Merge pull request #6510 from Carreau/removecython

Remove cython extension and examples.

docs/source/whatsnew/pr/remove_cythonmagic.rst

@@ -0,0 +1,1 b''
+* The ``%cython`` magic, is now part of the Cython module. Use `%load_ext Cython` with a version of Cython >= 0.21 to have access to the magic now. 

IPython/extensions/cythonmagic.py

@@ -1,345 +1,43 b''
 # -*- coding: utf-8 -*-
 """
-=====================
-Cython related magics
-=====================
+The cython magic has been integrated into Cython itself, 
+which is now released in version 0.21.
 
-Magic command interface for interactive work with Cython
-
-.. note::
-
-  The ``Cython`` package needs to be installed separately. It
-  can be obtained using ``easy_install`` or ``pip``.
-
-Usage
-=====
-
-To enable the magics below, execute ``%load_ext cythonmagic``.
-
-``%%cython``
-
-{CYTHON_DOC}
-
-``%%cython_inline``
-
-{CYTHON_INLINE_DOC}
-
-``%%cython_pyximport``
-
-{CYTHON_PYXIMPORT_DOC}
-
-Author:
-* Brian Granger
-
-Parts of this code were taken from Cython.inline.
+cf github `Cython` organisation, `Cython` repo, under the 
+file `Cython/Build/IpythonMagic.py`
 """
 #-----------------------------------------------------------------------------
 # Copyright (C) 2010-2011, IPython Development Team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file COPYING.txt, distributed with this software.
 #-----------------------------------------------------------------------------
 
 from __future__ import print_function
 
-import imp
-import io
-import os
-import re
-import sys
-import time
+import IPython.utils.version as version
 
 try:
-    reload
-except NameError:   # Python 3
-    from imp import reload
-
-try:
-    import hashlib
-except ImportError:
-    import md5 as hashlib
-
-from distutils.core import Distribution, Extension
-from distutils.command.build_ext import build_ext
-
-from IPython.core import display
-from IPython.core import magic_arguments
-from IPython.core.magic import Magics, magics_class, cell_magic
-from IPython.utils import py3compat
-from IPython.utils.path import get_ipython_cache_dir
-from IPython.utils.text import dedent
-
 import Cython
-from Cython.Compiler.Errors import CompileError
-from Cython.Build.Dependencies import cythonize
-
-
-@magics_class
-class CythonMagics(Magics):
-
-    def __init__(self, shell):
-        super(CythonMagics,self).__init__(shell)
-        self._reloads = {}
-        self._code_cache = {}
-
-    def _import_all(self, module):
-        for k,v in module.__dict__.items():
-            if not k.startswith('__'):
-                self.shell.push({k:v})
-
-    @cell_magic
-    def cython_inline(self, line, cell):
-        """Compile and run a Cython code cell using Cython.inline.
-
-        This magic simply passes the body of the cell to Cython.inline
-        and returns the result. If the variables `a` and `b` are defined
-        in the user's namespace, here is a simple example that returns
-        their sum::
-
-            %%cython_inline
-            return a+b
-
-        For most purposes, we recommend the usage of the `%%cython` magic.
-        """
-        locs = self.shell.user_global_ns
-        globs = self.shell.user_ns
-        return Cython.inline(cell, locals=locs, globals=globs)
-
-    @cell_magic
-    def cython_pyximport(self, line, cell):
-        """Compile and import a Cython code cell using pyximport.
-
-        The contents of the cell are written to a `.pyx` file in the current
-        working directory, which is then imported using `pyximport`. This
-        magic requires a module name to be passed::
-
-            %%cython_pyximport modulename
-            def f(x):
-                return 2.0*x
-
-        The compiled module is then imported and all of its symbols are
-        injected into the user's namespace. For most purposes, we recommend
-        the usage of the `%%cython` magic.
-        """
-        module_name = line.strip()
-        if not module_name:
-            raise ValueError('module name must be given')
-        fname = module_name + '.pyx'
-        with io.open(fname, 'w', encoding='utf-8') as f:
-            f.write(cell)
-        if 'pyximport' not in sys.modules:
-            import pyximport
-            pyximport.install(reload_support=True)
-        if module_name in self._reloads:
-            module = self._reloads[module_name]
-            reload(module)
-        else:
-            __import__(module_name)
-            module = sys.modules[module_name]
-            self._reloads[module_name] = module
-        self._import_all(module)
+except:
+    Cython = None
 
