From 66f642b6a742ae8097a1c9732e8b4292a83c5e51 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Wed, 29 Apr 2020 17:59:51 +0200
Subject: [PATCH 01/18] Augment Section parent test with indirect access

---
 nixio/test/test_section.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nixio/test/test_section.py b/nixio/test/test_section.py
index 2f950ac7..ba77aae1 100644
--- a/nixio/test/test_section.py
+++ b/nixio/test/test_section.py
@@ -231,6 +231,9 @@ def test_parent(self):
         grp.metadata = child
         self.assertEqual(grp.metadata.parent, self.section)
 
+        # indirect access parent check
+        self.assertEqual(block.groups["group"].metadata.parent, self.section)
+
     def test_inverse_search(self):
         block = self.file.create_block("a block", "block with metadata")
         block.metadata = self.section

From 90abd221067536eb5457613aacc84202d30fc9f7 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Wed, 29 Apr 2020 19:19:11 +0200
Subject: [PATCH 02/18] Common method rename: _create_new -> create_new

The creator method is meant to be used by parent classes.  I had
originally made it "private" to imply it's for internal library use
only.

In the future, we might fold the creation functionality into the
__init__ function along with the instantiation of objects from a file.
---
 nixio/block.py               | 28 ++++++++++++++--------------
 nixio/data_array.py          | 24 ++++++++++++------------
 nixio/data_frame.py          |  8 ++++----
 nixio/dimensions.py          | 22 +++++++++++-----------
 nixio/entity.py              |  2 +-
 nixio/feature.py             |  2 +-
 nixio/file.py                |  4 ++--
 nixio/group.py               |  6 +++---
 nixio/multi_tag.py           |  6 +++---
 nixio/property.py            |  4 ++--
 nixio/section.py             | 12 ++++++------
 nixio/source.py              |  8 ++++----
 nixio/tag.py                 |  8 ++++----
 nixio/test/test_validator.py |  4 ++--
 14 files changed, 69 insertions(+), 69 deletions(-)

diff --git a/nixio/block.py b/nixio/block.py
index 1bf849d9..326d4032 100644
--- a/nixio/block.py
+++ b/nixio/block.py
@@ -49,9 +49,9 @@ def __init__(self, nixparent, h5group, compression=Compression.Auto):
         self._data_frames = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_, compression):
-        newentity = super(Block, cls)._create_new(nixparent, h5parent,
-                                                  name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_, compression):
+        newentity = super(Block, cls).create_new(nixparent, h5parent,
+                                                 name, type_)
         newentity._compr = compression
         return newentity
 
@@ -101,8 +101,8 @@ def create_multi_tag(self, name="", type_="", positions=None,
                                                  "{}-extents".format(type_),
                                                  data=extents)
                 extcreated = True
-            mtag = MultiTag._create_new(self, multi_tags,
-                                        name, type_, positions)
+            mtag = MultiTag.create_new(self, multi_tags,
+                                       name, type_, positions)
         except Exception as e:
             msg = "MultiTag Creation Failed"
             if poscreated:
@@ -150,7 +150,7 @@ def create_tag(self, name="", type_="", position=0,
         tags = self._h5group.open_group("tags")
         if name in tags:
             raise exceptions.DuplicateName("create_tag")
-        tag = Tag._create_new(self, tags, name, type_, position)
+        tag = Tag.create_new(self, tags, name, type_, position)
         return tag
 
     # Source
@@ -170,7 +170,7 @@ def create_source(self, name, type_):
         sources = self._h5group.open_group("sources")
         if name in sources:
             raise exceptions.DuplicateName("create_source")
-        src = Source._create_new(self, sources, name, type_)
+        src = Source.create_new(self, sources, name, type_)
         return src
 
     # Group
@@ -190,7 +190,7 @@ def create_group(self, name, type_):
         groups = self._h5group.open_group("groups")
         if name in groups:
             raise exceptions.DuplicateName("open_group")
-        grp = Group._create_new(self, groups, name, type_)
+        grp = Group.create_new(self, groups, name, type_)
         return grp
 
     def create_data_array(self, name="", array_type="", dtype=None, shape=None,
@@ -250,8 +250,8 @@ def create_data_array(self, name="", array_type="", dtype=None, shape=None,
             raise exceptions.DuplicateName("create_data_array")
         if compression == Compression.Auto:
             compression = self._compr
-        da = DataArray._create_new(self, data_arrays, name, array_type,
-                                   dtype, shape, compression)
+        da = DataArray.create_new(self, data_arrays, name, array_type,
+                                  dtype, shape, compression)
         if data is not None:
             da.write_direct(data)
         return da
@@ -328,7 +328,7 @@ def create_data_frame(self, name="", type_="", col_dict=None,
                     )
                 else:  # col_dtypes is None and data is None
                     raise ValueError(
-                           "The data type of each column have to be specified"
+                        "The data type of each column have to be specified"
                     )
                 if len(col_names) != len(col_dict):
                     raise exceptions.DuplicateColumnName
@@ -348,7 +348,7 @@ def create_data_frame(self, name="", type_="", col_dict=None,
                     # data is None or type(data[0]) != np.void
                     # data_type doesnt matter
                     raise ValueError(
-                           "No information about column names is provided!"
+                        "No information about column names is provided!"
                     )
 
         if col_dict is not None:
@@ -362,8 +362,8 @@ def create_data_frame(self, name="", type_="", col_dict=None,
             dt_arr = list(col_dict.items())
             col_dtype = np.dtype(dt_arr)
 
-        df = DataFrame._create_new(self, data_frames, name,
-                                   type_, shape, col_dtype, compression)
+        df = DataFrame.create_new(self, data_frames, name,
+                                  type_, shape, col_dtype, compression)
 
         if data is not None:
             if type(data[0]) == np.void:
diff --git a/nixio/data_array.py b/nixio/data_array.py
index 7384f51a..5a25be78 100644
--- a/nixio/data_array.py
+++ b/nixio/data_array.py
@@ -38,10 +38,10 @@ def __init__(self, nixparent, h5group):
         self._dimensions = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_, data_type, shape,
-                    compression):
-        newentity = super(DataArray, cls)._create_new(nixparent, h5parent,
-                                                      name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_, data_type, shape,
+                   compression):
+        newentity = super(DataArray, cls).create_new(nixparent, h5parent,
+                                                     name, type_)
         datacompr = False
         if compression == Compression.DeflateNormal:
             datacompr = True
@@ -87,7 +87,7 @@ def append_set_dimension(self, labels=None):
         """
         dimgroup = self._h5group.open_group("dimensions")
         index = len(dimgroup) + 1
-        setdim = SetDimension._create_new(dimgroup, index)
+        setdim = SetDimension.create_new(dimgroup, index)
         if labels:
             setdim.labels = labels
         if self._parent._parent.time_auto_update:
@@ -109,8 +109,8 @@ def append_sampled_dimension(self, sampling_interval, label=None,
         """
         dimgroup = self._h5group.open_group("dimensions")
         index = len(dimgroup) + 1
-        smpldim = SampledDimension._create_new(dimgroup, index,
-                                               sampling_interval)
+        smpldim = SampledDimension.create_new(dimgroup, index,
+                                              sampling_interval)
         if label:
             smpldim.label = label
         if unit:
@@ -134,7 +134,7 @@ def append_range_dimension(self, ticks, label=None, unit=None):
         """
         dimgroup = self._h5group.open_group("dimensions")
         index = len(dimgroup) + 1
-        rdim = RangeDimension._create_new(dimgroup, index, ticks)
+        rdim = RangeDimension.create_new(dimgroup, index, ticks)
         if label:
             rdim.label = label
             rdim.unit = unit
@@ -160,8 +160,8 @@ def append_data_frame_dimension(self, data_frame, column_idx=None):
         """
         dimgroup = self._h5group.open_group("dimensions")
         index = len(dimgroup) + 1
-        dfdim = DataFrameDimension._create_new(dimgroup, index,
-                                               data_frame, column_idx)
+        dfdim = DataFrameDimension.create_new(dimgroup, index,
+                                              data_frame, column_idx)
         if self._parent._parent.time_auto_update:
             self.force_updated_at()
         return dfdim
@@ -194,7 +194,7 @@ def append_alias_range_dimension(self):
                     "Current SI unit is {}".format(u),
                     "DataArray.append_alias_range_dimension"
                 )
-        return RangeDimension._create_new_alias(dimgroup, 1, self)
+        return RangeDimension.create_new_alias(dimgroup, 1, self)
 
     def delete_dimensions(self):
         """
@@ -315,7 +315,7 @@ def unit(self, u):
             u = None
         util.check_attr_type(u, str)
         if (self._dimension_count() == 1 and
-            self.dimensions[0].dimension_type == DimensionType.Range and
+                self.dimensions[0].dimension_type == DimensionType.Range and
                 self.dimensions[0].is_alias and u is not None):
             if not (util.units.is_si(u) or util.units.is_compound(u)):
                 raise InvalidUnit(
diff --git a/nixio/data_frame.py b/nixio/data_frame.py
index ab5fea36..016fd48b 100644
--- a/nixio/data_frame.py
+++ b/nixio/data_frame.py
@@ -33,10 +33,10 @@ def __init__(self, nixparent, h5group):
         self._rows = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent,
-                    name, type_, shape, col_dtype, compression):
-        newentity = super(DataFrame, cls)._create_new(nixparent, h5parent,
-                                                      name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_,
+                   shape, col_dtype, compression):
+        newentity = super(DataFrame, cls).create_new(nixparent, h5parent,
+                                                     name, type_)
         newentity._h5group.create_dataset("data", (shape, ), col_dtype)
         return newentity
 
diff --git a/nixio/dimensions.py b/nixio/dimensions.py
index 7f1e2e8b..1413e6c9 100644
--- a/nixio/dimensions.py
+++ b/nixio/dimensions.py
@@ -42,7 +42,7 @@ def __init__(self, h5group, index):
         self.dim_index = int(index)
 
     @classmethod
-    def _create_new(cls, parent, index):
+    def create_new(cls, parent, index):
         h5group = parent.open_group(str(index))
         newdim = cls(h5group, index)
         return newdim
@@ -76,8 +76,8 @@ def __init__(self, h5group, index):
         super(SampledDimension, self).__init__(h5group, index)
 
     @classmethod
-    def _create_new(cls, parent, index, sample):
-        newdim = super(SampledDimension, cls)._create_new(parent, index)
+    def create_new(cls, parent, index, sample):
+        newdim = super(SampledDimension, cls).create_new(parent, index)
         newdim._set_dimension_type(DimensionType.Sample)
         newdim.sampling_interval = sample
         return newdim
@@ -172,15 +172,15 @@ def __init__(self, h5group, index):
         super(RangeDimension, self).__init__(h5group, index)
 
     @classmethod
-    def _create_new(cls, parent, index, ticks):
-        newdim = super(RangeDimension, cls)._create_new(parent, index)
+    def create_new(cls, parent, index, ticks):
+        newdim = super(RangeDimension, cls).create_new(parent, index)
         newdim._set_dimension_type(DimensionType.Range)
         newdim._h5group.write_data("ticks", ticks, dtype=DataType.Double)
         return newdim
 
     @classmethod
-    def _create_new_alias(cls, parent, index, da):
-        newdim = super(RangeDimension, cls)._create_new(parent, index)
+    def create_new_alias(cls, parent, index, da):
+        newdim = super(RangeDimension, cls).create_new(parent, index)
         newdim._set_dimension_type(DimensionType.Range)
         newdim._h5group.create_link(da, da.id)
         return newdim
@@ -301,8 +301,8 @@ def __init__(self, h5group, index):
         super(SetDimension, self).__init__(h5group, index)
 
     @classmethod
-    def _create_new(cls, parent, index):
-        newdim = super(SetDimension, cls)._create_new(parent, index)
+    def create_new(cls, parent, index):
+        newdim = super(SetDimension, cls).create_new(parent, index)
         newdim._set_dimension_type(DimensionType.Set)
         return newdim
 
@@ -325,7 +325,7 @@ def __init__(self, h5group, index):
         super(DataFrameDimension, self).__init__(h5group, index)
 
     @classmethod
-    def _create_new(cls, parent, index, data_frame, column):
+    def create_new(cls, parent, index, data_frame, column):
         """
         Create a new Dimension that points to a DataFrame
 
@@ -338,7 +338,7 @@ def _create_new(cls, parent, index, data_frame, column):
 
