intermediate changes

ref:cde9a383711a11544ce7e107a78147fb96cc4029

4 files changed, 1361 insertions, 0 deletions

diff --git a/contrib/python/ipython/py2/IPython/sphinxext/__init__.py b/contrib/python/ipython/py2/IPython/sphinxext/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/contrib/python/ipython/py2/IPython/sphinxext/__init__.py
diff --git a/contrib/python/ipython/py2/IPython/sphinxext/custom_doctests.py b/contrib/python/ipython/py2/IPython/sphinxext/custom_doctests.py
new file mode 100644
index 0000000000..7678fd6801
--- /dev/null
+++ b/contrib/python/ipython/py2/IPython/sphinxext/custom_doctests.py
@@ -0,0 +1,155 @@
+"""
+Handlers for IPythonDirective's @doctest pseudo-decorator.
+
+The Sphinx extension that provides support for embedded IPython code provides
+a pseudo-decorator @doctest, which treats the input/output block as a
+doctest, raising a RuntimeError during doc generation if the actual output
+(after running the input) does not match the expected output.
+
+An example usage is:
+
+.. code-block:: rst
+
+   .. ipython::
+
+        In [1]: x = 1
+
+        @doctest
+        In [2]: x + 2
+        Out[3]: 3
+
+One can also provide arguments to the decorator. The first argument should be
+the name of a custom handler. The specification of any other arguments is
+determined by the handler. For example,
+
+.. code-block:: rst
+
+      .. ipython::
+
+         @doctest float
+         In [154]: 0.1 + 0.2
+         Out[154]: 0.3
+
+allows the actual output ``0.30000000000000004`` to match the expected output
+due to a comparison with `np.allclose`.
+
+This module contains handlers for the @doctest pseudo-decorator. Handlers
+should have the following function signature::
+
+    handler(sphinx_shell, args, input_lines, found, submitted)
+
+where `sphinx_shell` is the embedded Sphinx shell, `args` contains the list
+of arguments that follow: '@doctest handler_name', `input_lines` contains
+a list of the lines relevant to the current doctest, `found` is a string
+containing the output from the IPython shell, and `submitted` is a string
+containing the expected output from the IPython shell.
+
+Handlers must be registered in the `doctests` dict at the end of this module.
+
+"""
+
+def str_to_array(s):
+    """
+    Simplistic converter of strings from repr to float NumPy arrays.
+
+    If the repr representation has ellipsis in it, then this will fail.
+
+    Parameters
+    ----------
+    s : str
+        The repr version of a NumPy array.
+
+    Examples
+    --------
+    >>> s = "array([ 0.3,  inf,  nan])"
+    >>> a = str_to_array(s)
+
+    """
+    import numpy as np
+
+    # Need to make sure eval() knows about inf and nan.
+    # This also assumes default printoptions for NumPy.
+    from numpy import inf, nan
+
+    if s.startswith(u'array'):
+        # Remove array( and )
+        s = s[6:-1]
+
+    if s.startswith(u'['):
+        a = np.array(eval(s), dtype=float)
+    else:
+        # Assume its a regular float. Force 1D so we can index into it.
+        a = np.atleast_1d(float(s))
+    return a
+
+def float_doctest(sphinx_shell, args, input_lines, found, submitted):
+    """
+    Doctest which allow the submitted output to vary slightly from the input.
+
+    Here is how it might appear in an rst file:
+
+    .. code-block:: rst
+
+       .. ipython::
+
+          @doctest float
+          In [1]: 0.1 + 0.2
+          Out[1]: 0.3
+
+    """
+    import numpy as np
+
+    if len(args) == 2:
+        rtol = 1e-05
+        atol = 1e-08
+    else:
+        # Both must be specified if any are specified.
+        try:
+            rtol = float(args[2])
+            atol = float(args[3])
+        except IndexError:
+            e = ("Both `rtol` and `atol` must be specified "
+                 "if either are specified: {0}".format(args))
+            raise IndexError(e)
+
+    try:
+        submitted = str_to_array(submitted)
+        found = str_to_array(found)
+    except:
+        # For example, if the array is huge and there are ellipsis in it.
+        error = True
+    else:
+        found_isnan = np.isnan(found)
+        submitted_isnan = np.isnan(submitted)
+        error = not np.allclose(found_isnan, submitted_isnan)
+        error |= not np.allclose(found[~found_isnan],
+                                 submitted[~submitted_isnan],
+                                 rtol=rtol, atol=atol)
+
+    TAB = ' ' * 4
+    directive = sphinx_shell.directive
+    if directive is None:
+        source = 'Unavailable'
+        content = 'Unavailable'
+    else:
+        source = directive.state.document.current_source
+        # Add tabs and make into a single string.
+        content = '\n'.join([TAB + line for line in directive.content])
+
+    if error:
+
+        e = ('doctest float comparison failure\n\n'
+             'Document source: {0}\n\n'
+             'Raw content: \n{1}\n\n'
+             'On input line(s):\n{TAB}{2}\n\n'
+             'we found output:\n{TAB}{3}\n\n'
+             'instead of the expected:\n{TAB}{4}\n\n')
+        e = e.format(source, content, '\n'.join(input_lines), repr(found),
+                     repr(submitted), TAB=TAB)
+        raise RuntimeError(e)
+
+# dict of allowable doctest handlers. The key represents the first argument
+# that must be given to @doctest in order to activate the handler.
+doctests = {
+    'float': float_doctest,
+}
diff --git a/contrib/python/ipython/py2/IPython/sphinxext/ipython_console_highlighting.py b/contrib/python/ipython/py2/IPython/sphinxext/ipython_console_highlighting.py
new file mode 100644
index 0000000000..b93a151fb3
--- /dev/null
+++ b/contrib/python/ipython/py2/IPython/sphinxext/ipython_console_highlighting.py
@@ -0,0 +1,28 @@
+"""
+reST directive for syntax-highlighting ipython interactive sessions.
