Add the matplotlib sphinx extensions, authored by the MPL team.

docs/sphinxext/inheritance_diagram.py

@@ -0,0 +1,423 b''
+"""
+Defines a docutils directive for inserting inheritance diagrams.
+
+Provide the directive with one or more classes or modules (separated
+by whitespace).  For modules, all of the classes in that module will
+be used.
+
+Example::
+
+   Given the following classes:
+
+   class A: pass
+   class B(A): pass
+   class C(A): pass
+   class D(B, C): pass
+   class E(B): pass
+
+   .. inheritance-diagram: D E
+
+   Produces a graph like the following:
+
+               A
+              / \
+             B   C
+            / \ /
+           E   D
+
+The graph is inserted as a PNG+image map into HTML and a PDF in
+LaTeX.
+"""
+
+import inspect
+import os
+import re
+import subprocess
+try:
+    from hashlib import md5
+except ImportError:
+    from md5 import md5
+
+from docutils.nodes import Body, Element
+from docutils.writers.html4css1 import HTMLTranslator
+from sphinx.latexwriter import LaTeXTranslator
+from docutils.parsers.rst import directives
+from sphinx.roles import xfileref_role
+
+class DotException(Exception):
+    pass
+
+class InheritanceGraph(object):
+    """
+    Given a list of classes, determines the set of classes that
+    they inherit from all the way to the root "object", and then
+    is able to generate a graphviz dot graph from them.
+    """
+    def __init__(self, class_names, show_builtins=False):
+        """
+        *class_names* is a list of child classes to show bases from.
+
+        If *show_builtins* is True, then Python builtins will be shown
+        in the graph.
+        """
+        self.class_names = class_names
+        self.classes = self._import_classes(class_names)
+        self.all_classes = self._all_classes(self.classes)
+        if len(self.all_classes) == 0:
+            raise ValueError("No classes found for inheritance diagram")
+        self.show_builtins = show_builtins
+
+    py_sig_re = re.compile(r'''^([\w.]*\.)?    # class names
+                           (\w+)  \s* $        # optionally arguments
+                           ''', re.VERBOSE)
+
+    def _import_class_or_module(self, name):
+        """
+        Import a class using its fully-qualified *name*.
+        """
+        try:
+            path, base = self.py_sig_re.match(name).groups()
+        except:
+            raise ValueError(
+                "Invalid class or module '%s' specified for inheritance diagram" % name)
+        fullname = (path or '') + base
+        path = (path and path.rstrip('.'))
+        if not path:
+            path = base
+        if not path:
+            raise ValueError(
+                "Invalid class or module '%s' specified for inheritance diagram" % name)
+        try:
+            module = __import__(path, None, None, [])
+        except ImportError:
+            raise ValueError(
+                "Could not import class or module '%s' specified for inheritance diagram" % name)
+
+        try:
+            todoc = module
+            for comp in fullname.split('.')[1:]:
+                todoc = getattr(todoc, comp)
+        except AttributeError:
+            raise ValueError(
+                "Could not find class or module '%s' specified for inheritance diagram" % name)
+
+        # If a class, just return it
+        if inspect.isclass(todoc):
+            return [todoc]
+        elif inspect.ismodule(todoc):
+            classes = []
+            for cls in todoc.__dict__.values():
+                if inspect.isclass(cls) and cls.__module__ == todoc.__name__:
+                    classes.append(cls)
+            return classes
+        raise ValueError(
+            "'%s' does not resolve to a class or module" % name)
+
+    def _import_classes(self, class_names):
+        """
+        Import a list of classes.
+        """
+        classes = []
+        for name in class_names:
+            classes.extend(self._import_class_or_module(name))
+        return classes
+
+    def _all_classes(self, classes):
+        """
+        Return a list of all classes that are ancestors of *classes*.
+        """
+        all_classes = {}
+
+        def recurse(cls):
+            all_classes[cls] = None
+            for c in cls.__bases__:
+                if c not in all_classes:
+                    recurse(c)
+
+        for cls in classes:
+            recurse(cls)
+
+        return all_classes.keys()
+
+    def class_name(self, cls, parts=0):
+        """
+        Given a class object, return a fully-qualified name.  This
+        works for things I've tested in matplotlib so far, but may not
+        be completely general.