         :return: The new DataFrameDimension
         """
-        newdim = super(DataFrameDimension, cls)._create_new(parent, index)
+        newdim = super(DataFrameDimension, cls).create_new(parent, index)
         newdim.data_frame = data_frame
         newdim.column_idx = column
         newdim._set_dimension_type(DimensionType.DataFrame)
diff --git a/nixio/entity.py b/nixio/entity.py
index fc8b99dd..ebdf6d79 100644
--- a/nixio/entity.py
+++ b/nixio/entity.py
@@ -18,7 +18,7 @@ def __init__(self, nixparent, h5group):
         self._parent = nixparent
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name=None, type_=None):
+    def create_new(cls, nixparent, h5parent, name=None, type_=None):
         if name and type_:
             util.check_entity_name_and_type(name, type_)
             id_ = util.create_id()
diff --git a/nixio/feature.py b/nixio/feature.py
index bedca5ea..865ec308 100644
--- a/nixio/feature.py
+++ b/nixio/feature.py
@@ -20,7 +20,7 @@ def __init__(self, nixparent, h5group):
         self._parent = nixparent
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, data, link_type):
+    def create_new(cls, nixparent, h5parent, data, link_type):
         id_ = util.create_id()
         h5group = h5parent.open_group(id_)
         h5group.set_attr("entity_id", id_)
diff --git a/nixio/file.py b/nixio/file.py
index 3f415aa5..cbf0c33d 100644
--- a/nixio/file.py
+++ b/nixio/file.py
@@ -416,7 +416,7 @@ def create_block(self, name="", type_="", compression=Compression.Auto,
             raise ValueError("Block with the given name already exists!")
         if compression == Compression.Auto:
             compression = self._compr
-        block = Block._create_new(self, self._data, name, type_, compression)
+        block = Block.create_new(self, self._data, name, type_, compression)
         return block
 
     # Section
@@ -437,7 +437,7 @@ def create_section(self, name, type_="undefined", oid=None):
         """
         if name in self.sections:
             raise DuplicateName("create_section")
-        sec = Section._create_new(self, self._metadata, name, type_, oid)
+        sec = Section.create_new(self, self._metadata, name, type_, oid)
         return sec
 
     @property
diff --git a/nixio/group.py b/nixio/group.py
index 628aaff8..a7a03309 100644
--- a/nixio/group.py
+++ b/nixio/group.py
@@ -28,9 +28,9 @@ def __init__(self, nixparent, h5group):
         self._sources = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_):
-        newentity = super(Group, cls)._create_new(nixparent, h5parent,
-                                                  name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_):
+        newentity = super(Group, cls).create_new(nixparent, h5parent,
+                                                 name, type_)
         return newentity
 
     @property
diff --git a/nixio/multi_tag.py b/nixio/multi_tag.py
index 7ad3402b..2cb9a0d8 100644
--- a/nixio/multi_tag.py
+++ b/nixio/multi_tag.py
@@ -29,9 +29,9 @@ def __init__(self, nixparent, h5group):
         self._features = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_, positions):
-        newentity = super(MultiTag, cls)._create_new(nixparent, h5parent,
-                                                     name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_, positions):
+        newentity = super(MultiTag, cls).create_new(nixparent, h5parent,
+                                                    name, type_)
         newentity.positions = positions
         return newentity
 
diff --git a/nixio/property.py b/nixio/property.py
index 0145126d..38981c21 100644
--- a/nixio/property.py
+++ b/nixio/property.py
@@ -97,8 +97,8 @@ def __init__(self, nixparent, h5dataset):
         self._h5dataset = self._h5group
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name,
-                    dtype, shape=None, oid=None):
+    def create_new(cls, nixparent, h5parent, name,
+                   dtype, shape=None, oid=None):
         if shape is None or shape[0] == 0:
             shape = (8, )
         util.check_entity_name(name)
diff --git a/nixio/section.py b/nixio/section.py
index 8837f2f0..48d82a15 100644
--- a/nixio/section.py
+++ b/nixio/section.py
@@ -55,9 +55,9 @@ def __init__(self, nixparent, h5group):
         self._properties = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_, oid=None):
-        newentity = super(Section, cls)._create_new(nixparent, h5parent,
-                                                    name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_, oid=None):
+        newentity = super(Section, cls).create_new(nixparent, h5parent,
+                                                   name, type_)
         if util.is_uuid(oid):
             newentity._h5group.set_attr("entity_id", oid)
 
@@ -83,7 +83,7 @@ def create_section(self, name, type_="undefined", oid=None):
         sections = self._h5group.open_group("sections", True)
         if name in sections:
             raise exceptions.DuplicateName("create_section")
-        sec = Section._create_new(self, sections, name, type_, oid)
+        sec = Section.create_new(self, sections, name, type_, oid)
         sec._sec_parent = self
         return sec
 
@@ -169,7 +169,7 @@ def create_property(self, name="", values_or_dtype=0, oid=None,
                     raise TypeError("Array contains inconsistent values.")
         shape = (len(vals),)
 
-        prop = Property._create_new(self, properties, name, dtype, shape, oid)
+        prop = Property.create_new(self, properties, name, dtype, shape, oid)
         prop.values = vals
 
         return prop
@@ -293,7 +293,7 @@ def parent(self):
         if self._sec_parent is not None:
             return self._sec_parent
         rootmd = self._h5group.file.open_group("metadata")
-        # Assuming most metadata trees are shallow---doing BFS
+        # BFS
         sections = [Section(None, sg) for sg in rootmd]
         if self in sections:
             # Top-level section
diff --git a/nixio/source.py b/nixio/source.py
index ec2e7ab0..2ffe338c 100644
--- a/nixio/source.py
+++ b/nixio/source.py
@@ -23,9 +23,9 @@ def __init__(self, nixparent, h5group):
         self._sources = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_):
-        newentity = super(Source, cls)._create_new(nixparent, h5parent,
-                                                   name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_):
+        newentity = super(Source, cls).create_new(nixparent, h5parent,
+                                                  name, type_)
         return newentity
 
     # Source
@@ -45,7 +45,7 @@ def create_source(self, name, type_):
         sources = self._h5group.open_group("sources", True)
         if name in sources:
             raise exceptions.DuplicateName("create_source")
-        src = Source._create_new(self, sources, name, type_)
+        src = Source.create_new(self, sources, name, type_)
         return src
 
     @property
diff --git a/nixio/tag.py b/nixio/tag.py
index 7e5ba127..78c6669d 100644
--- a/nixio/tag.py
+++ b/nixio/tag.py
@@ -105,7 +105,7 @@ def create_feature(self, data, link_type):
             link_type = link_type.lower()
         link_type = LinkType(link_type)
         features = self._h5group.open_group("features")
-        feat = Feature._create_new(self, features, data, link_type)
+        feat = Feature.create_new(self, features, data, link_type)
         return feat
 
     @staticmethod
@@ -173,9 +173,9 @@ def __init__(self, nixparent, h5group):
         self._features = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_, position):
-        newentity = super(Tag, cls)._create_new(nixparent, h5parent,
-                                                name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_, position):
+        newentity = super(Tag, cls).create_new(nixparent, h5parent,
+                                               name, type_)
         newentity.position = position
         return newentity
 
diff --git a/nixio/test/test_validator.py b/nixio/test/test_validator.py
index ad8486ae..77d34b2d 100644
--- a/nixio/test/test_validator.py
+++ b/nixio/test/test_validator.py
@@ -247,7 +247,7 @@ def test_incorrect_dim_index(self):
         da.delete_dimensions()
         dimgroup = da._h5group.open_group("dimensions")
         # This wont work if we ever change the internals
-        nix.SetDimension._create_new(dimgroup, "10")
+        nix.SetDimension.create_new(dimgroup, "10")
         res = self.file.validate()
         assert VE.IncorrectDimensionIndex.format(1, 10) in res["errors"][da]
 
@@ -256,7 +256,7 @@ def test_invalid_dim_index(self):
         da.delete_dimensions()
         dimgroup = da._h5group.open_group("dimensions")
         # This wont work if we ever change the internals
-        nix.SetDimension._create_new(dimgroup, "-1")
+        nix.SetDimension.create_new(dimgroup, "-1")
         res = self.file.validate()
         assert VE.InvalidDimensionIndex.format(1) in res["errors"][da]
 

From 9e0eeb4f2214bdc242a2c45e7cbaba2adc6de880 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Wed, 29 Apr 2020 19:38:17 +0200
Subject: [PATCH 03/18] Add file read-only property to Entity

---
 nixio/entity.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/nixio/entity.py b/nixio/entity.py
index ebdf6d79..e8ccbac8 100644
--- a/nixio/entity.py
+++ b/nixio/entity.py
@@ -16,6 +16,7 @@ def __init__(self, nixparent, h5group):
         util.check_entity_id(h5group.get_attr("entity_id"))
         self._h5group = h5group
         self._parent = nixparent
+        self._file = None
 
     @classmethod
     def create_new(cls, nixparent, h5parent, name=None, type_=None):
@@ -54,6 +55,16 @@ def created_at(self):
         """
         return util.str_to_time(self._h5group.get_attr("created_at"))
 
+    @property
+    def file(self):
+        """
+        Reference to the NIX File object.
+        This is a read-only property.
+
+        :rtype: nixio.File
+        """
+        return self._file
+
     def force_created_at(self, t=None):
         """
         Sets the creation time `created_at` to the given time

From 92bb2fb0173d80946fcb472cff49897b88d71b63 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Wed, 29 Apr 2020 21:43:45 +0200
Subject: [PATCH 04/18] Remove old unused function

---
 nixio/multi_tag.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/nixio/multi_tag.py b/nixio/multi_tag.py
index 2cb9a0d8..de5c9c93 100644
--- a/nixio/multi_tag.py
+++ b/nixio/multi_tag.py
@@ -109,11 +109,6 @@ def features(self):
             self._features = FeatureContainer("features", self, Feature)
         return self._features
 
-    def _get_slice(self, data, index):
-        offset, count = self._get_offset_and_count(data, index)
-        sl = tuple(slice(o, o + c) for o, c in zip(offset, count))
-        return sl
-
     def _calc_data_slices(self, data, index):
         positions = self.positions
         extents = self.extents

From 1cfec74d635033ecf2748b968b9092e3ca6d6683 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 00:21:36 +0200
Subject: [PATCH 05/18] Initialise all Entity objects with reference to File

All Entities are initialised with and keep a reference to the File
object.
Containers keep the same reference to initialise objects that it
instantiates from the file.
Non-Entity objects that also require this reference:
- Feature
- Dimension objects
---
 nixio/block.py               | 38 ++++++++++++---------
 nixio/container.py           | 10 +++---
 nixio/data_array.py          | 43 +++++++++++-------------
 nixio/data_frame.py          | 13 ++++----
 nixio/dimensions.py          | 64 ++++++++++++++++++++----------------
 nixio/entity.py              |  9 ++---
 nixio/feature.py             |  9 ++---
 nixio/file.py                |  6 ++--
 nixio/group.py               | 11 ++++---
 nixio/multi_tag.py           | 24 +++++++-------
 nixio/property.py            |  8 ++---
 nixio/section.py             | 29 ++++++++--------
 nixio/source.py              | 14 ++++----
 nixio/tag.py                 | 18 +++++-----
 nixio/test/test_validator.py |  6 ++--
 15 files changed, 159 insertions(+), 143 deletions(-)

diff --git a/nixio/block.py b/nixio/block.py
index 326d4032..622f7b04 100644
--- a/nixio/block.py
+++ b/nixio/block.py
@@ -38,8 +38,9 @@
 
 class Block(Entity):
 
-    def __init__(self, nixparent, h5group, compression=Compression.Auto):
-        super(Block, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group,
+                 compression=Compression.Auto):
+        super(Block, self).__init__(nixfile, nixparent, h5group)
         self._groups = None
         self._data_arrays = None
         self._tags = None
@@ -50,7 +51,8 @@ def __init__(self, nixparent, h5group, compression=Compression.Auto):
 
     @classmethod
     def create_new(cls, nixparent, h5parent, name, type_, compression):
-        newentity = super(Block, cls).create_new(nixparent, h5parent,
+        nixfile = nixparent  # file is parent
+        newentity = super(Block, cls).create_new(nixfile, nixparent, h5parent,
                                                  name, type_)
         newentity._compr = compression
         return newentity
@@ -101,7 +103,7 @@ def create_multi_tag(self, name="", type_="", positions=None,
                                                  "{}-extents".format(type_),
                                                  data=extents)
                 extcreated = True
-            mtag = MultiTag.create_new(self, multi_tags,
+            mtag = MultiTag.create_new(self.file, self, multi_tags,
                                        name, type_, positions)
         except Exception as e:
             msg = "MultiTag Creation Failed"
@@ -150,7 +152,7 @@ def create_tag(self, name="", type_="", position=0,
         tags = self._h5group.open_group("tags")
         if name in tags:
             raise exceptions.DuplicateName("create_tag")
-        tag = Tag.create_new(self, tags, name, type_, position)
+        tag = Tag.create_new(self.file, self, tags, name, type_, position)
         return tag
 
     # Source
@@ -170,7 +172,7 @@ def create_source(self, name, type_):
         sources = self._h5group.open_group("sources")
         if name in sources:
             raise exceptions.DuplicateName("create_source")
-        src = Source.create_new(self, sources, name, type_)
+        src = Source.create_new(self.file, self, sources, name, type_)
         return src
 
