From 09876408fc3f04c32bbf352ba09460ab0ef7e592 Mon Sep 17 00:00:00 2001 From: Steven Silvester Date: Sun, 25 Jan 2015 15:13:16 -0600 Subject: [PATCH] Fix some sphinx warnings and add to build Fix some sphinx warnings Add documentation build to test Add documentation build to test Remove change in numpydoc Remove change in apigen Add makefile target for html and add to travis script Add a makefile target for html and add to travis script Fix more sphinx warnings --- CONTRIBUTING.txt | 8 +++----- DEPENDS.txt | 10 +++++----- Makefile | 4 ++++ skimage/draw/draw.py | 1 + skimage/filters/thresholding.py | 6 ++++-- skimage/future/graph/rag.py | 2 +- skimage/measure/_ccomp.pyx | 2 +- skimage/segmentation/boundaries.py | 14 +++++++------- skimage/util/noise.py | 18 +++++++++--------- tools/travis_script.sh | 3 +++ 10 files changed, 38 insertions(+), 30 deletions(-) diff --git a/CONTRIBUTING.txt b/CONTRIBUTING.txt index fcb36547..58b83296 100644 --- a/CONTRIBUTING.txt +++ b/CONTRIBUTING.txt @@ -123,9 +123,7 @@ Guidelines * All code should have tests (see `test coverage`_ below for more details). * All code should be documented, to the same - `standard -<://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_ - as NumPy and SciPy. + `standard <://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_ as NumPy and SciPy. * For new functionality, always add an example to the gallery. * No changes are ever committed without review. Ask on the @@ -195,8 +193,8 @@ successfully passes all tests. To do so, * Go to `Travis-CI `__ and follow the Sign In link at the top - * Go to your `profile page `__ and switch on your - scikit-image fork + * Go to your `profile page `__ and switch + on your scikit-image fork It corresponds to steps one and two in `Travis-CI documentation `__ diff --git a/DEPENDS.txt b/DEPENDS.txt index 02ee007f..5cf37564 100644 --- a/DEPENDS.txt +++ b/DEPENDS.txt @@ -45,12 +45,12 @@ functionality is only available with the following installed: * `Astropy `__ provides FITS io capability. -*`SimpleITK ` - Optional io plugin providing a wide variety of `formats `__. - including specialized formats using in medical imaging. +* `SimpleITK ` + Optional io plugin providing a wide variety of `formats `__. + including specialized formats using in medical imaging. -*`imread ` - Optional io plugin providing most standard `formats `__. +* `imread ` + Optional io plugin providing most standard `formats `__. Testing requirements diff --git a/Makefile b/Makefile index 2ace534e..270aee98 100644 --- a/Makefile +++ b/Makefile @@ -14,3 +14,7 @@ doctest: coverage: nosetests skimage --with-coverage --cover-package=skimage + +html: + pip install sphinx + make -C docs html diff --git a/skimage/draw/draw.py b/skimage/draw/draw.py index be59e268..dbeb6ba0 100644 --- a/skimage/draw/draw.py +++ b/skimage/draw/draw.py @@ -95,6 +95,7 @@ def circle(cy, cx, radius, shape=None): Pixel coordinates of circle. May be used to directly index into an array, e.g. ``img[rr, cc] = 1``. + Notes ----- This function is a wrapper for skimage.draw.ellipse() diff --git a/skimage/filters/thresholding.py b/skimage/filters/thresholding.py index 74c5fc14..00e3763c 100644 --- a/skimage/filters/thresholding.py +++ b/skimage/filters/thresholding.py @@ -200,8 +200,10 @@ def threshold_isodata(image, nbins=256, return_all=False): Histogram-based threshold, known as Ridler-Calvard method or inter-means. Threshold values returned satisfy the following equality: - threshold = (image[image <= threshold].mean() + - image[image > threshold].mean()) / 2.0 + + ``threshold = (image[image <= threshold].mean() +`` + ``image[image > threshold].mean()) / 2.0`` + That is, returned thresholds are intensities that separate the image into two groups of pixels, where the threshold intensity is midway between the mean intensities of these groups. diff --git a/skimage/future/graph/rag.py b/skimage/future/graph/rag.py index b0fd9240..11441800 100644 --- a/skimage/future/graph/rag.py +++ b/skimage/future/graph/rag.py @@ -220,7 +220,7 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance', labels : ndarray, shape(M, N, [..., P,]) The labelled image. This should