+        """
+        module = cls.__module__
+        if module == '__builtin__':
+            fullname = cls.__name__
+        else:
+            fullname = "%s.%s" % (module, cls.__name__)
+        if parts == 0:
+            return fullname
+        name_parts = fullname.split('.')
+        return '.'.join(name_parts[-parts:])
+
+    def get_all_class_names(self):
+        """
+        Get all of the class names involved in the graph.
+        """
+        return [self.class_name(x) for x in self.all_classes]
+
+    # These are the default options for graphviz
+    default_graph_options = {
+        "rankdir": "LR",
+        "size": '"8.0, 12.0"'
+        }
+    default_node_options = {
+        "shape": "box",
+        "fontsize": 10,
+        "height": 0.25,
+        "fontname": "Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",
+        "style": '"setlinewidth(0.5)"'
+        }
+    default_edge_options = {
+        "arrowsize": 0.5,
+        "style": '"setlinewidth(0.5)"'
+        }
+
+    def _format_node_options(self, options):
+        return ','.join(["%s=%s" % x for x in options.items()])
+    def _format_graph_options(self, options):
+        return ''.join(["%s=%s;\n" % x for x in options.items()])
+
+    def generate_dot(self, fd, name, parts=0, urls={},
+                     graph_options={}, node_options={},
+                     edge_options={}):
+        """
+        Generate a graphviz dot graph from the classes that
+        were passed in to __init__.
+
+        *fd* is a Python file-like object to write to.
+
+        *name* is the name of the graph
+
+        *urls* is a dictionary mapping class names to http urls
+
+        *graph_options*, *node_options*, *edge_options* are
+        dictionaries containing key/value pairs to pass on as graphviz
+        properties.
+        """
+        g_options = self.default_graph_options.copy()
+        g_options.update(graph_options)
+        n_options = self.default_node_options.copy()
+        n_options.update(node_options)
+        e_options = self.default_edge_options.copy()
+        e_options.update(edge_options)
+
+        fd.write('digraph %s {\n' % name)
+        fd.write(self._format_graph_options(g_options))
+
+        for cls in self.all_classes:
+            if not self.show_builtins and cls in __builtins__.values():
+                continue
+
+            name = self.class_name(cls, parts)
+
+            # Write the node
+            this_node_options = n_options.copy()
+            url = urls.get(self.class_name(cls))
+            if url is not None:
+                this_node_options['URL'] = '"%s"' % url
+            fd.write('  "%s" [%s];\n' %
+                     (name, self._format_node_options(this_node_options)))
+
+            # Write the edges
+            for base in cls.__bases__:
+                if not self.show_builtins and base in __builtins__.values():
+                    continue
+
+                base_name = self.class_name(base, parts)
+                fd.write('  "%s" -> "%s" [%s];\n' %
+                         (base_name, name,
+                          self._format_node_options(e_options)))
+        fd.write('}\n')
+
+    def run_dot(self, args, name, parts=0, urls={},
+                graph_options={}, node_options={}, edge_options={}):
+        """
+        Run graphviz 'dot' over this graph, returning whatever 'dot'
+        writes to stdout.
+
+        *args* will be passed along as commandline arguments.
+
+        *name* is the name of the graph
+
+        *urls* is a dictionary mapping class names to http urls
+
+        Raises DotException for any of the many os and
+        installation-related errors that may occur.
+        """
+        try:
+            dot = subprocess.Popen(['dot'] + list(args),
+                                   stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+                                   close_fds=True)
+        except OSError:
+            raise DotException("Could not execute 'dot'.  Are you sure you have 'graphviz' installed?")
