Give .run_cell a store_history option, so that it can be used to run raw IPython code outside of the sequence of commands making the session. This also doesn't incremement the execution_count.

IPython/core/history.py

@@ -630,18 +630,20 b" def magic_rerun(self, parameter_s=''):"
     opts, args = self.parse_options(parameter_s, 'l:g:', mode='string')
     if "l" in opts:         # Last n lines
         n = int(opts['l'])
-        hist = self.history_manager.get_hist_tail(n, raw=False)
+        hist = self.history_manager.get_hist_tail(n)
     elif "g" in opts:       # Search
         p = "*"+opts['g']+"*"
-        hist = self.history_manager.get_hist_search(p, raw=False)
-        hist = list(hist)
-        if 'magic("rerun' in hist[-1][2]:
-            hist = hist[:-1]   # We can ignore the current line
-        hist = hist[-1:]       # Just get the last match
+        hist = list(self.history_manager.get_hist_search(p))
+        for l in reversed(hist):
+            if "rerun" not in l[2]:
+                hist = [l]     # The last match which isn't a %rerun
+                break
+        else:
+            hist = []          # No matches except %rerun
     elif args:              # Specify history ranges
         hist = self.history_manager.get_hist_from_rangestr(args)
     else:                   # Last line
-        hist = self.history_manager.get_hist_tail(1, raw=False)
+        hist = self.history_manager.get_hist_tail(1)
     hist = [x[2] for x in hist]
     if not hist:
         print("No lines in history match specification")
@@ -650,7 +652,7 b" def magic_rerun(self, parameter_s=''):"
     print("=== Executing: ===")
     print(histlines)
     print("=== Output: ===")
-    self.run_source("\n".join(hist), symbol="exec")
+    self.run_cell("\n".join(hist), store_history=False)
 
 
 def init_ipython(ip):

IPython/core/interactiveshell.py

@@ -2060,7 +2060,7 b' class InteractiveShell(Configurable, Magic):'
                 self.showtraceback()
                 warn('Unknown failure executing file: <%s>' % fname)
 
-    def run_cell(self, cell):
+    def run_cell(self, cell, store_history=True):
         """Run the contents of an entire multiline 'cell' of code, and store it
         in the history.
 
@@ -2111,7 +2111,9 b' class InteractiveShell(Configurable, Magic):'
         cell = ''.join(blocks)
 
         # Store raw and processed history
-        self.history_manager.store_inputs(self.execution_count, cell, raw_cell)
+        if store_history:
+            self.history_manager.store_inputs(self.execution_count, 
+                                                        cell, raw_cell)
 
         self.logger.log(cell, raw_cell)
 
@@ -2123,6 +2125,7 b' class InteractiveShell(Configurable, Magic):'
                 out = self.run_source(blocks[0])
                 # Write output to the database. Does nothing unless
                 # history output logging is enabled.
+                if store_history:
                 self.history_manager.store_output(self.execution_count)
                 # since we return here, we need to update the execution count
                 self.execution_count += 1
@@ -2154,6 +2157,7 b' class InteractiveShell(Configurable, Magic):'
 
         # Write output to the database. Does nothing unless
         # history output logging is enabled.
+        if store_history:
         self.history_manager.store_output(self.execution_count)
         # Each cell is a *single* input, regardless of how many lines it has
         self.execution_count += 1

IPython/core/magic.py

@@ -2369,7 +2369,8 b' Currently the magic system has the following functions:\\n"""'
         else:
             print 'done. Executing edited code...'
             if opts_raw:
-                self.shell.run_cell(file_read(filename))
+                self.shell.run_cell(file_read(filename),
+                                                    store_history=False)
             else:
                 self.shell.safe_execfile(filename,self.shell.user_ns,
                                          self.shell.user_ns)