diff --git a/doc/developers/index.rst b/doc/developers/index.rst
index 80e46ae41bcd0bd71711471f152f9280f4209511..78387281ba2285051b455d8c8696277c285c97de 100644
--- a/doc/developers/index.rst
+++ b/doc/developers/index.rst
@@ -18,6 +18,7 @@ You are also welcome to post there feature requests or links to pull-requests.
.. _git_repo:
+
Retrieving the latest code
==========================
@@ -51,18 +52,17 @@ Contributing code
https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
-
How to contribute
-----------------
-The prefered way to contribute to `scikit-learn` is to fork the main
+The prefered way to contribute to Scikit-Learn is to fork the main
repository on
`github <http://github.com/scikit-learn/scikit-learn/>`__:
1. `Create an account <https://github.com/signup/free>`_ on
github if you don't have one already.
- 2. Fork the `scikit-learn repo
+ 2. Fork the `project repository
<http://github.com/scikit-learn/scikit-learn>`__: click on the 'Fork'
button, at the top, center of the page. This creates a copy of
the code on the github server where you can work.
@@ -148,7 +148,6 @@ You can also check for common programming errors with the following tools:
$ pip install pep8
$ pep8 path/to/module.py
-
Bonus points for contributions that include a performance analysis with
a benchmark script and profiling output (please report on the mailing
list or on the github wiki).
@@ -163,7 +162,6 @@ details on profiling and cython optimizations.
on all new contributions will get the overall code base quality in the
right direction.
-
EasyFix Issues
--------------
@@ -275,19 +273,20 @@ In addition, we add the following guidelines:
A good example of code that we like can be found `here
<https://svn.enthought.com/enthought/browser/sandbox/docs/coding_standard.py>`_.
-
Input validation
----------------
-The module ``sklearn.utils`` contains various functions for doing input
+.. currentmodule:: sklearn.utils
+
+The module :mod:`sklearn.utils` contains various functions for doing input
validation/conversion. Sometimes, ``np.asarray`` suffices for validation;
do `not` use ``np.asanyarray`` or ``np.atleast_2d``, since those let NumPy's
``np.matrix`` through, which has a different API
(e.g., ``*`` means dot product on ``np.matrix``,
but Hadamard product on ``np.ndarray``).
-In other cases, be sure to call ``safe_asarray``, ``atleast2d_or_csr``,
-``as_float_array`` or ``array2d`` on any array-like argument passed to a
+In other cases, be sure to call :func:`safe_asarray`, :func:`atleast2d_or_csr`,
+:func:`as_float_array` or :func:`array2d` on any array-like argument passed to a
scikit-learn API function. The exact function to use depends mainly on whether
``scipy.sparse`` matrices must be accepted.
@@ -296,12 +295,12 @@ For more information, refer to the :ref:`developers-utils` page.
Random Numbers
--------------
-If your code depends on a random number generator, do not use
-``numpy.random.random()`` or similar routines. To ensure
+If your code depends on a random number generator, do not use
+``numpy.random.random()`` or similar routines. To ensure
repeatability in error checking, the routine should accept a keyword
``random_state`` and use this to construct a
``numpy.random.RandomState`` object.
-See ``sklearn.utils.check_random_state`` in :ref:`developers-utils`.
+See :func:`sklearn.utils.check_random_state` in :ref:`developers-utils`.
Here's a simple example of code using some of the above guidelines:
@@ -340,7 +339,6 @@ objects. In addition, to avoid the proliferation of framework code, we
try to adopt simple conventions and limit to a minimum the number of
methods an object has to implement.
-
Different objects
-----------------
@@ -378,7 +376,6 @@ multiple interfaces):
score = obj.score(data)
-
Estimators
----------
@@ -442,10 +439,9 @@ following is wrong::
# the argument in the constructor
self.param3 = param2
-The scikit-learn relies on this mechanism to introspect object to set
+Scikit-Learn relies on this mechanism to introspect object to set
their parameters by cross-validation.
