use shutdown_kernel instead of hard kill in notebook

IPython/frontend/html/notebook/handlers.py

@@ -344,7 +344,7 class KernelHandler(AuthenticatedHandler):
     @web.authenticated
     def delete(self, kernel_id):
         km = self.application.kernel_manager
-        km.kill_kernel(kernel_id)
+        km.shutdown_kernel(kernel_id)
         self.set_status(204)
         self.finish()
 

IPython/frontend/html/notebook/kernelmanager.py

@@ -87,11 +87,22 class MultiKernelManager(LoggingConfigurable):
                     config=self.config,
         )
         km.start_kernel(**kwargs)
-        # start the shell channel, needed for graceful restart
+        # start just the shell channel, needed for graceful restart
         km.start_channels(shell=True, sub=False, stdin=False, hb=False)
         self._kernels[kernel_id] = km
         return kernel_id
 
+    def shutdown_kernel(self, kernel_id):
+        """Shutdown a kernel by its kernel uuid.
+
+        Parameters
+        ==========
+        kernel_id : uuid
+            The id of the kernel to shutdown.
+        """
+        self.get_kernel(kernel_id).shutdown_kernel()
+        del self._kernels[kernel_id]
+
     def kill_kernel(self, kernel_id):
         """Kill a kernel by its kernel uuid.
 
@@ -269,6 +280,13 class MappingKernelManager(MultiKernelManager):
             self.log.info("Using existing kernel: %s" % kernel_id)
         return kernel_id
 
+    def shutdown_kernel(self, kernel_id):
+        """Shutdown a kernel and remove its notebook association."""
+        self._check_kernel_id(kernel_id)
+        super(MappingKernelManager, self).shutdown_kernel(kernel_id)
+        self.delete_mapping_for_kernel(kernel_id)
+        self.log.info("Kernel shutdown: %s" % kernel_id)
+
     def kill_kernel(self, kernel_id):
         """Kill a kernel and remove its notebook association."""
         self._check_kernel_id(kernel_id)

IPython/frontend/html/notebook/notebookapp.py

@@ -532,9 +532,9 class NotebookApp(BaseIPythonApplication):
         """
         self.log.info('Shutting down kernels')
         km = self.kernel_manager
-        # copy list, since kill_kernel deletes keys
+        # copy list, since shutdown_kernel deletes keys
         for kid in list(km.kernel_ids):
-            km.kill_kernel(kid)
+            km.shutdown_kernel(kid)
 
     def start(self):
         ip = self.ip if self.ip else '[all ip addresses on your system]'