi
-    - if [[ $PYVER == '3.2' ]]; then sudo pip-$PYVER install git+git://github.com/matplotlib/matplotlib.git@v1.2.x; fi
-    - sudo pip-$PYVER install flake8
-    - sudo pip-$PYVER install six
-    - $PYTHON setup.py build
-    - sudo $PYTHON setup.py install
+
+    - if [[ $PYVER == '2.x' ]]; then
+    -   sudo apt-get install $PYTHON-qt4;
+    -   sudo apt-get install $PYTHON-matplotlib;
+    - fi
+    - if [[ $PYVER == '3.x' ]]; then
+    -   sudo apt-get install $PYTHON-pyqt4;
+    -   pip install matplotlib;
+    - fi
+
+    - pip install cython
+    - pip install flake8
+    - pip install six
+
+    - python check_bento_build.py
+
+install:
+    - python setup.py build_ext --inplace
+
 script:
-    # Check if setup.py's match bento.info
-    - $PYTHON check_bento_build.py
-    # Change into an innocuous directory and find tests from installation
+    # Setup matplotlib settings
     - mkdir $HOME/.matplotlib
+    - touch $HOME/.matplotlib/matplotlibrc
     - "echo 'backend : Agg' > $HOME/.matplotlib/matplotlibrc"
     - "echo 'backend.qt4 : PyQt4' >> $HOME/.matplotlib/matplotlibrc"
-    - mkdir for_test
-    - cd for_test
-    - nosetests-$PYVER --exe -v --cover-package=skimage skimage
-    # Change back to repository root directory and run all doc examples
-    - cd ..
+    # Run all tests
+    - python -c "import skimage, sys, io; sys.exit(skimage.test_verbose())"
+    - python -c "import skimage, sys, io; sys.exit(skimage.doctest_verbose())"
+    # Run all doc examples
+    - export PYTHONPATH=$(pwd):$PYTHONPATH
     - for f in doc/examples/*.py; do $PYTHON "$f"; if [ $? -ne 0 ]; then exit 1; fi done
     - for f in doc/examples/applications/*.py; do $PYTHON "$f"; if [ $? -ne 0 ]; then exit 1; fi done
     # Run pep8 and flake tests

Makefile

@@ -7,7 +7,10 @@ clean:
 	find . -name "*.so" -o -name "*.pyc" -o -name "*.pyx.md5" | xargs rm -f
 
 test:
-	nosetests skimage
+	python -c "import skimage, sys, io; sys.exit(skimage.test_verbose())"
+
+doctest:
+	python -c "import skimage, sys, io; sys.exit(skimage.doctest_verbose())"
 
 coverage:
 	nosetests skimage --with-coverage --cover-package=skimage

TODO.txt

@@ -4,6 +4,7 @@ Version 0.10
 * Remove deprecated parameter `epsilon` of `skimage.viewer.LineProfile`
 * Remove backwards-compatability of `skimage.measure.regionprops`
 * Remove {`ratio`, `sigma`} deprecation warnings of `skimage.segmentation.slic`
+  and also remove explicit `sigma` parameter from doc-string example
 * Change default mode of random_walker segmentation to 'cg_mg' > 'cg' > 'bf',
   depending on which optional dependencies are available.
 * Remove deprecated `out` parameter of `skimage.morphology.binary_*`
@@ -12,4 +13,4 @@ Version 0.10
 * Remove deprecated function `filter.median_filter`
 * Remove deprecated `skimage.color.is_gray` and `skimage.color.is_rgb`
   functions
-
+* Enable doctests of experimental `skimage.feature.brief`

bento.info

@@ -45,9 +45,9 @@ Library:
     Extension: skimage.io._plugins._colormixer
         Sources:
             skimage/io/_plugins/_colormixer.pyx
-    Extension: skimage.measure._find_contours
+    Extension: skimage.measure._find_contours_cy
         Sources:
-            skimage/measure/_find_contours.pyx
+            skimage/measure/_find_contours_cy.pyx
     Extension: skimage.measure._moments
         Sources:
             skimage/measure/_moments.pyx

skimage/__init__.py

@@ -52,6 +52,7 @@
 import os.path as _osp
 import imp as _imp
 import functools as _functools
+import warnings as _warnings
 from skimage._shared.utils import deprecated as _deprecated
 