     # Group
@@ -190,7 +192,7 @@ def create_group(self, name, type_):
         groups = self._h5group.open_group("groups")
         if name in groups:
             raise exceptions.DuplicateName("open_group")
-        grp = Group.create_new(self, groups, name, type_)
+        grp = Group.create_new(self.file, self, groups, name, type_)
         return grp
 
     def create_data_array(self, name="", array_type="", dtype=None, shape=None,
@@ -250,7 +252,7 @@ def create_data_array(self, name="", array_type="", dtype=None, shape=None,
             raise exceptions.DuplicateName("create_data_array")
         if compression == Compression.Auto:
             compression = self._compr
-        da = DataArray.create_new(self, data_arrays, name, array_type,
+        da = DataArray.create_new(self.file, self, data_arrays, name, array_type,
                                   dtype, shape, compression)
         if data is not None:
             da.write_direct(data)
@@ -362,7 +364,7 @@ def create_data_frame(self, name="", type_="", col_dict=None,
             dt_arr = list(col_dict.items())
             col_dtype = np.dtype(dt_arr)
 
-        df = DataFrame.create_new(self, data_frames, name,
+        df = DataFrame.create_new(self.file, self, data_frames, name,
                                   type_, shape, col_dtype, compression)
 
         if data is not None:
@@ -510,7 +512,7 @@ def sources(self):
         This is a read only attribute.
         """
         if self._sources is None:
-            self._sources = SourceContainer("sources", self, Source)
+            self._sources = SourceContainer("sources", self.file, self, Source)
         return self._sources
 
     @property
@@ -522,7 +524,8 @@ def multi_tags(self):
         This is a read only attribute.
         """
         if self._multi_tags is None:
-            self._multi_tags = Container("multi_tags", self, MultiTag)
+            self._multi_tags = Container("multi_tags", self.file,
+                                         self, MultiTag)
         return self._multi_tags
 
     @property
@@ -534,7 +537,7 @@ def tags(self):
         This is a read only attribute.
         """
         if self._tags is None:
-            self._tags = Container("tags", self, Tag)
+            self._tags = Container("tags", self.file, self, Tag)
         return self._tags
 
     @property
@@ -547,13 +550,15 @@ def data_arrays(self):
         This is a read only attribute.
         """
         if self._data_arrays is None:
-            self._data_arrays = Container("data_arrays", self, DataArray)
+            self._data_arrays = Container("data_arrays", self.file,
+                                          self, DataArray)
         return self._data_arrays
 
     @property
     def data_frames(self):
         if self._data_frames is None:
-            self._data_frames = Container("data_frames", self, DataFrame)
+            self._data_frames = Container("data_frames", self.file,
+                                          self, DataFrame)
         return self._data_frames
 
     @property
@@ -565,7 +570,7 @@ def groups(self):
         This is a read only attribute.
         """
         if self._groups is None:
-            self._groups = Container("groups", self, Group)
+            self._groups = Container("groups", self.file, self, Group)
         return self._groups
 
     # metadata
@@ -579,7 +584,8 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None,
+                           self._h5group.open_group("metadata"))
         else:
             return None
 
diff --git a/nixio/container.py b/nixio/container.py
index bd2e2a79..ac4febb9 100644
--- a/nixio/container.py
+++ b/nixio/container.py
@@ -23,14 +23,15 @@ class Container(object):
     checking and instantiations)
     """
 
-    def __init__(self, name, parent, itemclass):
+    def __init__(self, name, nixfile, parent, itemclass):
         self._backend = parent._h5group.open_group(name)
         self._itemclass = itemclass
+        self._file = nixfile
         self._parent = parent
         self._name = name
 
     def _inst_item(self, item):
-        return self._itemclass(self._parent, item)
+        return self._itemclass(self._file, self._parent, item)
 
     def __len__(self):
         return len(self._backend)
@@ -180,7 +181,8 @@ class LinkContainer(Container):
     """
 
     def __init__(self, name, parent, itemclass, itemstore):
-        super(LinkContainer, self).__init__(name, parent, itemclass)
+        super(LinkContainer, self).__init__(name, parent.file,
+                                            parent, itemclass)
         self._itemstore = itemstore
 
     def __delitem__(self, item):
@@ -249,7 +251,7 @@ def __contains__(self, item):
         return False
 
     def _inst_item(self, item):
-        return self._itemclass(self._itemstore._parent, item)
+        return self._itemclass(self._file, self._itemstore._parent, item)
 
     @staticmethod
     def _item_key(item):
diff --git a/nixio/data_array.py b/nixio/data_array.py
index 5a25be78..5bd5c118 100644
--- a/nixio/data_array.py
+++ b/nixio/data_array.py
@@ -32,16 +32,16 @@ class DataSliceMode(Enum):
 
 class DataArray(Entity, DataSet):
 
-    def __init__(self, nixparent, h5group):
-        super(DataArray, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(DataArray, self).__init__(nixfile, nixparent, h5group)
         self._sources = None
         self._dimensions = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_, data_type, shape,
-                   compression):
-        newentity = super(DataArray, cls).create_new(nixparent, h5parent,
-                                                     name, type_)
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_,
+                   data_type, shape, compression):
+        newentity = super(DataArray, cls).create_new(nixfile, nixparent,
+                                                     h5parent, name, type_)
         datacompr = False
         if compression == Compression.DeflateNormal:
             datacompr = True
@@ -85,9 +85,8 @@ def append_set_dimension(self, labels=None):
         :returns: The newly created SetDimension.
         :rtype: SetDimension
         """
-        dimgroup = self._h5group.open_group("dimensions")
-        index = len(dimgroup) + 1
-        setdim = SetDimension.create_new(dimgroup, index)
+        index = len(self.dimensions) + 1
+        setdim = SetDimension.create_new(self, index)
         if labels:
             setdim.labels = labels
         if self._parent._parent.time_auto_update:
@@ -107,10 +106,8 @@ def append_sampled_dimension(self, sampling_interval, label=None,
         :returns: The newly created SampledDimension.
         :rtype: SampledDimension
         """
-        dimgroup = self._h5group.open_group("dimensions")
-        index = len(dimgroup) + 1
-        smpldim = SampledDimension.create_new(dimgroup, index,
-                                              sampling_interval)
+        index = len(self.dimensions) + 1
+        smpldim = SampledDimension.create_new(self, index, sampling_interval)
         if label:
             smpldim.label = label
         if unit:
@@ -132,9 +129,8 @@ def append_range_dimension(self, ticks, label=None, unit=None):
         :returns: The newly created RangeDimension.
         :rtype: RangeDimension
         """
-        dimgroup = self._h5group.open_group("dimensions")
-        index = len(dimgroup) + 1
-        rdim = RangeDimension.create_new(dimgroup, index, ticks)
+        index = len(self.dimensions) + 1
+        rdim = RangeDimension.create_new(self, index, ticks)
         if label:
             rdim.label = label
             rdim.unit = unit
@@ -158,9 +154,8 @@ def append_data_frame_dimension(self, data_frame, column_idx=None):
         :returns: Thew newly created DataFrameDimension.
         :rtype: DataFrameDimension
         """
-        dimgroup = self._h5group.open_group("dimensions")
-        index = len(dimgroup) + 1
-        dfdim = DataFrameDimension.create_new(dimgroup, index,
+        index = len(self.dimensions) + 1
+        dfdim = DataFrameDimension.create_new(self, index,
                                               data_frame, column_idx)
         if self._parent._parent.time_auto_update:
             self.force_updated_at()
@@ -183,7 +178,6 @@ def append_alias_range_dimension(self):
         if self._dimension_count() > 0:
             raise ValueError("Cannot append additional alias dimension. "
                              "There must only be one!")
-        dimgroup = self._h5group.open_group("dimensions")
         # check if existing unit is SI
         if self.unit:
             u = self.unit
@@ -194,7 +188,7 @@ def append_alias_range_dimension(self):
                     "Current SI unit is {}".format(u),
                     "DataArray.append_alias_range_dimension"
                 )
-        return RangeDimension.create_new_alias(dimgroup, 1, self)
+        return RangeDimension.create_new_alias(self, 1)
 
     def delete_dimensions(self):
         """
@@ -390,8 +384,8 @@ def dimensions(self):
         :type: Container of dimension descriptors.
         """
         if self._dimensions is None:
-            self._dimensions = DimensionContainer("dimensions", self,
-                                                  Dimension)
+            self._dimensions = DimensionContainer("dimensions", self.file,
+                                                  self, Dimension)
         return self._dimensions
 
     # metadata
@@ -406,7 +400,8 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None,
+                           self._h5group.open_group("metadata"))
         else:
             return None
 
diff --git a/nixio/data_frame.py b/nixio/data_frame.py
index 016fd48b..983a9d09 100644
--- a/nixio/data_frame.py
+++ b/nixio/data_frame.py
@@ -26,17 +26,17 @@
 
 class DataFrame(Entity, DataSet):
 
-    def __init__(self, nixparent, h5group):
-        super(DataFrame, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(DataFrame, self).__init__(nixfile, nixparent, h5group)
         self._sources = None
         self._columns = None
         self._rows = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_,
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_,
                    shape, col_dtype, compression):
-        newentity = super(DataFrame, cls).create_new(nixparent, h5parent,
-                                                     name, type_)
+        newentity = super(DataFrame, cls).create_new(nixfile, nixparent,
+                                                     h5parent, name, type_)
         newentity._h5group.create_dataset("data", (shape, ), col_dtype)
         return newentity
 
@@ -423,7 +423,8 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None,
+                           self._h5group.open_group("metadata"))
         else:
             return None
 
diff --git a/nixio/dimensions.py b/nixio/dimensions.py
index 1413e6c9..0eda9d22 100644
--- a/nixio/dimensions.py
+++ b/nixio/dimensions.py
@@ -32,20 +32,18 @@ def _inst_item(self, item):
             DimensionType.DataFrame: DataFrameDimension,
         }[DimensionType(item.get_attr("dimension_type"))]
         idx = item.name
-        return cls(item, idx)
+        return cls(self._parent, idx)
 
 
 class Dimension(object):
 
-    def __init__(self, h5group, index):
+    def __init__(self, nixfile, data_array, index):
+        dimgroup = data_array._h5group.open_group("dimensions")
+        h5group = dimgroup.open_group(str(index))
         self._h5group = h5group
         self.dim_index = int(index)
-
-    @classmethod
-    def create_new(cls, parent, index):
-        h5group = parent.open_group(str(index))
-        newdim = cls(h5group, index)
-        return newdim
+        self._parent = data_array
+        self._file = nixfile
 
     @property
     def dimension_type(self):
@@ -72,12 +70,13 @@ def __repr__(self):
 
 class SampledDimension(Dimension):
 
-    def __init__(self, h5group, index):
-        super(SampledDimension, self).__init__(h5group, index)
+    def __init__(self, data_array, index):
+        nixfile = data_array.file
+        super(SampledDimension, self).__init__(nixfile, data_array, index)
 
     @classmethod
-    def create_new(cls, parent, index, sample):
-        newdim = super(SampledDimension, cls).create_new(parent, index)
+    def create_new(cls, data_array, index, sample):
+        newdim = cls(data_array, index)
         newdim._set_dimension_type(DimensionType.Sample)
         newdim.sampling_interval = sample
         return newdim
@@ -168,21 +167,22 @@ def offset(self, o):
 
 class RangeDimension(Dimension):
 
-    def __init__(self, h5group, index):
-        super(RangeDimension, self).__init__(h5group, index)
+    def __init__(self, data_array, index):
+        nixfile = data_array.file
+        super(RangeDimension, self).__init__(nixfile, data_array, index)
 
     @classmethod
-    def create_new(cls, parent, index, ticks):
-        newdim = super(RangeDimension, cls).create_new(parent, index)
+    def create_new(cls, data_array, index, ticks):
+        newdim = cls(data_array, index)
         newdim._set_dimension_type(DimensionType.Range)
         newdim._h5group.write_data("ticks", ticks, dtype=DataType.Double)
         return newdim
 
     @classmethod
-    def create_new_alias(cls, parent, index, da):
-        newdim = super(RangeDimension, cls).create_new(parent, index)
+    def create_new_alias(cls, data_array, index):
+        newdim = cls(data_array, index)
         newdim._set_dimension_type(DimensionType.Range)
-        newdim._h5group.create_link(da, da.id)
+        newdim._h5group.create_link(data_array, data_array.id)
         return newdim
 
     @property
@@ -297,12 +297,13 @@ def axis(self, count, start=0):
 
 class SetDimension(Dimension):
 
-    def __init__(self, h5group, index):
-        super(SetDimension, self).__init__(h5group, index)
+    def __init__(self, data_array, index):
+        nixfile = data_array.file
+        super(SetDimension, self).__init__(nixfile, data_array, index)
 
     @classmethod
-    def create_new(cls, parent, index):
-        newdim = super(SetDimension, cls).create_new(parent, index)
+    def create_new(cls, data_array, index):
+        newdim = cls(data_array, index)
         newdim._set_dimension_type(DimensionType.Set)
         return newdim
 
@@ -321,15 +322,18 @@ def labels(self, labels):
 
 class DataFrameDimension(Dimension):
 
