Provide helpful error messages on doctest failures.

IPython/sphinxext/custom_doctests.py

@@ -1,92 +1,108 b''
 """
 Module containing custom doctests.
 
 """
 
 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 for input_lines={0} with '
-             'found_output={1} and submitted '
-             'output="{2}"'.format(input_lines, repr(found), repr(submitted)) )
+
+        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)
 
 doctests = {
     'float': float_doctest,
 }

IPython/sphinxext/ipython_directive.py

@@ -1,925 +1,958 b''
 # -*- 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 specified in conf.py as `None` or not specified in conf.py at
     all, then no call to `matplotlib.use()` is made. Then, matplotlib is loaded
     only if specified in `ipython_execlines` or if the @savefig pseudo
     decorator is used. In the latter case, matplotlib is imported and its
     default backend is used.
 ipython_execlines:
     A list of strings to be exec'd for 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` or not specified in conf.py at all, then the default
     value of ['import numpy as np', 'from pylab import *'] is used.
 
 As an example, to use the IPython directive when `matplotlib` is not available,
 one sets the backend to `None`::
 
     ipython_mplbacked = 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 more additional
 documentation.
 
 ToDo
 ----
 
 - 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 os
 import re
 import sys
 import tempfile
 import ast
 
 # To keep compatibility with various python versions
 try:
     from hashlib import md5
 except ImportError:
     from md5 import md5
 
 # Third-party
 import sphinx
 from docutils.parsers.rst import directives
 from docutils import nodes
 from sphinx.util.compat import Directive
 
 # Our own
 from IPython import Config, 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 ouput, 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('@'):
             # we're assuming at most one decorator -- may need to
             # rethink
             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):
                     inputline += '\n' + nextline[Nc:]
                 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.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)
 
         # io.stdout redirect must be done *after* instantiating InteractiveShell
         io.stdout = self.cout
         io.stderr = self.cout
 
         # For debugging, so we can see normal output, use this:
         #from IPython.utils.io import Tee
         #io.stdout = Tee(self.cout, channel='stdout') # dbg
         #io.stderr = Tee(self.cout, channel='stderr') # dbg
 
         # 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.is_verbatim = False
         self.is_doctest = False
         self.is_suppress = False
 
+        # Optionally, provide more detailed information to shell.
+        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 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"""
-        #print "input='%s'"%self.input
+
         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.source_raw_reset()[1]
                 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
         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."""
+        """
+        Process data block for INPUT token.
+
+        """
         decorator, input, rest = data
         image_file = None
         image_directive = None
-        #print 'INPUT:', data  # dbg
+
         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_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))
         Nc = len(continuation)
 
         if is_savefig:
             image_file, image_directive = self.process_image(decorator)
 
         ret = []
         is_semicolon = False
 
         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=True)
                 formatted_line = '%s %s'%(input_prompt, line)
             else:
                 # process a continuation line
                 if not is_verbatim:
                     self.process_input_line(line, store_history=True)
 
                 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, which needs to be added in
             # verbatim mode
             ret.append(rest)
 
         self.cout.seek(0)
         output = self.cout.read()
         if not is_suppress and not is_semicolon:
             ret.append(output)
         elif is_semicolon: # get spacing right
             ret.append('')
 
         self.cout.truncate(0)
         return (ret, input_lines, output, is_doctest, decorator, image_file,
                     image_directive)
-        #print 'OUTPUT', output  # dbg
+
 
     def process_output(self, data, output_prompt,
                        input_lines, output, is_doctest, decorator, image_file):
-        """Process data block for OUTPUT token."""
+        """
+        Process data block for OUTPUT token.
+
+        """
+        TAB = ' ' * 4
+
         if is_doctest and output is not None:
 
             found = 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 prompt="{0}" does '
-                     'not match out line={1}'.format(output_prompt, found))
+                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 for input_lines="{0}" with '
-                         'found_output="{1}" and submitted '
-                         'output="{2}"'.format(input_lines, 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)
 
     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
 
         for token, data in block:
             if token==COMMENT:
                 out_data = self.process_comment(data)
             elif token==INPUT:
                 (out_data, input_lines, output, is_doctest, decorator,
                     image_file, image_directive) = \
                           self.process_input(data, input_prompt, lineno)
             elif token==OUTPUT:
                 out_data = \
                     self.process_output(data, output_prompt,
                                         input_lines, output, is_doctest,
                                         decorator, image_file)
             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):
         if self._pyplot_imported:
             return
         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,
                   }
 
     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
         confdir = self.state.document.settings.env.app.confdir
         savefig_dir = config.ipython_savefig_dir
         source_dir = os.path.dirname(self.state.document.current_source)
         if savefig_dir is None:
             savefig_dir = config.html_static_path
         if isinstance(savefig_dir, list):
             savefig_dir = savefig_dir[0] # safe to assume only one path?
         savefig_dir = os.path.join(confdir, 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
 
         # Handle None uniformly, whether specified in conf.py as `None` or
         # omitted entirely from conf.py.
 
         if mplbackend is None:
             mplbackend = 'agg'
         if exec_lines is None:
             exec_lines = ['import numpy as np', 'from pylab import *']
 
         return (savefig_dir, source_dir, rgxin, rgxout,
                 promptin, promptout, mplbackend, exec_lines)
 
     def setup(self):
         # Get configuration values.
         (savefig_dir, source_dir, rgxin, rgxout, promptin,
          promptout, mplbackend, exec_lines) = self.get_config_options()
 
         if self.shell is None:
             if mplbackend:
                 import matplotlib
                 # Repeated calls to use() will not hurt us since `mplbackend`
                 # is the same each time.
                 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
 
         # 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
 
         # handle pure python code
         if 'python' in self.arguments:
             content = self.content
             self.content = self.shell.process_pure_python(content)
 
         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(['   %s'%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 is what makes the lines appear in the final output.
+                # 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 []#, imgnode]
 
 # Enable as a proper Sphinx directive
 def setup(app):
     setup.app = app
 
     app.add_directive('ipython', IPythonDirective)
     app.add_config_value('ipython_savefig_dir', None, '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')
     app.add_config_value('ipython_mplbackend', None, 'env')
     app.add_config_value('ipython_execlines', None, 'env')
 
 # 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/')