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

@@ -1,37 +1,10 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.
@@ -43,303 +16,28 b' Parts of this code were taken from Cython.inline.'
 
 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

@@ -131,7 +131,6 b" 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')
@@ -240,9 +239,6 b" 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

docs/source/config/extensions/cythonmagic.rst

@@ -4,4 +4,4 b''
 cythonmagic
 ===========
 
-.. automodule:: IPython.extensions.cythonmagic
+The `cython` magic has been moved in the `Cython` package.

docs/source/config/extensions/index.rst

@@ -100,3 +100,5 b' Extensions bundled with IPython'
 * ``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

@@ -41,7 +41,7 b' 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