-    @magic_arguments.magic_arguments()
-    @magic_arguments.argument(
-        '-c', '--compile-args', action='append', default=[],
-        help="Extra flags to pass to compiler via the `extra_compile_args` "
-             "Extension flag (can be specified  multiple times)."
-    )
-    @magic_arguments.argument(
-        '--link-args', action='append', default=[],
-        help="Extra flags to pass to linker via the `extra_link_args` "
-             "Extension flag (can be specified  multiple times)."
-    )
-    @magic_arguments.argument(
-        '-l', '--lib', action='append', default=[],
-        help="Add a library to link the extension against (can be specified "
-             "multiple times)."
-    )
-    @magic_arguments.argument(
-        '-n', '--name',
-        help="Specify a name for the Cython module."
-    )
-    @magic_arguments.argument(
-        '-L', dest='library_dirs', metavar='dir', action='append', default=[],
-        help="Add a path to the list of libary directories (can be specified "
-             "multiple times)."
-    )
-    @magic_arguments.argument(
-        '-I', '--include', action='append', default=[],
-        help="Add a path to the list of include directories (can be specified "
-             "multiple times)."
-    )
-    @magic_arguments.argument(
-        '-+', '--cplus', action='store_true', default=False,
-        help="Output a C++ rather than C file."
-    )
-    @magic_arguments.argument(
-        '-f', '--force', action='store_true', default=False,
-        help="Force the compilation of a new module, even if the source has been "
-             "previously compiled."
-    )
-    @magic_arguments.argument(
-        '-a', '--annotate', action='store_true', default=False,
-        help="Produce a colorized HTML version of the source."
-    )
-    @cell_magic
-    def cython(self, line, cell):
-        """Compile and import everything from a Cython code cell.
-
-        The contents of the cell are written to a `.pyx` file in the
-        directory `IPYTHONDIR/cython` using a filename with the hash of the
-        code. This file is then cythonized and compiled. The resulting module
-        is imported and all of its symbols are injected into the user's
-        namespace. The usage is similar to that of `%%cython_pyximport` but
-        you don't have to pass a module name::
-
-            %%cython
-            def f(x):
-                return 2.0*x
-
-        To compile OpenMP codes, pass the required  `--compile-args`
-        and `--link-args`.  For example with gcc::
-
-            %%cython --compile-args=-fopenmp --link-args=-fopenmp
-            ...
-        """
-        args = magic_arguments.parse_argstring(self.cython, line)
-        code = cell if cell.endswith('\n') else cell+'\n'
-        lib_dir = os.path.join(get_ipython_cache_dir(), 'cython')
-        quiet = True
-        key = code, sys.version_info, sys.executable, Cython.__version__
-
-        if not os.path.exists(lib_dir):
-            os.makedirs(lib_dir)
-
-        if args.force:
-            # Force a new module name by adding the current time to the
-            # key which is hashed to determine the module name.
-            key += time.time(),
-
-        if args.name:
-            module_name = py3compat.unicode_to_str(args.name)
-        else:
-            module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
-        module_path = os.path.join(lib_dir, module_name + self.so_ext)
-
-        have_module = os.path.isfile(module_path)
-        need_cythonize = not have_module
-
-        if args.annotate:
-            html_file = os.path.join(lib_dir, module_name + '.html')
-            if not os.path.isfile(html_file):
-                need_cythonize = True
-
-        if need_cythonize:
-            c_include_dirs = args.include
-            if 'numpy' in code:
-                import numpy
-                c_include_dirs.append(numpy.get_include())
-            pyx_file = os.path.join(lib_dir, module_name + '.pyx')
-            pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding())
-            with io.open(pyx_file, 'w', encoding='utf-8') as f:
-                f.write(code)
-            extension = Extension(
-                name = module_name,
-                sources = [pyx_file],
-                include_dirs = c_include_dirs,
-                library_dirs = args.library_dirs,
-                extra_compile_args = args.compile_args,
-                extra_link_args = args.link_args,
-                libraries = args.lib,
-                language = 'c++' if args.cplus else 'c',
-            )
-            build_extension = self._get_build_extension()
-            try:
-                opts = dict(
-                    quiet=quiet,
-                    annotate = args.annotate,
-                    force = True,
-                    )
-                build_extension.extensions = cythonize([extension], **opts)
-            except CompileError:
-                return
-
-        if not have_module:
-            build_extension.build_temp = os.path.dirname(pyx_file)
-            build_extension.build_lib  = lib_dir
-            build_extension.run()
-            self._code_cache[key] = module_name
-
-        module = imp.load_dynamic(module_name, module_path)
-        self._import_all(module)
-
-        if args.annotate:
             try:
-                with io.open(html_file, encoding='utf-8') as f:
-                    annotated_html = f.read()
-            except IOError as e:
-                # File could not be opened. Most likely the user has a version
-                # of Cython before 0.15.1 (when `cythonize` learned the
-                # `force` keyword argument) and has already compiled this
-                # exact source without annotation.
-                print('Cython completed successfully but the annotated '
-                      'source could not be read.', file=sys.stderr)
-                print(e, file=sys.stderr)
-            else:
-                return display.HTML(self.clean_annotated_html(annotated_html))
-
-    @property
-    def so_ext(self):
-        """The extension suffix for compiled modules."""
-        try:
-            return self._so_ext
-        except AttributeError:
-            self._so_ext = self._get_build_extension().get_ext_filename('')
-            return self._so_ext
-
-    def _clear_distutils_mkpath_cache(self):
-        """clear distutils mkpath cache
-        
-        prevents distutils from skipping re-creation of dirs that have been removed
-        """
-        try:
-            from distutils.dir_util import _path_created
-        except ImportError:
+    from Cython.Build.IpythonMagic import CythonMagics
+except :
             pass
-        else:
-            _path_created.clear()
     
