more doc scripts

__transit/index.txt

-.. theano documentation master file, created by sphinx-quickstart on Tue Oct  7 02:53:58 2008.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to theano's documentation!
-==================================
-
-Contents:
-
-.. toctree::
-   :maxdepth: 2
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-

doc/README.txt

@@ -194,18 +194,9 @@ Getting Help
 If these installation instructions don't work, search the theano-users archive for similar cases.  If you don't find a solution, write to theano-users and explain the situation.
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
 .. _README: README.html
 .. _Download: README.html#downloading-theano
 .. _Documentation: doc/index.html
 .. _Wiki: http://pylearn.org/theano
 .. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
 
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18

__transit/scripts/local.epydoc → doc/api/epydoc.conf

@@ -7,12 +7,7 @@
 # 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: __init__.py,
-    [a-z]*.py,
-    [A-Z]*.py,
-    gof/__init__.py,
-    gof/[a-z]*.py,
-    gof/[A-Z]*.py
+modules: theano
 
 # The type of output that should be generated.  Should be one
 # of: html, text, latex, dvi, ps, pdf.
@@ -125,9 +120,9 @@ separate-classes: no
 
 # 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
+# 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
 

doc/conf.py

+# -*- coding: utf-8 -*-
+#
+# theano documentation build configuration file, created by
+# sphinx-quickstart on Tue Oct  7 16:34:06 2008.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# The contents of this file are pickled, so don't put values in the namespace
+# that aren't pickleable (module imports are okay, they're removed automatically).
+#
+# All configuration values have a default value; values that are commented out
+# serve to show the default value.
+
+import sys, os
+
+# If your extensions are in another directory, add it here. If the directory
+# is relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#sys.path.append(os.path.abspath('some/directory'))
+
+# General configuration
+# ---------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'ext']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.txt'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General substitutions.
+project = 'theano'
+copyright = '2008, Olivier Breuleux, James Bergstra'
+
+# The default replacements for |version| and |release|, also used in various
+# other places throughout the built documents.
+#
+# The short X.Y version.
+version = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.1'
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directories, that shouldn't be searched
+# for source files.
+#exclude_dirs = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# Options for HTML output
+# -----------------------
+
+# The style sheet to use for HTML and HTML Help pages. A file of that name
+# must exist either in Sphinx' static/ path, or in one of the custom paths
+# given in html_static_path.
+html_style = 'default.css'
+
+# 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
+
+# The name of an image file (within the static path) to place at the top of
+# the sidebar.
+#html_logo = None
+
+# 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
+
+# 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 = ['.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'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, the reST sources are included in the HTML build as _sources/<name>.
+#html_copy_source = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'theanodoc'
+
+
+# Options for LaTeX output
+# ------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, document class [howto/manual]).
+latex_documents = [
+  ('index', 'theano.tex', 'theano Documentation',
+   'Olivier Breuleux, James Bergstra', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

__transit/DevStartGuide.txt → doc/doc/dev_start_guide.txt

@@ -60,16 +60,6 @@ When you install a package, only the package name can be imported directly. If y
 .. _basicnumpy: http://lgcm.iro.umontreal.ca/theano/wiki/BasicNumpy
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
 .. _README: ../README.html
 .. _Download: ../README.html#downloading-theano
 .. _Documentation: index.html

__transit/graph.txt → doc/doc/graph.txt

@@ -87,16 +87,6 @@ If we had wanted a more brute-force approach to graph construction, we could hav
 Note how the call to `Apply` modifies the `owner` and `index` fields of the `Result` s passed as outputs to point to itself and the rank they occupy in the output list. This whole machinery builds a DAG (Directed Acyclic Graph) representing the computation, a graph that theano can compile and optimize.
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
 .. _README: ../README.html
 .. _Download: ../README.html#downloading-theano
 .. _Documentation: index.html

doc/doc/index.txt

+=====================================
+Theano Project Documentation Overview
+=====================================
+
+.. toctree::
+   :glob:
+
+   *
+
+Documentation is divided broadly into two kinds: user documentation and
+developer documentation.  
+
+- `Using Theano` covers how to *use* what is already in the Theano library to
+  build graphs and evaluate them.
+
+- `Extending Theano` introduces how Theano works and explains how to add new
+  data and expression types, as well as optimizations to accompany them.
+
+- `Hacking Theano` introduces you to what's under the hood: the compilation
+  process, the Env, C code generation.
+
+
+Using Theano
+============
+
+- First of all, read the `n00b guide`_.  It is a cut-and-paste, tutorial-style intro to what Theano can do.
+
+- Familiarize yourself with the `glossary of terminology`_.
+
+- Join `theano-users`_.
+
+- Learn to use the typelist_, and the oplist_.  These are the building blocks
+  of theano expression graphs.
+
+- Browse through some of the `Howto`_ recipes on the wiki.
+
+.. _Howto: 
+.. _theano-users: http://groups.google.com/group/theano-users?pli=1
+.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
+.. _n00b guide: n00b.html
+.. _glossary of terminology: ../api/term-index.html
+.. _typelist: typelist.html
+.. _oplist: oplist.html
+
+Extending Theano
+================
+
+- Read about `How Theano Works <UserAdvanced.html>`__.  This introduces the
+  major interface data structures: Op, Type, Result, Apply.
+
+- How to make a new Op.
+
+- How to make a new Optimization.
+
+- How to make a new data Type.
+
+Hacking Theano
+==============
+
+- `Get Started as a Developer <DevStartGuide.html>`__ by setting up mercurial, getting a few accounts,
+  setting up your environment, and getting some background in mercurial, python,
+  and numpy.
+
+- Join `theano-dev`_ to participate in development discussion.
+
+- Pick a task from the `task list`_, or suggest one on `theano-users`_.
+  Features/ideas are generally discussed on `theano-users`_.   Technical
+  discussions of how to actually implement something should be on
+  `theano-dev`_.
+
+- Browse `Theano's API <../api/>`__.
+
+- Keep an eye on the `Mercurial Changelog <http://pylearn.org/hg/theano>`__.
+
+- Send us your work as a patch to `theano-dev`_ or commit directly to the trunk.
+
+.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
+.. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
+.. _reStructuredText: http://docutils.sourceforge.net/rst.html
+
+
+
+

