Merge pull request #3631 from hantek/doctest

.travis.yml

@@ -29,8 +29,14 @@ install:
   - source activate pyenv
   - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then pip install pydot; fi
   - pip install . --no-deps
+  - pip install -U Sphinx
 
 # command to run tests
+env:
+  - PART="theano/sandbox theano/sparse theano/scalar theano/tensor/nnet theano/scan_module"
+  - PART="theano/tensor/tests/test_basic.py theano/tensor/signal theano/compile theano/gof theano/misc theano/tests theano/compat"
+  - PART="-e test_basic.py theano/tensor/tests"
+
 matrix:
   fast_finish: true
   include:
@@ -38,11 +44,8 @@ matrix:
       env: PART="." THEANO_FLAGS="mode=FAST_COMPILE"
     - python: "2.6"
       env: PART="." THEANO_FLAGS="mode=FAST_COMPILE,floatX=float32"
-
-env:
-  - PART="sandbox sparse scalar tensor/nnet scan_module"
-  - PART="tensor/tests/test_basic.py tensor/signal compile gof misc tests compat"
-  - PART="-e test_basic.py tensor/tests"
+    - python: 2.6
+      env: PART="." DOC=1
 
 script:
   - export THEANO_FLAGS=$THEANO_FLAGS,warn.ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc.cxxflags=-pipe
@@ -56,7 +59,9 @@ script:
   # Move to the path of the installed version
   - cd $(python -c 'import theano; import os; print(os.path.split(theano.__file__)[0])')
   - echo "$PART"
-  - theano-nose -v $PART
+  - cd -; cd Theano
+  - if [[ $DOC == "1" ]]; then python doc/scripts/docgen.py --nopdf; else theano-nose -v $PART; fi
+  - if [[ $DOC == "1" ]]; then python doc/scripts/docgen.py --test; fi
 #  - theano-cache list
 
 #after_script:

README.txt

@@ -2,7 +2,6 @@ To install the package, see this page:
 
    http://deeplearning.net/software/theano/install.html
 
-
 For the documentation, see the project website:
 
    http://deeplearning.net/software/theano/
@@ -14,7 +13,7 @@ Related Projects:
 We recommend you look at the documentation on the website, since it
 will be more current than the documentation included with the package.
 If you really wish to build the documentation yourself, you will need
-epydoc and sphinx. Issue the following command:
+sphinx. Issue the following command:
 
