diff --git a/doc/conf.py b/doc/conf.py
index c0a3b4de901a7d30971c0414e39d58ae2cde6b80..7f2b4eb81ac333e5540daaeaa4695e536577bef2 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -103,7 +103,7 @@ pygments_style = 'sphinx'
# The theme to use for HTML and HTML Help pages. Major themes that come with
# Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'default'
+html_theme = 'scikit-learn'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
@@ -111,23 +111,23 @@ html_theme = 'default'
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+html_theme_path = ['themes']
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
+html_short_title = 'scikits.learn'
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
-#html_logo = None
+html_logo = 'logos/scikit-learn-logo-small.png'
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
-#html_favicon = None
+html_favicon = 'logos/favicon.ico'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
diff --git a/doc/images/plot_digits_classification.png b/doc/images/plot_digits_classification.png
new file mode 100644
index 0000000000000000000000000000000000000000..e56cf364a35710695308660f384e9c43be7d94a8
Binary files /dev/null and b/doc/images/plot_digits_classification.png differ
diff --git a/doc/index.rst b/doc/index.rst
index a951e80af87ec605090ba43191aeb6098912fd39..b32c329f326f4015d9fbc859240c610c1e8284ad 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -1,36 +1,6 @@
-.. raw:: html
-
- <style type="text/css">
- li.toctree-l1 {
- padding: 0.5em 0 1em 0 ;
- list-style-type: none;
- font-size: 150% ;
- }
-
- li.toctree-l2 {
- font-size: 70% ;
- list-style-type: square;
- }
-
- li.toctree-l3 {
- font-size: 85% ;
- list-style-type: circle;
- }
-
- div.bodywrapper h1 {
- text-align: center;
- font-size: 300% ;
- color: #000;
- border: none;
- background-color: #FFFFFF;
- padding: 3px 0 0 0;
- margin: 0 0 -16px 0;
- }
-
- </style>
===========================================
-Scikits.learn: machine learning in Python
+scikits.learn: machine learning in python
===========================================
.. |banner1| image:: auto_examples/cluster/images/plot_affinity_propagation.png
@@ -38,7 +8,7 @@ Scikits.learn: machine learning in Python
:target: auto_examples/cluster/plot_affinity_propagation.html
-.. |banner2| image:: auto_examples/svm/images/plot_custom_kernel.png
+.. |banner2| image:: auto_examples/glm/images/plot_lasso_lars.png
:height: 150
:target: auto_examples/svm/plot_custom_kernel.html
@@ -75,10 +45,22 @@ Scikits.learn: machine learning in Python
engineering**.
+
+:Features:
+ * **Solid**: :ref:`supervised-learning`: classification, regression
+
+ * **Work in progress**: :ref:`unsupervised-learning`: :ref:`clustering`,
+ :ref:`gmm`, manifold learning, ICA
+
+ * **Planed**: Gaussian graphical models, matrix factorization
+
+:License:
+ Open source, commercially usable: **BSD license** (3 clause)
+
+
.. raw:: html
- <small>
- <a href="auto_examples/plot_digits_classification.html"><img src="_images/plot_digits_classification.png" align="right" style="width: 400px"/></a>
+ <div class="example_digits">
:ref:`A simple Example: recognizing hand-written digits <example_plot_digits_classification.py>` ::
@@ -101,22 +83,15 @@ Scikits.learn: machine learning in Python
pl.subplot(2, 4, index+5)
pl.imshow(image, cmap=pl.cm.gray_r)
pl.title('Prediction: %i' % classifier.predict(image.ravel()))
-
-.. raw:: html
-
- </small>
+.. image:: images/plot_digits_classification.png
+ :height: 140
+ :target: auto_examples/plot_digits_classification.html
-:Features:
- * **Solid**: :ref:`supervised-learning`: classification, regression
-
