Fix off-by-one bug in history because we weren't correctly updating it.

Fix was to manage history in run_cell, which is the entity that gets
cells of source, and have no history handling at all in runcode, which
is meant *purely* for code execution.

IPython/core/history.py

@@ -54,7 +54,7 b" def magic_history(self, parameter_s = ''):"
        confirmation first if it already exists.
     """
 
-    if not self.displayhook.do_full_cache:
+    if not self.shell.displayhook.do_full_cache:
         print 'This feature is only available if numbered prompts are in use.'
         return
     opts,args = self.parse_options(parameter_s,'gnoptsrf:',mode='list')
@@ -76,12 +76,12 b" def magic_history(self, parameter_s = ''):"
         close_at_end = True
 
     if 't' in opts:
-        input_hist = self.input_hist
+        input_hist = self.shell.input_hist
     elif 'r' in opts:
-        input_hist = self.input_hist_raw
+        input_hist = self.shell.input_hist_raw
     else:
         # Raw history is the default
-        input_hist = self.input_hist_raw
+        input_hist = self.shell.input_hist_raw
             
     default_length = 40
     pattern = None
@@ -114,7 +114,7 b" def magic_history(self, parameter_s = ''):"
     
     found = False
     if pattern is not None:
-        sh = self.shadowhist.all()
+        sh = self.shell.shadowhist.all()
         for idx, s in sh:
             if fnmatch.fnmatch(s, pattern):
                 print >> outfile, "0%d: %s" %(idx, s.expandtabs(4))
@@ -126,11 +126,12 b" def magic_history(self, parameter_s = ''):"
               "shadow history ends, fetch by %rep <number> (must start with 0)"
         print >> outfile, "=== start of normal history ==="
         
-    for in_num in range(init,final):
+    for in_num in range(init, final):
         # Print user history with tabs expanded to 4 spaces.  The GUI clients
         # use hard tabs for easier usability in auto-indented code, but we want
         # to produce PEP-8 compliant history for safe pasting into an editor.
         inline = input_hist[in_num].expandtabs(4)
+
         if pattern is not None and not fnmatch.fnmatch(inline, pattern):
             continue
             
@@ -149,7 +150,7 b" def magic_history(self, parameter_s = ''):"
         else:
             print >> outfile, inline,
         if print_outputs:
-            output = self.shell.user_ns['Out'].get(in_num)
+            output = self.shell.output_hist.get(in_num)
             if output is not None:
                 print >> outfile, repr(output)
 
@@ -195,7 +196,7 b' def rep_f(self, arg):'
     
     opts,args = self.parse_options(arg,'',mode='list')
     if not args:
-        self.set_next_input(str(self.user_ns["_"]))
+        self.set_next_input(str(self.shell.user_ns["_"]))
         return
 
     if len(args) == 1 and not '-' in args[0]:
@@ -203,17 +204,17 b' def rep_f(self, arg):'
         if len(arg) > 1 and arg.startswith('0'):
             # get from shadow hist
             num = int(arg[1:])
-            line = self.shadowhist.get(num)
+            line = self.shell.shadowhist.get(num)
             self.set_next_input(str(line))
             return
         try:
             num = int(args[0])
-            self.set_next_input(str(self.input_hist_raw[num]).rstrip())
+            self.set_next_input(str(self.shell.input_hist_raw[num]).rstrip())
             return
         except ValueError:
             pass
         
-        for h in reversed(self.input_hist_raw):
+        for h in reversed(self.shell.input_hist_raw):
             if 'rep' in h:
                 continue
             if fnmatch.fnmatch(h,'*' + arg + '*'):
@@ -231,7 +232,7 b' def rep_f(self, arg):'
 _sentinel = object()
 
 class ShadowHist(object):
-    def __init__(self,db):
+    def __init__(self, db):
         # cmd => idx mapping
         self.curidx = 0
         self.db = db

IPython/core/interactiveshell.py

@@ -2121,10 +2121,21 b' class InteractiveShell(Configurable, Magic):'
         # just feed the whole thing to runcode.
         # This seems like a reasonable usability design.
         last = blocks[-1]
+        
+        # Note: below, whenever we call runcode, we must sync history
+        # ourselves, because runcode is NOT meant to manage history at all.
         if len(last.splitlines()) < 2:
-            self.runcode(''.join(blocks[:-1]), post_execute=False)
+            # Get the main body to run as a cell
+            body = ''.join(blocks[:-1])
+            self.input_hist.append(body)
+            self.input_hist_raw.append(body)
+            self.runcode(body, post_execute=False)
+            # And the last expression via runlines so it produces output
             self.runlines(last)
         else:
+            # Run the whole cell as one entity
+            self.input_hist.append(cell)
+            self.input_hist_raw.append(cell)
             self.runcode(cell)
 
     def runlines(self, lines, clean=False):
@@ -2245,11 +2256,6 b' class InteractiveShell(Configurable, Magic):'
           - 1: an error occurred.
         """
 
-        # It's also possible that we've been fed a plain string.  In that case,
-        # we must store it in the input history.
-        if isinstance(code_obj, basestring):
-            self.input_hist_raw.append(code_obj)
-
         # Set our own excepthook in case the user code tries to call it
         # directly, so that the IPython crash handler doesn't get triggered
         old_excepthook,sys.excepthook = sys.excepthook, self.excepthook