     python ./doc/scripts/docgen.py
 

doc/api/epydoc.conf

-# TODO:
-#   Get all graphs to work!
-
-
-[epydoc] # Epydoc section marker (required by ConfigParser)
-
-# The list of objects to document.  Objects can be named using
-# dotted names, module filenames, or package directory names.
-# Alases for this option include "objects" and "values".
-modules: theano scipy.sparse
-
-# The type of output that should be generated.  Should be one
-# of: html, text, latex, dvi, ps, pdf.
-output: html
-
-# An integer indicating how verbose epydoc should be.  The default
-# value is 0; negative values will supress warnings and errors;
-# positive values will give more verbose output.
-verbosity: 1
-
-# A boolean value indicating that Epydoc should show a tracaback
-# in case of unexpected error. By default don't show tracebacks
-debug: 1
-
-# If True, don't try to use colors or cursor control when doing
-# textual output. The default False assumes a rich text prompt
-simple-term: 0
-
-
-### Generation options
-
-# The default markup language for docstrings, for modules that do
-# not define __docformat__.  Defaults to epytext.
-docformat: epytext
-
-# Whether or not parsing should be used to examine objects.
-parse: yes
-
-# Whether or not introspection should be used to examine objects.
-introspect: yes
-
-# Don't examine in any way the modules whose dotted name match this
-# regular expression pattern.
-#exclude
-
-# Don't perform introspection on the modules whose dotted name match this
-# regular expression pattern.
-#exclude-introspect
-
-# Don't perform parsing on the modules whose dotted name match this
-# regular expression pattern.
-#exclude-parse
-
-# The format for showing inheritance objects.
-# It should be one of: 'grouped', 'listed', 'included'.
-inheritance: grouped
-
-# Whether or not to inclue private variables.  (Even if included,
-# private variables will be hidden by default.)
-private: yes
-
-# Whether or not to list each module's imports.
-imports: yes
-
-# Whether or not to include syntax highlighted source code in
-# the output (HTML only).
-sourcecode: yes
-
-# Whether or not to includea a page with Epydoc log, containing
-# effective option at the time of generation and the reported logs.
-include-log: yes
-
-
-### Output options
-
-# The documented project's name.
-name: Theano
-
-# The CSS stylesheet for HTML output.  Can be the name of a builtin
-# stylesheet, or the name of a file.
-css: white
-
-# The documented project's URL.
-url: http://lgcm.iro.umontreal.ca/theano/
-
-# HTML code for the project link in the navigation bar.  If left
-# unspecified, the project link will be generated based on the
-# project's name and URL.
-#link: <a href="somewhere">My Cool Project</a>
-
-# The "top" page for the documentation.  Can be a URL, the name
-# of a module or class, or one of the special names "trees.html",
-# "indices.html", or "help.html"
-#top: os.path
-
-# An alternative help file.  The named file should contain the
-# body of an HTML file; navigation bars will be added to it.
-#help: my_helpfile.html
-
-# Whether or not to include a frames-based table of contents.
-#frames: yes
-frames: no
-
-# Whether each class should be listed in its own section when
-# generating LaTeX or PDF output.
-separate-classes: no
-
-
-### API linking options
-
-# Define a new API document.  A new interpreted text role
-# will be created
-#external-api: epydoc
-
-# Use the records in this file to resolve objects in the API named NAME.
-#external-api-file: epydoc:api-objects.txt
-
-# Use this URL prefix to configure the string returned for external API.
-#external-api-root: epydoc:http://epydoc.sourceforge.net/api
-# external-api: wiki doc
-# external-api-root: wiki:http://lgcm.iro.umontreal.ca/theano/wiki/ doc:http://lgcm.iro.umontreal.ca/auto_theano/doc/
-# external-api-file: wiki:wiki.idx doc:doc/doc.idx
-
-### Graph options
-
-# The list of graph types that should be automatically included
-# in the output.  Graphs are generated using the Graphviz "dot"
-# executable.  Graph types include: "classtree", "callgraph",
-# "umlclass".  Use "all" to include all graph types
-graph: all
-
-# The path to the Graphviz "dot" executable, used to generate
-# graphs.
-dotpath: /usr/bin/dot
-
-# The name of one or more pstat files (generated by the profile
-# or hotshot module).  These are used to generate call graphs.
-#pstat: autotest.pstat
-
-# Specify the font used to generate Graphviz graphs.
-# (e.g., helvetica or times).
-graph-font: Helvetica
-
-# Specify the font size used to generate Graphviz graphs.
-graph-font-size: 10
-
-
-### Return value options
-
-# The condition upon which Epydoc should exit with a non-zero
-# exit status. Possible values are error, warning, docstring_warning
-#fail-on: error

doc/dev_start_guide.txt

@@ -21,12 +21,11 @@ To get up to speed, you'll need to
 - Learn some non-basic Python to understand what's going on in some of the
   trickier files (like tensor.py).
 - Go through the `NumPy documentation`_.
-- Learn to write reStructuredText_ for epydoc_ and Sphinx_.
+- Learn to write reStructuredText_ for Sphinx_.
 - Learn about how unittest_ and nose_ work
 
 .. _Sphinx: http://sphinx.pocoo.org/
 .. _reStructuredText: http://docutils.sourceforge.net/rst.html
-.. _epydoc: http://epydoc.sourceforge.net/
 .. _NumPy documentation: http://docs.scipy.org/numpy/
 .. _unittest: http://docs.python.org/library/unittest.html
 .. _nose: http://somethingaboutorange.com/mrl/projects/nose/

doc/extending/op.txt

@@ -672,13 +672,14 @@ is a :ref:`variable` we statically know the value of.
 
 .. doctest:: mul
 
+   >>> import numpy
    >>> x = double('x')
    >>> z = mul(x, 2)
    >>> f = theano.function([x], z)
    >>> f(10)
    20.0
-   >>> f(3.4)
-   6.8
+   >>> numpy.allclose(f(3.4), 6.8)
+   True
 
 Now the code works the way we want it to.
 

doc/extending/using_params.txt

@@ -146,7 +146,7 @@ the params type.
 
        def make_node(self, inp):
            inp = as_scalar(inp)
-           return Apply(self, [inp], [inp.type()]
+           return Apply(self, [inp], [inp.type()])
 
        def perform(self, node, inputs, output_storage, params):
            # Here params is a python float so this is ok
@@ -193,7 +193,7 @@ weights.
        def make_node(self, x, y):
            x = as_scalar(x)
            y = as_scalar(y)
-           return Apply(self, [x, y], [x.type()]
+           return Apply(self, [x, y], [x.type()])
 
        def c_support_code_struct(self, node, name):
            return """

doc/install.txt

@@ -886,7 +886,7 @@ We recommend you look at the documentation on the website, since it
 will be more current than the documentation included with the package.
 