-    def _get_build_extension(self):
-        self._clear_distutils_mkpath_cache()
-        dist = Distribution()
-        config_files = dist.find_config_files()
-        try:
-            config_files.remove('setup.cfg')
-        except ValueError:
-            pass
-        dist.parse_config_files(config_files)
-        build_extension = build_ext(dist)
-        build_extension.finalize_options()
-        return build_extension
-
-    @staticmethod
-    def clean_annotated_html(html):
-        """Clean up the annotated HTML source.
-
-        Strips the link to the generated C or C++ file, which we do not
-        present to the user.
-        """
-        r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>')
-        html = '\n'.join(l for l in html.splitlines() if not r.match(l))
-        return html
-
-__doc__ = __doc__.format(
-                # rST doesn't see the -+ flag as part of an option list, so we
-                # hide it from the module-level docstring.
-                CYTHON_DOC = dedent(CythonMagics.cython.__doc__\
-                            .replace('-+, --cplus','--cplus    ')),
-                CYTHON_INLINE_DOC = dedent(CythonMagics.cython_inline.__doc__),
-                CYTHON_PYXIMPORT_DOC = dedent(CythonMagics.cython_pyximport.__doc__),
-)
 
+## still load the magic in IPython 3.x, remove completely in future versions.
 def load_ipython_extension(ip):
     """Load the extension in IPython."""
-    ip.register_magics(CythonMagics)
+    
+    print("""The Cython magic has been move to the Cython package, hence """)
+    print("""`%load_ext cythonmagic` is deprecated; Please use `%load_ext Cython` instead.""")
+    
+    if Cython is None or not version.check_version(Cython.__version__, "0.21"):
+        print("You need Cython version >=0.21 to use the Cython magic")
+        return 
+    print("""\nThough, because I am nice, I'll still try to load it for you this time.""")
+    Cython.load_ipython_extension(ip)

IPython/testing/iptest.py

@@ -1,516 +1,512 b''
 # -*- coding: utf-8 -*-
 """IPython Test Suite Runner.
 
 This module provides a main entry point to a user script to test IPython
 itself from the command line. There are two ways of running this script:
 
 1. With the syntax `iptest all`.  This runs our entire test suite by
    calling this script (with different arguments) recursively.  This
    causes modules and package to be tested in different processes, using nose
    or trial where appropriate.
 2. With the regular nose syntax, like `iptest -vvs IPython`.  In this form
    the script simply calls nose, but with special command line flags and
    plugins loaded.
 
 """
 
 # Copyright (c) IPython Development Team.
 # Distributed under the terms of the Modified BSD License.
 
 from __future__ import print_function
 
 import glob
 from io import BytesIO
 import os
 import os.path as path
 import sys
 from threading import Thread, Lock, Event
 import warnings
 
 import nose.plugins.builtin
 from nose.plugins.xunit import Xunit
 from nose import SkipTest
 from nose.core import TestProgram
 from nose.plugins import Plugin
 from nose.util import safe_str
 
 from IPython.utils.process import is_cmd_found
 from IPython.utils.importstring import import_item
 from IPython.testing.plugin.ipdoctest import IPythonDoctest
 from IPython.external.decorators import KnownFailure, knownfailureif
 
 pjoin = path.join
 
 
 #-----------------------------------------------------------------------------
 # Globals
 #-----------------------------------------------------------------------------
 
 
 #-----------------------------------------------------------------------------
 # Warnings control
 #-----------------------------------------------------------------------------
 
 # Twisted generates annoying warnings with Python 2.6, as will do other code
 # that imports 'sets' as of today
 warnings.filterwarnings('ignore', 'the sets module is deprecated',
                         DeprecationWarning )
 
 # This one also comes from Twisted
 warnings.filterwarnings('ignore', 'the sha module is deprecated',
                         DeprecationWarning)
 
 # Wx on Fedora11 spits these out
 warnings.filterwarnings('ignore', 'wxPython/wxWidgets release number mismatch',
                         UserWarning)
 
 # ------------------------------------------------------------------------------
 # Monkeypatch Xunit to count known failures as skipped.
 # ------------------------------------------------------------------------------
 def monkeypatch_xunit():
     try:
         knownfailureif(True)(lambda: None)()
     except Exception as e:
         KnownFailureTest = type(e)
 
     def addError(self, test, err, capt=None):
         if issubclass(err[0], KnownFailureTest):
             err = (SkipTest,) + err[1:]
         return self.orig_addError(test, err, capt)
 
     Xunit.orig_addError = Xunit.addError
     Xunit.addError = addError
 
 #-----------------------------------------------------------------------------
 # Check which dependencies are installed and greater than minimum version.
 #-----------------------------------------------------------------------------
 def extract_version(mod):
     return mod.__version__
 
 def test_for(item, min_version=None, callback=extract_version):
     """Test to see if item is importable, and optionally check against a minimum
     version.
 
