Select adequate highlighter for cell magic languages

Detect cells that use language extension magics such as %%R or %%bash
and call the appropriate pygmentize lexer.

Closes  #4184

IPython/nbconvert/filters/highlight.py

@@ -14,6 +14,8 b' from within Jinja templates.'
 # Imports
 #-----------------------------------------------------------------------------
 
+import re
+
 from  pygments import highlight as pygements_highlight
 from pygments.lexers import get_lexer_by_name
 from pygments.formatters import HtmlFormatter
@@ -28,6 +30,20 b' from IPython.nbconvert.utils.lexers import IPythonLexer'
 
 MULTILINE_OUTPUTS = ['text', 'html', 'svg', 'latex', 'javascript', 'json']
 
+# list of magic language extensions and their associated pygment lexers
+magic_languages = {'%%R': 'r',
+                   '%%bash': 'bash',
+                   '%%octave': 'octave',
+                   '%%perl': 'perl',
+                   '%%ruby': 'ruby'
+                   }
+
+# build a RE to catch language extensions and choose an adequate
+# pygments lexer
+re_languages = "|".join(magic_languages.keys())
+re_magic_language = re.compile(r'^\s*({})\s+'.format(re_languages),
+                               re.MULTILINE)
+
 #-----------------------------------------------------------------------------
 # Utility functions
 #-----------------------------------------------------------------------------
@@ -67,6 +83,29 b" def highlight2latex(source, language='ipython'):"
     return _pygment_highlight(source, LatexFormatter(), language)
 
 
+def which_magic_language(source):
+    """
+    When a cell uses another language through a magic extension,
+    the other language is returned.
+    If no language magic is detected, this function returns None.
+
+    Parameters
+    ----------
+    source: str
+        Source code of the cell to highlight
+    """
+
+    m = re_magic_language.search(source)
+
+    if m:
+        # By construction of the re, the matched language must be in the
+        # language dictionnary
+        assert(m.group(1) in magic_languages)
+        return magic_languages[m.group(1)]
+    else:
+        return None
+
+
 def _pygment_highlight(source, output_formatter, language='ipython'):
     """
     Return a syntax-highlighted version of the input source
@@ -80,6 +119,10 b" def _pygment_highlight(source, output_formatter, language='ipython'):"
         Language to highlight the syntax of.
     """
     
+    magic_language = which_magic_language(source)
+    if magic_language:
+        language = magic_language
+
     if language == 'ipython':
         lexer = IPythonLexer()
     else:

IPython/nbconvert/filters/tests/test_highlight.py

@@ -15,7 +15,7 b' Module with tests for Highlight'
 #-----------------------------------------------------------------------------
 
 from ...tests.base import TestsBase
-from ..highlight import highlight2html, highlight2latex
+from ..highlight import highlight2html, highlight2latex, which_magic_language
 
 
 #-----------------------------------------------------------------------------
@@ -45,21 +45,53 b' class TestHighlight(TestsBase):'
         ['Hello World Example', 'say', 'text', 'print', 'def'],
         ['pylab', 'plot']]
 
-
     def test_highlight2html(self):
         """highlight2html test"""
         for index, test in enumerate(self.tests):
             self._try_highlight(highlight2html, test, self.tokens[index])
 
-
     def test_highlight2latex(self):
         """highlight2latex test"""
         for index, test in enumerate(self.tests):
             self._try_highlight(highlight2latex, test, self.tokens[index])
 
-
     def _try_highlight(self, method, test, tokens):
         """Try highlighting source, look for key tokens"""
         results = method(test)
         for token in tokens:
             assert token in results
+
+    magic_tests = {
+            'r':
+                """%%R -i x,y -o XYcoef
+                lm.fit <- lm(y~x)
+                par(mfrow=c(2,2))
+                print(summary(lm.fit))
+                plot(lm.fit)
+                XYcoef <- coef(lm.fit)
+                """,
+            'bash':
+                """# the following code is in bash
+                %%bash
+                echo "test" > out
+                """,
+            'ipython':
+                """# this should not be detected
+                print("%%R")
+                """
+            }
+
+    def test_highlight_rmagic(self):
+        """Test %%R magic highlighting"""
+        language = which_magic_language(self.magic_tests['r'])
+        assert language == 'r'
+
+    def test_highlight_bashmagic(self):
+        """Test %%bash magic highlighting"""
+        language = which_magic_language(self.magic_tests['bash'])
+        assert language == 'bash'
+
+    def test_highlight_interferemagic(self):
+        """Test that magic highlighting does not interfere with ipython code"""
+        language = which_magic_language(self.magic_tests['ipython'])
+        assert language == None
  No newline at end of file