-    def __init__(self, h5group, index):
-        super(DataFrameDimension, self).__init__(h5group, index)
+    def __init__(self, data_array, index):
+        nixfile = data_array.file
+        super(DataFrameDimension, self).__init__(nixfile, data_array, index)
 
     @classmethod
-    def create_new(cls, parent, index, data_frame, column):
+    def create_new(cls, data_array, index, data_frame, column):
         """
         Create a new Dimension that points to a DataFrame
 
-        :param parent: DataArray the dimension will be attached to
+        :param data_array: The DataArray this Dimension belongs to
+
+        :param parent: The H5Group for the dimensions
 
         :param data_frame: the referenced DataFrame for this Dimension
 
@@ -338,7 +342,7 @@ def create_new(cls, parent, index, data_frame, column):
 
         :return: The new DataFrameDimension
         """
-        newdim = super(DataFrameDimension, cls).create_new(parent, index)
+        newdim = cls(data_array, index)
         newdim.data_frame = data_frame
         newdim.column_idx = column
         newdim._set_dimension_type(DimensionType.DataFrame)
@@ -419,7 +423,9 @@ def get_label(self, index=None):
     def data_frame(self):
         dfname = self._h5group.get_by_pos(0).name
         grp = self._h5group.open_group(dfname)
-        df = DataFrame(grp.h5root.group["data_frames"], grp)
+        nixblock = self._parent._parent
+        nixfile = self._file
+        df = DataFrame(nixfile, nixblock, grp)
         return df
 
     @data_frame.setter
diff --git a/nixio/entity.py b/nixio/entity.py
index e8ccbac8..e51f32fc 100644
--- a/nixio/entity.py
+++ b/nixio/entity.py
@@ -12,14 +12,14 @@
 
 class Entity(object):
 
-    def __init__(self, nixparent, h5group):
+    def __init__(self, nixfile, nixparent, h5group):
         util.check_entity_id(h5group.get_attr("entity_id"))
         self._h5group = h5group
         self._parent = nixparent
-        self._file = None
+        self._file = nixfile
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name=None, type_=None):
+    def create_new(cls, nixfile, nixparent, h5parent, name=None, type_=None):
         if name and type_:
             util.check_entity_name_and_type(name, type_)
             id_ = util.create_id()
@@ -30,7 +30,8 @@ def create_new(cls, nixparent, h5parent, name=None, type_=None):
         h5group.set_attr("name", name)
         h5group.set_attr("type", type_)
         h5group.set_attr("entity_id", id_)
-        newentity = cls(nixparent, h5group)
+
+        newentity = cls(nixfile, nixparent, h5group)
         newentity.force_created_at()
         newentity.force_updated_at()
         return newentity
diff --git a/nixio/feature.py b/nixio/feature.py
index 865ec308..d5e3fc9c 100644
--- a/nixio/feature.py
+++ b/nixio/feature.py
@@ -14,17 +14,18 @@
 
 class Feature(object):
 
-    def __init__(self, nixparent, h5group):
+    def __init__(self, nixfile, nixparent, h5group):
         util.check_entity_id(h5group.get_attr("entity_id"))
         self._h5group = h5group
         self._parent = nixparent
+        self._file = nixfile
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, data, link_type):
+    def create_new(cls, nixfile, nixparent, h5parent, data, link_type):
         id_ = util.create_id()
         h5group = h5parent.open_group(id_)
         h5group.set_attr("entity_id", id_)
-        newfeature = cls(nixparent, h5group)
+        newfeature = cls(nixfile, nixparent, h5group)
         newfeature.link_type = link_type
         newfeature.data = data
         newfeature._h5group.set_attr("created_at",
@@ -56,7 +57,7 @@ def link_type(self, lt):
     def data(self):
         if "data" not in self._h5group:
             raise RuntimeError("Feature.data: DataArray not found!")
-        return DataArray(self._parent._parent,
+        return DataArray(self._file, self._parent._parent,
                          self._h5group.open_group("data"))
 
     @data.setter
diff --git a/nixio/file.py b/nixio/file.py
index cbf0c33d..9f7873dd 100644
--- a/nixio/file.py
+++ b/nixio/file.py
@@ -437,7 +437,7 @@ def create_section(self, name, type_="undefined", oid=None):
         """
         if name in self.sections:
             raise DuplicateName("create_section")
-        sec = Section.create_new(self, self._metadata, name, type_, oid)
+        sec = Section.create_new(self, self, self._metadata, name, type_, oid)
         return sec
 
     @property
@@ -450,7 +450,7 @@ def blocks(self):
         create_block method of File. This is a read-only attribute.
         """
         if self._blocks is None:
-            self._blocks = Container("data", self, Block)
+            self._blocks = Container("data", self, self, Block)
         return self._blocks
 
     def find_sections(self, filtr=lambda _: True, limit=None):
@@ -486,7 +486,7 @@ def sections(self):
         This is a read-only property.
         """
         if self._sections is None:
-            self._sections = SectionContainer("metadata", self, Section)
+            self._sections = SectionContainer("metadata", self, self, Section)
         return self._sections
 
 
diff --git a/nixio/group.py b/nixio/group.py
index a7a03309..9360509f 100644
--- a/nixio/group.py
+++ b/nixio/group.py
@@ -19,8 +19,8 @@
 
 class Group(Entity):
 
-    def __init__(self, nixparent, h5group):
-        super(Group, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(Group, self).__init__(nixfile, nixparent, h5group)
         self._data_arrays = None
         self._data_frames = None
         self._tags = None
@@ -28,8 +28,8 @@ def __init__(self, nixparent, h5group):
         self._sources = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_):
-        newentity = super(Group, cls).create_new(nixparent, h5parent,
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_):
+        newentity = super(Group, cls).create_new(nixfile, nixparent, h5parent,
                                                  name, type_)
         return newentity
 
@@ -115,7 +115,8 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None,
+                           self._h5group.open_group("metadata"))
         else:
             return None
 
diff --git a/nixio/multi_tag.py b/nixio/multi_tag.py
index de5c9c93..6d1be56d 100644
--- a/nixio/multi_tag.py
+++ b/nixio/multi_tag.py
@@ -22,16 +22,16 @@
 
 class MultiTag(BaseTag):
 
-    def __init__(self, nixparent, h5group):
-        super(MultiTag, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(MultiTag, self).__init__(nixfile, nixparent, h5group)
         self._sources = None
         self._references = None
         self._features = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_, positions):
-        newentity = super(MultiTag, cls).create_new(nixparent, h5parent,
-                                                    name, type_)
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_, positions):
+        newentity = super(MultiTag, cls).create_new(nixfile, nixparent,
+                                                    h5parent, name, type_)
         newentity.positions = positions
         return newentity
 
@@ -44,7 +44,8 @@ def positions(self):
         """
         if "positions" not in self._h5group:
             raise RuntimeError("MultiTag.positions: DataArray not found!")
-        return DataArray(self._parent, self._h5group.open_group("positions"))
+        return DataArray(self.file, self._parent,
+                         self._h5group.open_group("positions"))
 
     @positions.setter
     def positions(self, da):
@@ -65,9 +66,9 @@ def extents(self):
         :type: DataArray or None
         """
         if "extents" in self._h5group:
-            return DataArray(self._parent, self._h5group.open_group("extents"))
-        else:
-            return None
+            return DataArray(self.file, self._parent,
+                             self._h5group.open_group("extents"))
+        return None
 
     @extents.setter
     def extents(self, da):
@@ -106,7 +107,8 @@ def features(self):
         :type: Container of Feature.
         """
         if self._features is None:
-            self._features = FeatureContainer("features", self, Feature)
+            self._features = FeatureContainer("features", self.file,
+                                              self, Feature)
         return self._features
 
     def _calc_data_slices(self, data, index):
@@ -261,7 +263,7 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None, self._h5group.open_group("metadata"))
         else:
             return None
 
diff --git a/nixio/property.py b/nixio/property.py
index 38981c21..bf18729a 100644
--- a/nixio/property.py
+++ b/nixio/property.py
@@ -92,12 +92,12 @@ def get_odml_type(cls, dtype):
 
 class Property(Entity):
     """An odML Property"""
-    def __init__(self, nixparent, h5dataset):
-        super(Property, self).__init__(nixparent, h5dataset)
+    def __init__(self, nixfile, nixparent, h5dataset):
+        super(Property, self).__init__(nixfile, nixparent, h5dataset)
         self._h5dataset = self._h5group
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name,
+    def create_new(cls, nixfile, nixparent, h5parent, name,
                    dtype, shape=None, oid=None):
         if shape is None or shape[0] == 0:
             shape = (8, )
@@ -112,7 +112,7 @@ def create_new(cls, nixparent, h5parent, name,
 
         h5dataset.set_attr("entity_id", oid)
 
-        newentity = cls(nixparent, h5dataset)
+        newentity = cls(nixfile, nixparent, h5dataset)
         newentity.force_created_at()
         newentity.force_updated_at()
 
diff --git a/nixio/section.py b/nixio/section.py
index 48d82a15..6ec0df3f 100644
--- a/nixio/section.py
+++ b/nixio/section.py
@@ -48,16 +48,16 @@ def __getattribute__(self, item):
 
 class Section(Entity):
 
-    def __init__(self, nixparent, h5group):
-        super(Section, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(Section, self).__init__(nixfile, nixparent, h5group)
         self._sec_parent = None
         self._sections = None
         self._properties = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_, oid=None):
-        newentity = super(Section, cls).create_new(nixparent, h5parent,
-                                                   name, type_)
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_, oid=None):
+        newentity = super(Section, cls).create_new(nixfile, nixparent,
+                                                   h5parent, name, type_)
         if util.is_uuid(oid):
             newentity._h5group.set_attr("entity_id", oid)
 
@@ -83,7 +83,7 @@ def create_section(self, name, type_="undefined", oid=None):
         sections = self._h5group.open_group("sections", True)
         if name in sections:
             raise exceptions.DuplicateName("create_section")
-        sec = Section.create_new(self, sections, name, type_, oid)
+        sec = Section.create_new(self.file, self, sections, name, type_, oid)
         sec._sec_parent = self
         return sec
 
@@ -169,7 +169,8 @@ def create_property(self, name="", values_or_dtype=0, oid=None,
                     raise TypeError("Array contains inconsistent values.")
         shape = (len(vals),)
 
-        prop = Property.create_new(self, properties, name, dtype, shape, oid)
+        prop = Property.create_new(self.file, self, properties,
+                                   name, dtype, shape, oid)
         prop.values = vals
 
         return prop
@@ -240,7 +241,7 @@ def link(self):
         if "link" not in self._h5group:
             return None
 
-        return Section(self, self._h5group.open_group("link"))
+        return Section(self.file, self, self._h5group.open_group("link"))
 
     @link.setter
     def link(self, id_or_sec):
@@ -249,7 +250,7 @@ def link(self, id_or_sec):
         if isinstance(id_or_sec, Section):
             sec = id_or_sec
         else:
-            rootsec = Section(self, self._h5group.h5root)
+            rootsec = Section(self.file, self, self._h5group.h5root)
             sec = rootsec.find_sections(filtr=lambda x: x.id == id_or_sec)
 
         self._h5group.create_link(sec, "link")
@@ -258,7 +259,7 @@ def link(self, id_or_sec):
 
     def inherited_properties(self):
         properties = self._h5group.open_group("properties")
-        inhprops = [Property(self, h5prop) for h5prop in properties]
+        inhprops = [Property(self.file, self, h5prop) for h5prop in properties]
         if self.link:
             inhprops.extend(self.link.inherited_properties())
         return inhprops
@@ -294,7 +295,7 @@ def parent(self):
             return self._sec_parent
         rootmd = self._h5group.file.open_group("metadata")
         # BFS
-        sections = [Section(None, sg) for sg in rootmd]
+        sections = [Section(self.file, None, sg) for sg in rootmd]
         if self in sections:
             # Top-level section
             return None
@@ -444,7 +445,8 @@ def sections(self):
         :type: Container of Section
         """
         if self._sections is None:
-            self._sections = SectionContainer("sections", self, Section)
+            self._sections = SectionContainer("sections", self.file,
+                                              self, Section)
         return self._sections
 
     def __len__(self):
@@ -504,7 +506,8 @@ def props(self):
         :type: Container of Property
         """
         if self._properties is None:
-            self._properties = Container("properties", self, Property)
+            self._properties = Container("properties", self.file,
+                                         self, Property)
         return self._properties
 
     def pprint(self, indent=2, max_depth=1, max_length=80, current_depth=0):
diff --git a/nixio/source.py b/nixio/source.py
index 2ffe338c..dc33987c 100644
--- a/nixio/source.py
+++ b/nixio/source.py
@@ -18,13 +18,13 @@
 
 class Source(Entity):
 
-    def __init__(self, nixparent, h5group):
-        super(Source, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(Source, self).__init__(nixfile, nixparent, h5group)
         self._sources = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_):
-        newentity = super(Source, cls).create_new(nixparent, h5parent,
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_):
+        newentity = super(Source, cls).create_new(nixfile, nixparent, h5parent,
                                                   name, type_)
         return newentity
 