 If you really wish to build the documentation yourself, you will need
-epydoc and sphinx, as described above. Issue the following command::
+sphinx, as described above. Issue the following command::
 
     python ./doc/scripts/docgen.py
 

doc/internal/metadocumentation.txt

@@ -40,8 +40,8 @@ Use ReST for documentation
 --------------------------
 
  * `ReST <http://docutils.sourceforge.net/rst.html>`__ is standardized.
-   epydoc is not. trac wiki-markup is not.
-   This means that ReST can be cut-and-pasted between epydoc, code, other
+   trac wiki-markup is not.
+   This means that ReST can be cut-and-pasted between code, other
    docs, and TRAC.  This is a huge win!
  * ReST is extensible: we can write our own roles and directives to automatically link to WIKI, for example.
  * ReST has figure and table directives, and can be converted (using a standard tool) to latex documents.

doc/library/compile/shared.txt

@@ -5,7 +5,7 @@
 :mod:`shared` - defines theano.shared
 ===========================================
 
-.. module:: shared
+.. module:: theano.compile.sharedvalue
    :platform: Unix, Windows
    :synopsis: defines theano.shared and related classes
 .. moduleauthor:: LISA
@@ -47,7 +47,7 @@
 
         :type: class:`Container`
 
-.. autofunction:: theano.compile.sharedvalue.shared
+.. autofunction:: shared
 
 .. function:: shared_constructor(ctor)
 

doc/library/sandbox/cuda/op.txt

@@ -19,7 +19,7 @@ Blas Op
 
 .. automodule:: theano.sandbox.cuda.blas
     :members:
-.. autofunction:: theano.sandbox.cuda.blas.batched_dot
+.. autoclass:: theano.sandbox.cuda.blas.BatchedDotOp
 
 Nnet Op
 =======

doc/library/tensor/nnet/conv.txt

@@ -104,7 +104,7 @@ TODO: Give examples on how to use these things! They are pretty complicated.
       as a manual replacement for nnet.conv2d.
     - :func:`GpuCorrMM <theano.sandbox.cuda.blas.GpuCorrMM>`
       This is a GPU-only 2d correlation implementation taken from
-      `caffe <https://github.com/BVLC/caffe/blob/master/src/caffe/layers/conv_layer.cu>`_
+      `caffe's CUDA implementation <https://github.com/BVLC/caffe/blob/master/src/caffe/layers/conv_layer.cu>`_
       and also used by Torch. It does not flip the kernel.
 
       For each element in a batch, it first creates a
@@ -122,7 +122,7 @@ TODO: Give examples on how to use these things! They are pretty complicated.
       If using it, please see the warning about a bug in CUDA 5.0 to 6.0 below.
     - :func:`CorrMM <theano.tensor.nnet.corr.CorrMM>`
       This is a CPU-only 2d correlation implementation taken from
-      `caffe <https://github.com/BVLC/caffe/blob/master/src/caffe/layers/conv_layer.cpp>`_
+      `caffe's cpp implementation <https://github.com/BVLC/caffe/blob/master/src/caffe/layers/conv_layer.cpp>`_
       and also used by Torch. It does not flip the kernel. As it provides a gradient,
       you can use it as a replacement for nnet.conv2d. For convolutions done on
       CPU, nnet.conv2d will be replaced by CorrMM. To explicitly disable it, set

doc/library/tensor/shared_randomstreams.txt

@@ -21,7 +21,7 @@ object for each such variable, and draw from it as necessary.  We will call this
 random numbers a *random stream*.
 
 For an example of how to use random numbers, see
-:ref:`using_random_numbers`.
+:ref:`Using Random Numbers <using_random_numbers>`.
 
 
 Reference

doc/proposals/pfunc.txt

@@ -89,7 +89,7 @@ The proposal is for two new ways of creating a *shared* variable:
     def shared(value, name=None, strict=False, **kwargs):
         """Return a SharedVariable Variable, initialized with a copy or reference of `value`.
 
-        This function iterates over constructor functions (see `shared_constructor`) to find a
+        This function iterates over constructor functions (see :func:`shared_constructor`) to find a
         suitable SharedVariable subclass.
 