     If min_version is given, the default behavior is to check against the
     `__version__` attribute of the item, but specifying `callback` allows you to
     extract the value you are interested in. e.g::
 
         In [1]: import sys
 
         In [2]: from IPython.testing.iptest import test_for
 
         In [3]: test_for('sys', (2,6), callback=lambda sys: sys.version_info)
         Out[3]: True
 
     """
     try:
         check = import_item(item)
     except (ImportError, RuntimeError):
         # GTK reports Runtime error if it can't be initialized even if it's
         # importable.
         return False
     else:
         if min_version:
             if callback:
                 # extra processing step to get version to compare
                 check = callback(check)
 
             return check >= min_version
         else:
             return True
 
 # Global dict where we can store information on what we have and what we don't
 # have available at test run time
 have = {}
 
 have['curses'] = test_for('_curses')
 have['matplotlib'] = test_for('matplotlib')
 have['numpy'] = test_for('numpy')
 have['pexpect'] = test_for('IPython.external.pexpect')
 have['pymongo'] = test_for('pymongo')
 have['pygments'] = test_for('pygments')
 have['qt'] = test_for('IPython.external.qt')
 have['sqlite3'] = test_for('sqlite3')
-have['cython'] = test_for('Cython')
 have['tornado'] = test_for('tornado.version_info', (3,1,0), callback=None)
 have['jinja2'] = test_for('jinja2')
 have['mistune'] = test_for('mistune')
 have['requests'] = test_for('requests')
 have['sphinx'] = test_for('sphinx')
 have['jsonschema'] = test_for('jsonschema')
 have['casperjs'] = is_cmd_found('casperjs')
 have['phantomjs'] = is_cmd_found('phantomjs')
 have['slimerjs'] = is_cmd_found('slimerjs')
 
 min_zmq = (2,1,11)
 
 have['zmq'] = test_for('zmq.pyzmq_version_info', min_zmq, callback=lambda x: x())
 
 #-----------------------------------------------------------------------------
 # Test suite definitions
 #-----------------------------------------------------------------------------
 
 test_group_names = ['parallel', 'kernel', 'kernel.inprocess', 'config', 'core',
                     'extensions', 'lib', 'terminal', 'testing', 'utils',
                     'nbformat', 'qt', 'html', 'nbconvert'
                    ]
 
 class TestSection(object):
     def __init__(self, name, includes):
         self.name = name
         self.includes = includes
         self.excludes = []
         self.dependencies = []
         self.enabled = True
     
     def exclude(self, module):
         if not module.startswith('IPython'):
             module = self.includes[0] + "." + module
         self.excludes.append(module.replace('.', os.sep))
     
     def requires(self, *packages):
         self.dependencies.extend(packages)
     
     @property
     def will_run(self):
         return self.enabled and all(have[p] for p in self.dependencies)
 
 # Name -> (include, exclude, dependencies_met)
 test_sections = {n:TestSection(n, ['IPython.%s' % n]) for n in test_group_names}
 
 # Exclusions and dependencies
 # ---------------------------
 
 # core:
 sec = test_sections['core']
 if not have['sqlite3']:
     sec.exclude('tests.test_history')
     sec.exclude('history')
 if not have['matplotlib']:
     sec.exclude('pylabtools'),
     sec.exclude('tests.test_pylabtools')
 
 # lib:
 sec = test_sections['lib']
 if not have['zmq']:
     sec.exclude('kernel')
 # We do this unconditionally, so that the test suite doesn't import
 # gtk, changing the default encoding and masking some unicode bugs.
 sec.exclude('inputhookgtk')
 # We also do this unconditionally, because wx can interfere with Unix signals.
 # There are currently no tests for it anyway.
 sec.exclude('inputhookwx')
 # Testing inputhook will need a lot of thought, to figure out
 # how to have tests that don't lock up with the gui event
 # loops in the picture
 sec.exclude('inputhook')
 
 # testing:
 sec = test_sections['testing']
 # These have to be skipped on win32 because they use echo, rm, cd, etc.
 # See ticket https://github.com/ipython/ipython/issues/87
 if sys.platform == 'win32':
     sec.exclude('plugin.test_exampleip')
     sec.exclude('plugin.dtexample')
 