@@ -45,7 +45,7 @@ def create_source(self, name, type_):
         sources = self._h5group.open_group("sources", True)
         if name in sources:
             raise exceptions.DuplicateName("create_source")
-        src = Source.create_new(self, sources, name, type_)
+        src = Source.create_new(self.file, self, sources, name, type_)
         return src
 
     @property
@@ -99,7 +99,7 @@ def sources(self):
         This is a read only attribute.
         """
         if self._sources is None:
-            self._sources = SourceContainer("sources", self, Source)
+            self._sources = SourceContainer("sources", self.file, self, Source)
         return self._sources
 
     # metadata
@@ -114,7 +114,7 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None, self._h5group.open_group("metadata"))
         else:
             return None
 
diff --git a/nixio/tag.py b/nixio/tag.py
index 78c6669d..e4a8c19a 100644
--- a/nixio/tag.py
+++ b/nixio/tag.py
@@ -105,7 +105,7 @@ def create_feature(self, data, link_type):
             link_type = link_type.lower()
         link_type = LinkType(link_type)
         features = self._h5group.open_group("features")
-        feat = Feature.create_new(self, features, data, link_type)
+        feat = Feature.create_new(self.file, self, features, data, link_type)
         return feat
 
     @staticmethod
@@ -166,15 +166,15 @@ def _pos_to_idx(pos, unit, dim):
 
 class Tag(BaseTag):
 
-    def __init__(self, nixparent, h5group):
-        super(Tag, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group):
+        super(Tag, self).__init__(nixfile, nixparent, h5group)
         self._sources = None
         self._references = None
         self._features = None
 
     @classmethod
-    def create_new(cls, nixparent, h5parent, name, type_, position):
-        newentity = super(Tag, cls).create_new(nixparent, h5parent,
+    def create_new(cls, nixfile, nixparent, h5parent, name, type_, position):
+        newentity = super(Tag, cls).create_new(nixfile, nixparent, h5parent,
                                                name, type_)
         newentity.position = position
         return newentity
@@ -347,7 +347,8 @@ def features(self):
         :type: Container of Feature.
         """
         if self._features is None:
-            self._features = FeatureContainer("features", self, Feature)
+            self._features = FeatureContainer("features", self.file,
+                                              self, Feature)
         return self._features
 
     @property
@@ -375,9 +376,8 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
-        else:
-            return None
+            return Section(self.file, None, self._h5group.open_group("metadata"))
+        return None
 
     @metadata.setter
     def metadata(self, sect):
diff --git a/nixio/test/test_validator.py b/nixio/test/test_validator.py
index 77d34b2d..ac5f5893 100644
--- a/nixio/test/test_validator.py
+++ b/nixio/test/test_validator.py
@@ -245,18 +245,16 @@ def test_check_data_array_invalid_unit(self):
     def test_incorrect_dim_index(self):
         da = self.file.blocks[1].data_arrays["data-1d"]
         da.delete_dimensions()
-        dimgroup = da._h5group.open_group("dimensions")
         # This wont work if we ever change the internals
-        nix.SetDimension.create_new(dimgroup, "10")
+        nix.SetDimension.create_new(da, "10")
         res = self.file.validate()
         assert VE.IncorrectDimensionIndex.format(1, 10) in res["errors"][da]
 
     def test_invalid_dim_index(self):
         da = self.file.blocks[1].data_arrays["data-1d"]
         da.delete_dimensions()
-        dimgroup = da._h5group.open_group("dimensions")
         # This wont work if we ever change the internals
-        nix.SetDimension.create_new(dimgroup, "-1")
+        nix.SetDimension.create_new(da, "-1")
         res = self.file.validate()
         assert VE.InvalidDimensionIndex.format(1) in res["errors"][da]
 

From 9aaefe316c544891f13ec79dc97ad5adce07dc24 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Wed, 29 Apr 2020 21:39:01 +0200
Subject: [PATCH 06/18] Test object file references

Testing in container for convenience (has all objects) and because
instantiating objects through containers is where an object might lose
references to parent objects.
---
 nixio/test/test_container.py | 40 ++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/nixio/test/test_container.py b/nixio/test/test_container.py
index d8ed5b79..21e5b393 100644
--- a/nixio/test/test_container.py
+++ b/nixio/test/test_container.py
@@ -73,13 +73,53 @@ def test_link_container_index_getter(self):
         self.assertEqual(self.multi_tag,
                          self.group.multi_tags[0])
 
+    def test_file_references(self):
+        # add some sources
+        self.source = self.block.create_source("test source", "containertest")
+        self.child_source = self.source.create_source("test source 2",
+                                                      "containertest")
+        # using assertIs since the reference should be the same instance as
+        # the original
+
+        # created objects
+        self.assertIs(self.block.file, self.file)
+        self.assertIs(self.group.file, self.file)
+        self.assertIs(self.dataarray.file, self.file)
+        self.assertIs(self.tag.file, self.file)
+        self.assertIs(self.multi_tag.file, self.file)
+        self.assertIs(self.positions.file, self.file)
+        self.assertIs(self.source.file, self.file)
+        self.assertIs(self.child_source.file, self.file)
+
+        # instantiated through container getters
+        blk = self.file.blocks[0]
+        self.assertIs(blk.file, self.file)
+        self.assertIs(blk.groups[0].file, self.file)
+        self.assertIs(blk.data_arrays[0].file, self.file)
+        self.assertIs(blk.tags[0].file, self.file)
+        self.assertIs(blk.multi_tags[0].file, self.file)
+        self.assertIs(blk.sources[0].file, self.file)
+        self.assertIs(blk.sources[0].sources[0].file, self.file)
+
+        # linked through group
+        self.assertIs(self.group.data_arrays[0].file, self.file)
+        self.assertIs(self.group.tags[0].file, self.file)
+        self.assertIs(self.group.multi_tags[0].file, self.file)
+
     def test_parent_references(self):
+        # add some sources
+        self.source = self.block.create_source("test source", "containertest")
+        self.child_source = self.source.create_source("test source 2",
+                                                      "containertest")
+
         self.assertEqual(self.block._parent, self.file)
         self.assertEqual(self.group._parent, self.block)
         self.assertEqual(self.dataarray._parent, self.block)
         self.assertEqual(self.tag._parent, self.block)
         self.assertEqual(self.multi_tag._parent, self.block)
         self.assertEqual(self.positions._parent, self.block)
+        self.assertEqual(self.source._parent, self.block)
+        self.assertEqual(self.child_source._parent, self.source)
 
     def test_link_parent_references(self):
         self.assertEqual(self.group.data_arrays[0]._parent, self.block)

From da44eb7a9a05f510541661c74a2ca3f4762a6ecc Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 02:10:29 +0200
Subject: [PATCH 07/18] Use file property to read time_auto_update setting

---
 nixio/data_array.py | 16 ++++++++--------
 nixio/data_frame.py |  2 +-
 nixio/entity.py     | 10 ++--------
 nixio/feature.py    |  4 ++--
 nixio/multi_tag.py  |  4 ++--
 nixio/tag.py        |  6 +++---
 6 files changed, 18 insertions(+), 24 deletions(-)

diff --git a/nixio/data_array.py b/nixio/data_array.py
index 5bd5c118..770db9fb 100644
--- a/nixio/data_array.py
+++ b/nixio/data_array.py
@@ -89,7 +89,7 @@ def append_set_dimension(self, labels=None):
         setdim = SetDimension.create_new(self, index)
         if labels:
             setdim.labels = labels
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
         return setdim
 
@@ -114,7 +114,7 @@ def append_sampled_dimension(self, sampling_interval, label=None,
             smpldim.unit = unit
         if offset:
             smpldim.offset = offset
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
         return smpldim
 
@@ -134,7 +134,7 @@ def append_range_dimension(self, ticks, label=None, unit=None):
         if label:
             rdim.label = label
             rdim.unit = unit
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
         return rdim
 
@@ -157,7 +157,7 @@ def append_data_frame_dimension(self, data_frame, column_idx=None):
         index = len(self.dimensions) + 1
         dfdim = DataFrameDimension.create_new(self, index,
                                               data_frame, column_idx)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
         return dfdim
 
@@ -252,7 +252,7 @@ def polynom_coefficients(self, coeff):
         else:
             dtype = DataType.Double
             self._h5group.write_data("polynom_coefficients", coeff, dtype)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
@@ -270,7 +270,7 @@ def expansion_origin(self):
     def expansion_origin(self, eo):
         util.check_attr_type(eo, Number)
         self._h5group.set_attr("expansion_origin", eo)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
@@ -288,7 +288,7 @@ def label(self):
     def label(self, l):
         util.check_attr_type(l, str)
         self._h5group.set_attr("label", l)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
@@ -318,7 +318,7 @@ def unit(self, u):
                     "DataArray.unit"
                 )
         self._h5group.set_attr("unit", u)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     def get_slice(self, positions, extents=None, mode=DataSliceMode.Index):
diff --git a/nixio/data_frame.py b/nixio/data_frame.py
index 983a9d09..aa3309bc 100644
--- a/nixio/data_frame.py
+++ b/nixio/data_frame.py
@@ -348,7 +348,7 @@ def units(self, u):
                 util.check_attr_type(i, str)
         unit = np.array(u, util.vlen_str_dtype)
         self._h5group.set_attr("units", unit)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
diff --git a/nixio/entity.py b/nixio/entity.py
index e51f32fc..94608b90 100644
--- a/nixio/entity.py
+++ b/nixio/entity.py
@@ -120,10 +120,7 @@ def definition(self):
     def definition(self, d):
         util.check_attr_type(d, str)
         self._h5group.set_attr("definition", d)
-        par = self._parent
-        while isinstance(par, Entity):
-            par = par._parent
-        if par.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
@@ -154,10 +151,7 @@ def type(self, t):
             raise AttributeError("type can't be None")
         util.check_attr_type(t, str)
         self._h5group.set_attr("type", t)
-        par = self._parent
-        while isinstance(par, Entity):
-            par = par._parent
-        if par.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     def __eq__(self, other):
diff --git a/nixio/feature.py b/nixio/feature.py
index d5e3fc9c..d88e4cf8 100644
--- a/nixio/feature.py
+++ b/nixio/feature.py
@@ -49,7 +49,7 @@ def link_type(self, lt):
             lt = lt.lower()
         lt = LinkType(lt)
         self._h5group.set_attr("link_type", lt.value)
-        if self._parent._parent._parent.time_auto_update:
+        if self._file.time_auto_update:
             t = util.now_int()
             self._h5group.set_attr("updated_at", util.time_to_str(t))
 
@@ -70,7 +70,7 @@ def data(self, da):
         if "data" in self._h5group:
             del self._h5group["data"]
         self._h5group.create_link(da, "data")
-        if self._parent._parent._parent.time_auto_update:
+        if self._file.time_auto_update:
             t = util.now_int()
             self._h5group.set_attr("updated_at", util.time_to_str(t))
 
diff --git a/nixio/multi_tag.py b/nixio/multi_tag.py
index 6d1be56d..a230766c 100644
--- a/nixio/multi_tag.py
+++ b/nixio/multi_tag.py
@@ -54,7 +54,7 @@ def positions(self, da):
         if "positions" in self._h5group:
             del self._h5group["positions"]
         self._h5group.create_link(da, "positions")
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
@@ -76,7 +76,7 @@ def extents(self, da):
             del self._h5group["extents"]
         else:
             self._h5group.create_link(da, "extents")
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
diff --git a/nixio/tag.py b/nixio/tag.py
index e4a8c19a..364c7e46 100644
--- a/nixio/tag.py
+++ b/nixio/tag.py
@@ -86,7 +86,7 @@ def units(self, units):
 
             dtype = DataType.String
             self._h5group.write_data("units", sanitized, dtype)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     def create_feature(self, data, link_type):
@@ -196,7 +196,7 @@ def position(self, pos):
         else:
             dtype = DataType.Double
             self._h5group.write_data("position", pos, dtype)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     @property
@@ -217,7 +217,7 @@ def extent(self, ext):
         else:
             dtype = DataType.Double
             self._h5group.write_data("extent", ext, dtype)
-        if self._parent._parent.time_auto_update:
+        if self.file.time_auto_update:
             self.force_updated_at()
 
     def _calc_data_slices(self, data):

From 3602171aa110976588f56db0294919e2bca1f319 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 02:13:45 +0200
Subject: [PATCH 08/18] Feature.file property (read only)

---
 nixio/feature.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/nixio/feature.py b/nixio/feature.py
index d88e4cf8..efc2adbc 100644
--- a/nixio/feature.py
+++ b/nixio/feature.py
@@ -39,6 +39,10 @@ def create_new(cls, nixfile, nixparent, h5parent, data, link_type):
     def id(self):
         return self._h5group.get_attr("entity_id")
 