+
+"""
+
+from sphinx import highlighting
+from IPython.lib.lexers import IPyLexer
+
+def setup(app):
+    """Setup as a sphinx extension."""
+
+    # This is only a lexer, so adding it below to pygments appears sufficient.
+    # But if somebody knows what the right API usage should be to do that via
+    # sphinx, by all means fix it here.  At least having this setup.py
+    # suppresses the sphinx warning we'd get without it.
+    metadata = {'parallel_read_safe': True, 'parallel_write_safe': True}
+    return metadata
+
+# Register the extension as a valid pygments lexer.
+# Alternatively, we could register the lexer with pygments instead. This would
+# require using setuptools entrypoints: http://pygments.org/docs/plugins
+
+ipy2 = IPyLexer(python3=False)
+ipy3 = IPyLexer(python3=True)
+
+highlighting.lexers['ipython'] = ipy2
+highlighting.lexers['ipython2'] = ipy2
+highlighting.lexers['ipython3'] = ipy3
diff --git a/contrib/python/ipython/py2/IPython/sphinxext/ipython_directive.py b/contrib/python/ipython/py2/IPython/sphinxext/ipython_directive.py
new file mode 100644
index 0000000000..8df9ace1f3
--- /dev/null
+++ b/contrib/python/ipython/py2/IPython/sphinxext/ipython_directive.py
@@ -0,0 +1,1178 @@
+# -*- coding: utf-8 -*-
+"""
+Sphinx directive to support embedded IPython code.
+
+This directive allows pasting of entire interactive IPython sessions, prompts
+and all, and their code will actually get re-executed at doc build time, with
+all prompts renumbered sequentially. It also allows you to input code as a pure
+python input by giving the argument python to the directive. The output looks
+like an interactive ipython section.
+
+To enable this directive, simply list it in your Sphinx ``conf.py`` file
+(making sure the directory where you placed it is visible to sphinx, as is
+needed for all Sphinx directives). For example, to enable syntax highlighting
+and the IPython directive::
+
+    extensions = ['IPython.sphinxext.ipython_console_highlighting',
+                  'IPython.sphinxext.ipython_directive']
+
+The IPython directive outputs code-blocks with the language 'ipython'. So
+if you do not have the syntax highlighting extension enabled as well, then
+all rendered code-blocks will be uncolored. By default this directive assumes
+that your prompts are unchanged IPython ones, but this can be customized.
+The configurable options that can be placed in conf.py are:
+
+ipython_savefig_dir:
+    The directory in which to save the figures. This is relative to the
+    Sphinx source directory. The default is `html_static_path`.
+ipython_rgxin:
+    The compiled regular expression to denote the start of IPython input
+    lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You
+    shouldn't need to change this.
+ipython_rgxout:
+    The compiled regular expression to denote the start of IPython output
+    lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You
+    shouldn't need to change this.
+ipython_promptin:
+    The string to represent the IPython input prompt in the generated ReST.
+    The default is 'In [%d]:'. This expects that the line numbers are used
+    in the prompt.
+ipython_promptout:
+    The string to represent the IPython prompt in the generated ReST. The
+    default is 'Out [%d]:'. This expects that the line numbers are used
+    in the prompt.
+ipython_mplbackend:
+    The string which specifies if the embedded Sphinx shell should import
+    Matplotlib and set the backend. The value specifies a backend that is
+    passed to `matplotlib.use()` before any lines in `ipython_execlines` are
+    executed. If not specified in conf.py, then the default value of 'agg' is
+    used. To use the IPython directive without matplotlib as a dependency, set
+    the value to `None`. It may end up that matplotlib is still imported
+    if the user specifies so in `ipython_execlines` or makes use of the
+    @savefig pseudo decorator.
+ipython_execlines:
+    A list of strings to be exec'd in the embedded Sphinx shell. Typical
+    usage is to make certain packages always available. Set this to an empty
+    list if you wish to have no imports always available. If specified in
+    conf.py as `None`, then it has the effect of making no imports available.
+    If omitted from conf.py altogether, then the default value of
+    ['import numpy as np', 'import matplotlib.pyplot as plt'] is used.
+ipython_holdcount
+    When the @suppress pseudo-decorator is used, the execution count can be
+    incremented or not. The default behavior is to hold the execution count,
+    corresponding to a value of `True`. Set this to `False` to increment
+    the execution count after each suppressed command.
+
+As an example, to use the IPython directive when `matplotlib` is not available,
+one sets the backend to `None`::
+
+    ipython_mplbackend = None
+
+An example usage of the directive is:
+
+.. code-block:: rst
+
+    .. ipython::
+
+        In [1]: x = 1
+
+        In [2]: y = x**2
+
+        In [3]: print(y)
+
+See http://matplotlib.org/sampledoc/ipython_directive.html for additional
+documentation.
+
+Pseudo-Decorators
+=================
+
+Note: Only one decorator is supported per input. If more than one decorator
+is specified, then only the last one is used.
+
+In addition to the Pseudo-Decorators/options described at the above link,
+several enhancements have been made. The directive will emit a message to the
+console at build-time if code-execution resulted in an exception or warning.
+You can suppress these on a per-block basis by specifying the :okexcept:
+or :okwarning: options:
+
+.. code-block:: rst
+
+    .. ipython::
+        :okexcept:
+        :okwarning:
+
+        In [1]: 1/0
+        In [2]: # raise warning.
+
+To Do
+-----
+
+- Turn the ad-hoc test() function into a real test suite.
+- Break up ipython-specific functionality from matplotlib stuff into better
+  separated code.
+
+Authors
+-------
+
+- John D Hunter: orignal author.