 # terminal:
 if (not have['pexpect']) or (not have['zmq']):
     test_sections['terminal'].exclude('console')
 
 # parallel
 sec = test_sections['parallel']
 sec.requires('zmq')
 if not have['pymongo']:
     sec.exclude('controller.mongodb')
     sec.exclude('tests.test_mongodb')
 
 # kernel:
 sec = test_sections['kernel']
 sec.requires('zmq')
 # The in-process kernel tests are done in a separate section
 sec.exclude('inprocess')
 # importing gtk sets the default encoding, which we want to avoid
 sec.exclude('zmq.gui.gtkembed')
 sec.exclude('zmq.gui.gtk3embed')
 if not have['matplotlib']:
     sec.exclude('zmq.pylab')
 
 # kernel.inprocess:
 test_sections['kernel.inprocess'].requires('zmq')
 
 # extensions:
 sec = test_sections['extensions']
-if not have['cython']:
-    sec.exclude('cythonmagic')
-    sec.exclude('tests.test_cythonmagic')
 # This is deprecated in favour of rpy2
 sec.exclude('rmagic')
 # autoreload does some strange stuff, so move it to its own test section
 sec.exclude('autoreload')
 sec.exclude('tests.test_autoreload')
 test_sections['autoreload'] = TestSection('autoreload',
         ['IPython.extensions.autoreload', 'IPython.extensions.tests.test_autoreload'])
 test_group_names.append('autoreload')
 
 # qt:
 test_sections['qt'].requires('zmq', 'qt', 'pygments')
 
 # html:
 sec = test_sections['html']
 sec.requires('zmq', 'tornado', 'requests', 'sqlite3', 'jsonschema')
 # The notebook 'static' directory contains JS, css and other
 # files for web serving.  Occasionally projects may put a .py
 # file in there (MathJax ships a conf.py), so we might as
 # well play it safe and skip the whole thing.
 sec.exclude('static')
 sec.exclude('fabfile')
 if not have['jinja2']:
     sec.exclude('notebookapp')
 if not have['pygments'] or not have['jinja2']:
     sec.exclude('nbconvert')
 
 # config:
 # Config files aren't really importable stand-alone
 test_sections['config'].exclude('profile')
 
 # nbconvert:
 sec = test_sections['nbconvert']
 sec.requires('pygments', 'jinja2', 'jsonschema', 'mistune')
 # Exclude nbconvert directories containing config files used to test.
 # Executing the config files with iptest would cause an exception.
 sec.exclude('tests.files')
 sec.exclude('exporters.tests.files')
 if not have['tornado']:
     sec.exclude('nbconvert.post_processors.serve')
     sec.exclude('nbconvert.post_processors.tests.test_serve')
 
 # nbformat:
 test_sections['nbformat'].requires('jsonschema')
 
 #-----------------------------------------------------------------------------
 # Functions and classes
 #-----------------------------------------------------------------------------
 
 def check_exclusions_exist():
     from IPython.utils.path import get_ipython_package_dir
     from IPython.utils.warn import warn
     parent = os.path.dirname(get_ipython_package_dir())
     for sec in test_sections:
         for pattern in sec.exclusions:
             fullpath = pjoin(parent, pattern)
             if not os.path.exists(fullpath) and not glob.glob(fullpath + '.*'):
                 warn("Excluding nonexistent file: %r" % pattern)
 
 
 class ExclusionPlugin(Plugin):
     """A nose plugin to effect our exclusions of files and directories.
     """
     name = 'exclusions'
     score = 3000  # Should come before any other plugins
     
     def __init__(self, exclude_patterns=None):
         """
         Parameters
         ----------
 
         exclude_patterns : sequence of strings, optional
           Filenames containing these patterns (as raw strings, not as regular
           expressions) are excluded from the tests.
         """
         self.exclude_patterns = exclude_patterns or []
         super(ExclusionPlugin, self).__init__()
 
     def options(self, parser, env=os.environ):
         Plugin.options(self, parser, env)
     
     def configure(self, options, config):
         Plugin.configure(self, options, config)
         # Override nose trying to disable plugin.
         self.enabled = True
         
     def wantFile(self, filename):
         """Return whether the given filename should be scanned for tests.
         """
         if any(pat in filename for pat in self.exclude_patterns):
             return False
         return None
 
     def wantDirectory(self, directory):
         """Return whether the given directory should be scanned for tests.
         """
         if any(pat in directory for pat in self.exclude_patterns):
             return False
         return None
 
 
 class StreamCapturer(Thread):
     daemon = True  # Don't hang if main thread crashes
     started = False
     def __init__(self):
         super(StreamCapturer, self).__init__()
         self.streams = []
         self.buffer = BytesIO()
         self.readfd, self.writefd = os.pipe()
         self.buffer_lock = Lock()
         self.stop = Event()
 
