Refactor use of deepcopy by docval (#238)

* Remove use of deepcopy by docval

* Use deepcopy on default value in case a complex obj is used

* Remove unused helper function

* Fix flake8 unused import

* Remove other unnecessary uses of deepcopy

src/hdmf/build/map.py

@@ -1,6 +1,6 @@
 import numpy as np
 from collections import OrderedDict
-from copy import copy, deepcopy
+from copy import copy
 from datetime import datetime
 
 from ..utils import docval, getargs, ExtenderMeta, get_docval, call_docval_func, fmt_docval_args
@@ -449,7 +449,7 @@ def __get_cls_dict(self, base, addl_fields, name=None, default_name=None):
         fields = list()
 
         # copy docval args from superclass
-        for arg in deepcopy(get_docval(base.__init__)):
+        for arg in get_docval(base.__init__):
             existing_args.add(arg['name'])
             if arg['name'] in addl_fields:
                 continue

src/hdmf/spec/namespace.py

@@ -1,6 +1,6 @@
 from collections import OrderedDict
 from datetime import datetime
-from copy import deepcopy, copy
+from copy import copy
 import ruamel.yaml as yaml
 import os.path
 import string
@@ -36,7 +36,7 @@ class SpecNamespace(dict):
 
     __types_key = 'data_types'
 
-    @docval(*deepcopy(_namespace_args))
+    @docval(*_namespace_args)
     def __init__(self, **kwargs):
         doc, full_name, name, version, date, author, contact, schema, catalog = \
             popargs('doc', 'full_name', 'name', 'version', 'date', 'author', 'contact', 'schema', 'catalog', kwargs)

src/hdmf/spec/spec.py

@@ -297,7 +297,7 @@ class BaseStorageSpec(Spec):
     __type_key = 'data_type'
     __id_key = 'object_id'
 
-    @docval(*deepcopy(_attrbl_args))
+    @docval(*_attrbl_args)
     def __init__(self, **kwargs):
         name, doc, parent, quantity, attributes, linkable, data_type_def, data_type_inc =\
              getargs('name', 'doc', 'parent', 'quantity', 'attributes',
@@ -477,7 +477,7 @@ def quantity(self):
         ''' The number of times the object being specified should be present '''
         return self.get('quantity', DEF_QUANTITY)
 
-    @docval(*deepcopy(_attr_args))
+    @docval(*_attr_args)
     def add_attribute(self, **kwargs):
         ''' Add an attribute to this specification '''
         pargs, pkwargs = fmt_docval_args(AttributeSpec.__init__, kwargs)
@@ -618,7 +618,7 @@ class DatasetSpec(BaseStorageSpec):
     To specify a table-like dataset i.e. a compound data type.
     '''
 
-    @docval(*deepcopy(_dataset_args))
+    @docval(*_dataset_args)
     def __init__(self, **kwargs):
         doc, shape, dims, dtype, default_value = popargs('doc', 'shape', 'dims', 'dtype', 'default_value', kwargs)
         if shape is not None:
@@ -811,7 +811,7 @@ class GroupSpec(BaseStorageSpec):
     ''' Specification for groups
     '''
 
-    @docval(*deepcopy(_group_args))
+    @docval(*_group_args)
     def __init__(self, **kwargs):
         doc, groups, datasets, links = popargs('doc', 'groups', 'datasets', 'links', kwargs)
         self.__data_types = dict()
@@ -1095,7 +1095,7 @@ def links(self):
         ''' The links specificed in this GroupSpec '''
         return tuple(self.get('links', tuple()))
 
-    @docval(*deepcopy(_group_args))
+    @docval(*_group_args)
     def add_group(self, **kwargs):
         ''' Add a new specification for a subgroup to this group specification '''
         doc = kwargs.pop('doc')
@@ -1127,7 +1127,7 @@ def get_group(self, **kwargs):
         name = getargs('name', kwargs)
         return self.__groups.get(name, self.__links.get(name))
 
-    @docval(*deepcopy(_dataset_args))
+    @docval(*_dataset_args)
     def add_dataset(self, **kwargs):
         ''' Add a new specification for a dataset to this group specification '''
         doc = kwargs.pop('doc')

src/hdmf/utils.py

@@ -1,5 +1,4 @@
 import copy as _copy
-import itertools as _itertools
 from abc import ABCMeta
 import collections
 import h5py
@@ -225,7 +224,7 @@ def __parse_args(validator, args, kwargs, enforce_type=True, enforce_shape=True,
                 ret[argname] = args[argsi]
                 argsi += 1
             else:
-                ret[argname] = arg['default']
+                ret[argname] = _copy.deepcopy(arg['default'])
             argval = ret[argname]
             if enforce_type:
                 if not __type_okay(argval, arg['type'], arg['default'] is None):
@@ -265,17 +264,6 @@ def __parse_args(validator, args, kwargs, enforce_type=True, enforce_shape=True,
     return {'args': ret, 'type_errors': type_errors, 'value_errors': value_errors}
 
 
-def __sort_args(validator):
-    pos = list()
-    kw = list()
-    for arg in validator:
-        if "default" in arg:
-            kw.append(arg)
-        else:
-            pos.append(arg)
-    return list(_itertools.chain(pos, kw))
-
-
 docval_idx_name = '__dv_idx__'
 docval_attr_name = '__docval__'
 __docval_args_loc = 'args'
@@ -411,7 +399,6 @@ def foo(self, **kwargs):
     rtype = options.pop('rtype', None)
     is_method = options.pop('is_method', True)
     allow_extra = options.pop('allow_extra', False)
-    val_copy = __sort_args(_copy.deepcopy(validator))
 
     def dec(func):
         _docval = _copy.copy(options)
@@ -420,7 +407,7 @@ def dec(func):
         func.__doc__ = _docval.get('doc', func.__doc__)
         pos = list()
         kw = list()
-        for a in val_copy:
+        for a in validator:
             try:
                 a['type'] = __resolve_type(a['type'])
             except Exception as e:
@@ -436,7 +423,7 @@ def dec(func):
             def func_call(*args, **kwargs):
                 self = args[0]
                 parsed = __parse_args(
-                            _copy.deepcopy(loc_val),
+                            loc_val,
                             args[1:],
                             kwargs,
                             enforce_type=enforce_type,
@@ -453,7 +440,7 @@ def func_call(*args, **kwargs):
                 return func(self, **parsed['args'])
         else:
             def func_call(*args, **kwargs):
-                parsed = __parse_args(_copy.deepcopy(loc_val),
+                parsed = __parse_args(loc_val,
                                       args,
                                       kwargs,
                                       enforce_type=enforce_type,