- * **Work in progress**: :ref:`unsupervised-learning`: :ref:`clustering`,
- :ref:`gmm`, manifold learning, ICA
+.. raw:: html
- * **Planed**: Gaussian graphical models, matrix factorization
+ </div>
-:License:
- Open source, commercially usable: **BSD license** (3 clause)
User guide
======================
@@ -131,16 +106,39 @@ User guide
:maxdepth: 3
install
+
+Tutorial
+========
+
+.. toctree::
+ :maxdepth: 2
+
tutorial
+
+Reference
+=========
+
+.. toctree::
+ :maxdepth: 2
+
supervised_learning
unsupervised_learning
model_selection
cross_validation
+ modules/classes
+
+Gallery
+=======
.. toctree::
:maxdepth: 2
auto_examples/index
- modules/classes
+
+Developement
+============
+.. toctree::
+ :maxdepth: 2
+
developers/index
performance
diff --git a/doc/logos/favicon.ico b/doc/logos/favicon.ico
new file mode 100755
index 0000000000000000000000000000000000000000..80d4aa51e352a38566f1a6addb60794fe381bfdc
Binary files /dev/null and b/doc/logos/favicon.ico differ
diff --git a/doc/logos/scikit-learn-logo-small.png b/doc/logos/scikit-learn-logo-small.png
new file mode 100644
index 0000000000000000000000000000000000000000..7cc5fbde5dd7646d51001f5ec92db0182f60c3e3
Binary files /dev/null and b/doc/logos/scikit-learn-logo-small.png differ
diff --git a/doc/modules/glm.rst b/doc/modules/glm.rst
index 93d74dadc25fbd0cb2c6c45685ed5657617c4d49..36bb1f77eff5e013641c681a88be6738fdb4d772 100644
--- a/doc/modules/glm.rst
+++ b/doc/modules/glm.rst
@@ -29,7 +29,6 @@ responses predicted by the linear approximation.
.. figure:: ../auto_examples/glm/images/plot_ols.png
:target: ../auto_examples/glm/plot_ols.html
:scale: 50%
- :align: center
:class:`LinearRegression` will take in its `fit` method arrays X, y
and will store the coefficients :math:`w` of the linear model in its
diff --git a/doc/support.rst b/doc/support.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d05ec89ab1fc4434ac619e44645248f26a356442
--- /dev/null
+++ b/doc/support.rst
@@ -0,0 +1,24 @@
+There are several ways to get in touch with the developers
+
+Mailing List
+============
+
+Main mailing list is `scikit-learn-general
+<https://lists.sourceforge.net/lists/listinfo/scikit-learn-general>`_. There
+is also a commit list, where updates to the main repo get notified: `scikit-learn-commits <https://lists.sourceforge.net/lists/listinfo/scikit-learn-commits>`_
+
+
+
+Bug tracker
+===========
+
+If you think you've encoutered a bug, please report it to the issue tracker:
+
+http://sourceforge.net/apps/trac/scikit-learn/report/1
+
+IRC
+===
+Some devs like to hang out on channel #learn on irc.freenode.net
+
+If you do not have an irc client or are behind a firewall this web
+client works fine: http://webchat.freenode.net
diff --git a/doc/templates/layout.html b/doc/templates/layout.html
deleted file mode 100644
index 88b01661ed19fa307be285982fc5f7f1ad573537..0000000000000000000000000000000000000000
--- a/doc/templates/layout.html
+++ /dev/null
@@ -1,36 +0,0 @@
-{% extends '!layout.html' %}
-
-{%- if pagename == 'index' %}
- {%- block sidebartoc %}
- <br/> <!-- These 'br' should die once we have the logo -->
- <br/>
- <br/>
- <hr/>
- <h3>Quick links</h3>
- <h4><a href="https://sourceforge.net/projects/scikit-learn/files/">
- Download packages</a></h3>
- <h4><a href="https://lists.sourceforge.net/lists/listinfo/scikit-learn-general">
- Mailing list</a></h3>
- <h3><a href="{{ pathto(master_doc) }}">{{ _('Table Of Contents') }}</a></h3>
-
- {{ toc }}
- {%- endblock %}
- {%- set next = False %}
- {%- block relbar1 %}
- {%- endblock %}
-{%- endif %}
-
-{%- block sidebarsourcelink %}
-{% endblock %}
-
-{%- block sidebarsearch %}
- <hr/>
-{{ super() }}
-{%- if show_source and has_source and sourcename %}
-<hr/>
-<small><a href="{{ pathto('_sources/' + sourcename, true)|e }}"
- rel="nofollow">{{ _('Show this page source') }}</a>
-</small>
-{%- endif %}
-{% endblock %}
-
diff --git a/doc/themes/scikit-learn/layout.html b/doc/themes/scikit-learn/layout.html
new file mode 100644
index 0000000000000000000000000000000000000000..27b58ca1047f823ba1db40e6bb9ee55e53f4b4d5
--- /dev/null
+++ b/doc/themes/scikit-learn/layout.html
@@ -0,0 +1,108 @@
+{#
+ scikit-learn/layout.html
+ ~~~~~~~~~~~~~~~~~
+
+ Layout for scikit-learn, after a design made by Angel Soler
+ (http://webylimonada.org)
+
+ :copyright: Fabian Pedregosa
+ :license: BSD
+#}
+{% extends "basic/layout.html" %}
+
+{% block header %}
+ <div class="header-wrapper">
+ <div class="header">
+ {%- if logo %}
+ <p class="logo"><a href="{{ pathto(master_doc) }}">
+ <img src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/>
+ </a>
+ </p>
+ {%- endif %}
+
+
+
+ {%- block navbar -%}
+ <div class="navbar">
+ <ul>
+ <li><a href="http://sourceforge.net/projects/scikit-learn/files/">download</a></li>
+ <li><a href="{{pathto('support')}}">support</a></li>
+ <li><a href="{{pathto('modules/classes')}}">reference</a></li>
+ <li><a href="{{pathto('auto_examples/index')}}">gallery</a></li>
+ <li><a href="{{pathto('developers/index')}}">development</a></li>
+ </ul>
+
+ <form class="search" action="{{ pathto('search') }}" method="get">
+ <input id="search_input"
+ type="text" name="q" size="18" value=" search..."
+ onfocus="if(this.value==this.defaultValue)this.value='';this.style.color='black'"
+ onblur="if(this.value=='') { this.value=this.defaultValue;this.style.color='#cccccc'}"/>
+ <input type="submit" value="{{ _('Go') }}" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div> <!-- end navbar -->
+ {%- endblock -%}
+
+
+ </div>
+ </div>
+{% endblock %}
+
+{% block content %}
+ <div class="content-wrapper">
+
+ <!-- <div id="blue_tile"></div> -->
+
+ <div class="sphinxsidebar">
+
+ {%- if pagename != 'index' %}
+ <div class="rel">
+ {%- for rellink in rellinks|reverse %}
+ <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+ {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+ {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+ {%- endfor %}
+ </div>
+ {% endif %}
+
+ <h3><a href="{{ pathto(master_doc) }}">{{ _('Table Of Contents') }}</a></h3>
+ {{ toc }}
+
+ </div>
+
+ <div class="content">
+ {%- block document %}
+ {{ super() }}
+ {%- endblock %}
+ <div class="clearer"></div>
+ </div>
+ </div>
+{% endblock %}
+
+{% block footer %}
+ <div class="footer-wrapper">
+ <div class="footer">
+ <div class="left">
+ {%- for rellink in rellinks|reverse %}
+ <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+ {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+ {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+ {%- endfor %}
+ {%- if show_source and has_source and sourcename %}
+ <br/>
+ <a href="{{ pathto('_sources/' + sourcename, true)|e }}"
+ rel="nofollow">{{ _('Show Source') }}</a>
+ {%- endif %}
+ </div>
+
+ <div class="right">
+ {{ super() }}
+ </div>
+ <div class="clearer"></div>
+ </div>
+ </div>
+{% endblock %}
+
+{% block relbar1 %}{% endblock %}
+{% block relbar2 %}{% endblock %}
diff --git a/doc/themes/scikit-learn/static/nature.css_t b/doc/themes/scikit-learn/static/nature.css_t
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b7173490d6af70cac3e77b1e6140b3c56cf40
--- /dev/null
+++ b/doc/themes/scikit-learn/static/nature.css_t
@@ -0,0 +1,368 @@
+/*
+ * nature.css_t
+ * ~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- nature theme.
+ *
+ * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+@import url("basic.css");
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+ font-family: Helvetica, Arial, sans-serif;
+ font-size: 100%;
+ background-color: #4eacc5;
+ margin: 0;
+ padding: 0;
+}
+
+div.header-wrapper {
+ background-color: #ffffff;
+ max-width: 1024px;
+ min-height: 50px;
+ margin-left: auto;
+ margin-right: auto;
+ border-radius: 15px;
+ -moz-border-radius: 15px;
+ margin-top: 10px;
+}
+
+
+p.logo {
+ margin-top: auto;
+ margin-left: 20px;
+ float: left;
+ margin: 0 0 0 20px;
+}
+
+span.legend {
+ font-family: Verdana;
+ font-size: 13px;
+ position: relative;
+ left: -35px;
+ top: -3px;
+}
+
+div.navbar {
+ padding-top: 13px;
+ margin-left: 230px;
+}
+
+div.navbar ul {
+ background-color: #ff9c34;
+ color: white;
+ border-radius: 5px;
+ -moz-border-radius: 5px;
+ list-style: none;
+}
+
+div.navbar ul, div.navbar li {
+ display: inline;
+ padding: 4px 15px 5px 15px;
+}
+
+div.navbar ul li a,
+div.navbar ul li a:link,
+div.navbar ul li a:visited,
+div.navbar ul li a:hover {
+ color: white;
+ text-decoration: none;
+ font-weight: bold;
+ font-size: 14px;
+}
+
+div.navbar ul li a:hover {
+ color: #EEE;
+}
+
+/* #search_top { */
+/* margin-top: 12px; */
+/* margin-right: 20px; */
+/* display: inline; */
+/* } */
+
+form.search {
+ margin-left: 15px;
+ display: inline;
+}
+#search_input {
+ color: #CCC;
+}
+
+div.content-wrapper {
+ background-color: #ffffff;
+ color: #3E4349;
+ max-width: 1024px;
+ margin-top: 10px;
+ margin-left: auto;
+ margin-right: auto;
+ border-radius: 15px;
+ -moz-border-radius: 15px;
+}
+
+div.content {
+ margin-left: 200px;
+ padding-bottom: 10px;
+}
+
+div.example_digits {
+ max-width: 700px;
+ font-size: 85%;
+}
+
+
+div.document {
+ padding-left: 240px;
+ padding-right: 20px;
+}
+
+hr {
+ border: 1px solid #B1B4B6;
+}
+
+
+div.body {
+ font-size: 0.9em;
+ margin: 10px;
+}
+
+div.footer {
+ color: #555;
+ width: 100%;
+ padding: 13px 0;
+ text-align: center;
+ font-size: 75%;
+}
+
+div.footer a {
+ color: #444;
+ text-decoration: underline;
+}
+
+div.related {
+ background-color: #6BA81E;
+ line-height: 32px;
+ color: #fff;
+ text-shadow: 0px 1px 0 #444;
+ font-size: 0.9em;
+}
+
+div.related a {
+ color: #E2F3CC;
+}
+
+div.rel {
+ padding: 15px 15px 0 15px;
+}
+
+div.sphinxsidebar h3,
+div.sphinxsidebar h4 {
+ margin: 0;
+ padding: 5px 10px;
+ text-shadow: 1px 1px 0 white
+}
+
+
+div.sphinxsidebar p {
+ padding: 5px 20px;
+}
+
+div.sphinxsidebar p.topless {
+}
+
+div.sphinxsidebar ul {
+ margin: 10px 20px;
+ padding: 0;
+ color: #000;
+}
+
+div.sphinxsidebar ul ul {
+ margin-right: 0;
+}
+
+div.sphinxsidebar a {
+ color: #444;
+}
+
+
+div.sphinxsidebar {
+ width: 170px;
+ float: left;
+ margin-left: 0;
+ background-color: inherit;
+ border-top-left-radius: 15px;
+ -moz-border-radius:15px;
+ border-top-width: 0;
+ border-left-width: 0;
+ border-bottom-width: 0;
+}
+
+div.sphinxsidebar h3 {
+ margin-top: 10px;
+ text-align: center;