     def run(self):
         self.started = True
 
         while not self.stop.is_set():
             chunk = os.read(self.readfd, 1024)
 
             with self.buffer_lock:
                 self.buffer.write(chunk)
     
         os.close(self.readfd)
         os.close(self.writefd)
 
     def reset_buffer(self):
         with self.buffer_lock:
             self.buffer.truncate(0)
             self.buffer.seek(0)
 
     def get_buffer(self):
         with self.buffer_lock:
             return self.buffer.getvalue()
 
     def ensure_started(self):
         if not self.started:
             self.start()
 
     def halt(self):
         """Safely stop the thread."""
         if not self.started:
             return
 
         self.stop.set()
         os.write(self.writefd, b'wake up')  # Ensure we're not locked in a read()
         self.join()
 
 class SubprocessStreamCapturePlugin(Plugin):
     name='subprocstreams'
     def __init__(self):
         Plugin.__init__(self)
         self.stream_capturer = StreamCapturer()
         self.destination = os.environ.get('IPTEST_SUBPROC_STREAMS', 'capture')
         # This is ugly, but distant parts of the test machinery need to be able
         # to redirect streams, so we make the object globally accessible.
         nose.iptest_stdstreams_fileno = self.get_write_fileno
 
     def get_write_fileno(self):
         if self.destination == 'capture':
             self.stream_capturer.ensure_started()
             return self.stream_capturer.writefd
         elif self.destination == 'discard':
             return os.open(os.devnull, os.O_WRONLY)
         else:
             return sys.__stdout__.fileno()
     
     def configure(self, options, config):
         Plugin.configure(self, options, config)
         # Override nose trying to disable plugin.
         if self.destination == 'capture':
             self.enabled = True
     
     def startTest(self, test):
         # Reset log capture
         self.stream_capturer.reset_buffer()
     
     def formatFailure(self, test, err):
         # Show output
         ec, ev, tb = err
         captured = self.stream_capturer.get_buffer().decode('utf-8', 'replace')
         if captured.strip():
             ev = safe_str(ev)
             out = [ev, '>> begin captured subprocess output <<',
                     captured,
                     '>> end captured subprocess output <<']
             return ec, '\n'.join(out), tb
 
         return err
     
     formatError = formatFailure
     
     def finalize(self, result):
         self.stream_capturer.halt()
 
 
 def run_iptest():
     """Run the IPython test suite using nose.
 
     This function is called when this script is **not** called with the form
     `iptest all`.  It simply calls nose with appropriate command line flags
     and accepts all of the standard nose arguments.
     """
     # Apply our monkeypatch to Xunit
     if '--with-xunit' in sys.argv and not hasattr(Xunit, 'orig_addError'):
         monkeypatch_xunit()
 
     warnings.filterwarnings('ignore',
         'This will be removed soon.  Use IPython.testing.util instead')
     
     arg1 = sys.argv[1]
     if arg1 in test_sections:
         section = test_sections[arg1]
         sys.argv[1:2] = section.includes
     elif arg1.startswith('IPython.') and arg1[8:] in test_sections:
         section = test_sections[arg1[8:]]
         sys.argv[1:2] = section.includes
     else:
         section = TestSection(arg1, includes=[arg1])
         
 
     argv = sys.argv + [ '--detailed-errors',  # extra info in tracebacks
 
                         '--with-ipdoctest',
                         '--ipdoctest-tests','--ipdoctest-extension=txt',
 
                         # We add --exe because of setuptools' imbecility (it
                         # blindly does chmod +x on ALL files).  Nose does the
                         # right thing and it tries to avoid executables,
                         # setuptools unfortunately forces our hand here.  This
                         # has been discussed on the distutils list and the
                         # setuptools devs refuse to fix this problem!
                         '--exe',
                         ]
     if '-a' not in argv and '-A' not in argv:
         argv = argv + ['-a', '!crash']
 
     if nose.__version__ >= '0.11':
         # I don't fully understand why we need this one, but depending on what
         # directory the test suite is run from, if we don't give it, 0 tests
         # get run.  Specifically, if the test suite is run from the source dir
         # with an argument (like 'iptest.py IPython.core', 0 tests are run,
         # even if the same call done in this directory works fine).  It appears
         # that if the requested package is in the current dir, nose bails early
         # by default.  Since it's otherwise harmless, leave it in by default
         # for nose >= 0.11, though unfortunately nose 0.10 doesn't support it.
         argv.append('--traverse-namespace')
 
     # use our plugin for doctesting.  It will remove the standard doctest plugin
     # if it finds it enabled
     plugins = [ExclusionPlugin(section.excludes), IPythonDoctest(), KnownFailure(),
                SubprocessStreamCapturePlugin() ]
     
