Work on documentation

Included logos, added docuentation thumbnail and organized contents
in a way that navigating in the python and c++ reference will be
easier. Applications appear in a special sidebar.

doc/_templates/sideb.html

@@ -0,0 +1,15 @@
+<p>
+<a href="http://ipht.cea.fr"> <img style="width: 60px; margin: 10px 5px 0 0" src='_static/logo_cea.png' alt="CEA"/> </a>
+<a href="http://www.cpht.polytechnique.fr"> <img style="width: 60px; margin: 10px 5px 0 5px" src='_static/logo_x.png' alt="Ecole Polytechnique"/> </a>
+<a href="http://www.cnrs.fr"> <img style="width: 60px; margin: 10px 0 0 5px" src='_static/logo_cnrs.png' alt="CNRS"/> </a>
+</p>
+
+<h3>TRIQS applications</h3>
+
+<p>
+Some applications are supported by the TRIQS collaboration, 
+<a class="reference external" href="{{ pathto("applications") }}">check them out!</a>
+Note that you can obtain
+<a class="reference external" href="{{ pathto("bundles") }}">bundled sources</a>
+that contain both the TRIQS library and the supported applications.
+</p>

doc/applications.rst

@@ -11,7 +11,9 @@ Wien2TRIQS is an interface to Wien2k for LDA+DMFT calculation. It allows
 you to turn band-structure calculations obtained from the Wien2k package to
 inputs to full-fledged LDA+DMFT calculations in a few lines!
 
-More info `here <http://ipht.cea.fr/triqs/new/cthyb_matrix/contents.html>`_.
+| *Homepage:* `<http://ipht.cea.fr/triqs/new/dft_tools/index.html>`_
+| *Documentation:* `<http://ipht.cea.fr/triqs/new/dft_tools/documentation.html>`_
+| *Installation:* `<http://ipht.cea.fr/triqs/new/dft_tools/install.html>`_
 
 Hybridization-expansion matrix solver
 -------------------------------------
@@ -21,7 +23,9 @@ of a quantum impurity embedded in a conduction bath. It is based on a quantum
 Monte Carlo algorithm that stochastically samples the diagrams of a
 hybridization expansion of the partition function.
 
-More info here
+| *Homepage:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/index.html>`_
+| *Documentation:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/documentation.html>`_
+| *Installation:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/install.html>`_
 
 Hubbard I solver
 ----------------
@@ -30,4 +34,6 @@ This solver gives the Hubbard I solution of a quantum impurity problem,
 i.e. it solves the atomic limit. This simple approximation allows to have
 very quick answer even for large multiband systems.
 
-More info here
+| *Homepage:* `<http://ipht.cea.fr/triqs/new/hubbardI/index.html>`_
+| *Documentation:* `<http://ipht.cea.fr/triqs/new/hubbardI/documentation.html>`_
+| *Installation:* `<http://ipht.cea.fr/triqs/new/hubbardI/install.html>`_

doc/authors.rst

@@ -1,4 +1,3 @@
-:orphan:
 
 Authors
 =======

doc/bugs.rst

@@ -1,4 +1,3 @@
-:orphan:
 
 Reporting bugs
 ==============

doc/conf.py.in

@@ -35,7 +35,7 @@ extensions += [
         'matplotlib.sphinxext.only_directives',
         'plot_directive',
        # 'matplotlib.sphinxext.ipython_directive',
-       # 'ipython_console_highlighting',
+        'ipython_console_highlighting',
        # 'inheritance_diagram',
         'numpydoc']
 
@@ -61,7 +61,7 @@ autoclass_content = "both"
 mathjax_path = "@MATHJAX_PATH@/MathJax.js?config=default"
 
 # Add any paths that contain templates here, relative to this directory.
-#templates_path = ['@TRIQS_SOURCE_DIR@/doc/_templates']
+templates_path = ['@TRIQS_SOURCE_DIR@/doc/_templates']
 
 # The suffix of source filenames.
 source_suffix = '.rst'
@@ -74,7 +74,7 @@ master_doc = 'contents'
 
 # General information about the project.
 project = u'TRIQS'
-copyright = u'2011, The TRIQS collaboration'
+copyright = u'2011-2013, The TRIQS collaboration'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -83,7 +83,7 @@ copyright = u'2011, The TRIQS collaboration'
 # The short X.Y version.
 version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = '1.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -144,6 +144,7 @@ doxylink = { 'doxy' : ('@CMAKE_CURRENT_BINARY_DIR@/doxy.tag', 'doxy_triqs') }
 #html_style = 'default.css'
 html_theme_path = ["@TRIQS_SOURCE_DIR@/doc/themes/"]
 html_theme = "triqs"
+html_show_sphinx = False
 
 #html_theme_options = { "pagewidth": "80em", "documentwidth" : "60em" }
 
@@ -166,11 +167,11 @@ html_theme = "triqs"
 # 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['@TRIQS_SOURCE_DIR@/doc/_static']
+html_static_path = ['@TRIQS_SOURCE_DIR@/doc/_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-html_last_updated_fmt = '%b %d, %Y'
+#html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
@@ -178,6 +179,7 @@ html_last_updated_fmt = '%b %d, %Y'
 
 # Custom sidebar templates, maps document names to template names.
 #html_sidebars = {}
+html_sidebars = {'index': ['sideb.html', 'searchbox.html']}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

doc/contents.rst

@@ -1,4 +1,3 @@
-.. _documentation:
 
 Table of contents
 =================
@@ -6,9 +5,11 @@ Table of contents
 .. toctree::
    :maxdepth: 2
 
-   overview
-   installation/install
-   tutorials/contents
-   reference/python/contents
-   reference/c++/contents
+   index
+   install
+   documentation
+   applications
+   bundles
+   bugs
+   authors
 

doc/documentation.rst

@@ -0,0 +1,29 @@
+.. _documentation:
+
+Documentation
+=============
+
+A quick tour
+------------
+
+.. toctree::
+   :maxdepth: 1
+
+   overview
+   tutorials/contents
+
+C++ libraries
+-------------
+
+.. toctree::
+   :maxdepth: 1
+
+   reference/c++/contents
+
+Python modules
+--------------
+
+.. toctree::
+   :maxdepth: 1
+
+   reference/python/contents

doc/index.rst

@@ -1,27 +1,51 @@
-Welcome to TRIQS
-================
+.. _welcome:
+
+Welcome
+=======
 
 TRIQS is a scientific project that provides a set of tools for the study of
 interacting quantum systems. It allows to quickly implement many-body
 calculations and explore new theoretical and phenomenological ideas within a
 flexible, easy-to-use python environment (à la Matlab). 
 
-Documentation
-=============
+Powerful c++ libraries
+----------------------
 
-Link to :ref:`documentation <documentation>`.
+.. code-block:: c++
 
-TRIQS-based applications
-========================
+  #include <triqs/arrays.hpp>
+  #include <triqs/arrays/linalg/inverse.hpp>
+  #include <triqs/arrays/linalg/determinant.hpp>
 
-Some applications are supported by the TRIQS collaboration.
-Link to :ref:`applications <applications>`.
+  using triqs::arrays::array;  using triqs::arrays::matrix;  using triqs::clef::placeholder;
+  int main(){
+    placeholder<0> i_;
+    placeholder<1> j_;
+    matrix<double> A(2,2);
+    A(i_,j_) << i_+j_;
 
-Download
-========
+    matrix<double> B = inverse(A);
+    double C = determinant(A);
 
-From git as described in :ref:`install <installation>`.
+    std::cout << "A^(-1) = "<< B << std::endl;
+    std::cout << "det(A) = " <<C <<std::endl;
+  }
 
-Or get a :ref:`bundled version <bundles>` which provides both the
-TRIQS library and all supported applications.
+User-friendly python interface
+------------------------------
 