have one dimension less than `image`. If `image` has dimensions `(M, N, 3)` `labels` should have - dimensions `(M, N)`. + dimensions `(M, N)`. connectivity : int, optional Pixels with a squared distance less than `connectivity` from each other are considered adjacent. It can range from 1 to `labels.ndim`. Its diff --git a/skimage/measure/_ccomp.pyx b/skimage/measure/_ccomp.pyx index 56b31a9f..a3b27593 100644 --- a/skimage/measure/_ccomp.pyx +++ b/skimage/measure/_ccomp.pyx @@ -368,7 +368,7 @@ def label(input, neighbors=None, background=None, return_num=False, Two pixels are connected when they are neighbors and have the same value. In 2D, they can be neighbors either in a 1- or 2-connected sense. The value refers to the maximum number of orthogonal hops to consider a - pixel/voxel a neighbor. + pixel/voxel a neighbor:: 1-connectivity 2-connectivity diagonal connection close-up diff --git a/skimage/segmentation/boundaries.py b/skimage/segmentation/boundaries.py index 1975d879..9400e306 100644 --- a/skimage/segmentation/boundaries.py +++ b/skimage/segmentation/boundaries.py @@ -65,15 +65,15 @@ def find_boundaries(label_img, connectivity=1, mode='thick', background=0): How to mark the boundaries: - thick: any pixel not completely surrounded by pixels of the - same label (defined by `connectivity`) is marked as a boundary. - This results in boundaries that are 2 pixels thick. + same label (defined by `connectivity`) is marked as a boundary. + This results in boundaries that are 2 pixels thick. - inner: outline the pixels *just inside* of objects, leaving - background pixels untouched. + background pixels untouched. - outer: outline pixels in the background around object - boundaries. When two objects touch, their boundary is also - marked. + boundaries. When two objects touch, their boundary is also + marked. - subpixel: return a doubled image, with pixels *between* the - original pixels marked as boundary where appropriate. + original pixels marked as boundary where appropriate. background: int, optional For modes 'inner' and 'outer', a definition of a background label is required. See `mode` for descriptions of these two. @@ -197,7 +197,7 @@ def mark_boundaries(image, label_img, color=(1, 1, 0), See Also -------- - ``find_boundaries``. + find_boundaries """ marked = img_as_float(image, force_copy=True) if marked.ndim == 2: diff --git a/skimage/util/noise.py b/skimage/util/noise.py index 9283f537..ff20084a 100644 --- a/skimage/util/noise.py +++ b/skimage/util/noise.py @@ -16,15 +16,15 @@ def random_noise(image, mode='gaussian', seed=None, clip=True, **kwargs): mode : str One of the following strings, selecting the type of noise to add: - 'gaussian' Gaussian-distributed additive noise. - 'localvar' Gaussian-distributed additive noise, with specified - local variance at each point of `image` - 'poisson' Poisson-distributed noise generated from the data. - 'salt' Replaces random pixels with 1. - 'pepper' Replaces random pixels with 0. - 's&p' Replaces random pixels with 0 or 1. - 'speckle' Multiplicative noise using out = image + n*image, where - n is uniform noise with specified mean & variance. + - 'gaussian' Gaussian-distributed additive noise. + - 'localvar' Gaussian-distributed additive noise, with specified + local variance at each point of `image` + - 'poisson' Poisson-distributed noise generated from the data. + - 'salt' Replaces random pixels with 1. + - 'pepper' Replaces random pixels with 0. + - 's&p' Replaces random pixels with 0 or 1. + - 'speckle' Multiplicative noise using out = image + n*image, where + n is uniform noise with specified mean & variance. seed : int If provided, this will set the random seed before generating noise, for valid pseudo-random comparisons. diff --git a/tools/travis_script.sh b/tools/travis_script.sh index f76467bb..38e2f72a 100755 --- a/tools/travis_script.sh +++ b/tools/travis_script.sh @@ -5,6 +5,9 @@ section "Test.with.min.requirements" nosetests $TEST_ARGS skimage section_end "Test.with.min.requirements" +section "Build.docs" +make html +section_end "Build.docs" section "Flake8.test" flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples