Initial doc framework and several docstrings

doc/clustering.rst

+.. automodule:: graph_tool.clustering
+   :members:

doc/conf.py

+# -*- coding: utf-8 -*-
+#
+# graph-tool documentation build configuration file, created by
+# sphinx-quickstart on Sun Oct 26 18:29:16 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; values that are commented out
+# serve to show the default.
+
+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('.'))
+
+# 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', 'sphinx.ext.doctest',
+              'sphinx.ext.intersphinx', 'sphinx.ext.jsmath',
+              'sphinxext.numpydoc']
+
+jsmath_path = "jsMath/easy/load.js"
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'graph-tool'
+copyright = u'2008, Tiago de Paula Peixoto'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '2.0'
+# The full version, including alpha/beta/rc tags.
+release = '2.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# 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 directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['.build']
+
+# 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 (relative to this directory) 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 = 'graph-tooldoc'
+
+
+# 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', 'graph-tool.tex', ur'graph-tool Documentation',
+   ur'Tiago de Paula Peixoto', '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
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/dev': None}

doc/graph_tool.rst

+.. automodule:: graph_tool
+   :members:
+
+Available subpackages
+=====================
+
+.. toctree::
+
+   clustering

doc/index.rst

+.. graph-tool documentation master file, created by sphinx-quickstart on Sun Oct 26 18:29:16 2008.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to graph-tool's documentation!
+======================================
+
+Contents:
+
+.. toctree::
+   :glob:
+
+   quickstart
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/modules.rst

+Module documentation
+====================
+
+.. toctree::
+
+   graph_tool

doc/numpydoc.py

+"""
+========
+numpydoc
+========
+
+Sphinx extension that handles docstrings in the Numpy standard format. [1]
+
+It will:
+
+- Convert Parameters etc. sections to field lists.
+- Convert See Also section to a See also entry.
+- Renumber references.
+- Extract the signature from the docstring, if it can't be determined otherwise.
+
+.. [1] http://projects.scipy.org/scipy/numpy/wiki/CodingStyleGuidelines#docstring-standard
+
+"""
+
+import os, re, pydoc
+from docscrape_sphinx import get_doc_object, SphinxDocString
+import inspect
+
+def mangle_docstrings(app, what, name, obj, options, lines,
+                      reference_offset=[0]):
+    if what == 'module':
+        # Strip top title
+        title_re = re.compile(r'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
+                              re.I|re.S)
+        lines[:] = title_re.sub('', "\n".join(lines)).split("\n")
+    else:
+        doc = get_doc_object(obj, what)
+        lines[:] = str(doc).split("\n")
+
+    if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \
+           obj.__name__:
+        if hasattr(obj, '__module__'):
+            v = dict(full_name="%s.%s" % (obj.__module__, obj.__name__))
+        else:
+            v = dict(full_name=obj.__name__)
+        lines += ['', '.. htmlonly::', '']
+        lines += ['    %s' % x for x in
+                  (app.config.numpydoc_edit_link % v).split("\n")]
+
+    # replace reference numbers so that there are no duplicates
+    references = []
+    for l in lines:
+        l = l.strip()
+        if l.startswith('.. ['):
+            try:
+                references.append(int(l[len('.. ['):l.index(']')]))
+            except ValueError:
+                print "WARNING: invalid reference in %s docstring" % name
+
+    # Start renaming from the biggest number, otherwise we may
+    # overwrite references.
+    references.sort()
+    if references:
+        for i, line in enumerate(lines):
+            for r in references:
+                new_r = reference_offset[0] + r
+                lines[i] = lines[i].replace('[%d]_' % r,
+                                            '[%d]_' % new_r)
+                lines[i] = lines[i].replace('.. [%d]' % r,
+                                            '.. [%d]' % new_r)
+
+    reference_offset[0] += len(references)
+
+def mangle_signature(app, what, name, obj, options, sig, retann):
+    # Do not try to inspect classes that don't define `__init__`
+    if (inspect.isclass(obj) and
+        'initializes x; see ' in pydoc.getdoc(obj.__init__)):
+        return '', ''
+
+    if not (callable(obj) or hasattr(obj, '__argspec_is_invalid_')): return
+    if not hasattr(obj, '__doc__'): return
+
+    doc = SphinxDocString(pydoc.getdoc(obj))
+    if doc['Signature']:
+        sig = re.sub("^[^(]*", "", doc['Signature'])
+        return sig, ''
+
+def initialize(app):
+    try:
+        app.connect('autodoc-process-signature', mangle_signature)
+    except:
+        monkeypatch_sphinx_ext_autodoc()
+
+def setup(app, get_doc_object_=get_doc_object):
+    global get_doc_object
+    get_doc_object = get_doc_object_
+    
+    app.connect('autodoc-process-docstring', mangle_docstrings)
+    app.connect('builder-inited', initialize)
+    app.add_config_value('numpydoc_edit_link', None, True)
+
+#------------------------------------------------------------------------------
+# Monkeypatch sphinx.ext.autodoc to accept argspecless autodocs (Sphinx < 0.5)
+#------------------------------------------------------------------------------
+
+def monkeypatch_sphinx_ext_autodoc():
+    global _original_format_signature
+    import sphinx.ext.autodoc
+
+    if sphinx.ext.autodoc.format_signature is our_format_signature:
+        return
+
+    print "[numpydoc] Monkeypatching sphinx.ext.autodoc ..."
+    _original_format_signature = sphinx.ext.autodoc.format_signature
+    sphinx.ext.autodoc.format_signature = our_format_signature
+
+def our_format_signature(what, obj):
+    r = mangle_signature(None, what, None, obj, None, None, None)
+    if r is not None:
+        return r[0]
+    else:
+        return _original_format_signature(what, obj)

