prior

src/hdmf/backends/hdf5/h5tools.py

@@ -383,7 +383,10 @@ def copy_file(self, **kwargs):
              'default': True},
             {'name': 'herd', 'type': 'hdmf.common.resources.HERD',
              'doc': 'A HERD object to populate with references.',
-             'default': None})
+             'default': None},
+            {'name': 'expandable', 'type': bool, 'default': True,
+             'doc': ('Bool to set whether datasets are expandable by setting the max shape for all dimensions',
+                     'of a dataset to None and enabling auto-chunking by default.')})
     def write(self, **kwargs):
         """Write the container to an HDF5 file."""
         if self.__mode == 'r':
@@ -826,10 +829,16 @@ def close_linked_files(self):
              'doc': 'exhaust DataChunkIterators one at a time. If False, exhaust them concurrently',
              'default': True},
             {'name': 'export_source', 'type': str,
-             'doc': 'The source of the builders when exporting', 'default': None})
+             'doc': 'The source of the builders when exporting', 'default': None},
+            {'name': 'expandable', 'type': bool, 'default': True,
+             'doc': ('Bool to set whether datasets are expandable by setting the max shape for all dimensions',
+                     'of a dataset to None and enabling auto-chunking by default.')})
     def write_builder(self, **kwargs):
         f_builder = popargs('builder', kwargs)
-        link_data, exhaust_dci, export_source = getargs('link_data', 'exhaust_dci', 'export_source', kwargs)
+        link_data, exhaust_dci, export_source = getargs('link_data',
+                                                        'exhaust_dci',
+                                                        'export_source',
+                                                        kwargs)
         self.logger.debug("Writing GroupBuilder '%s' to path '%s' with kwargs=%s"
                           % (f_builder.name, self.source, kwargs))
         for name, gbldr in f_builder.groups.items():
@@ -1000,6 +1009,9 @@ def _filler():
              'default': True},
             {'name': 'export_source', 'type': str,
              'doc': 'The source of the builders when exporting', 'default': None},
+            {'name': 'expandable', 'type': bool, 'default': True,
+             'doc': ('Bool to set whether datasets are expandable by setting the max shape for all dimensions',
+                     'of a dataset to None and enabling auto-chunking by default.')},
             returns='the Group that was created', rtype=Group)
     def write_group(self, **kwargs):
         parent, builder = popargs('parent', 'builder', kwargs)
@@ -1100,14 +1112,17 @@ def write_link(self, **kwargs):
              'default': True},
             {'name': 'export_source', 'type': str,
              'doc': 'The source of the builders when exporting', 'default': None},
+            {'name': 'expandable', 'type': bool, 'default': True,
+             'doc': ('Bool to set whether datasets are expandable by setting the max shape for all dimensions',
+                     'of a dataset to None and enabling auto-chunking by default.')},
             returns='the Dataset that was created', rtype=Dataset)
     def write_dataset(self, **kwargs):  # noqa: C901
         """ Write a dataset to HDF5
 
         The function uses other dataset-dependent write functions, e.g,
         ``__scalar_fill__``, ``__list_fill__``, and ``__setup_chunked_dset__`` to write the data.
         """
-        parent, builder = popargs('parent', 'builder', kwargs)
+        parent, builder, expandable = popargs('parent', 'builder', 'expandable', kwargs)
         link_data, exhaust_dci, export_source = getargs('link_data', 'exhaust_dci', 'export_source', kwargs)
         self.logger.debug("Writing DatasetBuilder '%s' to parent group '%s'" % (builder.name, parent.name))
         if self.get_written(builder):
@@ -1228,7 +1243,7 @@ def _filler():
                 return
             # If the compound data type contains only regular data (i.e., no references) then we can write it as usual
             else:
-                dset = self.__list_fill__(parent, name, data, options)
+                dset = self.__list_fill__(parent, name, data, expandable, options)
         # Write a dataset containing references, i.e., a region or object reference.
         # NOTE: we can ignore options['io_settings'] for scalar data
         elif self.__is_ref(options['dtype']):
@@ -1323,7 +1338,7 @@ def _filler():
                 self.__dci_queue.append(dataset=dset, data=data)
             # Write a regular in memory array (e.g., numpy array, list etc.)
             elif hasattr(data, '__len__'):
-                dset = self.__list_fill__(parent, name, data, options)
+                dset = self.__list_fill__(parent, name, data, expandable, options)
             # Write a regular scalar dataset
             else:
                 dset = self.__scalar_fill__(parent, name, data, options)
@@ -1451,7 +1466,7 @@ def __chunked_iter_fill__(cls, parent, name, data, options=None):
         return dset
 
     @classmethod
-    def __list_fill__(cls, parent, name, data, options=None):
+    def __list_fill__(cls, parent, name, data, expandable, options=None):
         # define the io settings and data type if necessary
         io_settings = {}
         dtype = None