datacontainer open HDF5 file only once - unless the object implements…

… its own to_hdf() function

pyiron_base/storage/datacontainer.py

@@ -15,6 +15,7 @@
 
 from pyiron_base.storage.fileio import read, write
 from pyiron_base.storage.hdfstub import HDFStub
+from pyiron_base.storage.helper_functions import open_hdf5, write_hdf5_with_json_support
 from pyiron_base.interfaces.has_groups import HasGroups
 from pyiron_base.interfaces.has_hdf import HasHDF
 
@@ -784,7 +785,7 @@ def _get_hdf_group_name(self):
         return self.table_name
 
     def _to_hdf(self, hdf):
-        hdf["READ_ONLY"] = self.read_only
+        data_dict = {"READ_ONLY": self.read_only}
         written_keys = _internal_hdf_nodes.copy()
         for i, (k, v) in enumerate(self.items()):
             if isinstance(k, str) and "__index_" in k:
@@ -803,10 +804,15 @@ def _to_hdf(self, hdf):
                     del hdf[k]
                 v.to_hdf(hdf=hdf, group_name=k)
             else:
+                data_dict[k] = v
+        with open_hdf5(hdf.file_name, mode="a") as store:
+            for k, v in data_dict.items():
                 # if the value doesn't know how to serialize itself, assume
                 # that h5py knows how to
                 try:
-                    hdf[k] = v
+                    write_hdf5_with_json_support(
+                        file_handle=store, value=v, path=hdf.get_h5_path(k)
+                    )
                 except TypeError:
                     raise TypeError(
                         "Error saving {} (key {}): DataContainer doesn't support saving elements "