+        except ValueError:
+            raise DotException("'dot' called with invalid arguments")
+        except:
+            raise DotException("Unexpected error calling 'dot'")
+
+        self.generate_dot(dot.stdin, name, parts, urls, graph_options,
+                          node_options, edge_options)
+        dot.stdin.close()
+        result = dot.stdout.read()
+        returncode = dot.wait()
+        if returncode != 0:
+            raise DotException("'dot' returned the errorcode %d" % returncode)
+        return result
+
+class inheritance_diagram(Body, Element):
+    """
+    A docutils node to use as a placeholder for the inheritance
+    diagram.
+    """
+    pass
+
+def inheritance_diagram_directive_run(class_names, options, state):
+    """
+    Run when the inheritance_diagram directive is first encountered.
+    """
+    node = inheritance_diagram()
+
+    # Create a graph starting with the list of classes
+    graph = InheritanceGraph(class_names)
+
+    # Create xref nodes for each target of the graph's image map and
+    # add them to the doc tree so that Sphinx can resolve the
+    # references to real URLs later.  These nodes will eventually be
+    # removed from the doctree after we're done with them.
+    for name in graph.get_all_class_names():
+        refnodes, x = xfileref_role(
+            'class', ':class:`%s`' % name, name, 0, state)
+        node.extend(refnodes)
+    # Store the graph object so we can use it to generate the
+    # dot file later
+    node['graph'] = graph
+    # Store the original content for use as a hash
+    node['parts'] = options.get('parts', 0)
+    node['content'] = " ".join(class_names)
+    return [node]
+
+def get_graph_hash(node):
+    return md5(node['content'] + str(node['parts'])).hexdigest()[-10:]
+
+def html_output_graph(self, node):
+    """
+    Output the graph for HTML.  This will insert a PNG with clickable
+    image map.
+    """
+    graph = node['graph']
+    parts = node['parts']
+
+    graph_hash = get_graph_hash(node)
+    name = "inheritance%s" % graph_hash
+    png_path = os.path.join('_static', name + ".png")
+
+    path = '_static'
+    source = self.document.attributes['source']
+    count = source.split('/doc/')[-1].count('/')
+    for i in range(count):
+        if os.path.exists(path): break
+        path = '../'+path
+    path = '../'+path #specifically added for matplotlib
+
+    # Create a mapping from fully-qualified class names to URLs.
+    urls = {}
+    for child in node:
+        if child.get('refuri') is not None:
+            urls[child['reftitle']] = child.get('refuri')
+        elif child.get('refid') is not None:
+            urls[child['reftitle']] = '#' + child.get('refid')
+
+    # These arguments to dot will save a PNG file to disk and write
+    # an HTML image map to stdout.
+    image_map = graph.run_dot(['-Tpng', '-o%s' % png_path, '-Tcmapx'],
+                              name, parts, urls)
+    return ('<img src="%s/%s.png" usemap="#%s" class="inheritance"/>%s' %
+            (path, name, name, image_map))
+
+def latex_output_graph(self, node):
+    """
+    Output the graph for LaTeX.  This will insert a PDF.
+    """
+    graph = node['graph']
+    parts = node['parts']
+
+    graph_hash = get_graph_hash(node)
+    name = "inheritance%s" % graph_hash
+    pdf_path = os.path.join('_static', name + ".pdf")
+
+    graph.run_dot(['-Tpdf', '-o%s' % pdf_path],
+                  name, parts, graph_options={'size': '"6.0,6.0"'})
+    return '\\includegraphics{../../%s}' % pdf_path
+
+def visit_inheritance_diagram(inner_func):
+    """
+    This is just a wrapper around html/latex_output_graph to make it
+    easier to handle errors and insert warnings.