+- Fernando Perez: refactoring, documentation, cleanups, port to 0.11.
+- VáclavŠmilauer <eudoxos-AT-arcig.cz>: Prompt generalizations.
+- Skipper Seabold, refactoring, cleanups, pure python addition
+"""
+from __future__ import print_function
+
+#-----------------------------------------------------------------------------
+# Imports
+#-----------------------------------------------------------------------------
+
+# Stdlib
+import atexit
+import errno
+import os
+import re
+import sys
+import tempfile
+import ast
+import warnings
+import shutil
+
+
+# Third-party
+from docutils.parsers.rst import directives
+from docutils.parsers.rst import Directive
+
+# Our own
+from traitlets.config import Config
+from IPython import InteractiveShell
+from IPython.core.profiledir import ProfileDir
+from IPython.utils import io
+from IPython.utils.py3compat import PY3
+
+if PY3:
+    from io import StringIO
+else:
+    from StringIO import StringIO
+
+#-----------------------------------------------------------------------------
+# Globals
+#-----------------------------------------------------------------------------
+# for tokenizing blocks
+COMMENT, INPUT, OUTPUT =  range(3)
+
+#-----------------------------------------------------------------------------
+# Functions and class declarations
+#-----------------------------------------------------------------------------
+
+def block_parser(part, rgxin, rgxout, fmtin, fmtout):
+    """
+    part is a string of ipython text, comprised of at most one
+    input, one output, comments, and blank lines.  The block parser
+    parses the text into a list of::
+
+      blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...]
+
+    where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and
+    data is, depending on the type of token::
+
+      COMMENT : the comment string
+
+      INPUT: the (DECORATOR, INPUT_LINE, REST) where
+         DECORATOR: the input decorator (or None)
+         INPUT_LINE: the input as string (possibly multi-line)
+         REST : any stdout generated by the input line (not OUTPUT)
+
+      OUTPUT: the output string, possibly multi-line
+
+    """
+    block = []
+    lines = part.split('\n')
+    N = len(lines)
+    i = 0
+    decorator = None
+    while 1:
+
+        if i==N:
+            # nothing left to parse -- the last line
+            break
+
+        line = lines[i]
+        i += 1
+        line_stripped = line.strip()
+        if line_stripped.startswith('#'):
+            block.append((COMMENT, line))
+            continue
+
+        if line_stripped.startswith('@'):
+            # Here is where we assume there is, at most, one decorator.
+            # Might need to rethink this.
+            decorator = line_stripped
+            continue
+
+        # does this look like an input line?
+        matchin = rgxin.match(line)
+        if matchin:
+            lineno, inputline = int(matchin.group(1)), matchin.group(2)
+
+            # the ....: continuation string
+            continuation = '   %s:'%''.join(['.']*(len(str(lineno))+2))
+            Nc = len(continuation)
+            # input lines can continue on for more than one line, if
+            # we have a '\' line continuation char or a function call
+            # echo line 'print'.  The input line can only be
+            # terminated by the end of the block or an output line, so
+            # we parse out the rest of the input line if it is
+            # multiline as well as any echo text
+
+            rest = []
+            while i<N:
+
+                # look ahead; if the next line is blank, or a comment, or
+                # an output line, we're done
+
+                nextline = lines[i]
+                matchout = rgxout.match(nextline)
+                #print "nextline=%s, continuation=%s, starts=%s"%(nextline, continuation, nextline.startswith(continuation))
+                if matchout or nextline.startswith('#'):
+                    break
+                elif nextline.startswith(continuation):
+                    # The default ipython_rgx* treat the space following the colon as optional.
+                    # However, If the space is there we must consume it or code
+                    # employing the cython_magic extension will fail to execute.
+                    #
+                    # This works with the default ipython_rgx* patterns,
+                    # If you modify them, YMMV.
+                    nextline = nextline[Nc:]
+                    if nextline and nextline[0] == ' ':
+                        nextline = nextline[1:]
+
+                    inputline += '\n' +  nextline
+                else:
+                    rest.append(nextline)
+                i+= 1
+
+            block.append((INPUT, (decorator, inputline, '\n'.join(rest))))
+            continue
+
+        # if it looks like an output line grab all the text to the end
+        # of the block
+        matchout = rgxout.match(line)
+        if matchout:
+            lineno, output = int(matchout.group(1)), matchout.group(2)
+            if i<N-1:
+                output = '\n'.join([output] + lines[i:])
+
+            block.append((OUTPUT, output))
+            break
+
+    return block
+
+
+class EmbeddedSphinxShell(object):
+    """An embedded IPython instance to run inside Sphinx"""
+
+    def __init__(self, exec_lines=None):
+
+        self.cout = StringIO()
+
+        if exec_lines is None:
+            exec_lines = []
+
+        # Create config object for IPython
+        config = Config()
+        config.HistoryManager.hist_file = ':memory:'
+        config.InteractiveShell.autocall = False
+        config.InteractiveShell.autoindent = False
+        config.InteractiveShell.colors = 'NoColor'
+
+        # create a profile so instance history isn't saved
+        tmp_profile_dir = tempfile.mkdtemp(prefix='profile_')
+        profname = 'auto_profile_sphinx_build'
+        pdir = os.path.join(tmp_profile_dir,profname)
+        profile = ProfileDir.create_profile_dir(pdir)
+
+        # Create and initialize global ipython, but don't start its mainloop.
+        # This will persist across different EmbededSphinxShell instances.
+        IP = InteractiveShell.instance(config=config, profile_dir=profile)
+        atexit.register(self.cleanup)
+
+        # Store a few parts of IPython we'll need.