-
Fitting
^^^^^^^
@@ -501,14 +497,12 @@ Any attribute that ends with ``_`` is expected to be overridden when
you call ``fit`` a second time without taking any previous value into
account: **fit should be idempotent**.
-
Optional Arguments
^^^^^^^^^^^^^^^^^^
In iterative algorithms, number of iterations should be specified by
an int called ``n_iter``.
-
Unresolved API issues
----------------------
@@ -518,7 +512,6 @@ Some things are must still be decided:
* which exception should be raised when arrays' shape do not match
in fit() ?
-
Working notes
---------------
@@ -526,7 +519,6 @@ For unresolved issues, TODOs, remarks on ongoing work, developers are
adviced to maintain notes on the github wiki:
https://github.com/scikit-learn/scikit-learn/wiki
-
Specific models
-----------------
diff --git a/doc/developers/utilities.rst b/doc/developers/utilities.rst
index e1232657dcce7511f5207a0e79bf36a32ed34ef2..c85e73366e291bc61850241147fb2606722c971e 100644
--- a/doc/developers/utilities.rst
+++ b/doc/developers/utilities.rst
@@ -3,19 +3,22 @@
========================
Utilities for Developers
========================
-Scikit-learn contains a number of utilities to help with development. These
-are located in ``sklearn.utils``, and include tools in a number of categories.
-All the following functions and classes are in the module ``sklearn.utils``.
-Please note that these utilities are meant to be used internally within
+Scikit-learn contains a number of utilities to help with development. These are
+located in :mod:`sklearn.utils`, and include tools in a number of categories.
+All the following functions and classes are in the module :mod:`sklearn.utils`.
+
+Please note that these utilities are meant to be used internally within
scikit-learn. They are not guaranteed to be stable between versions of
scikit-learn. Backports, in particular, will be removed as the scikit-learn
dependencies evolve.
+
.. currentmodule:: sklearn.utils
Validation Tools
-----------------
+================
+
These are tools used to check and validate input. When you write a function
which accepts arrays, matrices, or sparse matrices as arguments, the following
should be used when applicable.
@@ -30,7 +33,7 @@ should be used when applicable.
- :func:`array2d`: equivalent to ``np.atleast_2d``, but the ``order`` and
``dtype`` of the input are maintained.
-
+
- :func:`atleast2d_or_csr`: equivalent to ``array2d``, but if a sparse matrix
is passed, will convert to csr format. Also calls ``assert_all_finite``.
@@ -50,7 +53,7 @@ number generator object.
- :func:`check_random_state`: create a ``np.random.RandomState`` object from
a parameter ``random_state``.
-
+
- If ``random_state`` is ``None`` or ``np.random``, then a
randomly-initialized ``RandomState`` object is returned.
- If ``random_state`` is an integer, then it is used to seed a new
@@ -67,7 +70,7 @@ For example:
Efficient Linear Algebra & Array Operations
--------------------------------------------
+===========================================
- :func:`extmath.randomized_range_finder`: construct an orthonormal matrix
whose range approximates the range of the input. This is used in
@@ -113,12 +116,13 @@ Efficient Linear Algebra & Array Operations
- :func:`shuffle`: Shuffle arrays or sparse matrices in a consistent way.
Used in ``sklearn.cluster.k_means``.
+
Graph Routines
---------------
+==============
- :func:`graph.single_source_shortest_path_length`:
(not currently used in scikit-learn)
- Return the shortest path from a single source
+ Return the shortest path from a single source
to all connected nodes on a graph. Code is adapted from networkx.
If this is ever needed again, it would be far faster to use a single
iteration of Dijkstra's algorithm from ``graph_shortest_path``.
@@ -127,7 +131,7 @@ Graph Routines
(used in :func:`sklearn.cluster.spectral.spectral_embedding`)
Return the Laplacian of a given graph. There is specialized code for
both dense and sparse connectivity matrices.
-
+
- :func:`graph_shortest_path.graph_shortest_path`:
(used in :class:``sklearn.manifold.Isomap``)
Return the shortest path between all pairs of connected points on a directed
@@ -135,15 +139,16 @@ Graph Routines
algorithm are available. The algorithm is most efficient when the
connectivity matrix is a ``scipy.sparse.csr_matrix``.