         :note:

doc/scripts/docgen.py

@@ -4,56 +4,6 @@ import sys
 import os
 import shutil
 import inspect
-
-from epydoc import docintrospecter
-from epydoc.apidoc import RoutineDoc
-
-
-def Op_to_RoutineDoc(op, routine_doc, module_name=None):
-    routine_doc.specialize_to(RoutineDoc)
-
-    #NB: this code is lifted from epydoc/docintrospecter.py
-
-    # op should be an op instance
-    assert hasattr(op, 'perform')
-
-    # Record the function's docstring.
-    routine_doc.docstring = getattr(op, '__doc__', '')
-
-    # Record the function's signature.
-    func = op.__epydoc_asRoutine
-    if isinstance(func, type(Op_to_RoutineDoc)):
-        (args, vararg, kwarg, defaults) = inspect.getargspec(func)
-
-        # Add the arguments.
-        routine_doc.posargs = args
-        routine_doc.vararg = vararg
-        routine_doc.kwarg = kwarg
-
-        # Set default values for positional arguments.
-        routine_doc.posarg_defaults = [None] * len(args)
-
-        # Set the routine's line number.
-        if hasattr(func, '__code__'):
-            routine_doc.lineno = func.__code__.co_firstlineno
-    else:
-        # [XX] I should probably use UNKNOWN here??
-        # dvarrazzo: if '...' is to be changed, also check that
-        # `docstringparser.process_arg_field()` works correctly.
-        # See SF bug #1556024.
-        routine_doc.posargs = ['...']
-        routine_doc.posarg_defaults = [None]
-        routine_doc.kwarg = None
-        routine_doc.vararg = None
-
-    return routine_doc
-
-docintrospecter.register_introspecter(
-    lambda value: getattr(value, '__epydoc_asRoutine', False),
-    Op_to_RoutineDoc,
-    priority=-1)
-
-
 import getopt
 from collections import defaultdict
 
@@ -66,7 +16,7 @@ if __name__ == '__main__':
     opts, args = getopt.getopt(
         sys.argv[1:],
         'o:f:',
-        ['epydoc', 'rst', 'help', 'nopdf', 'cache', 'test'])
+        ['rst', 'help', 'nopdf', 'cache', 'test'])
     options.update(dict([x, y or True] for x, y in opts))
     if options['--help']:
         print('Usage: %s [OPTIONS] [files...]' % sys.argv[0])
@@ -74,8 +24,6 @@ if __name__ == '__main__':
         print('  --cache: use the doctree cache')
         print('  --rst: only compile the doc (requires sphinx)')
         print('  --nopdf: do not produce a PDF file from the doc, only HTML')
-        print('  --epydoc: only compile the api documentation', end=' ')
-        print('(requires epydoc)')
         print('  --test: run all the code samples in the documentaton')
         print('  --help: this help')
         print('If one or more files are specified after the options then only '
@@ -83,7 +31,7 @@ if __name__ == '__main__':
               'processed. Specifying files will implies --cache.')
         sys.exit(0)
 
-    if not (options['--epydoc'] or options['--rst'] or options['--test']):
+    if options['--rst'] or options['--test']:
         # Default is now rst
         options['--rst'] = True
 
@@ -105,26 +53,10 @@ if __name__ == '__main__':
     pythonpath = os.pathsep.join([throot, pythonpath])
     sys.path[0:0] = [throot]  # We must not use os.environ.
 
-    if options['--all'] or options['--epydoc']:
-        mkdir("api")
-
-        #Generate HTML doc
-
-        ## This causes problems with the subsequent generation of sphinx doc
-        #from epydoc.cli import cli
-        #sys.argv[:] = ['', '--config', '%s/doc/api/epydoc.conf' % throot,
-        #               '-o', 'api']
-        #cli()
-        ## So we use this instead
-        os.system("epydoc --config %s/doc/api/epydoc.conf -o api" % throot)
-
-        # Generate PDF doc
-        # TODO
-
     def call_sphinx(builder, workdir, extraopts=None):
         import sphinx
         if extraopts is None:
-            extraopts = []
+            extraopts = ['-W']
         if not options['--cache'] and files is None:
             extraopts.append('-E')
         docpath = os.path.join(throot, 'doc')

doc/tutorial/adding.txt

@@ -11,6 +11,7 @@ To get us started with Theano and get a feel of what we're working with,
 let's make a simple function: add two numbers together. Here is how you do
 it:
 