+        self.IP = IP
+        self.user_ns = self.IP.user_ns
+        self.user_global_ns = self.IP.user_global_ns
+
+        self.input = ''
+        self.output = ''
+        self.tmp_profile_dir = tmp_profile_dir
+
+        self.is_verbatim = False
+        self.is_doctest = False
+        self.is_suppress = False
+
+        # Optionally, provide more detailed information to shell.
+        # this is assigned by the SetUp method of IPythonDirective
+        # to point at itself.
+        #
+        # So, you can access handy things at self.directive.state
+        self.directive = None
+
+        # on the first call to the savefig decorator, we'll import
+        # pyplot as plt so we can make a call to the plt.gcf().savefig
+        self._pyplot_imported = False
+
+        # Prepopulate the namespace.
+        for line in exec_lines:
+            self.process_input_line(line, store_history=False)
+
+    def cleanup(self):
+        shutil.rmtree(self.tmp_profile_dir, ignore_errors=True)
+
+    def clear_cout(self):
+        self.cout.seek(0)
+        self.cout.truncate(0)
+
+    def process_input_line(self, line, store_history=True):
+        """process the input, capturing stdout"""
+
+        stdout = sys.stdout
+        splitter = self.IP.input_splitter
+        try:
+            sys.stdout = self.cout
+            splitter.push(line)
+            more = splitter.push_accepts_more()
+            if not more:
+                source_raw = splitter.raw_reset()
+                self.IP.run_cell(source_raw, store_history=store_history)
+        finally:
+            sys.stdout = stdout
+
+    def process_image(self, decorator):
+        """
+        # build out an image directive like
+        # .. image:: somefile.png
+        #    :width 4in
+        #
+        # from an input like
+        # savefig somefile.png width=4in
+        """
+        savefig_dir = self.savefig_dir
+        source_dir = self.source_dir
+        saveargs = decorator.split(' ')
+        filename = saveargs[1]
+        # insert relative path to image file in source (as absolute path for Sphinx)
+        outfile = '/' + os.path.relpath(os.path.join(savefig_dir,filename),
+                                        source_dir)
+
+        imagerows = ['.. image:: %s'%outfile]
+
+        for kwarg in saveargs[2:]:
+            arg, val = kwarg.split('=')
+            arg = arg.strip()
+            val = val.strip()
+            imagerows.append('   :%s: %s'%(arg, val))
+
+        image_file = os.path.basename(outfile) # only return file name
+        image_directive = '\n'.join(imagerows)
+        return image_file, image_directive
+
+    # Callbacks for each type of token
+    def process_input(self, data, input_prompt, lineno):
+        """
+        Process data block for INPUT token.
+
+        """
+        decorator, input, rest = data
+        image_file = None
+        image_directive = None
+
+        is_verbatim = decorator=='@verbatim' or self.is_verbatim
+        is_doctest = (decorator is not None and \
+                     decorator.startswith('@doctest')) or self.is_doctest
+        is_suppress = decorator=='@suppress' or self.is_suppress
+        is_okexcept = decorator=='@okexcept' or self.is_okexcept
+        is_okwarning = decorator=='@okwarning' or self.is_okwarning
+        is_savefig = decorator is not None and \
+                     decorator.startswith('@savefig')
+
+        input_lines = input.split('\n')
+        if len(input_lines) > 1:
+            if input_lines[-1] != "":
+                input_lines.append('') # make sure there's a blank line
+                                       # so splitter buffer gets reset
+
+        continuation = '   %s:'%''.join(['.']*(len(str(lineno))+2))
+
+        if is_savefig:
+            image_file, image_directive = self.process_image(decorator)
+
+        ret = []
+        is_semicolon = False
+
+        # Hold the execution count, if requested to do so.
+        if is_suppress and self.hold_count:
+            store_history = False
+        else:
+            store_history = True
+
+        # Note: catch_warnings is not thread safe
+        with warnings.catch_warnings(record=True) as ws:
+            for i, line in enumerate(input_lines):
+                if line.endswith(';'):
+                    is_semicolon = True
+
+                if i == 0:
+                    # process the first input line
+                    if is_verbatim:
+                        self.process_input_line('')
+                        self.IP.execution_count += 1 # increment it anyway
+                    else:
+                        # only submit the line in non-verbatim mode
+                        self.process_input_line(line, store_history=store_history)
+                    formatted_line = '%s %s'%(input_prompt, line)
+                else:
+                    # process a continuation line
+                    if not is_verbatim:
+                        self.process_input_line(line, store_history=store_history)
+
+                    formatted_line = '%s %s'%(continuation, line)
+
+                if not is_suppress:
+                    ret.append(formatted_line)
+
+        if not is_suppress and len(rest.strip()) and is_verbatim:
+            # The "rest" is the standard output of the input. This needs to be
+            # added when in verbatim mode. If there is no "rest", then we don't
+            # add it, as the new line will be added by the processed output.
+            ret.append(rest)
+
+        # Fetch the processed output. (This is not the submitted output.)
+        self.cout.seek(0)
+        processed_output = self.cout.read()
+        if not is_suppress and not is_semicolon:
+            #
+            # In IPythonDirective.run, the elements of `ret` are eventually
+            # combined such that '' entries correspond to newlines. So if
+            # `processed_output` is equal to '', then the adding it to `ret`
+            # ensures that there is a blank line between consecutive inputs
+            # that have no outputs, as in:
+            #
+            #    In [1]: x = 4
+            #
+            #    In [2]: x = 5
+            #
+            # When there is processed output, it has a '\n' at the tail end. So
+            # adding the output to `ret` will provide the necessary spacing
+            # between consecutive input/output blocks, as in:
+            #
+            #   In [1]: x
+            #   Out[1]: 5
+            #
+            #   In [2]: x
+            #   Out[2]: 5
+            #
+            # When there is stdout from the input, it also has a '\n' at the
+            # tail end, and so this ensures proper spacing as well. E.g.:
+            #
+            #   In [1]: print x
+            #   5
+            #
+            #   In [2]: x = 5
+            #
+            # When in verbatim mode, `processed_output` is empty (because
+            # nothing was passed to IP. Sometimes the submitted code block has
+            # an Out[] portion and sometimes it does not. When it does not, we
+            # need to ensure proper spacing, so we have to add '' to `ret`.