 pkg_dir = _osp.abspath(_osp.dirname(__file__))
@@ -68,24 +69,48 @@
     _imp.find_module('nose')
 except ImportError:
     def _test(verbose=False):
-        """This would invoke the skimage test suite, but nose couldn't be
+        """This would run all unit tests, but nose couldn't be
         imported so the test suite can not run.
         """
         raise ImportError("Could not load nose. Unit tests not available.")
+
+    def _doctest(verbose=False):
+        """This would run all doc tests, but nose couldn't be
+        imported so the test suite can not run.
+        """
+        raise ImportError("Could not load nose. Doctests not available.")
 else:
-    def _test(verbose=False):
-        """Invoke the skimage test suite."""
+    def _test(doctest=False, verbose=False):
+        """Run all unit tests."""
         import nose
-        args = ['', pkg_dir, '--exe']
+        args = ['', pkg_dir, '--exe', '--ignore-files=^_test']
         if verbose:
             args.extend(['-v', '-s'])
-        nose.run('skimage', argv=args)
+        if doctest:
+            args.extend(['--with-doctest', '--ignore-files=^\.',
+                         '--ignore-files=^setup\.py$$', '--ignore-files=test'])
+            # Make sure warnings do not break the doc tests
+            with _warnings.catch_warnings():
+                _warnings.simplefilter("ignore")
+                success = nose.run('skimage', argv=args)
+        else:
+            success = nose.run('skimage', argv=args)
+        # Return sys.exit code
+        if success:
+            return 0
+        else:
+            return 1
+
 
 # do not use `test` as function name as this leads to a recursion problem with
 # the nose test suite
 test = _test
 test_verbose = _functools.partial(test, verbose=True)
 test_verbose.__doc__ = test.__doc__
+doctest = _functools.partial(test, doctest=True)
+doctest.__doc__ = doctest.__doc__
+doctest_verbose = _functools.partial(test, doctest=True, verbose=True)
+doctest_verbose.__doc__ = doctest.__doc__
 
 
 class _Log(Warning):
@@ -105,10 +130,9 @@ def __init__(self, name):
         """
         self._name = name
 
-        import warnings
         warnings.simplefilter("always", _Log)
 
-        self._warnings = warnings
+        self._warnings = _warnings
 
     def _warn(self, msg, wtype):
         self._warnings.warn('%s: %s' % (wtype, msg), _Log)

skimage/color/colorlabel.py

@@ -112,7 +112,7 @@ def label2rgb(label, image=None, colors=None, alpha=0.3,
         label = label - offset  # Make sure you don't modify the input array.
         bg_label -= offset
 
-    new_type = np.min_scalar_type(label.max())
+    new_type = np.min_scalar_type(int(label.max()))
     if new_type == np.bool:
         new_type = np.uint8
     label = label.astype(new_type)

skimage/exposure/exposure.py

@@ -14,7 +14,6 @@
 def histogram(image, nbins=256):
     """Return histogram of image.
 
-
     Unlike `numpy.histogram`, this function returns the centers of bins and
     does not rebin integer arrays. For integer arrays, each integer value has
     its own bin, which improves speed and intensity-resolution.
@@ -40,11 +39,12 @@ def histogram(image, nbins=256):
 
     Examples
     --------
-    >>> from skimage import data
-    >>> hist = histogram(data.camera())
-    >>> import matplotlib.pyplot as plt
-    >>> plt.plot(hist[1], hist[0])  # doctest: +ELLIPSIS
-    [...]
+    >>> from skimage import data, exposure, util
+    >>> image = util.img_as_float(data.camera())
+    >>> np.histogram(image, bins=2)
+    (array([107432, 154712]), array([ 0. ,  0.5,  1. ]))
+    >>> exposure.histogram(image, nbins=2)
+    (array([107432, 154712]), array([ 0.25,  0.75]))
     """
     sh = image.shape
     if len(sh) == 3 and sh[-1] < 4:
@@ -339,7 +339,8 @@ def adjust_sigmoid(image, cutoff=0.5, gain=10, inv=False):
     References
     ----------
     .. [1] Gustav J. Braun, "Image Lightness Rescaling Using Sigmoidal Contrast
-    Enhancement Functions" http://www.cis.rit.edu/fairchild/PDFs/PAP07.pdf
+           Enhancement Functions",
+           http://www.cis.rit.edu/fairchild/PDFs/PAP07.pdf
 
     """
     _assert_non_negative(image)

skimage/feature/_brief.py

@@ -57,12 +57,11 @@ def brief(image, keypoints, descriptor_size=256, mode='normal', patch_size=49,
 
