Deprecate some hooks in favour of callbacks

IPython/core/callbacks.py

@@ -112,4 +112,13 b' def post_execute():'
 @_collect
 def post_execute_explicit():
     """Fires after user-entered code runs."""
-    pass
  No newline at end of file
+    pass
+
+@_collect
+def shell_initialised(ip):
+    """Fires after initialisation of :class:`~IPython.core.interactiveshell.InteractiveShell`.
+    
+    This is before extensions and startup scripts are loaded, so it can only be
+    set by subclassing.
+    """
+    pass

IPython/core/hooks.py

@@ -49,6 +49,11 b" __all__ = ['editor', 'fix_error_editor', 'synchronize_with_editor',"
            'show_in_pager','pre_prompt_hook',
            'pre_run_code_hook', 'clipboard_get']
 
+deprecated = {'pre_run_code_hook': "a callback for the 'pre_execute' or 'pre_execute_explicit' event",
+              'late_startup_hook': "a callback for the 'shell_initialised' event",
+              'shutdown_hook': "the atexit module",
+             }
+
 def editor(self, filename, linenum=None, wait=True):
     """Open the default editor at the given filename and linenumber.
 

IPython/core/interactiveshell.py

@@ -512,6 +512,7 b' class InteractiveShell(SingletonConfigurable):'
         self.init_payload()
         self.init_comms()
         self.hooks.late_startup_hook()
+        self.callbacks.fire('shell_initialised', self)
         atexit.register(self.atexit_operations)
 
     def get_ipython(self):
@@ -787,9 +788,10 b' class InteractiveShell(SingletonConfigurable):'
         for hook_name in hooks.__all__:
             # default hooks have priority 100, i.e. low; user hooks should have
             # 0-100 priority
-            self.set_hook(hook_name,getattr(hooks,hook_name), 100)
+            self.set_hook(hook_name,getattr(hooks,hook_name), 100, _warn_deprecated=False)
 
-    def set_hook(self,name,hook, priority = 50, str_key = None, re_key = None):
+    def set_hook(self,name,hook, priority=50, str_key=None, re_key=None,
+                 _warn_deprecated=True):
         """set_hook(name,hook) -> sets an internal IPython hook.
 
         IPython exposes some of its internal API as user-modifiable hooks.  By
@@ -818,6 +820,11 b' class InteractiveShell(SingletonConfigurable):'
         if name not in IPython.core.hooks.__all__:
             print("Warning! Hook '%s' is not one of %s" % \
                   (name, IPython.core.hooks.__all__ ))
+
+        if _warn_deprecated and (name in IPython.core.hooks.deprecated):
+            alternative = IPython.core.hooks.deprecated[name]
+            warn("Hook {} is deprecated. Use {} instead.".format(name, alternative))
+
         if not dp:
             dp = IPython.core.hooks.CommandChainDispatcher()