+    @property
+    def file(self):
+        return self._file
+
     @property
     def link_type(self):
         return LinkType(self._h5group.get_attr("link_type"))
@@ -49,7 +53,7 @@ def link_type(self, lt):
             lt = lt.lower()
         lt = LinkType(lt)
         self._h5group.set_attr("link_type", lt.value)
-        if self._file.time_auto_update:
+        if self.file.time_auto_update:
             t = util.now_int()
             self._h5group.set_attr("updated_at", util.time_to_str(t))
 
@@ -57,7 +61,7 @@ def link_type(self, lt):
     def data(self):
         if "data" not in self._h5group:
             raise RuntimeError("Feature.data: DataArray not found!")
-        return DataArray(self._file, self._parent._parent,
+        return DataArray(self.file, self._parent._parent,
                          self._h5group.open_group("data"))
 
     @data.setter
@@ -70,7 +74,7 @@ def data(self, da):
         if "data" in self._h5group:
             del self._h5group["data"]
         self._h5group.create_link(da, "data")
-        if self._file.time_auto_update:
+        if self.file.time_auto_update:
             t = util.now_int()
             self._h5group.set_attr("updated_at", util.time_to_str(t))
 

From 32e765bb9010ac8b4ffe6ec0ddf69c57c15805d7 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 02:16:52 +0200
Subject: [PATCH 09/18] Test auto_update_time setting

Type and Definition changes on Block.
---
 nixio/test/test_file.py | 55 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

diff --git a/nixio/test/test_file.py b/nixio/test/test_file.py
index 2266b5de..e386ae7e 100644
--- a/nixio/test/test_file.py
+++ b/nixio/test/test_file.py
@@ -10,6 +10,7 @@
 import unittest
 import h5py
 import numpy as np
+import time
 
 import nixio as nix
 import nixio.file as filepy
@@ -166,6 +167,60 @@ def test_copy_on_file(self):
         assert self.file.blocks[0] == self.file.blocks[1]  # ID stays the same
         assert self.file.blocks[0].name != self.file.blocks[1].name
 
+    def test_timestamp_autoupdate_definition(self):
+        blk = self.file.create_block("block", "timetest")
+        blktime = blk.updated_at
+        blk.definition = "updated"
+        # no update
+        self.assertEqual(blk.updated_at, blktime)
+
+        rblk = self.file.blocks["block"]  # read through container
+        rblk.definition = "updated again"
+        self.assertEqual(rblk.updated_at, blktime)
+
+        # close and recreate file with auto_update_time enabled
+        self.file.close()
+        self.file = nix.File(self.testfilename, nix.FileMode.Overwrite,
+                             auto_update_time=True)
+        blk = self.file.create_block("block", "timetest")
+        blktime = blk.updated_at
+        time.sleep(1)  # wait for time to change
+        blk.definition = "update"
+        self.assertNotEqual(blk.updated_at, blktime)
+
+        rblk = self.file.blocks["block"]  # read through container
+        rblktime = rblk.updated_at
+        time.sleep(1)  # wait for time to change
+        rblk.definition = "time should change"
+        self.assertNotEqual(rblk.updated_at, rblktime)
+
+    def test_timestamp_autoupdate_type(self):
+        blk = self.file.create_block("block", "timetest")
+        blktime = blk.updated_at
+        blk.type = "updated"
+        # no update
+        self.assertEqual(blk.updated_at, blktime)
+
+        rblk = self.file.blocks["block"]  # read through container
+        rblk.type = "updated again"
+        self.assertEqual(rblk.updated_at, blktime)
+
+        # close and recreate file with auto_update_time enabled
+        self.file.close()
+        self.file = nix.File(self.testfilename, nix.FileMode.Overwrite,
+                             auto_update_time=True)
+        blk = self.file.create_block("block", "timetest")
+        blktime = blk.updated_at
+        time.sleep(1)  # wait for time to change
+        blk.type = "update"
+        self.assertNotEqual(blk.updated_at, blktime)
+
+        rblk = self.file.blocks["block"]  # read through container
+        rblktime = rblk.updated_at
+        time.sleep(1)  # wait for time to change
+        rblk.type = "time should change"
+        self.assertNotEqual(rblk.updated_at, rblktime)
+
 
 class TestFileVer(unittest.TestCase):
 

From e8eaaa1c97dab99e623a2ee881d5fcee7f14cb65 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 17:21:46 +0200
Subject: [PATCH 10/18] Rename auto update timestamp option and true by default

- Rename 'time_auto_update' to 'auto_update_timestamp'
- Property and constructor argument are the same
- Enabled by default: Updating timestamps should be the default.  The
  overhead is probably minimal (perhaps even negligible) and should only
  be disabled for performance when required.
---
 nixio/data_array.py     | 16 ++++++++--------
 nixio/data_frame.py     |  2 +-
 nixio/entity.py         |  4 ++--
 nixio/feature.py        |  4 ++--
 nixio/file.py           | 33 +++++++++++++++++++++------------
 nixio/multi_tag.py      |  4 ++--
 nixio/section.py        |  6 +++---
 nixio/tag.py            |  6 +++---
 nixio/test/test_file.py | 34 ++++++++++++++++------------------
 9 files changed, 58 insertions(+), 51 deletions(-)

diff --git a/nixio/data_array.py b/nixio/data_array.py
index 770db9fb..2b0d85b8 100644
--- a/nixio/data_array.py
+++ b/nixio/data_array.py
@@ -89,7 +89,7 @@ def append_set_dimension(self, labels=None):
         setdim = SetDimension.create_new(self, index)
         if labels:
             setdim.labels = labels
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
         return setdim
 
@@ -114,7 +114,7 @@ def append_sampled_dimension(self, sampling_interval, label=None,
             smpldim.unit = unit
         if offset:
             smpldim.offset = offset
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
         return smpldim
 
@@ -134,7 +134,7 @@ def append_range_dimension(self, ticks, label=None, unit=None):
         if label:
             rdim.label = label
             rdim.unit = unit
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
         return rdim
 
@@ -157,7 +157,7 @@ def append_data_frame_dimension(self, data_frame, column_idx=None):
         index = len(self.dimensions) + 1
         dfdim = DataFrameDimension.create_new(self, index,
                                               data_frame, column_idx)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
         return dfdim
 
@@ -252,7 +252,7 @@ def polynom_coefficients(self, coeff):
         else:
             dtype = DataType.Double
             self._h5group.write_data("polynom_coefficients", coeff, dtype)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -270,7 +270,7 @@ def expansion_origin(self):
     def expansion_origin(self, eo):
         util.check_attr_type(eo, Number)
         self._h5group.set_attr("expansion_origin", eo)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -288,7 +288,7 @@ def label(self):
     def label(self, l):
         util.check_attr_type(l, str)
         self._h5group.set_attr("label", l)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -318,7 +318,7 @@ def unit(self, u):
                     "DataArray.unit"
                 )
         self._h5group.set_attr("unit", u)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     def get_slice(self, positions, extents=None, mode=DataSliceMode.Index):
diff --git a/nixio/data_frame.py b/nixio/data_frame.py
index aa3309bc..a4ce238e 100644
--- a/nixio/data_frame.py
+++ b/nixio/data_frame.py
@@ -348,7 +348,7 @@ def units(self, u):
                 util.check_attr_type(i, str)
         unit = np.array(u, util.vlen_str_dtype)
         self._h5group.set_attr("units", unit)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
diff --git a/nixio/entity.py b/nixio/entity.py
index 94608b90..6babde5f 100644
--- a/nixio/entity.py
+++ b/nixio/entity.py
@@ -120,7 +120,7 @@ def definition(self):
     def definition(self, d):
         util.check_attr_type(d, str)
         self._h5group.set_attr("definition", d)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -151,7 +151,7 @@ def type(self, t):
             raise AttributeError("type can't be None")
         util.check_attr_type(t, str)
         self._h5group.set_attr("type", t)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     def __eq__(self, other):
diff --git a/nixio/feature.py b/nixio/feature.py
index efc2adbc..9feccdf0 100644
--- a/nixio/feature.py
+++ b/nixio/feature.py
@@ -53,7 +53,7 @@ def link_type(self, lt):
             lt = lt.lower()
         lt = LinkType(lt)
         self._h5group.set_attr("link_type", lt.value)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             t = util.now_int()
             self._h5group.set_attr("updated_at", util.time_to_str(t))
 
@@ -74,7 +74,7 @@ def data(self, da):
         if "data" in self._h5group:
             del self._h5group["data"]
         self._h5group.create_link(da, "data")
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             t = util.now_int()
             self._h5group.set_attr("updated_at", util.time_to_str(t))
 
diff --git a/nixio/file.py b/nixio/file.py
index 9f7873dd..a2985549 100644
--- a/nixio/file.py
+++ b/nixio/file.py
@@ -85,7 +85,8 @@ def make_fcpl():
 class File(object):
 
     def __init__(self, path, mode=FileMode.ReadWrite,
-                 compression=Compression.Auto, auto_update_time=False):
+                 compression=Compression.Auto,
+                 auto_update_timestamps=True):
         """
         Open a NIX file, or create it if it does not exist.
 
@@ -93,6 +94,9 @@ def __init__(self, path, mode=FileMode.ReadWrite,
         :param mode: FileMode ReadOnly, ReadWrite, or Overwrite.
                     (default: ReadWrite)
         :param compression: No, DeflateNormal, Auto (default: Auto)
+        :param auto_update_timestamps: Enable/disable automatic updating of
+                    'updated_at' timestamp. (default: True)
+
         :return: nixio.File object
         """
         try:
@@ -120,7 +124,7 @@ def __init__(self, path, mode=FileMode.ReadWrite,
             self._root = H5Group(self._h5file, "/")
 
         self._h5group = self._root  # to match behaviour of other objects
-        self._time_auto_update = True
+        self._auto_update_timestamps = auto_update_timestamps
         self._check_header(mode)
         self.mode = mode
         self._data = self._root.open_group("data", create=True)
@@ -129,7 +133,6 @@ def __init__(self, path, mode=FileMode.ReadWrite,
             self.force_created_at()
         if "updated_at" not in self._h5file.attrs:
             self.force_updated_at()
-        self.time_auto_update = auto_update_time
         if compression == Compression.Auto:
             compression = Compression.No
         self._compr = compression
@@ -139,10 +142,10 @@ def __init__(self, path, mode=FileMode.ReadWrite,
 
     @classmethod
     def open(cls, path, mode=FileMode.ReadWrite, compression=Compression.Auto,
-             backend=None,  auto_update_time=False):
+             backend=None, auto_update_timestamps=True):
         if backend is not None:
             warn("Backend selection is deprecated. Ignoring value.")
-        return cls(path, mode, compression, auto_update_time)
+        return cls(path, mode, compression, auto_update_timestamps)
 
     def _create_header(self):
         self._set_format()
@@ -218,18 +221,24 @@ def _set_format(self):
         self._root.set_attr("format", FILE_FORMAT.encode("ascii"))
 
     @property
-    def time_auto_update(self):
+    def auto_update_timestamps(self):
         """
-        A user defined flag which decided if time should always be updated
-        when properties are changed.
+        If enabled, automatically updates the 'updated_at' attribute when an
+        object's data or attributes are changed.
 
         :type: bool
         """
-        return self._time_auto_update
+        return self._auto_update_timestamps
+
+    @auto_update_timestamps.setter
+    def auto_update_timestamps(self, enable):
+        """
+        If enabled, automatically updates the 'updated_at' attribute when an
+        object's data or attributes are changed.
 