     Examples
     --------
-    >>> import numpy as np
-    >>> from skimage.feature.corner import corner_peaks, corner_harris
-    >>> from skimage.feature import pairwise_hamming_distance, brief, match_keypoints_brief
-    >>> square1 = np.zeros([8, 8], dtype=np.int32)
-    >>> square1[2:6, 2:6] = 1
-    >>> square1
+    >> from skimage.feature import corner_peaks, corner_harris, \\
+    ..   pairwise_hamming_distance, brief, match_keypoints_brief
+    >> square1 = np.zeros([8, 8], dtype=np.int32)
+    >> square1[2:6, 2:6] = 1
+    >> square1
     array([[0, 0, 0, 0, 0, 0, 0, 0],
            [0, 0, 0, 0, 0, 0, 0, 0],
            [0, 0, 1, 1, 1, 1, 0, 0],
@@ -71,21 +70,21 @@ def brief(image, keypoints, descriptor_size=256, mode='normal', patch_size=49,
            [0, 0, 1, 1, 1, 1, 0, 0],
            [0, 0, 0, 0, 0, 0, 0, 0],
            [0, 0, 0, 0, 0, 0, 0, 0]], dtype=int32)
-    >>> keypoints1 = corner_peaks(corner_harris(square1), min_distance=1)
-    >>> keypoints1
+    >> keypoints1 = corner_peaks(corner_harris(square1), min_distance=1)
+    >> keypoints1
     array([[2, 2],
            [2, 5],
            [5, 2],
            [5, 5]])
-    >>> descriptors1, keypoints1 = brief(square1, keypoints1, patch_size=5)
-    >>> keypoints1
+    >> descriptors1, keypoints1 = brief(square1, keypoints1, patch_size=5)
+    >> keypoints1
     array([[2, 2],
            [2, 5],
            [5, 2],
            [5, 5]])
-    >>> square2 = np.zeros([9, 9], dtype=np.int32)
-    >>> square2[2:7, 2:7] = 1
-    >>> square2
+    >> square2 = np.zeros([9, 9], dtype=np.int32)
+    >> square2[2:7, 2:7] = 1
+    >> square2
     array([[0, 0, 0, 0, 0, 0, 0, 0, 0],
            [0, 0, 0, 0, 0, 0, 0, 0, 0],
            [0, 0, 1, 1, 1, 1, 1, 0, 0],
@@ -95,24 +94,25 @@ def brief(image, keypoints, descriptor_size=256, mode='normal', patch_size=49,
            [0, 0, 1, 1, 1, 1, 1, 0, 0],
            [0, 0, 0, 0, 0, 0, 0, 0, 0],
            [0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=int32)
-    >>> keypoints2 = corner_peaks(corner_harris(square2), min_distance=1)
-    >>> keypoints2
+    >> keypoints2 = corner_peaks(corner_harris(square2), min_distance=1)
+    >> keypoints2
     array([[2, 2],
            [2, 6],
            [6, 2],
            [6, 6]])
-    >>> descriptors2, keypoints2 = brief(square2, keypoints2, patch_size=5)
-    >>> keypoints2
+    >> descriptors2, keypoints2 = brief(square2, keypoints2, patch_size=5)
+    >> keypoints2
     array([[2, 2],
            [2, 6],
            [6, 2],
            [6, 6]])
-    >>> pairwise_hamming_distance(descriptors1, descriptors2)
+    >> pairwise_hamming_distance(descriptors1, descriptors2)
     array([[ 0.03125  ,  0.3203125,  0.3671875,  0.6171875],
            [ 0.3203125,  0.03125  ,  0.640625 ,  0.375    ],
            [ 0.375    ,  0.6328125,  0.0390625,  0.328125 ],
            [ 0.625    ,  0.3671875,  0.34375  ,  0.0234375]])
-    >>> match_keypoints_brief(keypoints1, descriptors1, keypoints2, descriptors2)
+    >> match_keypoints_brief(keypoints1, descriptors1,
+    ..                       keypoints2, descriptors2)
     array([[[ 2,  2],
             [ 2,  2]],
 
@@ -126,6 +126,7 @@ def brief(image, keypoints, descriptor_size=256, mode='normal', patch_size=49,
             [ 6,  6]]])
 
     """
+
     np.random.seed(sample_seed)
 
     image = np.squeeze(image)