+
Backports
----------
+=========
- :class:`fixes.Counter` (partial backport of ``collections.Counter`` from
Python 2.7) Used in ``sklearn.feature_extraction.text``.
- :func:`fixes.unique`: (backport of ``np.unique`` from numpy 1.4). Find the
unique entries in an array. In numpy versions < 1.4, ``np.unique`` is less
- flexible. Used in ``sklearn.cross_validation``.
+ flexible. Used in :mod:`sklearn.cross_validation`.
- :func:`fixes.copysign`: (backport of ``np.copysign`` from numpy 1.4).
Change the sign of ``x1`` to that of ``x2``, element-wise.
@@ -159,20 +164,21 @@ Backports
- :func:`fixes.count_nonzero` (backport of ``np.count_nonzero`` from
numpy 1.6). Count the nonzero elements of a matrix. Used in
- tests of ``sklearn.linear_model``.
+ tests of :mod:`sklearn.linear_model`.
- :func:`arrayfuncs.solve_triangular`
(Back-ported from scipy v0.9) Used in ``sklearn.linear_model.omp``,
- independent back-ports in ``sklearn.mixture.gmm`` and
- ``sklearn.gaussian_process``
+ independent back-ports in ``sklearn.mixture.gmm`` and
+ :mod:`sklearn.gaussian_process`.
- :func:`sparsetools.cs_graph_components`
(backported from ``scipy.sparse.cs_graph_components`` in scipy 0.9).
Used in ``sklearn.cluster.hierarchical``, as well as in tests for
- ``sklearn.feature_extraction``.
+ :mod:`sklearn.feature_extraction`.
+
ARPACK
-~~~~~~
+------
- :func:`arpack.eigs`
(backported from ``scipy.sparse.linalg.eigs`` in scipy 0.10)
@@ -194,22 +200,24 @@ ARPACK
Benchmarking
-~~~~~~~~~~~~
+------------
- :func:`bench.total_seconds` (back-ported from ``timedelta.total_seconds``
- in Python 2.7). Used in ``benchmarks/bench_glm.py``
+ in Python 2.7). Used in ``benchmarks/bench_glm.py``.
+
Testing Functions
------------------
+=================
- :func:`testing.assert_in`: Compare string elements within lists.
- Used in ``sklearn.datasets`` tests.
+ Used in :mod:`sklearn.datasets` tests.
- :class:`mock_urllib2`: Object which mocks the urllib2 module to fake
- requests of mldata. Used in tests of ``sklearn.datasets``.
+ requests of mldata. Used in tests of :mod:`sklearn.datasets`.
+
Helper Functions
-----------------
+================
- :class:`gen_even_slices`: generator to create ``n``-packs of slices going up
to ``n``. Used in ``sklearn.decomposition.dict_learning`` and
@@ -217,12 +225,13 @@ Helper Functions
- :class:`arraybuilder.ArrayBuilder`: Helper class to incrementally build
a 1-d numpy.ndarray. Currently used in
- ``sklearn.datasets._svmlight_format.pyx``
+ ``sklearn.datasets._svmlight_format.pyx``.
+
Warnings and Exceptions
------------------------
+=======================
- :class:`deprecated`: Decorator to mark a function or class as deprecated.
- :class:`ConvergenceWarning`: Custom warning to catch convergence problems.
- Used in ``sklearn.covariance.graph_lasso``
+ Used in ``sklearn.covariance.graph_lasso``.
diff --git a/doc/modules/classes.rst b/doc/modules/classes.rst
index eb4fac58bd6f89d39657ca197ae8eba4b5551226..1f69e971388628a1850963154c26f96f81910d57 100644
--- a/doc/modules/classes.rst
+++ b/doc/modules/classes.rst
@@ -847,6 +847,8 @@ Low-level methods
:no-members:
:no-inherited-members:
+**Developer guide:** See the :ref:`developers-utils` page for further details.
+
.. currentmodule:: sklearn
.. autosummary::