+            # However, if there is an Out[] in the submitted code, then we do
+            # not want to add a newline as `process_output` has stuff to add.
+            # The difficulty is that `process_input` doesn't know if
+            # `process_output` will be called---so it doesn't know if there is
+            # Out[] in the code block. The requires that we include a hack in
+            # `process_block`. See the comments there.
+            #
+            ret.append(processed_output)
+        elif is_semicolon:
+            # Make sure there is a newline after the semicolon.
+            ret.append('')
+
+        # context information
+        filename = "Unknown"
+        lineno = 0
+        if self.directive.state:
+            filename = self.directive.state.document.current_source
+            lineno = self.directive.state.document.current_line
+
+        # output any exceptions raised during execution to stdout
+        # unless :okexcept: has been specified.
+        if not is_okexcept and "Traceback" in processed_output:
+            s =  "\nException in %s at block ending on line %s\n" % (filename, lineno)
+            s += "Specify :okexcept: as an option in the ipython:: block to suppress this message\n"
+            sys.stdout.write('\n\n>>>' + ('-' * 73))
+            sys.stdout.write(s)
+            sys.stdout.write(processed_output)
+            sys.stdout.write('<<<' + ('-' * 73) + '\n\n')
+
+        # output any warning raised during execution to stdout
+        # unless :okwarning: has been specified.
+        if not is_okwarning:
+            for w in ws:
+                s =  "\nWarning in %s at block ending on line %s\n" % (filename, lineno)
+                s += "Specify :okwarning: as an option in the ipython:: block to suppress this message\n"
+                sys.stdout.write('\n\n>>>' + ('-' * 73))
+                sys.stdout.write(s)
+                sys.stdout.write(('-' * 76) + '\n')
+                s=warnings.formatwarning(w.message, w.category,
+                                         w.filename, w.lineno, w.line)
+                sys.stdout.write(s)
+                sys.stdout.write('<<<' + ('-' * 73) + '\n')
+
+        self.cout.truncate(0)
+
+        return (ret, input_lines, processed_output,
+                is_doctest, decorator, image_file, image_directive)
+
+
+    def process_output(self, data, output_prompt, input_lines, output,
+                       is_doctest, decorator, image_file):
+        """
+        Process data block for OUTPUT token.
+
+        """
+        # Recall: `data` is the submitted output, and `output` is the processed
+        # output from `input_lines`.
+
+        TAB = ' ' * 4
+
+        if is_doctest and output is not None:
+
+            found = output # This is the processed output
+            found = found.strip()
+            submitted = data.strip()
+
+            if self.directive is None:
+                source = 'Unavailable'
+                content = 'Unavailable'
+            else:
+                source = self.directive.state.document.current_source
+                content = self.directive.content
+                # Add tabs and join into a single string.
+                content = '\n'.join([TAB + line for line in content])
+
+            # Make sure the output contains the output prompt.
+            ind = found.find(output_prompt)
+            if ind < 0:
+                e = ('output does not contain output prompt\n\n'
+                     'Document source: {0}\n\n'
+                     'Raw content: \n{1}\n\n'
+                     'Input line(s):\n{TAB}{2}\n\n'
+                     'Output line(s):\n{TAB}{3}\n\n')
+                e = e.format(source, content, '\n'.join(input_lines),
+                             repr(found), TAB=TAB)
+                raise RuntimeError(e)
+            found = found[len(output_prompt):].strip()
+
+            # Handle the actual doctest comparison.
+            if decorator.strip() == '@doctest':
+                # Standard doctest
+                if found != submitted:
+                    e = ('doctest failure\n\n'
+                         'Document source: {0}\n\n'
+                         'Raw content: \n{1}\n\n'
+                         'On input line(s):\n{TAB}{2}\n\n'
+                         'we found output:\n{TAB}{3}\n\n'
+                         'instead of the expected:\n{TAB}{4}\n\n')
+                    e = e.format(source, content, '\n'.join(input_lines),
+                                 repr(found), repr(submitted), TAB=TAB)
+                    raise RuntimeError(e)
+            else:
+                self.custom_doctest(decorator, input_lines, found, submitted)
+
+        # When in verbatim mode, this holds additional submitted output
+        # to be written in the final Sphinx output.
+        # https://github.com/ipython/ipython/issues/5776
+        out_data = []
+
+        is_verbatim = decorator=='@verbatim' or self.is_verbatim
+        if is_verbatim and data.strip():
+            # Note that `ret` in `process_block` has '' as its last element if
+            # the code block was in verbatim mode. So if there is no submitted
+            # output, then we will have proper spacing only if we do not add
+            # an additional '' to `out_data`. This is why we condition on
+            # `and data.strip()`.
+
+            # The submitted output has no output prompt. If we want the
+            # prompt and the code to appear, we need to join them now
+            # instead of adding them separately---as this would create an
+            # undesired newline. How we do this ultimately depends on the
+            # format of the output regex. I'll do what works for the default
+            # prompt for now, and we might have to adjust if it doesn't work
+            # in other cases. Finally, the submitted output does not have
+            # a trailing newline, so we must add it manually.
+            out_data.append("{0} {1}\n".format(output_prompt, data))
+
+        return out_data
+
+    def process_comment(self, data):
+        """Process data fPblock for COMMENT token."""
+        if not self.is_suppress:
+            return [data]
+
+    def save_image(self, image_file):
+        """
+        Saves the image file to disk.
