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Message #12915
[Branch ~yade-pkg/yade/git-trunk] Rev 3964: Provide a proper functioning with IPython5.
------------------------------------------------------------
revno: 3964
author: Anton Gladky <gladk@xxxxxxxxxxx>
committer: Anton Gladky <gladk@xxxxxxxxxx>
timestamp: Wed 2016-11-02 23:08:33 +0100
message:
Provide a proper functioning with IPython5.
added:
doc/sphinx/ipython_directive500.py
modified:
doc/sphinx/book/confBook.py
doc/sphinx/book/confManual.py
doc/sphinx/book/confReference.py
doc/sphinx/book/confTheory.py
doc/sphinx/conf.py
--
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=== modified file 'doc/sphinx/book/confBook.py'
--- doc/sphinx/book/confBook.py 2016-02-10 17:07:12 +0000
+++ doc/sphinx/book/confBook.py 2016-11-02 22:08:33 +0000
@@ -364,10 +364,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
import ipython_directive012 as id
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
import ipython_directive013 as id
- else:
+ elif 200<=yade.runtime.ipython_version<500:
import ipython_directive200 as id
+ else:
+ import ipython_directive500 as id
#The next four lines are for compatibility with IPython 0.13.1
ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
@@ -414,10 +416,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
extensions.append('ipython_directive012')
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
extensions.append('ipython_directive013')
- else:
+ elif 200<=yade.runtime.ipython_version<500:
extensions.append('ipython_directive200')
+ else:
+ extensions.append('ipython_directive500')
# the sidebar extension
if False:
=== modified file 'doc/sphinx/book/confManual.py'
--- doc/sphinx/book/confManual.py 2015-12-04 06:19:11 +0000
+++ doc/sphinx/book/confManual.py 2016-11-02 22:08:33 +0000
@@ -357,10 +357,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
import ipython_directive012 as id
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
import ipython_directive013 as id
- else:
+ elif 200<=yade.runtime.ipython_version<500:
import ipython_directive200 as id
+ else:
+ import ipython_directive500 as id
#The next four lines are for compatibility with IPython 0.13.1
ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
@@ -407,10 +409,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
extensions.append('ipython_directive012')
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
extensions.append('ipython_directive013')
- else:
+ elif 200<=yade.runtime.ipython_version<500:
extensions.append('ipython_directive200')
+ else:
+ extensions.append('ipython_directive500')
# the sidebar extension
if False:
=== modified file 'doc/sphinx/book/confReference.py'
--- doc/sphinx/book/confReference.py 2015-12-04 06:19:11 +0000
+++ doc/sphinx/book/confReference.py 2016-11-02 22:08:33 +0000
@@ -357,10 +357,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
import ipython_directive012 as id
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
import ipython_directive013 as id
- else:
+ elif 200<=yade.runtime.ipython_version<500:
import ipython_directive200 as id
+ else:
+ import ipython_directive500 as id
#The next four lines are for compatibility with IPython 0.13.1
ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
@@ -407,10 +409,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
extensions.append('ipython_directive012')
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
extensions.append('ipython_directive013')
- else:
+ elif 200<=yade.runtime.ipython_version<500:
extensions.append('ipython_directive200')
+ else:
+ extensions.append('ipython_directive500')
# the sidebar extension
if False:
=== modified file 'doc/sphinx/book/confTheory.py'
--- doc/sphinx/book/confTheory.py 2015-12-04 06:19:11 +0000
+++ doc/sphinx/book/confTheory.py 2016-11-02 22:08:33 +0000
@@ -357,10 +357,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
import ipython_directive012 as id
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
import ipython_directive013 as id
- else:
+ elif 200<=yade.runtime.ipython_version<500:
import ipython_directive200 as id
+ else:
+ import ipython_directive500 as id
#The next four lines are for compatibility with IPython 0.13.1
ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
@@ -407,10 +409,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
extensions.append('ipython_directive012')
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
extensions.append('ipython_directive013')
- else:
+ elif 200<=yade.runtime.ipython_version<500:
extensions.append('ipython_directive200')
+ else:
+ extensions.append('ipython_directive500')
# the sidebar extension
if False:
=== modified file 'doc/sphinx/conf.py'
--- doc/sphinx/conf.py 2016-10-14 08:51:21 +0000
+++ doc/sphinx/conf.py 2016-11-02 22:08:33 +0000
@@ -357,10 +357,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
import ipython_directive012 as id
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
import ipython_directive013 as id
- else:
+ elif 200<=yade.runtime.ipython_version<500:
import ipython_directive200 as id
+ else:
+ import ipython_directive500 as id
#The next four lines are for compatibility with IPython 0.13.1
ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
@@ -407,10 +409,12 @@
else:
if 12<=yade.runtime.ipython_version<13:
extensions.append('ipython_directive012')
- elif 13<=yade.runtime.ipython_version<200:
+ elif 13<=yade.runtime.ipython_version<200:
extensions.append('ipython_directive013')
- else:
+ elif 200<=yade.runtime.ipython_version<500:
extensions.append('ipython_directive200')
+ else:
+ extensions.append('ipython_directive500')
# the sidebar extension
if False:
=== added file 'doc/sphinx/ipython_directive500.py'
--- doc/sphinx/ipython_directive500.py 1970-01-01 00:00:00 +0000
+++ doc/sphinx/ipython_directive500.py 2016-11-02 22:08:33 +0000
@@ -0,0 +1,1184 @@
+# -*- 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.
+
+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 atexit
+import os
+import re
+import sys
+import tempfile
+import ast
+import warnings
+import shutil
+
+
+# Third-party
+from docutils.parsers.rst import directives
+from sphinx.util.compat 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)
+
+ sys.stdout = self.cout
+ sys.stderr = self.cout
+
+ # For debugging, so we can see normal output, use this:
+ #from IPython.utils.io import Tee
+ #sys.stdout = Tee(self.cout, channel='stdout') # dbg
+ #sys.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.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
+ 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
+ outdir = self.state.document.settings.env.app.outdir
+ 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 or '_static'
+ if isinstance(savefig_dir, list):
+ savefig_dir = os.path.join(*savefig_dir)
+ savefig_dir = os.path.join(outdir, 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()
+
+ 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', 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')
+
+ # 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/')