-    @time_auto_update.setter
-    def time_auto_update(self, auto_update_flag):
-        self._time_auto_update = auto_update_flag
+        :type: bool
+        """
+        self._auto_update_timestamps = enable
 
     @property
     def created_at(self):
diff --git a/nixio/multi_tag.py b/nixio/multi_tag.py
index a230766c..2d208667 100644
--- a/nixio/multi_tag.py
+++ b/nixio/multi_tag.py
@@ -54,7 +54,7 @@ def positions(self, da):
         if "positions" in self._h5group:
             del self._h5group["positions"]
         self._h5group.create_link(da, "positions")
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -76,7 +76,7 @@ def extents(self, da):
             del self._h5group["extents"]
         else:
             self._h5group.create_link(da, "extents")
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
diff --git a/nixio/section.py b/nixio/section.py
index 6ec0df3f..85d1cdad 100644
--- a/nixio/section.py
+++ b/nixio/section.py
@@ -226,7 +226,7 @@ def reference(self):
     def reference(self, ref):
         util.check_attr_type(ref, str)
         self._h5group.set_attr("reference", ref)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -254,7 +254,7 @@ def link(self, id_or_sec):
             sec = rootsec.find_sections(filtr=lambda x: x.id == id_or_sec)
 
         self._h5group.create_link(sec, "link")
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     def inherited_properties(self):
@@ -278,7 +278,7 @@ def repository(self):
     def repository(self, r):
         util.check_attr_type(r, str)
         self._h5group.set_attr("repository", r)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
diff --git a/nixio/tag.py b/nixio/tag.py
index 364c7e46..d38fae22 100644
--- a/nixio/tag.py
+++ b/nixio/tag.py
@@ -86,7 +86,7 @@ def units(self, units):
 
             dtype = DataType.String
             self._h5group.write_data("units", sanitized, dtype)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     def create_feature(self, data, link_type):
@@ -196,7 +196,7 @@ def position(self, pos):
         else:
             dtype = DataType.Double
             self._h5group.write_data("position", pos, dtype)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     @property
@@ -217,7 +217,7 @@ def extent(self, ext):
         else:
             dtype = DataType.Double
             self._h5group.write_data("extent", ext, dtype)
-        if self.file.time_auto_update:
+        if self.file.auto_update_timestamps:
             self.force_updated_at()
 
     def _calc_data_slices(self, data):
diff --git a/nixio/test/test_file.py b/nixio/test/test_file.py
index e386ae7e..f6f5996b 100644
--- a/nixio/test/test_file.py
+++ b/nixio/test/test_file.py
@@ -170,56 +170,54 @@ def test_copy_on_file(self):
     def test_timestamp_autoupdate_definition(self):
         blk = self.file.create_block("block", "timetest")
         blktime = blk.updated_at
+        time.sleep(1)  # wait for time to change
         blk.definition = "updated"
         # no update
-        self.assertEqual(blk.updated_at, blktime)
+        self.assertNotEqual(blk.updated_at, blktime)
 
         rblk = self.file.blocks["block"]  # read through container
+        time.sleep(1)  # wait for time to change
         rblk.definition = "updated again"
-        self.assertEqual(rblk.updated_at, blktime)
+        self.assertNotEqual(rblk.updated_at, blktime)
 
-        # close and recreate file with auto_update_time enabled
-        self.file.close()
-        self.file = nix.File(self.testfilename, nix.FileMode.Overwrite,
-                             auto_update_time=True)
-        blk = self.file.create_block("block", "timetest")
+        # disable timestamp autoupdating
+        self.file.auto_update_timestamps = False
         blktime = blk.updated_at
         time.sleep(1)  # wait for time to change
         blk.definition = "update"
-        self.assertNotEqual(blk.updated_at, blktime)
+        self.assertEqual(blk.updated_at, blktime)
 
         rblk = self.file.blocks["block"]  # read through container
         rblktime = rblk.updated_at
         time.sleep(1)  # wait for time to change
         rblk.definition = "time should change"
-        self.assertNotEqual(rblk.updated_at, rblktime)
+        self.assertEqual(rblk.updated_at, rblktime)
 
     def test_timestamp_autoupdate_type(self):
         blk = self.file.create_block("block", "timetest")
         blktime = blk.updated_at
+        time.sleep(1)  # wait for time to change
         blk.type = "updated"
         # no update
-        self.assertEqual(blk.updated_at, blktime)
+        self.assertNotEqual(blk.updated_at, blktime)
 
         rblk = self.file.blocks["block"]  # read through container
+        time.sleep(1)  # wait for time to change
         rblk.type = "updated again"
-        self.assertEqual(rblk.updated_at, blktime)
+        self.assertNotEqual(rblk.updated_at, blktime)
 
-        # close and recreate file with auto_update_time enabled
-        self.file.close()
-        self.file = nix.File(self.testfilename, nix.FileMode.Overwrite,
-                             auto_update_time=True)
-        blk = self.file.create_block("block", "timetest")
+        # disable timestamp autoupdating
+        self.file.auto_update_timestamps = False
         blktime = blk.updated_at
         time.sleep(1)  # wait for time to change
         blk.type = "update"
-        self.assertNotEqual(blk.updated_at, blktime)
+        self.assertEqual(blk.updated_at, blktime)
 
         rblk = self.file.blocks["block"]  # read through container
         rblktime = rblk.updated_at
         time.sleep(1)  # wait for time to change
         rblk.type = "time should change"
-        self.assertNotEqual(rblk.updated_at, rblktime)
+        self.assertEqual(rblk.updated_at, rblktime)
 
 
 class TestFileVer(unittest.TestCase):

From fa40d413db704972c4f0b5632d26fdadfb1ec6c0 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 17:46:48 +0200
Subject: [PATCH 11/18] Split tests for enabled and disabled timestamp update

Instead of separating based on property, separate based on option state.
---
 nixio/test/test_file.py | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/nixio/test/test_file.py b/nixio/test/test_file.py
index f6f5996b..dc37ffae 100644
--- a/nixio/test/test_file.py
+++ b/nixio/test/test_file.py
@@ -167,7 +167,8 @@ def test_copy_on_file(self):
         assert self.file.blocks[0] == self.file.blocks[1]  # ID stays the same
         assert self.file.blocks[0].name != self.file.blocks[1].name
 
-    def test_timestamp_autoupdate_definition(self):
+    def test_timestamp_autoupdate(self):
+        # Using Block to test Entity.definition
         blk = self.file.create_block("block", "timetest")
         blktime = blk.updated_at
         time.sleep(1)  # wait for time to change
@@ -180,21 +181,7 @@ def test_timestamp_autoupdate_definition(self):
         rblk.definition = "updated again"
         self.assertNotEqual(rblk.updated_at, blktime)
 
-        # disable timestamp autoupdating
-        self.file.auto_update_timestamps = False
-        blktime = blk.updated_at
-        time.sleep(1)  # wait for time to change
-        blk.definition = "update"
-        self.assertEqual(blk.updated_at, blktime)
-
-        rblk = self.file.blocks["block"]  # read through container
-        rblktime = rblk.updated_at
-        time.sleep(1)  # wait for time to change
-        rblk.definition = "time should change"
-        self.assertEqual(rblk.updated_at, rblktime)
-
-    def test_timestamp_autoupdate_type(self):
-        blk = self.file.create_block("block", "timetest")
+        # Using Block to test Entity.type
         blktime = blk.updated_at
         time.sleep(1)  # wait for time to change
         blk.type = "updated"
@@ -206,8 +193,23 @@ def test_timestamp_autoupdate_type(self):
         rblk.type = "updated again"
         self.assertNotEqual(rblk.updated_at, blktime)
 
+    def test_timestamp_noautoupdate(self):
+        # Using Block to test Entity.definition
+        blk = self.file.create_block("block", "timetest")
+
         # disable timestamp autoupdating
         self.file.auto_update_timestamps = False
+        blktime = blk.updated_at
+        time.sleep(1)  # wait for time to change
+        blk.definition = "update"
+        self.assertEqual(blk.updated_at, blktime)
+
+        rblk = self.file.blocks["block"]  # read through container
+        rblktime = rblk.updated_at
+        time.sleep(1)  # wait for time to change
+        rblk.definition = "time should change"
+        self.assertEqual(rblk.updated_at, rblktime)
+
         blktime = blk.updated_at
         time.sleep(1)  # wait for time to change
         blk.type = "update"

From 1fbc6a9cd40f6e78b307d8d20198b743c1ae986c Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 18:08:40 +0200
Subject: [PATCH 12/18] Test timestamp autoupdate for DataArray properties

---
 nixio/data_array.py           |   5 +-
 nixio/test/test_data_array.py | 112 ++++++++++++++++++++++++++++++++++
 2 files changed, 116 insertions(+), 1 deletion(-)

diff --git a/nixio/data_array.py b/nixio/data_array.py
index 2b0d85b8..22d1a9a9 100644
--- a/nixio/data_array.py
+++ b/nixio/data_array.py
@@ -188,7 +188,10 @@ def append_alias_range_dimension(self):
                     "Current SI unit is {}".format(u),
                     "DataArray.append_alias_range_dimension"
                 )
-        return RangeDimension.create_new_alias(self, 1)
+        aliasdim = RangeDimension.create_new_alias(self, 1)
+        if self.file.auto_update_timestamps:
+            self.force_updated_at()
+        return aliasdim
 
     def delete_dimensions(self):
         """
diff --git a/nixio/test/test_data_array.py b/nixio/test/test_data_array.py
index 0cd41913..49fe0b54 100644
--- a/nixio/test/test_data_array.py
+++ b/nixio/test/test_data_array.py
@@ -7,6 +7,7 @@
 # modification, are permitted under the terms of the BSD License. See
 # LICENSE file in the root of the Project.
 import os
+import time
 from six import string_types
 import sys
 import unittest
@@ -476,3 +477,114 @@ def test_dim_one_based(self):
         for idx, dim in dim_container_one_based:
             assert self.array.dimensions[idx-1].dimension_type ==\
                 dim.dimension_type
+
+    def test_timestamp_autoupdate(self):
+        array = self.block.create_data_array("array.time", "signal",
+                                             nix.DataType.Double, (100, ))
+        # Append dimensions and check time
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_set_dimension()
+        self.assertNotEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_sampled_dimension(sampling_interval=0.1)
+        self.assertNotEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_range_dimension(ticks=[0.1])
+        self.assertNotEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        df = self.block.create_data_frame(
+            "df", "test.data_array.timestamp.data_frame",
+            col_dict={"idx": int}
+        )
+        array.append_data_frame_dimension(data_frame=df)
+        self.assertNotEqual(datime, array.updated_at)
+
+        array.delete_dimensions()
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_alias_range_dimension()
+        self.assertNotEqual(datime, array.updated_at)
+
+        # other properties
+        datime = array.updated_at
+        time.sleep(1)
+        array.polynom_coefficients = [1.1, 2.2]
+        self.assertNotEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.expansion_origin = -1
+        self.assertNotEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.label = "lbl"
+        self.assertNotEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.unit = "Ms"
+        self.assertNotEqual(datime, array.updated_at)
+
+    def test_timestamp_noautoupdate(self):
+        self.file.auto_update_timestamps = False
+        array = self.block.create_data_array("array.time", "signal",
+                                             nix.DataType.Double, (100, ))
+        # Append dimensions and check time
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_set_dimension()
+        self.assertEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_sampled_dimension(sampling_interval=0.1)
+        self.assertEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_range_dimension(ticks=[0.1])
+        self.assertEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        df = self.block.create_data_frame(
+            "df", "test.data_array.timestamp.data_frame",
+            col_dict={"idx": int}
+        )
+        array.append_data_frame_dimension(data_frame=df)
+        self.assertEqual(datime, array.updated_at)
+
+        array.delete_dimensions()
+        datime = array.updated_at
+        time.sleep(1)
+        array.append_alias_range_dimension()
+        self.assertEqual(datime, array.updated_at)
+
+        # other properties
+        datime = array.updated_at
+        time.sleep(1)
+        array.polynom_coefficients = [1.1, 2.2]
+        self.assertEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.expansion_origin = -1
+        self.assertEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.label = "lbl"
+        self.assertEqual(datime, array.updated_at)
+
+        datime = array.updated_at
+        time.sleep(1)
+        array.unit = "Ms"
+        self.assertEqual(datime, array.updated_at)

From 99bdae79fc4526a358117f391dad5367122f0d2f Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 18:33:41 +0200
Subject: [PATCH 13/18] Test timestamp autoupdate for DataFrame properties

---
 nixio/test/test_data_frame.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/nixio/test/test_data_frame.py b/nixio/test/test_data_frame.py
index 2b2655f0..61445f7b 100644
--- a/nixio/test/test_data_frame.py
+++ b/nixio/test/test_data_frame.py
@@ -3,6 +3,7 @@
 import nixio as nix
 from .tmp import TempDir
 import os
+import time
 import numpy as np
 from six import string_types
 try:
@@ -206,3 +207,21 @@ def test_creation_without_name(self):
         df = self.block.create_data_frame("without_name", "test", data=data)
         assert sorted(list(df.column_names)) == sorted(["name", "id", "val"])
         assert sorted(list(df["name"])) == ["a", "b", "c"]
+
+    def test_timestamp_autoupdate(self):
+        self.file.auto_update_timestamps = True
+        df = self.block.create_data_frame("df.time", "test.time",
+                                          col_dict={"idx": int})
+        dftime = df.updated_at
+        time.sleep(1)
+        df.units = "ly"
+        self.assertNotEqual(dftime, df.updated_at)
+
+    def test_timestamp_noautoupdate(self):
+        self.file.auto_update_timestamps = False
+        df = self.block.create_data_frame("df.time", "test.time",
+                                          col_dict={"idx": int})
+        dftime = df.updated_at
+        time.sleep(1)
+        df.units = "ly"
+        self.assertEqual(dftime, df.updated_at)

From d598d0a09885194aeee0562b098454f12a173669 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 18:33:41 +0200
Subject: [PATCH 14/18] Test timestamp autoupdate for Feature properties