+        """
+        self.ensure_pyplot()
+        command = 'plt.gcf().savefig("%s")'%image_file
+        #print 'SAVEFIG', command  # dbg
+        self.process_input_line('bookmark ipy_thisdir', store_history=False)
+        self.process_input_line('cd -b ipy_savedir', store_history=False)
+        self.process_input_line(command, store_history=False)
+        self.process_input_line('cd -b ipy_thisdir', store_history=False)
+        self.process_input_line('bookmark -d ipy_thisdir', store_history=False)
+        self.clear_cout()
+
+    def process_block(self, block):
+        """
+        process block from the block_parser and return a list of processed lines
+        """
+        ret = []
+        output = None
+        input_lines = None
+        lineno = self.IP.execution_count
+
+        input_prompt = self.promptin % lineno
+        output_prompt = self.promptout % lineno
+        image_file = None
+        image_directive = None
+
+        found_input = False
+        for token, data in block:
+            if token == COMMENT:
+                out_data = self.process_comment(data)
+            elif token == INPUT:
+                found_input = True
+                (out_data, input_lines, output, is_doctest,
+                 decorator, image_file, image_directive) = \
+                          self.process_input(data, input_prompt, lineno)
+            elif token == OUTPUT:
+                if not found_input:
+
+                    TAB = ' ' * 4
+                    linenumber = 0
+                    source = 'Unavailable'
+                    content = 'Unavailable'
+                    if self.directive:
+                        linenumber = self.directive.state.document.current_line
+                        source = self.directive.state.document.current_source
+                        content = self.directive.content
+                        # Add tabs and join into a single string.
+                        content = '\n'.join([TAB + line for line in content])
+
+                    e = ('\n\nInvalid block: Block contains an output prompt '
+                         'without an input prompt.\n\n'
+                         'Document source: {0}\n\n'
+                         'Content begins at line {1}: \n\n{2}\n\n'
+                         'Problematic block within content: \n\n{TAB}{3}\n\n')
+                    e = e.format(source, linenumber, content, block, TAB=TAB)
+
+                    # Write, rather than include in exception, since Sphinx
+                    # will truncate tracebacks.
+                    sys.stdout.write(e)
+                    raise RuntimeError('An invalid block was detected.')
+
+                out_data = \
+                    self.process_output(data, output_prompt, input_lines,
+                                        output, is_doctest, decorator,
+                                        image_file)
+                if out_data:
+                    # Then there was user submitted output in verbatim mode.
+                    # We need to remove the last element of `ret` that was
+                    # added in `process_input`, as it is '' and would introduce
+                    # an undesirable newline.
+                    assert(ret[-1] == '')
+                    del ret[-1]
+
+            if out_data:
+                ret.extend(out_data)
+
+        # save the image files
+        if image_file is not None:
+            self.save_image(image_file)
+
+        return ret, image_directive
+
+    def ensure_pyplot(self):
+        """
+        Ensures that pyplot has been imported into the embedded IPython shell.
+
+        Also, makes sure to set the backend appropriately if not set already.
+
+        """
+        # We are here if the @figure pseudo decorator was used. Thus, it's
+        # possible that we could be here even if python_mplbackend were set to
+        # `None`. That's also strange and perhaps worthy of raising an
+        # exception, but for now, we just set the backend to 'agg'.
+
+        if not self._pyplot_imported:
+            if 'matplotlib.backends' not in sys.modules:
+                # Then ipython_matplotlib was set to None but there was a
+                # call to the @figure decorator (and ipython_execlines did
+                # not set a backend).
+                #raise Exception("No backend was set, but @figure was used!")
+                import matplotlib
+                matplotlib.use('agg')
+
+            # Always import pyplot into embedded shell.
+            self.process_input_line('import matplotlib.pyplot as plt',
+                                    store_history=False)
+            self._pyplot_imported = True
+
+    def process_pure_python(self, content):
+        """
+        content is a list of strings. it is unedited directive content
+
+        This runs it line by line in the InteractiveShell, prepends
+        prompts as needed capturing stderr and stdout, then returns
+        the content as a list as if it were ipython code
+        """
+        output = []
+        savefig = False # keep up with this to clear figure
+        multiline = False # to handle line continuation
+        multiline_start = None
+        fmtin = self.promptin
+
+        ct = 0
+
+        for lineno, line in enumerate(content):
+
+            line_stripped = line.strip()
+            if not len(line):
+                output.append(line)
+                continue
+
+            # handle decorators
+            if line_stripped.startswith('@'):
+                output.extend([line])
+                if 'savefig' in line:
+                    savefig = True # and need to clear figure
+                continue
+
+            # handle comments
+            if line_stripped.startswith('#'):
+                output.extend([line])
+                continue
+
+            # deal with lines checking for multiline
+            continuation  = u'   %s:'% ''.join(['.']*(len(str(ct))+2))
+            if not multiline:
+                modified = u"%s %s" % (fmtin % ct, line_stripped)
+                output.append(modified)
+                ct += 1
+                try:
+                    ast.parse(line_stripped)
+                    output.append(u'')
+                except Exception: # on a multiline
+                    multiline = True
+                    multiline_start = lineno
+            else: # still on a multiline
+                modified = u'%s %s' % (continuation, line)
+                output.append(modified)
+
+                # if the next line is indented, it should be part of multiline
+                if len(content) > lineno + 1:
+                    nextline = content[lineno + 1]
+                    if len(nextline) - len(nextline.lstrip()) > 3:
+                        continue
+                try:
+                    mod = ast.parse(
+                            '\n'.join(content[multiline_start:lineno+1]))
+                    if isinstance(mod.body[0], ast.FunctionDef):
+                        # check to see if we have the whole function
+                        for element in mod.body[0].body:
+                            if isinstance(element, ast.Return):
+                                multiline = False
+                    else:
+                        output.append(u'')
+                        multiline = False
+                except Exception:
+                    pass
+
+            if savefig: # clear figure if plotted
+                self.ensure_pyplot()
+                self.process_input_line('plt.clf()', store_history=False)
+                self.clear_cout()
+                savefig = False
+
+        return output
+
+    def custom_doctest(self, decorator, input_lines, found, submitted):
+        """
+        Perform a specialized doctest.