__transit/n00b.txt → doc/doc/n00b.txt

@@ -237,16 +237,6 @@ code. The question is how to automatically extract the source files and inline
 them into this documentation.*
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
 .. _README: ../README.html
 .. _Download: ../README.html#downloading-theano
 .. _Documentation: index.html

doc/ext.py

+
+from docutils import nodes
+import epydoc.docwriter.xlink as xlink
+
+def role_fn(name, rawtext, text, lineno, inliner,
+            options={}, content=[]):
+    node = nodes.reference(rawtext, text, refuri = "http://pylearn.org/theano/wiki/%s" % text)
+    return [node], []
+
+def setup(app):
+#    print dir(xlink)
+    app.add_role("wiki", role_fn)

doc/index.txt

+
+======
+Theano
+======
+
+.. toctree::
+   :maxdepth: 2
+
+   README
+   doc/index
+
+-------------------------------------------------------------------
+A python library for manipulating and evaluating matrix expressions
+-------------------------------------------------------------------
+
+Theano is a library in Python, built to evaluate complicated
+expressions (especially matrix-valued ones) as quickly as possible.
+It was written at LISA_ to explore techniques for machine learning.
+Our project uses the name to honour the ancient Greek mathematician. 
+
+--------------------------------------------------------------------------------
+
+.. _not in the normal sense: :wiki:`WhatIsTheano`
+
+Overview
+========
+
+**To get up & running quickly** see README_.
+
+All **documentation** can be reached from the `Theano Project Documentation Overview`_.
+
+As developers of an open source project, we rely on **feedback** for
+determining what features to implement, and what documentation needs to be
+improved.  The best forum for feedback is the theano-users_ mailing list.
+
+All **discussion** about theano also takes place on the theano-users_ mailing list.
+
+If you find a **bug**, please file a `bug report`_ or send email to
+the theano-users_ mailing list.  **Patch** submissions should be
+sent to theano-dev_.
+
+We welcome all kinds of **contributions**.  Our `task list`_ is
+full of interesting ideas awaiting a champion.  If you have any
+questions regarding how to extend Theano, please feel free to ask on
+the Theano-dev_ mailing list.
+
+Theano is in active development and should be considered **experimental**.
+APIs are subject to change at any time.
+
+
+Download
+========
+
+We recommend that you use the `latest snapshot`_,
+Better yet, use `mercurial`_ to keep your installation fresh.
+The snapshots usually contain *more features* and *fewer bugs* than the
+"official" releases |---| they're not only for developers!
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+.. |---| unicode:: U+02014 .. em dash
+   :trim:
+.. _latest snapshot: http://pylearn.org/hg/theano/archive/tip.tar.gz
+.. _bug report: http://lgcm.iro.umontreal.ca/theano/newticket
+.. _theano-users: http://groups.google.com/group/theano-users?pli=1
+.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
+.. _reStructuredText: rst.html
+.. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
+.. _README: README.html
+.. _Quick-Start: README.html#quick-start
+
+.. _Theano Project Documentation Overview: doc/index.html
+.. _Mercurial: http://www.selenic.com/mercurial/wiki/
+.. _docutils: http://docutils.sourceforge.net
+.. _epydoc: http://epydoc.sourceforge.net/
+.. _scipy: http://scipy.org/
+.. _Python: http://www.python.org/
+.. _TRAC: http://trac.edgewall.org/
+.. _LISA:  http://www.iro.umontreal.ca/rubrique.php3?id_rubrique=27
+

scripts/docgen.py

+
+import sys
+import os
+
+throot = "/".join(sys.path[0].split("/")[:-1])
+
+os.chdir(throot)
+
+def mkdir(path):
+    try:
+        os.mkdir(path)
+    except OSError:
+        pass
+
+mkdir("html")
+mkdir("html/doc")
+mkdir("html/api")
+
+os.system("epydoc --config doc/api/epydoc.conf -o html/api")
+
+import sphinx
+sys.path[0:0] = [os.path.realpath('doc')]
+sphinx.main([sys.argv[0], 'doc', 'html'])
+
+