+ font-size: 16px;
+}
+
+div.sphinxsidebar ul {
+ list-style: none;
+}
+
+div.sphinxsidebar {
+ font-size: 80%;
+ line-height: 1.5em;
+}
+
+
+input {
+ border: 1px solid #ccc;
+ display: inline-block;
+ text-shadow: none;
+ font-family: Arial;
+ font-size: 1em;
+}
+
+div.sphinxsidebar input[type=text]{
+ margin-left: 20px;
+}
+
+/* -- body styles ----------------------------------------------------------- */
+
+a {
+ color: #355F7C;
+ text-decoration: none;
+}
+
+a:hover {
+ color: #355F7C;
+ text-decoration: underline;
+}
+
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+ font-family: Arial, sans-serif;
+ background-color: #BED4EB;
+ font-weight: normal;
+ color: #212224;
+}
+
+div.body h1,
+div.body h2,
+div.body h3 {
+ padding: 10px;
+ text-align: center;
+ border-radius: 10px;
+}
+
+div.bodywrapper h1 {
+ margin: 0 -10px 0 -10px;
+ text-align: center;
+ background-color: #cde8ef;
+ font-family: Helvetica, Arial, sans-serif;
+ font-size: 250%;
+ border-radius: 0 15px 0 15px;
+ -moz-border-radius: 0 15px 0 15px;
+}
+
+
+
+div.body h3 {
+ font-size: 120%;
+ background-color: #D8DEE3;
+ padding: 5px;
+ border-radius: 10px;
+
+}
+div.body h4 { font-size: 110%; background-color: #D8DEE3; }
+div.body h5 { font-size: 100%; background-color: #D8DEE3; }
+div.body h6 { font-size: 100%; background-color: #D8DEE3; }
+
+a.headerlink {
+ color: #c60f0f;
+ font-size: 0.8em;
+ padding: 0 4px 0 4px;
+ text-decoration: none;
+}
+
+a.headerlink:hover {
+ background-color: #c60f0f;
+ color: white;
+}
+
+div.body p, div.body dd, div.body li {
+ line-height: 1.5em;
+}
+
+div.admonition p.admonition-title + p {
+ display: inline;
+}
+
+div.highlight{
+ background-color: white;
+}
+
+div.note {
+ background-color: #eee;
+ border: 1px solid #ccc;
+}
+
+div.seealso {
+ background-color: #ffc;
+ border: 1px solid #ff6;
+}
+
+div.topic {
+ background-color: #eee;
+}
+
+div.warning {
+ background-color: #ffe4e4;
+ border: 1px solid #f66;
+}
+
+p.admonition-title {
+ display: inline;
+}
+
+p.admonition-title:after {
+ content: ":";
+}
+
+pre {
+ padding: 10px;
+ background-color: White;
+ color: #222;
+ line-height: 1.2em;
+ border: 1px solid #C6C9CB;
+ font-size: 1.1em;
+ margin: 1.5em 0 1.5em 0;
+ -webkit-box-shadow: 1px 1px 1px #d8d8d8;
+ -moz-box-shadow: 1px 1px 1px #d8d8d8;
+}
+
+div.highlight-python pre {
+ overflow-y: hidden;
+}
+
+tt {
+ background-color: #ecf0f3;
+ color: #222;
+ /* padding: 1px 2px; */
+ font-size: 1.1em;
+ font-family: monospace;
+}
+
+.viewcode-back {
+ font-family: Arial, sans-serif;
+}
+
+div.viewcode-block:target {
+ background-color: #f4debf;
+ border-top: 1px solid #ac9;
+ border-bottom: 1px solid #ac9;
+}
diff --git a/doc/themes/scikit-learn/theme.conf b/doc/themes/scikit-learn/theme.conf
new file mode 100644
index 0000000000000000000000000000000000000000..1cc40044646bb73870088ddc88543c58a3ca083e
--- /dev/null
+++ b/doc/themes/scikit-learn/theme.conf
@@ -0,0 +1,4 @@
+[theme]
+inherit = basic
+stylesheet = nature.css
+pygments_style = tango