doc/quickstart.rst

+Quick start using `graph-tool`
+==============================
+
+Testy test test
+
+.. math::
+
+   (a + b)^2 = a^2 + 2ab + b^2
+
+   (a - b)^2 = a^2 - 2ab + b^2

doc/sphinxext/LICENSE.txt

+-------------------------------------------------------------------------------
+    The files
+    - numpydoc.py
+    - autosummary.py
+    - autosummary_generate.py
+    - docscrape.py
+    - docscrape_sphinx.py
+    - phantom_import.py
+    have the following license:
+
+Copyright (C) 2008 Stefan van der Walt <stefan@mentat.za.net>, Pauli Virtanen <pav@iki.fi>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+-------------------------------------------------------------------------------
+    The files
+    - compiler_unparse.py
+    - comment_eater.py
+    - traitsdoc.py
+    have the following license:
+
+This software is OSI Certified Open Source Software.
+OSI Certified is a certification mark of the Open Source Initiative.
+
+Copyright (c) 2006, Enthought, Inc.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of Enthought, Inc. nor the names of its contributors may
+   be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+-------------------------------------------------------------------------------
+    The files
+    - only_directives.py
+    - plot_directive.py
+    originate from Matplotlib (http://matplotlib.sf.net/) which has
+    the following license:
+
+Copyright (c) 2002-2008 John D. Hunter; All Rights Reserved.
+
+1. This LICENSE AGREEMENT is between John D. Hunter (“JDH”), and the Individual or Organization (“Licensee”) accessing and otherwise using matplotlib software in source or binary form and its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, JDH hereby grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce, analyze, test, perform and/or display publicly, prepare derivative works, distribute, and otherwise use matplotlib 0.98.3 alone or in any derivative version, provided, however, that JDH’s License Agreement and JDH’s notice of copyright, i.e., “Copyright (c) 2002-2008 John D. Hunter; All Rights Reserved” are retained in matplotlib 0.98.3 alone or in any derivative version prepared by Licensee.
+
+3. In the event Licensee prepares a derivative work that is based on or incorporates matplotlib 0.98.3 or any part thereof, and wants to make the derivative work available to others as provided herein, then Licensee hereby agrees to include in any such work a brief summary of the changes made to matplotlib 0.98.3.
+
+4. JDH is making matplotlib 0.98.3 available to Licensee on an “AS IS” basis. JDH MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, JDH MAKES NO AND DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF MATPLOTLIB 0.98.3 WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. JDH SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF MATPLOTLIB 0.98.3 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING MATPLOTLIB 0.98.3, OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material breach of its terms and conditions.
+
+7. Nothing in this License Agreement shall be deemed to create any relationship of agency, partnership, or joint venture between JDH and Licensee. This License Agreement does not grant permission to use JDH trademarks or trade name in a trademark sense to endorse or promote products or services of Licensee, or any third party.
+
+8. By copying, installing or otherwise using matplotlib 0.98.3, Licensee agrees to be bound by the terms and conditions of this License Agreement.
+

