Merge pull request #6290 from takluyver/deprecate-rmagic

Deprecate rmagic

docs/source/whatsnew/pr/incompat-rmagic-deprecated.rst

@@ -0,0 +1,2 b''
+- The ``rmagic`` extension is deprecated, as it is now part of rpy2. See
+  :mod:`rpy2.ipython.rmagic`.

IPython/extensions/rmagic.py

@@ -48,6 +48,7 b' import sys'
 import tempfile
 from glob import glob
 from shutil import rmtree
+import warnings
 
 # numpy and rpy2 imports
 
@@ -689,6 +690,16 b' __doc__ = __doc__.format('
 
 def load_ipython_extension(ip):
     """Load the extension in IPython."""
+    warnings.warn("The rmagic extension in IPython is deprecated in favour of "
+            "rpy2.ipython. If available, that will be loaded instead.\n"
+            "http://rpy.sourceforge.net/")
+    try:
+        import rpy2.ipython
+    except ImportError:
+        pass  # Fall back to our own implementation for now
+    else:
+        return rpy2.ipython.load_ipython_extension(ip)
+
     ip.register_magics(RMagics)
     # Initialising rpy2 interferes with readline. Since, at this point, we've
     # probably just loaded rpy2, we reset the delimiters. See issue gh-2759.

IPython/testing/iptest.py

@@ -140,7 +140,6 b" 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['rpy2'] = test_for('rpy2')
 have['sqlite3'] = test_for('sqlite3')
 have['cython'] = test_for('Cython')
 have['tornado'] = test_for('tornado.version_info', (3,1,0), callback=None)
@@ -255,9 +254,8 b" sec = test_sections['extensions']"
 if not have['cython']:
     sec.exclude('cythonmagic')
     sec.exclude('tests.test_cythonmagic')
-if not have['rpy2'] or not have['numpy']:
-    sec.exclude('rmagic')
-    sec.exclude('tests.test_rmagic')
+# 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')

docs/source/conf.py

@@ -189,7 +189,8 b' html_additional_pages = {'
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'ipythondoc'
 
-intersphinx_mapping = {'python': ('http://docs.python.org/2/', None)}
+intersphinx_mapping = {'python': ('http://docs.python.org/2/', None),
+                       'rpy2': ('http://rpy.sourceforge.net/rpy2/doc-2.4/html/', None)}
 
 # Options for LaTeX output
 # ------------------------

docs/source/config/extensions/index.rst

@@ -92,9 +92,11 b' Extensions bundled with IPython'
 
    autoreload
    cythonmagic
-   rmagic
    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.

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('rmagic')
+    c.InteractiveShellApp.extensions.append('cythonmagic')
 
 .. versionadded:: 2.0
    list, dict and set methods for config values

docs/source/whatsnew/version0.13.rst

@@ -317,7 +317,7 b' extremely useful. The following extensions are provided:'
 .. _octave: http://www.gnu.org/software/octave
 .. _oct2py: http://pypi.python.org/pypi/oct2py
 
-**R magics** (extension :ref:`rmagic <extensions_rmagic>`)
+**R magics** (extension ``rmagic``)
     This extension provides several magics that support calling code written in
     the R_ language for statistical data analysis.  You can execute
     single-lines or whole blocks of R code, capture both output and figures