Remove deepcopy (#694)

* Remove deepcopy

Just found this one after updating something internal and hitting serialization issue again. See previous PR regarding deepcopy (they have no purpose).

* Fixed flake8 issues

* Add deepcopy to test

Engine input isolation removed, update test with deepcopy.

* Isolation no longer expected

Remove test with this expectation.

* Reconfigure tests no isolation nb.

Used deepcopy where necessary when tests used the isolated nb
expectation in unittest logic for assertion checks.

Co-authored-by: Matthew Seal <mseal007@gmail.com>

papermill/engines.py

@@ -1,6 +1,5 @@
 """Engines to perform different roles"""
 import sys
-import copy
 import datetime
 import dateutil
 
@@ -99,8 +98,7 @@ class NotebookExecutionManager(object):
     def __init__(
         self, nb, output_path=None, log_output=False, progress_bar=True, autosave_cell_every=30
     ):
-        # Deep copy the input to isolate the object being executed against
-        self.nb = copy.deepcopy(nb)
+        self.nb = nb
         self.output_path = output_path
         self.log_output = log_output
         self.start_time = None

papermill/tests/test_engines.py

@@ -36,14 +36,6 @@ def setUp(self):
         self.foo_nb = copy.deepcopy(self.nb)
         self.foo_nb.metadata['foo'] = 'bar'
 
-    def test_nb_isolation(self):
-        """
-        Tests that the engine notebook is isolated from source notebook
-        """
-        nb_man = NotebookExecutionManager(self.nb)
-        nb_man.nb.metadata['foo'] = 'bar'
-        self.assertNotEqual(nb_man.nb, self.nb)
-
     def test_basic_pbar(self):
         nb_man = NotebookExecutionManager(self.nb)
 
@@ -343,7 +335,11 @@ def execute_managed_notebook(cls, nb_man, kernel_name, **kwargs):
                     nb_man.cell_complete(cell)
 
         with patch.object(NotebookExecutionManager, 'save') as save_mock:
-            nb = CellCallbackEngine.execute_notebook(self.nb, 'python', output_path='foo.ipynb')
+            nb = CellCallbackEngine.execute_notebook(
+                copy.deepcopy(self.nb),
+                'python',
+                output_path='foo.ipynb'
+            )
 
             self.assertEqual(nb, AnyMock(NotebookNode))
             self.assertNotEqual(self.nb, nb)
@@ -373,7 +369,9 @@ def execute_managed_notebook(cls, nb_man, kernel_name, **kwargs):
         with patch.object(NotebookExecutionManager, 'save') as save_mock:
             with patch.object(NotebookExecutionManager, 'complete_pbar') as pbar_comp_mock:
                 nb = NoCellCallbackEngine.execute_notebook(
-                    self.nb, 'python', output_path='foo.ipynb'
+                    copy.deepcopy(self.nb),
+                    'python',
+                    output_path='foo.ipynb'
                 )
 
                 self.assertEqual(nb, AnyMock(NotebookNode))
@@ -407,7 +405,7 @@ def test_nb_convert_engine(self):
         with patch.object(engines, 'PapermillNotebookClient') as client_mock:
             with patch.object(NotebookExecutionManager, 'save') as save_mock:
                 nb = NBClientEngine.execute_notebook(
-                    self.nb,
+                    copy.deepcopy(self.nb),
                     'python',
                     output_path='foo.ipynb',
                     progress_bar=False,