doc/sphinxext/autosummary_generate.py

+#!/usr/bin/env python
+r"""
+autosummary_generate.py OPTIONS FILES
+
+Generate automatic RST source files for items referred to in
+autosummary:: directives.
+
+Each generated RST file contains a single auto*:: directive which
+extracts the docstring of the referred item.
+
+Example Makefile rule::
+
+    generate:
+            ./ext/autosummary_generate.py -o source/generated source/*.rst
+
+"""
+import glob, re, inspect, os, optparse, pydoc
+from autosummary import import_by_name
+
+try:
+    from phantom_import import import_phantom_module
+except ImportError:
+    import_phantom_module = lambda x: x
+
+def main():
+    p = optparse.OptionParser(__doc__.strip())
+    p.add_option("-p", "--phantom", action="store", type="string",
+                 dest="phantom", default=None,
+                 help="Phantom import modules from a file")
+    p.add_option("-o", "--output-dir", action="store", type="string",
+                 dest="output_dir", default=None,
+                 help=("Write all output files to the given directory (instead "
+                       "of writing them as specified in the autosummary:: "
+                       "directives)"))
+    options, args = p.parse_args()
+
+    if len(args) == 0:
+        p.error("wrong number of arguments")
+
+    if options.phantom and os.path.isfile(options.phantom):
+        import_phantom_module(options.phantom)
+
+    # read
+    names = {}
+    for name, loc in get_documented(args).items():
+        for (filename, sec_title, keyword, toctree) in loc:
+            if toctree is not None:
+                path = os.path.join(os.path.dirname(filename), toctree)
+                names[name] = os.path.abspath(path)
+
+    # write
+    for name, path in sorted(names.items()):
+        if options.output_dir is not None:
+            path = options.output_dir
+        
+        if not os.path.isdir(path):
+            os.makedirs(path)
+
+        try:
+            obj, name = import_by_name(name)
+        except ImportError, e:
+            print "Failed to import '%s': %s" % (name, e)
+            continue
+
+        fn = os.path.join(path, '%s.rst' % name)
+
+        if os.path.exists(fn):
+            # skip
+            continue
+
+        f = open(fn, 'w')
+
+        try:
+            f.write('%s\n%s\n\n' % (name, '='*len(name)))
+
+            if inspect.isclass(obj):
+                if issubclass(obj, Exception):
+                    f.write(format_modulemember(name, 'autoexception'))
+                else:
+                    f.write(format_modulemember(name, 'autoclass'))
+            elif inspect.ismodule(obj):
+                f.write(format_modulemember(name, 'automodule'))
+            elif inspect.ismethod(obj) or inspect.ismethoddescriptor(obj):
+                f.write(format_classmember(name, 'automethod'))
+            elif callable(obj):
+                f.write(format_modulemember(name, 'autofunction'))
+            elif hasattr(obj, '__get__'):
+                f.write(format_classmember(name, 'autoattribute'))
+            else:
+                f.write(format_modulemember(name, 'autofunction'))
+        finally:
+            f.close()
+
+def format_modulemember(name, directive):
+    parts = name.split('.')
+    mod, name = '.'.join(parts[:-1]), parts[-1]
+    return ".. currentmodule:: %s\n\n.. %s:: %s\n" % (mod, directive, name)
+
+def format_classmember(name, directive):
+    parts = name.split('.')
+    mod, name = '.'.join(parts[:-2]), '.'.join(parts[-2:])
+    return ".. currentmodule:: %s\n\n.. %s:: %s\n" % (mod, directive, name)
+
+def get_documented(filenames):
+    """
+    Find out what items are documented in source/*.rst
+    See `get_documented_in_lines`.
+
+    """
+    documented = {}
+    for filename in filenames:
+        f = open(filename, 'r')
+        lines = f.read().splitlines()
+        documented.update(get_documented_in_lines(lines, filename=filename))
+        f.close()
+    return documented
+
+def get_documented_in_docstring(name, module=None, filename=None):
+    """
+    Find out what items are documented in the given object's docstring.
+    See `get_documented_in_lines`.
+    
+    """
+    try:
+        obj, real_name = import_by_name(name)
+        lines = pydoc.getdoc(obj).splitlines()
+        return get_documented_in_lines(lines, module=name, filename=filename)
+    except AttributeError:
+        pass
+    except ImportError, e:
+        print "Failed to import '%s': %s" % (name, e)
+    return {}
+
+def get_documented_in_lines(lines, module=None, filename=None):
+    """
+    Find out what items are documented in the given lines
+    
+    Returns
+    -------
+    documented : dict of list of (filename, title, keyword, toctree)
+        Dictionary whose keys are documented names of objects.
+        The value is a list of locations where the object was documented.
+        Each location is a tuple of filename, the current section title,
+        the name of the directive, and the value of the :toctree: argument
+        (if present) of the directive.
+
+    """
+    title_underline_re = re.compile("^[-=*_^#]{3,}\s*$")
+    autodoc_re = re.compile(".. auto(function|method|attribute|class|exception|module)::\s*([A-Za-z0-9_.]+)\s*$")
+    autosummary_re = re.compile(r'^\.\.\s+autosummary::\s*')
+    module_re = re.compile(r'^\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
+    autosummary_item_re = re.compile(r'^\s+([_a-zA-Z][a-zA-Z0-9_.]*)\s*')
+    toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$')
+    
+    documented = {}
+   
+    current_title = []
+    last_line = None
+    toctree = None
+    current_module = module
+    in_autosummary = False
+    
+    for line in lines:
+        try:
+            if in_autosummary:
+                m = toctree_arg_re.match(line)
+                if m:
+                    toctree = m.group(1)
+                    continue
+
+                if line.strip().startswith(':'):
+                    continue # skip options
+
+                m = autosummary_item_re.match(line)
+                if m:
+                    name = m.group(1).strip()
+                    if current_module and not name.startswith(current_module + '.'):
+                        name = "%s.%s" % (current_module, name)
+                    documented.setdefault(name, []).append(
+