Use copy(deepcopy=true) for checkpointing

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+* Use `copy(deepcopy=True)` when checkpointing to make checkpointing more user-friendly and secure. IMPORTANT: might increase runtime, please open an issue if you face serious problems. [#172](https://github.com/precice/fenics-adapter/pull/172)
 * Add unit tests for checkpointing. [#173](https://github.com/precice/fenics-adapter/pull/173)
 
 ## 2.1.0

fenicsprecice/solverstate.py

@@ -13,9 +13,9 @@ def __init__(self, payload, t, n):
             Iteration number.
         """
         try:
-            self.payload = payload.copy()
-        except AttributeError:  # if .copy() does not exist, it probably is a list
-            self.payload = [item.copy() for item in payload]
+            self.payload = payload.copy(deepcopy=True)
+        except (AttributeError, TypeError):  # AttributeError, if .copy() does not exist; TypeError, if .copy(deepcopy) does not exist. -> Probably a list
+            self.payload = [item.copy(deepcopy=True) for item in payload]
 
         self.t = t
         self.n = n
@@ -34,9 +34,9 @@ def get_state(self):
             Iteration number.
         """
         try:
-            return self.payload.copy(), self.t, self.n
-        except AttributeError:  # if .copy() does not exist, it probably is a list
-            return [item.copy() for item in self.payload], self.t, self.n
+            return self.payload.copy(deepcopy=True), self.t, self.n
+        except (AttributeError, TypeError):  # AttributeError, if .copy() does not exist; TypeError, if .copy(deepcopy) does not exist. -> Probably a list
+            return [item.copy(deepcopy=True) for item in self.payload], self.t, self.n
 
     def print_state(self):
         payload, t, n = self.get_state()

tests/integration/test_fenicsprecice.py

@@ -25,7 +25,11 @@ def assign(self, new_value):
         """
         self.value = new_value.value
 
-    def copy(self):
+    def copy(self, deepcopy=False):
+        """
+        mock of dolfin.Function.copy
+        :param deepcopy: has no effect but we need to provide it to avoid throwing TypeError if copy(deepcopy=True) is called
+        """
         returned_array = MockedArray()
         returned_array.value = self.value
         return returned_array