introduce write_dict_to_hdf()

pyiron_base/storage/hdfio.py

@@ -21,14 +21,14 @@
     open_hdf5,
     read_hdf5,
     write_hdf5_with_json_support,
+    write_dict_to_hdf,
     _is_ragged_in_1st_dim_only,
 )
 from pyiron_base.interfaces.has_groups import HasGroups
 from pyiron_base.state import state
 from pyiron_base.jobs.dynamic import JOB_DYN_DICT, class_constructor
 from pyiron_base.jobs.job.util import _get_safe_job_name
 import pyiron_base.project.maintenance
-import warnings
 
 __author__ = "Joerg Neugebauer, Jan Janssen"
 __copyright__ = (
@@ -846,8 +846,7 @@ def hd_copy(self, hdf_old, hdf_new, exclude_groups=None, exclude_nodes=None):
                 (set(hdf_old.list_nodes()) ^ set(check_nodes))
                 & set(hdf_old.list_nodes())
             )
-        for p in node_list:
-            hdf_new[p] = hdf_old[p]
+        write_dict_to_hdf(hdf=hdf_new, data_dict={p: hdf_old[p] for p in node_list})
         for p in group_list:
             h_new = hdf_new.create_group(p)
             ex_n = [e[-1] for e in exclude_nodes_split if p == e[0] or len(e) == 1]

pyiron_base/storage/helper_functions.py

@@ -57,13 +57,34 @@ def write_hdf5(
 
 def write_hdf5_with_json_support(value, path, file_handle):
     value, use_json = _check_json_conversion(value=value)
-    write_hdf5(
-        file_handle,
-        value,
-        title=path,
-        overwrite="update",
-        use_json=use_json,
-    )
+    try:
+        write_hdf5(
+            file_handle,
+            value,
+            title=path,
+            overwrite="update",
+            use_json=use_json,
+        )
+    except TypeError:
+        raise TypeError(
+            "Error saving {} (key {}): DataContainer doesn't support saving elements "
+            'of type "{}" to HDF!'.format(value, path, type(value))
+        ) from None
+
+
+def write_dict_to_hdf(hdf, data_dict, groups=[]):
+    with open_hdf5(hdf.file_name, mode="a") as store:
+        for k, v in data_dict.items():
+            if k not in groups:
+                write_hdf5_with_json_support(
+                    file_handle=store, value=v, path=hdf.get_h5_path(k)
+                )
+        for group in groups:
+            hdf_group = hdf.create_group(group)
+            for k, v in data_dict[group].items():
+                write_hdf5_with_json_support(
+                    file_handle=store, value=v, path=hdf_group.get_h5_path(k)
+                )
 
 
 def _check_json_conversion(value):