+    """
+    def visitor(self, node):
+        try:
+            content = inner_func(self, node)
+        except DotException, e:
+            # Insert the exception as a warning in the document
+            warning = self.document.reporter.warning(str(e), line=node.line)
+            warning.parent = node
+            node.children = [warning]
+        else:
+            source = self.document.attributes['source']
+            self.body.append(content)
+            node.children = []
+    return visitor
+
+def do_nothing(self, node):
+    pass
+
+options_spec = {
+    'parts': directives.nonnegative_int
+    }
+
+# Deal with the old and new way of registering directives
+try:
+    from docutils.parsers.rst import Directive
+except ImportError:
+    from docutils.parsers.rst.directives import _directives
+    def inheritance_diagram_directive(name, arguments, options, content, lineno,
+                                      content_offset, block_text, state,
+                                      state_machine):
+        return inheritance_diagram_directive_run(arguments, options, state)
+    inheritance_diagram_directive.__doc__ = __doc__
+    inheritance_diagram_directive.arguments = (1, 100, 0)
+    inheritance_diagram_directive.options = options_spec
+    inheritance_diagram_directive.content = 0
+    _directives['inheritance-diagram'] = inheritance_diagram_directive
+else:
+    class inheritance_diagram_directive(Directive):
+        has_content = False
+        required_arguments = 1
+        optional_arguments = 100
+        final_argument_whitespace = False
+        option_spec = options_spec
+
+        def run(self):
+            return inheritance_diagram_directive_run(
+                self.arguments, self.options, self.state)
+    inheritance_diagram_directive.__doc__ = __doc__
+
+    directives.register_directive('inheritance-diagram',
+                                  inheritance_diagram_directive)
+
+def setup(app):
+    app.add_node(inheritance_diagram)
+
+    HTMLTranslator.visit_inheritance_diagram = \
+        visit_inheritance_diagram(html_output_graph)
+    HTMLTranslator.depart_inheritance_diagram = do_nothing
+
+    LaTeXTranslator.visit_inheritance_diagram = \
+        visit_inheritance_diagram(latex_output_graph)
+    LaTeXTranslator.depart_inheritance_diagram = do_nothing

docs/sphinxext/ipython_console_highlighting.py

@@ -0,0 +1,75 b''
+from pygments.lexer import Lexer, do_insertions
+from pygments.lexers.agile import PythonConsoleLexer, PythonLexer, \
+    PythonTracebackLexer
+from pygments.token import Comment, Generic
+from sphinx import highlighting
+import re
+
+line_re = re.compile('.*?\n')
+
+class IPythonConsoleLexer(Lexer):
+    """
+    For IPython console output or doctests, such as:
+
+    Tracebacks are not currently supported.
+
+    .. sourcecode:: ipython
+
+      In [1]: a = 'foo'
+
+      In [2]: a
+      Out[2]: 'foo'
+
+      In [3]: print a
+      foo
+
+      In [4]: 1 / 0
+    """
+    name = 'IPython console session'
+    aliases = ['ipython']
+    mimetypes = ['text/x-ipython-console']
+    input_prompt = re.compile("(In \[[0-9]+\]: )|(   \.\.\.+:)")
+    output_prompt = re.compile("(Out\[[0-9]+\]: )|(   \.\.\.+:)")
+    continue_prompt = re.compile("   \.\.\.+:")
+    tb_start = re.compile("\-+")
+
+    def get_tokens_unprocessed(self, text):
+        pylexer = PythonLexer(**self.options)
+        tblexer = PythonTracebackLexer(**self.options)
+
+        curcode = ''
+        insertions = []
+        for match in line_re.finditer(text):
+            line = match.group()
+            input_prompt = self.input_prompt.match(line)
+            continue_prompt = self.continue_prompt.match(line.rstrip())
+            output_prompt = self.output_prompt.match(line)
+            if line.startswith("#"):
+                insertions.append((len(curcode),
+                                   [(0, Comment, line)]))
+            elif input_prompt is not None:
+                insertions.append((len(curcode),
+                                   [(0, Generic.Prompt, input_prompt.group())]))
+                curcode += line[input_prompt.end():]
+            elif continue_prompt is not None:
+                insertions.append((len(curcode),
+                                   [(0, Generic.Prompt, continue_prompt.group())]))
+                curcode += line[continue_prompt.end():]
+            elif output_prompt is not None:
+                insertions.append((len(curcode),
+                                   [(0, Generic.Output, output_prompt.group())]))
+                curcode += line[output_prompt.end():]
+            else:
+                if curcode:
+                    for item in do_insertions(insertions,
+                                              pylexer.get_tokens_unprocessed(curcode)):
+                        yield item
+                        curcode = ''
+                        insertions = []
+                yield match.start(), Generic.Output, line
+        if curcode:
+            for item in do_insertions(insertions,
+                                      pylexer.get_tokens_unprocessed(curcode)):
+                yield item
+
+highlighting.lexers['ipython'] = IPythonConsoleLexer()

docs/sphinxext/only_directives.py

@@ -0,0 +1,87 b''
+#
+# A pair of directives for inserting content that will only appear in
+# either html or latex.
