extract deep copy utility func

pyphare/pyphare/core/gridlayout.py

@@ -3,7 +3,7 @@
 import math
 import numpy as np
 
-from .phare_utilities import is_scalar, listify, np_array_ify
+from .phare_utilities import is_scalar, listify
 from .box import Box
 
 directions = ["x", "y", "z"]

pyphare/pyphare/core/phare_utilities.py

@@ -143,3 +143,19 @@ def print_trace():
     import sys, traceback
     _, _, tb = sys.exc_info()
     traceback.print_tb(tb)
+
+
+def deep_copy(item, memo, excludes=[]):
+    from copy import deepcopy
+
+    clazz = item.__class__
+    that = clazz.__new__(clazz)
+    memo[id(item)] = that
+    for key, value in item.__dict__.items():
+        # some objects are not picklable so cannot be deepcopied eg. h5py datasets
+        if key in excludes:
+            setattr(that, key, value)
+        else:
+            setattr(that, key, deepcopy(value, memo))
+    return that
+

pyphare/pyphare/pharesee/hierarchy.py

@@ -2,15 +2,14 @@
 
 import os
 import numpy as np
-from copy import deepcopy
 
 from .particles import Particles
 
 from ..core import box as boxm
 from ..core.box import Box
 from ..core.gridlayout import GridLayout
 import matplotlib.pyplot as plt
-from ..core.phare_utilities import refinement_ratio
+from ..core.phare_utilities import refinement_ratio, deep_copy
 
 
 
@@ -33,17 +32,8 @@ def __init__(self, layout, quantity):
 
 
     def __deepcopy__(self, memo):
-        # some objects are not picklable eg. h5py datasets
         no_copy_keys = ["dataset"] # do not copy these things
-        clazz = self.__class__
-        that = clazz.__new__(clazz)
-        memo[id(self)] = that
-        for key, value in self.__dict__.items():
-            if key in no_copy_keys:
-                setattr(that, key, value)
-            else:
-                setattr(that, key, deepcopy(value, memo))
-        return that
+        return deep_copy(self, memo, no_copy_keys)
 
 
 
@@ -214,6 +204,8 @@ def __repr__(self):
 
 
     def copy(self):
+        """does not copy patchdatas.datasets (see class PatchData)"""
+        from copy import deepcopy
         return deepcopy(self)