+
+        """
+        from .custom_doctests import doctests
+
+        args = decorator.split()
+        doctest_type = args[1]
+        if doctest_type in doctests:
+            doctests[doctest_type](self, args, input_lines, found, submitted)
+        else:
+            e = "Invalid option to @doctest: {0}".format(doctest_type)
+            raise Exception(e)
+
+
+class IPythonDirective(Directive):
+
+    has_content = True
+    required_arguments = 0
+    optional_arguments = 4 # python, suppress, verbatim, doctest
+    final_argumuent_whitespace = True
+    option_spec = { 'python': directives.unchanged,
+                    'suppress' : directives.flag,
+                    'verbatim' : directives.flag,
+                    'doctest' : directives.flag,
+                    'okexcept': directives.flag,
+                    'okwarning': directives.flag
+                  }
+
+    shell = None
+
+    seen_docs = set()
+
+    def get_config_options(self):
+        # contains sphinx configuration variables
+        config = self.state.document.settings.env.config
+
+        # get config variables to set figure output directory
+        savefig_dir = config.ipython_savefig_dir
+        source_dir = self.state.document.settings.env.srcdir
+        savefig_dir = os.path.join(source_dir, savefig_dir)
+
+        # get regex and prompt stuff
+        rgxin      = config.ipython_rgxin
+        rgxout     = config.ipython_rgxout
+        promptin   = config.ipython_promptin
+        promptout  = config.ipython_promptout
+        mplbackend = config.ipython_mplbackend
+        exec_lines = config.ipython_execlines
+        hold_count = config.ipython_holdcount
+
+        return (savefig_dir, source_dir, rgxin, rgxout,
+                promptin, promptout, mplbackend, exec_lines, hold_count)
+
+    def setup(self):
+        # Get configuration values.
+        (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout,
+         mplbackend, exec_lines, hold_count) = self.get_config_options()
+
+        try:
+            os.makedirs(savefig_dir)
+        except OSError as e:
+            if e.errno != errno.EEXIST:
+                raise
+
+        if self.shell is None:
+            # We will be here many times.  However, when the
+            # EmbeddedSphinxShell is created, its interactive shell member
+            # is the same for each instance.
+
+            if mplbackend and 'matplotlib.backends' not in sys.modules:
+                import matplotlib
+                matplotlib.use(mplbackend)
+
+            # Must be called after (potentially) importing matplotlib and
+            # setting its backend since exec_lines might import pylab.
+            self.shell = EmbeddedSphinxShell(exec_lines)
+
+            # Store IPython directive to enable better error messages
+            self.shell.directive = self
+
+        # reset the execution count if we haven't processed this doc
+        #NOTE: this may be borked if there are multiple seen_doc tmp files
+        #check time stamp?
+        if not self.state.document.current_source in self.seen_docs:
+            self.shell.IP.history_manager.reset()
+            self.shell.IP.execution_count = 1
+            self.seen_docs.add(self.state.document.current_source)
+
+        # and attach to shell so we don't have to pass them around
+        self.shell.rgxin = rgxin
+        self.shell.rgxout = rgxout
+        self.shell.promptin = promptin
+        self.shell.promptout = promptout
+        self.shell.savefig_dir = savefig_dir
+        self.shell.source_dir = source_dir
+        self.shell.hold_count = hold_count
+
+        # setup bookmark for saving figures directory
+        self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir,
+                                      store_history=False)
+        self.shell.clear_cout()
+
+        return rgxin, rgxout, promptin, promptout
+
+    def teardown(self):
+        # delete last bookmark
+        self.shell.process_input_line('bookmark -d ipy_savedir',
+                                      store_history=False)
+        self.shell.clear_cout()
+
+    def run(self):
+        debug = False
+
+        #TODO, any reason block_parser can't be a method of embeddable shell
+        # then we wouldn't have to carry these around
+        rgxin, rgxout, promptin, promptout = self.setup()
+
+        options = self.options
+        self.shell.is_suppress = 'suppress' in options
+        self.shell.is_doctest = 'doctest' in options
+        self.shell.is_verbatim = 'verbatim' in options
+        self.shell.is_okexcept = 'okexcept' in options
+        self.shell.is_okwarning = 'okwarning' in options
+
+        # handle pure python code
+        if 'python' in self.arguments:
+            content = self.content
+            self.content = self.shell.process_pure_python(content)
+
+        # parts consists of all text within the ipython-block.
+        # Each part is an input/output block.
+        parts = '\n'.join(self.content).split('\n\n')
+
+        lines = ['.. code-block:: ipython', '']
+        figures = []
+
+        for part in parts:
+            block = block_parser(part, rgxin, rgxout, promptin, promptout)
+            if len(block):
+                rows, figure = self.shell.process_block(block)
+                for row in rows:
+                    lines.extend(['   {0}'.format(line)
+                                  for line in row.split('\n')])
+
+                if figure is not None:
+                    figures.append(figure)
+
+        for figure in figures:
+            lines.append('')
+            lines.extend(figure.split('\n'))
+            lines.append('')
+
+        if len(lines) > 2:
+            if debug:
+                print('\n'.join(lines))
+            else:
+                # This has to do with input, not output. But if we comment
+                # these lines out, then no IPython code will appear in the
+                # final output.