     # Use working directory set by parent process (see iptestcontroller)
     if 'IPTEST_WORKING_DIR' in os.environ:
         os.chdir(os.environ['IPTEST_WORKING_DIR'])
     
     # We need a global ipython running in this process, but the special
     # in-process group spawns its own IPython kernels, so for *that* group we
     # must avoid also opening the global one (otherwise there's a conflict of
     # singletons).  Ultimately the solution to this problem is to refactor our
     # assumptions about what needs to be a singleton and what doesn't (app
     # objects should, individual shells shouldn't).  But for now, this
     # workaround allows the test suite for the inprocess module to complete.
     if 'kernel.inprocess' not in section.name:
         from IPython.testing import globalipapp
         globalipapp.start_ipython()
 
     # Now nose can run
     TestProgram(argv=argv, addplugins=plugins)
 
 if __name__ == '__main__':
     run_iptest()
 

docs/source/config/extensions/cythonmagic.rst

@@ -1,7 +1,7 b''
 .. _extensions_cythonmagic:
 
 ===========
 cythonmagic
 ===========
 
-.. automodule:: IPython.extensions.cythonmagic
+The `cython` magic has been moved in the `Cython` package.

docs/source/config/extensions/index.rst

@@ -1,102 +1,104 b''
 .. _extensions_overview:
 
 ==================
 IPython extensions
 ==================
 
 A level above configuration are IPython extensions, Python modules which modify
 the behaviour of the shell. They are referred to by an importable module name,
 and can be placed anywhere you'd normally import from, or in
 ``.ipython/extensions/``.
 
 Getting extensions
 ==================
 
 A few important extensions are :ref:`bundled with IPython <bundled_extensions>`.
 Others can be found on the `extensions index
 <https://github.com/ipython/ipython/wiki/Extensions-Index>`_ on the wiki, and
 the `Framework :: IPython tag <https://pypi.python.org/pypi?:action=browse&c=586>`_
 on PyPI.
 
 Extensions on PyPI can be installed using ``pip``, like any other Python package.
 Other simple extensions can be installed with the ``%install_ext`` magic. The
 latter does no validation, so be careful using it on untrusted networks like
 public wifi.
 
 Using extensions
 ================
 
 To load an extension while IPython is running, use the ``%load_ext`` magic:
 
 .. sourcecode:: ipython
 
     In [1]: %load_ext myextension
 
 To load it each time IPython starts, list it in your configuration file::
 
     c.InteractiveShellApp.extensions = [
         'myextension'
     ]
 
 Writing extensions
 ==================
 
 An IPython extension is an importable Python module that has a couple of special
 functions to load and unload it. Here is a template::
 
     # myextension.py
 
     def load_ipython_extension(ipython):
         # The `ipython` argument is the currently active `InteractiveShell`
         # instance, which can be used in any way. This allows you to register
         # new magics or aliases, for example.
 
     def unload_ipython_extension(ipython):
         # If you want your extension to be unloadable, put that logic here.
 
 This :func:`load_ipython_extension` function is called after your extension is
 imported, and the currently active :class:`~IPython.core.interactiveshell.InteractiveShell`
 instance is passed as the only argument. You can do anything you want with
 IPython at that point.
 
 :func:`load_ipython_extension` will be called again if you load or reload
 the extension again. It is up to the extension author to add code to manage
 that.
 
 Useful :class:`InteractiveShell` methods include :meth:`~IPython.core.interactiveshell.InteractiveShell.register_magic_function`, 
 :meth:`~IPython.core.interactiveshell.InteractiveShell.push` (to add variables to the user namespace) and 
 :meth:`~IPython.core.interactiveshell.InteractiveShell.drop_by_id` (to remove variables on unloading).
 
 .. seealso::
 
    :ref:`defining_magics`
 
 You can put your extension modules anywhere you want, as long as they can be
 imported by Python's standard import mechanism. However, to make it easy to
 write extensions, you can also put your extensions in :file:`extensions/`
 within the :ref:`IPython directory <ipythondir>`. This directory is
 added to :data:`sys.path` automatically.
 
 When your extension is ready for general use, please add it to the `extensions
 index <https://github.com/ipython/ipython/wiki/Extensions-Index>`_. We also
 encourage you to upload it to PyPI and use the ``Framework :: IPython``
 classifier, so that users can install it with standard packaging tools.
 