+#
+
+from docutils.nodes import Body, Element
+from docutils.writers.html4css1 import HTMLTranslator
+from sphinx.latexwriter import LaTeXTranslator
+from docutils.parsers.rst import directives
+
+class html_only(Body, Element):
+    pass
+
+class latex_only(Body, Element):
+    pass
+
+def run(content, node_class, state, content_offset):
+    text = '\n'.join(content)
+    node = node_class(text)
+    state.nested_parse(content, content_offset, node)
+    return [node]
+
+try:
+    from docutils.parsers.rst import Directive
+except ImportError:
+    from docutils.parsers.rst.directives import _directives
+
+    def html_only_directive(name, arguments, options, content, lineno,
+                            content_offset, block_text, state, state_machine):
+        return run(content, html_only, state, content_offset)
+
+    def latex_only_directive(name, arguments, options, content, lineno,
+                             content_offset, block_text, state, state_machine):
+        return run(content, latex_only, state, content_offset)
+
+    for func in (html_only_directive, latex_only_directive):
+        func.content = 1
+        func.options = {}
+        func.arguments = None
+
+    _directives['htmlonly'] = html_only_directive
+    _directives['latexonly'] = latex_only_directive
+else:
+    class OnlyDirective(Directive):
+        has_content = True
+        required_arguments = 0
+        optional_arguments = 0
+        final_argument_whitespace = True
+        option_spec = {}
+
+        def run(self):
+            self.assert_has_content()
+            return run(self.content, self.node_class,
+                       self.state, self.content_offset)
+
+    class HtmlOnlyDirective(OnlyDirective):
+        node_class = html_only
+
+    class LatexOnlyDirective(OnlyDirective):
+        node_class = latex_only
+
+    directives.register_directive('htmlonly', HtmlOnlyDirective)
+    directives.register_directive('latexonly', LatexOnlyDirective)
+
+def setup(app):
+    app.add_node(html_only)
+    app.add_node(latex_only)
+
+    # Add visit/depart methods to HTML-Translator:
+    def visit_perform(self, node):
+        pass
+    def depart_perform(self, node):
+        pass
+    def visit_ignore(self, node):
+        node.children = []
+    def depart_ignore(self, node):
+        node.children = []
+
+    HTMLTranslator.visit_html_only = visit_perform
+    HTMLTranslator.depart_html_only = depart_perform
+    HTMLTranslator.visit_latex_only = visit_ignore
+    HTMLTranslator.depart_latex_only = depart_ignore
+
+    LaTeXTranslator.visit_html_only = visit_ignore
+    LaTeXTranslator.depart_html_only = depart_ignore
+    LaTeXTranslator.visit_latex_only = visit_perform
+    LaTeXTranslator.depart_latex_only = depart_perform

docs/sphinxext/plot_directive.py

@@ -0,0 +1,155 b''
+"""A special directive for including a matplotlib plot.
+
+Given a path to a .py file, it includes the source code inline, then:
+
+- On HTML, will include a .png with a link to a high-res .png.
+
+- On LaTeX, will include a .pdf
+
+This directive supports all of the options of the `image` directive,
+except for `target` (since plot will add its own target).
+
+Additionally, if the :include-source: option is provided, the literal
+source will be included inline, as well as a link to the source.
