Merge pull request #151 from tonysyu/cleanup-tasks

DOC: Cleanup tasks list.

TASKS.txt

@@ -5,6 +5,15 @@
 How to contribute to ``skimage``
 ======================================
 
+.. toctree::
+   :hidden:
+
+   gitwash/index
+   gsoc2011
+   coverage_table
+   cell_profiler
+
+
 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.
@@ -33,13 +42,10 @@ Implement Algorithms
 - Convex hulls of objects in a labels matrix (simply adapt current convex hull 
   image code--this one's low hanging fruit).  Generalise this solution to also
   skeletonize objects in a labels matrix.
-- :strike:`Histograms of oriented gradients`
-- :strike:`Fast radon transform`
-- :strike:`Probabilistic Hough transform`
 
 Drawing (directly on an ndarray)
 ````````````````````````````````
-- Wu's algorithm for lines and circles
+- Wu's algorithm for circles
 - Text rendering
 
 Infrastructure
@@ -54,29 +60,19 @@ modified to work as part of the scikit, others may be lacking in documentation
 or tests.
 
    * :strike:`Connected components`
-   * :strike:`Grey-level co-occurrence matrices`
-   * :strike:`Marching squares`
    * Nadav's bilateral filtering (first compare against CellProfiler's
      code, based on http://groups.csail.mit.edu/graphics/bilagrid/bilagrid_web.pdf)
      Also see https://github.com/stefanv/scikits-image/tree/bilateral
-   * :strike:`2D iso-contour finding (sub-pixel precision) [ask Zach Pincus]`
    * 2D image warping via thin-plate splines [ask Zach Pincus]
 
 Merge code provided by `CellProfiler <http://www.cellprofiler.org>`_ team
 `````````````````````````````````````````````````````````````````````````
-* :strike:`Canny filter` (Canny, J., *A Computational Approach To Edge Detection*,
-  IEEE Trans. Pattern Analysis and Machine Intelligence, 8:679-714, 1986)
-* :strike:`Prewitt filter` - convolution with ``[[1,1,1], [0,0,0], [-1,-1,-1]]`` to
-  detect edges
-* :strike:`Sobel filter - convolution with` ``[[1,2,1], [0,0,0], [-1,-2,-1]]`` :strike:`to detect edges`
 * Roberts filter - convolution with diagonal and anti-diagonal
   kernels to detect edges
 * Minimum enclosing circles of objects in a labels matrix
-* :strike:`Map-coloring of a labels matrix - assign each label a color so that
-  all adjacent labels have different colors` -- simply plot with colormap "spectral".
-* :strike:`Skeletonize`, spur removal, thinning, thickening, and other morphological
-  operations on binary images, framework for creating arbitrary morphological
-  operations using a 3x3 grid.
+* spur removal, thinning, thickening, and other morphological operations on
+  binary images, framework for creating arbitrary morphological operations
+  using a 3x3 grid.
 
 Their SVN repository is read-accessible at
 
@@ -125,6 +121,4 @@ docs
 * Add examples to the gallery
 * Write topics for the `user guide
   <http://scikits-image.org/docs/dev/user_guide.html>`_
-* :strike:`Build docs outside source directory`
 * Integrate BiBTeX plugin into Sphinx build
-* :strike:`Create a kick-ass website`

doc/ext/gen_rst.py

@@ -47,6 +47,16 @@ plot_rst_template = """
     :lines: %(end_row)s-
     """
 
+
+toctree_template = """
+
+.. toctree::
+   :hidden:
+
+   %s
+
+"""
+
 # The following strings are used when we have several pictures: we use
 # an html div tag that our CSS uses to turn the lists into horizontal
 # lists.
@@ -144,13 +154,10 @@ def generate_dir_rst(dir, fhindex, example_dir, root_dir, plot_gallery):
         print 'Skipping this directory'
         print 80*'_'
         return
-    fhindex.write("""
 
+    example_description = file(os.path.join(src_dir, 'README.txt')).read()
+    fhindex.write("""\n\n%s\n\n""" % example_description)
 
-%s
-
-
-""" % file(os.path.join(src_dir, 'README.txt')).read())
     if not os.path.exists(target_dir):
         os.makedirs(target_dir)
 
@@ -159,20 +166,25 @@ def generate_dir_rst(dir, fhindex, example_dir, root_dir, plot_gallery):
         if not a.startswith('plot') and a.endswith('.py'):
             return 'zz' + a
         return a
-    for fname in sorted(os.listdir(src_dir), key=sort_key):
-        if fname.endswith('py'):
-            generate_file_rst(fname, target_dir, src_dir, plot_gallery)
-            thumb = os.path.join(dir, 'images', 'thumb', fname[:-3] + '.png')
-            link_name = os.path.join(dir, fname).replace(os.path.sep, '_')
-            fhindex.write('.. figure:: %s\n' % thumb)
-            if link_name.startswith('._'):
-                link_name = link_name[2:]
-            fhindex.write('   :figclass: gallery\n')
-            if dir != '.':
-                fhindex.write('   :target: ./%s/%s.html\n\n' % (dir, fname[:-3]))
-            else:
-                fhindex.write('   :target: ./%s.html\n\n' % link_name[:-3])
-            fhindex.write('   :ref:`example_%s`\n\n' % link_name)
+
+    examples = [fname for fname in sorted(os.listdir(src_dir), key=sort_key)
+                      if fname.endswith('py')]
+    ex_names = [ex[:-3] for ex in examples] # strip '.py' extension
+    fhindex.write(toctree_template % '\n   '.join(ex_names))
+
+    for fname in examples:
+        generate_file_rst(fname, target_dir, src_dir, plot_gallery)
+        thumb = os.path.join(dir, 'images', 'thumb', fname[:-3] + '.png')
+        link_name = os.path.join(dir, fname).replace(os.path.sep, '_')
+        fhindex.write('.. figure:: %s\n' % thumb)
+        if link_name.startswith('._'):
+            link_name = link_name[2:]
+        fhindex.write('   :figclass: gallery\n')
+        if dir != '.':
+            fhindex.write('   :target: ./%s/%s.html\n\n' % (dir, fname[:-3]))
+        else:
+            fhindex.write('   :target: ./%s.html\n\n' % link_name[:-3])
+        fhindex.write('   :ref:`example_%s`\n\n' % link_name)
     fhindex.write("""
 .. raw:: html
 

doc/source/index.txt

@@ -11,6 +11,19 @@ This SciKit_ is an image processing toolbox for SciPy_.
 Sections
 ========
 
+.. toctree::
+   :hidden:
+
+   overview
+   api
+   api_changes
+   install
+   user_guide
+   contribute
+   license
+   auto_examples/index
+
+
 .. list-table::
    :class: contentstable