+>>> import numpy
 >>> import theano.tensor as T
 >>> from theano import function
 >>> x = T.dscalar('x')
@@ -22,9 +23,8 @@ And now that we've created our function we can use it:
 
 >>> f(2, 3)
 array(5.0)
->>> f(16.3, 12.1)
-array(28.4)
-
+>>> numpy.allclose(f(16.3, 12.1), 28.4)
+True
 
 Let's break this down into several steps. The first step is to define
 two symbols (*Variables*) representing the quantities that you want
@@ -123,12 +123,13 @@ then be used like a normal Python function.
     the tutorial so far. It has the added benefit of not requiring
     you to import :func:`function` . Here is how :func:`eval` works:
 
+    >>> import numpy
     >>> import theano.tensor as T
     >>> x = T.dscalar('x')
     >>> y = T.dscalar('y')
     >>> z = x + y
-    >>> z.eval({x : 16.3, y : 12.1})
-    array(28.4)
+    >>> numpy.allclose(z.eval({x : 16.3, y : 12.1}), 28.4)
+    True
 
     We passed :func:`eval` a dictionary mapping symbolic theano
     variables to the values to substitute for them, and it returned

doc/tutorial/examples.txt

@@ -207,15 +207,15 @@ Let's try it out!
 .. theano/tests/test_tutorial.py:T_examples.test_examples_8
 
 >>> state.get_value()
-array(0)
+0
 >>> accumulator(1)
 array(0)
 >>> state.get_value()
-array(1)
+1
 >>> accumulator(300)
 array(1)
 >>> state.get_value()
-array(301)
+301
 
 It is possible to reset the state. Just use the ``.set_value()`` method:
 
@@ -223,7 +223,7 @@ It is possible to reset the state. Just use the ``.set_value()`` method:
 >>> accumulator(3)
 array(-1)
 >>> state.get_value()
-array(2)
+2
 
 As we mentioned above, you can define more than one function to use the same
 shared variable.  These functions can all update the value.
@@ -235,7 +235,7 @@ shared variable.  These functions can all update the value.
 >>> decrementor(2)
 array(2)
 >>> state.get_value()
-array(0)
+0
 
 You might be wondering why the updates mechanism exists.  You can always
 achieve a similar result by returning the new expressions, and working with
@@ -262,7 +262,7 @@ for the purpose of one particular function.
 >>> skip_shared(1, 3)  # we're using 3 for the state, not state.value
 array(7)
 >>> state.get_value()  # old state still there, but we didn't use it
-array(0)
+0
 
 The ``givens`` parameter can be used to replace any symbolic variable, not just a
 shared variable. You can replace constants, and expressions, in general.  Be

doc/tutorial/gradients.txt

@@ -23,6 +23,7 @@ Here is the code to compute this gradient:
 .. If you modify this code, also change :
 .. theano/tests/test_tutorial.py:T_examples.test_examples_4
 
+>>> import numpy
 >>> import theano
 >>> import theano.tensor as T
 >>> from theano import pp 
@@ -34,8 +35,8 @@ Here is the code to compute this gradient:
 >>> f = theano.function([x], gy)
 >>> f(4)
 array(8.0)
->>> f(94.2)
-array(188.4)
+>>> numpy.allclose(f(94.2), 188.4)
+True
 
 In this example, we can see from ``pp(gy)`` that we are computing
 the correct symbolic gradient.

doc/tutorial/profiling.txt

@@ -27,9 +27,7 @@ functions using either of the following two options:
       :attr:`profiling.n_ops` and :attr:`profiling.min_memory_size`
       to modify the quantify of information printed.
 
-2. Pass the argument :attr:`profile=True` to the function
-   :func:`theano.function <function.function>`. And then call
-   :attr:`f.profile.print_summary()` for a single function.
+2. Pass the argument :attr:`profile=True` to the function :func:`theano.function <function.function>`. And then call :attr:`f.profile.print_summary()` for a single function.
     - Use this option when you want to profile not all the
       functions but one or more specific function(s).
     - You can also combine the profile of many functions: 

theano/compile/function.py

@@ -50,9 +50,9 @@ def function_dump(filename, inputs, outputs=None, mode=None, updates=None,
     >>> f = theano.function(**d)  # doctest: +SKIP
 
     Note:
-      The parameter extra_tag_to_remove, is passed to the StripPickler used.
-      To pickle graph made by Blocks, it must be:
-          ['annotations', 'replacement_of', 'aggregation_scheme', 'rolesc']
+    The parameter extra_tag_to_remove, is passed to the StripPickler used.
+    To pickle graph made by Blocks, it must be:
+    ['annotations', 'replacement_of', 'aggregation_scheme', 'rolesc']
 
     """
     assert isinstance(filename, string_types)

theano/compile/sharedvalue.py

@@ -200,20 +200,25 @@ def shared_constructor(ctor, remove=False):
 
 
 def shared(value, name=None, strict=False, allow_downcast=None, **kwargs):
-    """
-    Return a SharedVariable Variable, initialized with a copy or
+    """Return a SharedVariable Variable, initialized with a copy or
     reference of `value`.
 