+"""
+
+import sys, os, glob, shutil
+from docutils.parsers.rst import directives
+
+try:
+    # docutils 0.4
+    from docutils.parsers.rst.directives.images import align
+except ImportError:
+    # docutils 0.5
+    from docutils.parsers.rst.directives.images import Image
+    align = Image.align
+
+
+import matplotlib
+import IPython.Shell
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+
+mplshell = IPython.Shell.MatplotlibShell('mpl')
+
+options = {'alt': directives.unchanged,
+           'height': directives.length_or_unitless,
+           'width': directives.length_or_percentage_or_unitless,
+           'scale': directives.nonnegative_int,
+           'align': align,
+           'class': directives.class_option,
+           'include-source': directives.flag }
+
+template = """
+.. htmlonly::
+
+   [`source code <../%(srcdir)s/%(basename)s.py>`__,
+   `png <../%(srcdir)s/%(basename)s.hires.png>`__,
+   `pdf <../%(srcdir)s/%(basename)s.pdf>`__]
+
+   .. image:: ../%(srcdir)s/%(basename)s.png
+%(options)s
+
+.. latexonly::
+   .. image:: ../%(srcdir)s/%(basename)s.pdf
+%(options)s
+
+"""
+
+def makefig(fullpath, outdir):
+    """
+    run a pyplot script and save the low and high res PNGs and a PDF in _static
+    """
+
+    fullpath = str(fullpath)  # todo, why is unicode breaking this
+    formats = [('png', 100),
+               ('hires.png', 200),
+               ('pdf', 72),
+               ]
+
+    basedir, fname = os.path.split(fullpath)
+    basename, ext = os.path.splitext(fname)
+    all_exists = True
+
+    if basedir != outdir:
+        shutil.copyfile(fullpath, os.path.join(outdir, fname))
+
+    for format, dpi in formats:
+        outname = os.path.join(outdir, '%s.%s' % (basename, format))
+        if not os.path.exists(outname):
+            all_exists = False
+            break
+
+    if all_exists:
+        print '    already have %s'%fullpath
+        return
+
+    print '    building %s'%fullpath
+    plt.close('all')    # we need to clear between runs
+    matplotlib.rcdefaults()
+
+    mplshell.magic_run(fullpath)
+    for format, dpi in formats:
+        outname = os.path.join(outdir, '%s.%s' % (basename, format))
+        if os.path.exists(outname): continue
+        plt.savefig(outname, dpi=dpi)
+
+def run(arguments, options, state_machine, lineno):
+    reference = directives.uri(arguments[0])
+    basedir, fname = os.path.split(reference)
+    basename, ext = os.path.splitext(fname)
+
+    # todo - should we be using the _static dir for the outdir, I am
+    # not sure we want to corrupt that dir with autogenerated files
+    # since it also has permanent files in it which makes it difficult
+    # to clean (save an rm -rf followed by and svn up)
+    srcdir = 'pyplots'
+
+    makefig(os.path.join(srcdir, reference), srcdir)
+
+    # todo: it is not great design to assume the makefile is putting
+    # the figs into the right place, so we may want to do that here instead.
+
+    if options.has_key('include-source'):
+        lines = ['.. literalinclude:: ../pyplots/%(reference)s' % locals()]
+        del options['include-source']
+    else:
+        lines = []
+
+    options = ['      :%s: %s' % (key, val) for key, val in
+               options.items()]
+    options = "\n".join(options)
+
+    lines.extend((template % locals()).split('\n'))
+
+    state_machine.insert_input(
+        lines, state_machine.input_lines.source(0))
+    return []
+
+
+try:
+    from docutils.parsers.rst import Directive
+except ImportError:
+    from docutils.parsers.rst.directives import _directives
+
+    def plot_directive(name, arguments, options, content, lineno,
+                       content_offset, block_text, state, state_machine):
+        return run(arguments, options, state_machine, lineno)
+    plot_directive.__doc__ = __doc__
+    plot_directive.arguments = (1, 0, 1)
+    plot_directive.options = options
+
+    _directives['plot'] = plot_directive
+else:
+    class plot_directive(Directive):
+        required_arguments = 1
+        optional_arguments = 0
+        final_argument_whitespace = True
+        option_spec = options
+        def run(self):
+            return run(self.arguments, self.options,
+                       self.state_machine, self.lineno)
+    plot_directive.__doc__ = __doc__
+
+    directives.register_directive('plot', plot_directive)
+