Merge pull request #13030 from rhshadrach/ipython_warning

Use Sphinx logging in IPython directive

docs/source/whatsnew/pr/ipython_directive_warnings.rst

@@ -0,0 +1,4 b''
+IPython directive warnings
+--------------------------
+
+The IPython directive now uses Sphinx logging for warnings.

IPython/sphinxext/ipython_directive.py

@@ -1,1251 +1,1260 b''
 # -*- coding: utf-8 -*-
 """
 Sphinx directive to support embedded IPython code.
 
 IPython provides an extension for `Sphinx <http://www.sphinx-doc.org/>`_ to
 highlight and run 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.
 
 Here is an example of how the IPython directive can
 **run** python code, at build time.
 
 .. ipython::
 
    In [1]: 1+1
 
    In [1]: import datetime
       ...: datetime.datetime.now()
 
 It supports IPython construct that plain
 Python does not understand (like magics):
 
 .. ipython::
 
    In [0]: import time
 
    In [0]: %timeit time.sleep(0.05)
 
 This will also support top-level async when using IPython 7.0+
 
 .. ipython::
 
    In [2]: import asyncio
       ...: print('before')
       ...: await asyncio.sleep(1)
       ...: print('after')
 
 
 The namespace will persist across multiple code chucks, Let's define a variable:
 
 .. ipython::
 
    In [0]: who = "World"
 
 And now say hello:
 
 .. ipython::
 
    In [0]: print('Hello,', who)
 
 If the current section raises an exception, you can add the ``:okexcept:`` flag
 to the current block, otherwise the build will fail.
 
 .. ipython::
    :okexcept:
 
    In [1]: 1/0
 
 IPython Sphinx directive module
 ===============================
 
 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_warning_is_error: [default to True]
     Fail the build if something unexpected happen, for example if a block raise
     an exception but does not have the `:okexcept:` flag. The exact behavior of
     what is considered strict, may change between the sphinx directive version.
 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: original author.
 # - Fernando Perez: refactoring, documentation, cleanups, port to 0.11.
 # - VáclavŠmilauer <eudoxos-AT-arcig.cz>: Prompt generalizations.
 # - Skipper Seabold, refactoring, cleanups, pure python addition
 
 #-----------------------------------------------------------------------------
 # Imports
 #-----------------------------------------------------------------------------
 
 # Stdlib
 import atexit
 import errno
 import os
 import pathlib
 import re
 import sys
 import tempfile
 import ast
 import warnings
 import shutil
 from io import StringIO
 
 # Third-party
 from docutils.parsers.rst import directives
 from docutils.parsers.rst import Directive
+from sphinx.util import logging
 
 # Our own
 from traitlets.config import Config
 from IPython import InteractiveShell
 from IPython.core.profiledir import ProfileDir
 
 use_matplotlib = False
 try:
     import matplotlib
     use_matplotlib = True
 except Exception:
     pass
 
 #-----------------------------------------------------------------------------
 # 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 EmbeddedSphinxShell 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):
         return self.process_input_lines([line], store_history=store_history)
 
     def process_input_lines(self, lines, store_history=True):
         """process the input, capturing stdout"""
         stdout = sys.stdout
         source_raw = '\n'.join(lines)
         try:
             sys.stdout = self.cout
             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
         # sphinx expects a posix path, even on Windows
         path = pathlib.Path(savefig_dir, filename)
         outfile = '/' + path.relative_to(source_dir).as_posix()
 
         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:
             if input_lines[0].endswith(';'):
                 is_semicolon = True
             #for i, line in enumerate(input_lines):
 
             # process the first input line
             if is_verbatim:
                 self.process_input_lines([''])
                 self.IP.execution_count += 1 # increment it anyway
             else:
                 # only submit the line in non-verbatim mode
                 self.process_input_lines(input_lines, store_history=store_history)
 
         if not is_suppress:
             for i, line in enumerate(input_lines):
                 if i == 0:
                     formatted_line = '%s %s'%(input_prompt, line)
                 else:
                     formatted_line = '%s %s'%(continuation, line)
                 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
 
+        # Use sphinx logger for warnings
+        logger = logging.getLogger(__name__)
+
         # output any exceptions raised during execution to stdout
         # unless :okexcept: has been specified.
-        if not is_okexcept and (("Traceback" in processed_output) or ("SyntaxError" in processed_output)):
-            s =  "\nException in %s at block ending on line %s\n" % (filename, lineno)
+        if not is_okexcept and (
+            ("Traceback" in processed_output) or ("SyntaxError" in processed_output)
+        ):
+            s = "\n>>>" + ("-" * 73) + "\n"
+            s += "Exception 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')
+            s += processed_output + "\n"
+            s += "<<<" + ("-" * 73)
+            logger.warning(s)
             if self.warning_is_error:
                 raise RuntimeError('Non Expected exception in `{}` line {}'.format(filename, lineno))
 
         # 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 = "\n>>>" + ("-" * 73) + "\n"
+                s += "Warning 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')
+                s += ("-" * 76) + "\n"
+                s += warnings.formatwarning(
+                    w.message, w.category, w.filename, w.lineno, w.line
+                )
+                s += "<<<" + ("-" * 73)
+                logger.warning(s)
                 if self.warning_is_error:
                     raise RuntimeError('Non Expected warning in `{}` line {}'.format(filename, lineno))
 
         self.clear_cout()
         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
         warning_is_error= config.ipython_warning_is_error
         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, warning_is_error)
 
     def setup(self):
         # Get configuration values.
         (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout,
          mplbackend, exec_lines, hold_count, warning_is_error) = 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 and use_matplotlib:
                 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
         self.shell.warning_is_error = warning_is_error
 
         # 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 = []
 
+        # Use sphinx logger for warnings
+        logger = logging.getLogger(__name__)
+
         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)
             else:
                 message = 'Code input with no code at {}, line {}'\
                             .format(
                                 self.state.document.current_source,
                                 self.state.document.current_line)
                 if self.shell.warning_is_error:
                     raise RuntimeError(message)
                 else:
-                    warnings.warn(message)
+                    logger.warning(message)
 
         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_warning_is_error', True, 'env')
     app.add_config_value('ipython_rgxin',
                          re.compile(r'In \[(\d+)\]:\s?(.*)\s*'), 'env')
     app.add_config_value('ipython_rgxout',
                          re.compile(r'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']
     if use_matplotlib:
         execlines.append('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 = {}
     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/')