-    This function iterates over
-    :ref:`constructor functions <shared_constructor>`
-    to find a suitable SharedVariable subclass.
-    The suitable one is the first constructor that accept the given value.
+    This function iterates over constructor functions to find a
+    suitable SharedVariable subclass.  The suitable one is the first
+    constructor that accept the given value.  See the documentation of
+    :func:`shared_constructor` for the definition of a contructor
+    function.
 
     This function is meant as a convenient default.  If you want to use a
     specific shared variable constructor, consider calling it directly.
 
     ``theano.shared`` is a shortcut to this function.
 
+    .. attribute:: constructors
+
+    A list of shared variable constructors that will be tried in reverse
+    order.
+
     Notes
     -----
     By passing kwargs, you effectively limit the set of potential constructors
@@ -229,11 +234,6 @@ def shared(value, name=None, strict=False, allow_downcast=None, **kwargs):
     This parameter allows you to create for example a `row` or `column` 2d
     tensor.
 
-    .. attribute:: constructors
-
-    A list of shared variable constructors that will be tried in reverse
-    order.
-
     """
 
     try:

theano/gof/graph.py

@@ -485,12 +485,13 @@ class Variable(Node):
         Examples
         --------
 
+        >>> import numpy
         >>> import theano.tensor as T
         >>> x = T.dscalar('x')
         >>> y = T.dscalar('y')
         >>> z = x + y
-        >>> z.eval({x : 16.3, y : 12.1})
-        array(28.4)
+        >>> numpy.allclose(z.eval({x : 16.3, y : 12.1}), 28.4)
+        True
 
         We passed :func:`eval` a dictionary mapping symbolic theano
         variables to the values to substitute for them, and it returned

theano/misc/pkl_utils.py

@@ -144,6 +144,7 @@ else:
                 u = CompatUnpickler(fp, encoding="latin1")
             else:
                 u = CompatUnpickler(fp)
+
             mat = u.load()
         """
         pass

theano/sparse/basic.py

@@ -273,7 +273,7 @@ def sp_ones_like(x):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         The same as `x` with data changed for ones.
 
     """
@@ -293,7 +293,7 @@ def sp_zeros_like(x):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         The same as `x` with zero entries for all element.
 
     """
@@ -1765,7 +1765,7 @@ def row_scale(x, s):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         A sparse matrix in the same format as `x` whose each row has been
         multiplied by the corresponding element of `s`.
 
@@ -2070,7 +2070,7 @@ def clean(x):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         The same as `x` with indices sorted and zeros
         removed.
 
@@ -2166,7 +2166,7 @@ y
 
 Returns
 -------
-matrix
+A sparse matrix
     The sum of the two sparse matrices element wise.
 
 Notes
@@ -2270,7 +2270,7 @@ y
 
 Returns
 -------
-matrix
+A sparse matrix
     A sparse matrix containing the addition of the vector to
     the data of the sparse matrix.
 
@@ -2297,7 +2297,7 @@ def add(x, y):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         `x` + `y`
 
     Notes
@@ -2348,7 +2348,7 @@ def sub(x, y):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         `x` - `y`
 
     Notes
@@ -2547,7 +2547,7 @@ y
 
 Returns
 -------
-matrix
+A sparse matrix
     The product x * y element wise.
 
 Notes
@@ -2572,7 +2572,7 @@ def mul(x, y):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         `x` + `y`
 
     Notes
@@ -3720,7 +3720,7 @@ def structured_dot(x, y):
 
     Returns
     -------
-    matrix
+    A sparse matrix
         The dot product of `a` and `b`.
 
     Notes

theano/tensor/elemwise.py

@@ -461,7 +461,7 @@ class Elemwise(OpenMPOp):
     scalar.ScalarOp to get help about controlling the output type)
 
     Parameters
-    -----------
+    ----------
     scalar_op
         An instance of a subclass of scalar.ScalarOp which works uniquely
         on scalars.