+                self.state_machine.insert_input(
+                    lines, self.state_machine.input_lines.source(0))
+
+        # cleanup
+        self.teardown()
+
+        return []
+
+# Enable as a proper Sphinx directive
+def setup(app):
+    setup.app = app
+
+    app.add_directive('ipython', IPythonDirective)
+    app.add_config_value('ipython_savefig_dir', 'savefig', 'env')
+    app.add_config_value('ipython_rgxin',
+                         re.compile('In \[(\d+)\]:\s?(.*)\s*'), 'env')
+    app.add_config_value('ipython_rgxout',
+                         re.compile('Out\[(\d+)\]:\s?(.*)\s*'), 'env')
+    app.add_config_value('ipython_promptin', 'In [%d]:', 'env')
+    app.add_config_value('ipython_promptout', 'Out[%d]:', 'env')
+
+    # We could just let matplotlib pick whatever is specified as the default
+    # backend in the matplotlibrc file, but this would cause issues if the
+    # backend didn't work in headless environments. For this reason, 'agg'
+    # is a good default backend choice.
+    app.add_config_value('ipython_mplbackend', 'agg', 'env')
+
+    # If the user sets this config value to `None`, then EmbeddedSphinxShell's
+    # __init__ method will treat it as [].
+    execlines = ['import numpy as np', 'import matplotlib.pyplot as plt']
+    app.add_config_value('ipython_execlines', execlines, 'env')
+
+    app.add_config_value('ipython_holdcount', True, 'env')
+
+    metadata = {'parallel_read_safe': True, 'parallel_write_safe': True}
+    return metadata
+
+# Simple smoke test, needs to be converted to a proper automatic test.
+def test():
+
+    examples = [
+        r"""
+In [9]: pwd
+Out[9]: '/home/jdhunter/py4science/book'
+
+In [10]: cd bookdata/
+/home/jdhunter/py4science/book/bookdata
+
+In [2]: from pylab import *
+
+In [2]: ion()
+
+In [3]: im = imread('stinkbug.png')
+
+@savefig mystinkbug.png width=4in
+In [4]: imshow(im)
+Out[4]: <matplotlib.image.AxesImage object at 0x39ea850>
+
+""",
+        r"""
+
+In [1]: x = 'hello world'
+
+# string methods can be
+# used to alter the string
+@doctest
+In [2]: x.upper()
+Out[2]: 'HELLO WORLD'
+
+@verbatim
+In [3]: x.st<TAB>
+x.startswith  x.strip
+""",
+    r"""
+
+In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\
+   .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv'
+
+In [131]: print url.split('&')
+['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv']
+
+In [60]: import urllib
+
+""",
+    r"""\
+
+In [133]: import numpy.random
+
+@suppress
+In [134]: numpy.random.seed(2358)
+
+@doctest
+In [135]: numpy.random.rand(10,2)
+Out[135]:
+array([[ 0.64524308,  0.59943846],
+       [ 0.47102322,  0.8715456 ],
+       [ 0.29370834,  0.74776844],
+       [ 0.99539577,  0.1313423 ],
+       [ 0.16250302,  0.21103583],
+       [ 0.81626524,  0.1312433 ],
+       [ 0.67338089,  0.72302393],
+       [ 0.7566368 ,  0.07033696],
+       [ 0.22591016,  0.77731835],
+       [ 0.0072729 ,  0.34273127]])
+
+""",
+
+    r"""
+In [106]: print x
+jdh
+
+In [109]: for i in range(10):
+   .....:     print i
+   .....:
+   .....:
+0
+1
+2
+3
+4
+5
+6
+7
+8
+9
+""",
+
+        r"""
+
+In [144]: from pylab import *
+
+In [145]: ion()
+
+# use a semicolon to suppress the output
+@savefig test_hist.png width=4in
+In [151]: hist(np.random.randn(10000), 100);
+
+
+@savefig test_plot.png width=4in
+In [151]: plot(np.random.randn(10000), 'o');
+   """,
+
+        r"""
+# use a semicolon to suppress the output
+In [151]: plt.clf()
+
+@savefig plot_simple.png width=4in
+In [151]: plot([1,2,3])
+
+@savefig hist_simple.png width=4in
+In [151]: hist(np.random.randn(10000), 100);
+
+""",
+     r"""
+# update the current fig
+In [151]: ylabel('number')
+
+In [152]: title('normal distribution')
+
+
+@savefig hist_with_text.png
+In [153]: grid(True)
+
+@doctest float
+In [154]: 0.1 + 0.2
+Out[154]: 0.3
+
+@doctest float
+In [155]: np.arange(16).reshape(4,4)
+Out[155]:
+array([[ 0,  1,  2,  3],
+       [ 4,  5,  6,  7],
+       [ 8,  9, 10, 11],
+       [12, 13, 14, 15]])
+
+In [1]: x = np.arange(16, dtype=float).reshape(4,4)
+
+In [2]: x[0,0] = np.inf
+
+In [3]: x[0,1] = np.nan
+
+@doctest float
+In [4]: x
+Out[4]:
+array([[ inf,  nan,   2.,   3.],
+       [  4.,   5.,   6.,   7.],
+       [  8.,   9.,  10.,  11.],
+       [ 12.,  13.,  14.,  15.]])
+
+
+        """,
+        ]
+    # skip local-file depending first example:
+    examples = examples[1:]
+
+    #ipython_directive.DEBUG = True  # dbg
+    #options = dict(suppress=True)  # dbg
+    options = dict()
+    for example in examples:
+        content = example.split('\n')
+        IPythonDirective('debug', arguments=None, options=options,
+                          content=content, lineno=0,
+                          content_offset=None, block_text=None,
+                          state=None, state_machine=None,
+                          )
+
+# Run test suite as a script
+if __name__=='__main__':
+    if not os.path.isdir('_static'):
+        os.mkdir('_static')
+    test()
+    print('All OK? Check figures in _static/')