 .. _bundled_extensions:
 
 Extensions bundled with IPython
 ===============================
 
 .. toctree::
    :maxdepth: 1
 
    autoreload
    cythonmagic
    storemagic
    sympyprinting
 
 * ``octavemagic`` used to be bundled, but is now part of `oct2py <http://blink1073.github.io/oct2py/docs/>`_.
   Use ``%load_ext oct2py.ipython`` to load it.
 * ``rmagic`` is now part of `rpy2 <http://rpy.sourceforge.net/>`_. Use
   ``%load_ext rpy2.ipython`` to load it, and see :mod:`rpy2.ipython.rmagic` for
   details of how to use it.
+* ``cythonmagic``used to be bundled, but is now part of `cython <https://github.com/cython/cython/>`_
+  Use ``%load_ext Cython`` to load it.

docs/source/config/intro.rst

@@ -1,156 +1,156 b''
 =====================================
 Introduction to IPython configuration
 =====================================
 
 .. _setting_config:
 
 Setting configurable options
 ============================
 
 Many of IPython's classes have configurable attributes (see
 :doc:`options/index` for the list). These can be
 configured in several ways.
 
 Python config files
 -------------------
 
 To create the blank config files, run::
 
     ipython profile create [profilename]
 
 If you leave out the profile name, the files will be created for the
 ``default`` profile (see :ref:`profiles`). These will typically be
 located in :file:`~/.ipython/profile_default/`, and will be named
 :file:`ipython_config.py`, :file:`ipython_notebook_config.py`, etc.
 The settings in :file:`ipython_config.py` apply to all IPython commands.
 
 The files typically start by getting the root config object::
 
     c = get_config()
 
 You can then configure class attributes like this::
 
     c.InteractiveShell.automagic = False
 
 Be careful with spelling--incorrect names will simply be ignored, with
 no error.
 
 To add to a collection which may have already been defined elsewhere,
 you can use methods like those found on lists, dicts and sets: append,
 extend, :meth:`~IPython.config.loader.LazyConfigValue.prepend` (like
 extend, but at the front), add and update (which works both for dicts
 and sets)::
 
-    c.InteractiveShellApp.extensions.append('cythonmagic')
+    c.InteractiveShellApp.extensions.append('Cython')
 
 .. versionadded:: 2.0
    list, dict and set methods for config values
 
 Example config file
 ```````````````````
 
 ::
 
     # sample ipython_config.py
     c = get_config()
 
     c.TerminalIPythonApp.display_banner = True
     c.InteractiveShellApp.log_level = 20
     c.InteractiveShellApp.extensions = [
         'myextension'
     ]
     c.InteractiveShellApp.exec_lines = [
         'import numpy',
         'import scipy'
     ]
     c.InteractiveShellApp.exec_files = [
         'mycode.py',
         'fancy.ipy'
     ]
     c.InteractiveShell.autoindent = True
     c.InteractiveShell.colors = 'LightBG'
     c.InteractiveShell.confirm_exit = False
     c.InteractiveShell.deep_reload = True
     c.InteractiveShell.editor = 'nano'
     c.InteractiveShell.xmode = 'Context'
 
     c.PromptManager.in_template  = 'In [\#]: '
     c.PromptManager.in2_template = '   .\D.: '
     c.PromptManager.out_template = 'Out[\#]: '
     c.PromptManager.justify = True
 
     c.PrefilterManager.multi_line_specials = True
 
     c.AliasManager.user_aliases = [
      ('la', 'ls -al')
     ]
 
 
 Command line arguments
 ----------------------
 
 Every configurable value can be set from the command line, using this
 syntax::
 
     ipython --ClassName.attribute=value
 
 Many frequently used options have short aliases and flags, such as
 ``--matplotlib`` (to integrate with a matplotlib GUI event loop) or
 ``--pdb`` (automatic post-mortem debugging of exceptions).
 
 To see all of these abbreviated options, run::
 
     ipython --help
     ipython notebook --help
     # etc.
 
 Options specified at the command line, in either format, override
 options set in a configuration file.
 
 The config magic
 ----------------
 
 You can also modify config from inside IPython, using a magic command::
 
     %config IPCompleter.greedy = True
 
 At present, this only affects the current session - changes you make to
 config are not saved anywhere. Also, some options are only read when
 IPython starts, so they can't be changed like this.
 
 .. _profiles:
 
 Profiles
 ========
 
 IPython can use multiple profiles, with separate configuration and
 history. By default, if you don't specify a profile, IPython always runs
 in the ``default`` profile. To use a new profile::
 
     ipython profile create foo   # create the profile foo
     ipython --profile=foo        # start IPython using the new profile
 
 Profiles are typically stored in :ref:`ipythondir`, but you can also keep
 a profile in the current working directory, for example to distribute it
 with a project. To find a profile directory on the filesystem::
 
     ipython locate profile foo
 
 .. _ipythondir:
 
 The IPython directory
 =====================
 
 IPython stores its files---config, command history and extensions---in
 the directory :file:`~/.ipython/` by default.
 
 .. envvar:: IPYTHONDIR
 
    If set, this environment variable should be the path to a directory,
    which IPython will use for user data. IPython will create it if it
    does not exist.
 
 .. option:: --ipython-dir=<path>
 
    This command line option can also be used to override the default
    IPython directory.