+.. plot::
+   :include-source:
+   :scale: 70
+
+    from pytriqs.gf.local import *
+    g = GfReFreq(indices = ['s','d'], window = [-2,2], n_points = 1000)
+    g['d','d'] = Omega - 0.3
+    g['d','s'] = 0.2
+    g['s','d'] = 0.2
+    g['s','s'] = inverse( Wilson(1.0) )
+    g.invert()
+
+    from pytriqs.plot.mpl_interface import oplot
+    oplot( g['d','d'], '-o', RI = 'S', x_window  = (-1.8,1.8), name = "Impurity" )
+    oplot( g['s','s'], '-x', RI = 'S', x_window  = (-1.8,1.8), name = "Bath" )

doc/reference/c++/contents.rst

@@ -1,5 +1,6 @@
-C++ librairies
-##########################
+
+C++ libraries
+=============
 
 .. toctree::
    :maxdepth: 1
@@ -13,3 +14,4 @@ C++ librairies
    parameters/parameters
    lectures/contents
    utilities/contents
+

doc/reference/c++/intro.rst

@@ -1,8 +0,0 @@
-* At lower level, a few general purpose libraries in Python and C++, e.g. :
-
-  * A new C++ multi-dimensional array library (triqs::arrays).
-  * A simple dictionary-like python :ref:`interface to HDF5 files<hdf5_base>`, which is the main data format in TRIQS.
-  * A thin :ref:`interface to matplotlib<plotting>` to visualize various objects via the definition of a :ref:`plot protocol<plotting>`.
-
-
-  

doc/reference/python/contents.rst

@@ -1,23 +1,12 @@
 
-.. role:: red
-
-.. index:: contents
-
-.. _contents:
-
 Python libraries
-================================
+================
 
 .. toctree::
-   :maxdepth: 2  
+   :maxdepth: 1
 
-   introduction/introduction
-   install/install
    green/green
+   operators/operators
    lattice/lattice
    data_analysis/contents
-   solvers/solvers
-   wien2k/wien2k
-   faq/faq
-   collaboration/collaboration
-   legal/legal
+

doc/themes/triqs/layout.html

@@ -34,11 +34,10 @@
 {% endblock %}
 
 {% block rootrellink %}
-      {% if hasdoc('index') %}
-        <li><a href="{{ pathto('index') }}">Home</a>&nbsp;|</li>
-        <li><a href="{{ pathto('contents') }}">Documentation</a> &raquo;</li>
+      {% if hasdoc('documentation') %}
+        <li><a href="{{ pathto('index') }}">Home</a> &raquo;</li>
       {% else %}
-        <li><a href="{{ pathto('contents') }}">Documentation</a> &raquo;</li>
+        <li><a href="{{ pathto('index') }}">Documentation</a> &raquo;</li>
       {% endif %}
 {% endblock %}
 
@@ -46,15 +45,12 @@
 <div class="pageheader">
   <ul>
     <li><a href="{{ pathto('install') }}">Install</a></li>
+    <li><a href="{{ pathto('documentation') }}">Documentation</a></li>
     <li><a href="{{ pathto('bugs') }}">Report Bugs</a></li>
     <li><a href="{{ pathto('authors') }}">Authors and Quote</a></li>
   </ul>
   <div>
-    {% if hasdoc('index') %}
-    <h1 style="padding:0; margin: 10px 0 0 0;"><a class="triqs" href="{{ pathto('index') }}">TRIQS</a></h1>
-    {% else %}
-    <h1 style="padding:0; margin: 10px 0 0 0;"><a class="triqs" href="{{ pathto('contents') }}">TRIQS</a></h1>
-    {% endif %}
+    <h1 style="padding:0; margin: 10px 0 0 0;"><a class="triqs" href="http://ipht.cea.fr/triqs">TRIQS</a></h1>
     <span style="font-size: 14px; margin: 0px; padding: 0px;">a Toolbox for Research on Interacting Quantum Systems</span>
   </div>
 </div>

doc/tutorials/contents.rst

@@ -4,7 +4,6 @@ Tutorials
 .. toctree::
    :maxdepth: 2  
 
-   intro
    python/introduction
    c++/contents
 

doc/tutorials/python/introduction.rst

@@ -36,5 +36,6 @@ The goal is not to explain them here in details but to quickly show some of TRIQ
    tour2
    tour3
    tour4
+   ipt/ipt
    reading