Finish fixing the at-exit spurious failures.

Mostly due to concurrent file access, and late calling

IPython/core/interactiveshell.py

@@ -3771,6 +3771,22 b' class InteractiveShell(SingletonConfigurable):'
         raise TypeError("%s is neither a string nor a macro." % target,
                         codeobj)
 
+    def _atexit_once(self):
+        """
+        At exist operation that need to be called at most once.
+        Second call to this function per instance will do nothing.
+        """
+
+        if not getattr(self, "_atexit_once_called", False):
+            self._atexit_once_called = True
+            # Clear all user namespaces to release all references cleanly.
+            self.reset(new_session=False)
+            # Close the history session (this stores the end time and line count)
+            # this must be *before* the tempfile cleanup, in case of temporary
+            # history db
+            self.history_manager.end_session()
+            self.history_manager = None
+
     #-------------------------------------------------------------------------
     # Things related to IPython exiting
     #-------------------------------------------------------------------------
@@ -3785,13 +3801,7 b' class InteractiveShell(SingletonConfigurable):'
         code that has the appropriate information, rather than trying to
         clutter
         """
-        # Clear all user namespaces to release all references cleanly.
-        self.reset(new_session=False)
-        # Close the history session (this stores the end time and line count)
-        # this must be *before* the tempfile cleanup, in case of temporary
-        # history db
-        self.history_manager.end_session()
-        del self.history_manager
+        self._atexit_once()
 
         # Cleanup all tempfiles and folders left around
         for tfile in self.tempfiles:

IPython/core/tests/test_pylabtools.py

@@ -146,8 +146,16 b' def test_import_pylab():'
     nt.assert_true('plt' in ns)
     nt.assert_equal(ns['np'], np)
 
+from traitlets.config import Config
+
+
 class TestPylabSwitch(object):
     class Shell(InteractiveShell):
+        def init_history(self):
+            """Sets up the command history, and starts regular autosaves."""
+            self.config.HistoryManager.hist_file = ":memory:"
+            super().init_history()
+
         def enable_gui(self, gui):
             pass
 
@@ -179,6 +187,7 b' class TestPylabSwitch(object):'
         matplotlib.rcParamsOrig = self._saved_rcParamsOrig
 
     def test_qt(self):
+
         s = self.Shell()
         gui, backend = s.enable_matplotlib(None)
         nt.assert_equal(gui, 'qt')

IPython/terminal/interactiveshell.py

@@ -615,6 +615,13 b' class TerminalInteractiveShell(InteractiveShell):'
 
                 self.restore_term_title()
 
+        # try to call some at-exit operation optimistically as some things can't
+        # be done during interpreter shutdown. this is technically inaccurate as
+        # this make mainlool not re-callable, but that should be a rare if not
+        # in existent use case.
+
+        self._atexit_once()
+
 
     _inputhook = None
     def inputhook(self, context):