---
 nixio/test/test_feature.py | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/nixio/test/test_feature.py b/nixio/test/test_feature.py
index 0b83eea2..e2d91f1e 100644
--- a/nixio/test/test_feature.py
+++ b/nixio/test/test_feature.py
@@ -7,6 +7,7 @@
 # modification, are permitted under the terms of the BSD License. See
 # LICENSE file in the root of the Project.
 import os
+import time
 import unittest
 import nixio as nix
 from .tmp import TempDir
@@ -84,3 +85,36 @@ def test_feature_on_group(self):
 
     def test_create_diff_link_type_style(self):
         self.stimuli_tag.create_feature(self.movie1, nix.LinkType.Tagged)
+
+    def test_timestamp_autoupdate(self):
+        array = self.block.create_data_array("array.time", "signal",
+                                             nix.DataType.Double, (100, ))
+        feature = self.stimuli_tag.create_feature(array, nix.LinkType.Tagged)
+
+        ftime = feature.updated_at
+        time.sleep(1)
+        feature.data = self.block.create_data_array("alt.array", "signal",
+                                                    nix.DataType.Int8, (1,))
+        self.assertNotEqual(ftime, feature.updated_at)
+
+        ftime = feature.updated_at
+        time.sleep(1)
+        feature.link_type = nix.LinkType.Untagged
+        self.assertNotEqual(ftime, feature.updated_at)
+
+    def test_timestamp_noautoupdate(self):
+        self.file.auto_update_timestamps = False
+        array = self.block.create_data_array("array.time", "signal",
+                                             nix.DataType.Double, (100, ))
+        feature = self.stimuli_tag.create_feature(array, nix.LinkType.Tagged)
+
+        ftime = feature.updated_at
+        time.sleep(1)
+        feature.data = self.block.create_data_array("alt.array", "signal",
+                                                    nix.DataType.Int8, (1,))
+        self.assertEqual(ftime, feature.updated_at)
+
+        ftime = feature.updated_at
+        time.sleep(1)
+        feature.link_type = nix.LinkType.Untagged
+        self.assertEqual(ftime, feature.updated_at)

From 69f4219d9cf0d2bb6c47783ab669a992b4d26db9 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 18:33:41 +0200
Subject: [PATCH 15/18] Test timestamp autoupdate for MultiTag positions and
 extents

---
 nixio/test/test_multi_tag.py | 40 ++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/nixio/test/test_multi_tag.py b/nixio/test/test_multi_tag.py
index c64956f8..628e8894 100644
--- a/nixio/test/test_multi_tag.py
+++ b/nixio/test/test_multi_tag.py
@@ -7,6 +7,7 @@
 # modification, are permitted under the terms of the BSD License. See
 # LICENSE file in the root of the Project.
 import os
+import time
 import unittest
 import numpy as np
 import nixio as nix
@@ -562,3 +563,42 @@ def out_of_bounds():
             self.feature_tag.feature_data(2, 1)
 
         self.assertRaises(IndexError, out_of_bounds)
+
+    def test_timestamp_autoupdate(self):
+        pos = self.block.create_data_array("positions.time", "test.time",
+                                           nix.DataType.Int16, (0, 0))
+        mtag = self.block.create_multi_tag("mtag.time", "test.time", pos)
+
+        mtagtime = mtag.updated_at
+        time.sleep(1)  # wait for time to change
+        mtag.positions = self.block.create_data_array("pos2.time",
+                                                      "test.time",
+                                                      nix.DataType.Int8, (0,))
+        self.assertNotEqual(mtag.updated_at, mtagtime)
+
+        mtagtime = mtag.updated_at
+        time.sleep(1)  # wait for time to change
+        mtag.extents = self.block.create_data_array("extents.time",
+                                                    "test.time",
+                                                    nix.DataType.Int8, (0,))
+        self.assertNotEqual(mtag.updated_at, mtagtime)
+
+    def test_timestamp_noautoupdate(self):
+        self.file.auto_update_timestamps = False
+        pos = self.block.create_data_array("positions.time", "test.time",
+                                           nix.DataType.Int16, (0, 0))
+        mtag = self.block.create_multi_tag("mtag.time", "test.time", pos)
+
+        mtagtime = mtag.updated_at
+        time.sleep(1)  # wait for time to change
+        mtag.positions = self.block.create_data_array("pos2.time",
+                                                      "test.time",
+                                                      nix.DataType.Int8, (0,))
+        self.assertEqual(mtag.updated_at, mtagtime)
+
+        mtagtime = mtag.updated_at
+        time.sleep(1)  # wait for time to change
+        mtag.extents = self.block.create_data_array("extents.time",
+                                                    "test.time",
+                                                    nix.DataType.Int8, (0,))
+        self.assertEqual(mtag.updated_at, mtagtime)

From 2798d748952f561e87fb5e633868d4daa633ab15 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 18:33:41 +0200
Subject: [PATCH 16/18] Test timestamp autoupdate for Section properties

---
 nixio/test/test_section.py | 40 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/nixio/test/test_section.py b/nixio/test/test_section.py
index ba77aae1..20571432 100644
--- a/nixio/test/test_section.py
+++ b/nixio/test/test_section.py
@@ -7,6 +7,7 @@
 # modification, are permitted under the terms of the BSD License. See
 # LICENSE file in the root of the Project.
 import os
+import time
 import unittest
 import nixio as nix
 from .tmp import TempDir
@@ -317,3 +318,42 @@ def test_copy_on_sections(self):
         assert sec2 == tarsec.sections[1]
         assert sec1.sections[0] == tarsec.sections[1]
         tarfile.close()
+
+    def test_timestamp_autoupdate(self):
+        section = self.file.create_section("section.time", "test.time")
+
+        sectime = section.updated_at
+        time.sleep(1)  # wait for time to change
+        section.reference = "whatever"
+        self.assertNotEqual(sectime, section.updated_at)
+
+        sectime = section.updated_at
+        linksec = self.file.create_section("link.section.time", "test.time")
+        time.sleep(1)  # wait for time to change
+        section.link = linksec
+        self.assertNotEqual(sectime, section.updated_at)
+
+        sectime = section.updated_at
+        time.sleep(1)  # wait for time to change
+        section.repository = "repo"
+        self.assertNotEqual(sectime, section.updated_at)
+
+    def test_timestamp_noautoupdate(self):
+        self.file.auto_update_timestamps = False
+        section = self.file.create_section("section.time", "test.time")
+
+        sectime = section.updated_at
+        time.sleep(1)  # wait for time to change
+        section.reference = "whatever"
+        self.assertEqual(sectime, section.updated_at)
+
+        sectime = section.updated_at
+        time.sleep(1)  # wait for time to change
+        linksec = self.file.create_section("link.section.time", "test.time")
+        section.link = linksec
+        self.assertEqual(sectime, section.updated_at)
+
+        sectime = section.updated_at
+        time.sleep(1)  # wait for time to change
+        section.repository = "repo"
+        self.assertEqual(sectime, section.updated_at)

From 2fc194ee644fd96f0cc3b15a2085963dcece34e8 Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Thu, 30 Apr 2020 18:33:41 +0200
Subject: [PATCH 17/18] Test timestamp autoupdate for Tag properties

---
 nixio/test/test_tag.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/nixio/test/test_tag.py b/nixio/test/test_tag.py
index c48d9d94..b10f4eb4 100644
--- a/nixio/test/test_tag.py
+++ b/nixio/test/test_tag.py
@@ -7,6 +7,7 @@
 # modification, are permitted under the terms of the BSD License. See
 # LICENSE file in the root of the Project.
 import os
+import time
 import unittest
 import numpy as np
 import nixio as nix
@@ -297,3 +298,40 @@ def test_tag_feature_data(self):
 
         assert (data1.size == 1)
         assert (data2.size == 3)
+
+    def test_timestamp_autoupdate(self):
+        tag = self.block.create_tag("tag.time", "test.time", [-1])
+
+        tagtime = tag.updated_at
+        time.sleep(1)  # wait for time to change
+        tag.position = [-100]
+        self.assertNotEqual(tag.updated_at, tagtime)
+
+        tagtime = tag.updated_at
+        time.sleep(1)  # wait for time to change
+        tag.extent = [30]
+        self.assertNotEqual(tag.updated_at, tagtime)
+
+        tagtime = tag.updated_at
+        time.sleep(1)  # wait for time to change
+        tag.units = "Mm"
+        self.assertNotEqual(tag.updated_at, tagtime)
+
+    def test_timestamp_noautoupdate(self):
+        self.file.auto_update_timestamps = False
+        tag = self.block.create_tag("tag.time", "test.time", [-1])
+
+        tagtime = tag.updated_at
+        time.sleep(1)  # wait for time to change
+        tag.position = [-100]
+        self.assertEqual(tag.updated_at, tagtime)
+
+        tagtime = tag.updated_at
+        time.sleep(1)  # wait for time to change
+        tag.extent = [30]
+        self.assertEqual(tag.updated_at, tagtime)
+
+        tagtime = tag.updated_at
+        time.sleep(1)  # wait for time to change
+        tag.units = "Mm"
+        self.assertEqual(tag.updated_at, tagtime)

From f76a283d5cf63c15e396463366cd78115710e7cb Mon Sep 17 00:00:00 2001
From: Achilleas Koutsou <achilleas.k@gmail.com>
Date: Mon, 4 May 2020 22:11:03 +0200
Subject: [PATCH 18/18] Cleanup: Use file references whenever appropriate

- Removed hacky parent traversal for getting root objects like the top
  level metadata container.
- Removed H5Group utility functions that are now obsolete.
- Containers that need to do a search from the root object to delete
  objects now use the file reference.
---
 nixio/container.py    | 12 +++-------
 nixio/hdf5/h5group.py | 53 -------------------------------------------
 nixio/section.py      | 15 +-----------
 3 files changed, 4 insertions(+), 76 deletions(-)

diff --git a/nixio/container.py b/nixio/container.py
index ac4febb9..0804a81a 100644
--- a/nixio/container.py
+++ b/nixio/container.py
@@ -57,10 +57,7 @@ def __delitem__(self, item):
                     self._itemclass.__name__)
             )
 
-        root = self._backend.h5root
-        if not root:
-            root = self._parent._h5group
-        root.delete_all([item.id])
+        self._file._h5group.delete_all([item.id])
 
     def __iter__(self):
         for group in self._backend:
@@ -122,8 +119,7 @@ def __delitem__(self, item):
         # the root block
         secids = [s.id for s in item.find_sections()]
 
-        root = self._backend.file
-        root.delete_all(secids)
+        self._file._h5group.delete_all(secids)
 
 
 class SourceContainer(Container):
@@ -146,9 +142,7 @@ def __delitem__(self, item):
         # the root block
         srcids = [s.id for s in item.find_sources()]
         srcids.append(item.id)
-
-        root = self._backend.h5root
-        root.delete_all(srcids)
+        self._file._h5group.delete_all(srcids)
 
 
 class LinkContainer(Container):
diff --git a/nixio/hdf5/h5group.py b/nixio/hdf5/h5group.py
index b7d6c703..28195042 100644
--- a/nixio/hdf5/h5group.py
+++ b/nixio/hdf5/h5group.py
@@ -12,11 +12,8 @@
 
 from .h5dataset import H5DataSet
 from ..datatype import DataType
-from ..block import Block
-from ..section import Section
 
 from .. import util
-from ..exceptions import InvalidEntity
 
 
 class H5Group(object):
@@ -297,56 +294,6 @@ def change_id(_, igrp):
             g.visititems(change_id)
         return g
 
-    @property
-    def file(self):
-        """
-        An H5Group object which represents the file root.
-
-        :return: H5Group at '/'
-        """
-        return H5Group(self.group.file, "/", create=False)
-
-    @property
-    def h5root(self):
-        """
-        Returns the H5Group of the Block or top-level Section which contains
-        this object. Returns None if requested on the file root '/' or the
-        /data or /metadata groups.
-
-        :return: Top level object containing this group (H5Group)
-        """
-        pathparts = self.group.name.split("/")
-        if len(pathparts) == 3:
-            return self
-        if self.group.name == "/":
-            return None
-        if len(pathparts) == 2:
-            return None
-
-        return self.parent.h5root
-
-    @property
-    def root(self):
-        """
-        Returns the Block or top-level Section which contains this object.
-        Returns None if requested on the file root '/' or the /data or
-        /metadata groups.
-
-        :return: Top level object containing this group (Block or Section)
-        """
-        h5root = self.h5root
-        if h5root is None:
-            return None
-        topgroup = self.group.name.split("/")[1]
-        if topgroup == "data":
-            cls = Block
-            return cls(h5root.parent, h5root)
-        elif topgroup == "metadata":
-            cls = Section
-            return cls(h5root.parent, h5root)
-        else:
-            raise InvalidEntity
-
     @property
     def parent(self):
         return self.create_from_h5obj(self._parent)
diff --git a/nixio/section.py b/nixio/section.py
index 85d1cdad..d3a14ab5 100644
--- a/nixio/section.py
+++ b/nixio/section.py
@@ -293,9 +293,8 @@ def parent(self):
         """
         if self._sec_parent is not None:
             return self._sec_parent
-        rootmd = self._h5group.file.open_group("metadata")
         # BFS
-        sections = [Section(self.file, None, sg) for sg in rootmd]
+        sections = list(self.file.sections)
         if self in sections:
             # Top-level section
             return None
@@ -309,18 +308,6 @@ def parent(self):
 
         return None
 
-    @property
-    def file(self):
-        """
-        Root file object.
-
-        :type: File
-        """
-        par = self._parent
-        while isinstance(par, Entity):
-            par = par._parent
-        return par
-
     @property
     def referring_objects(self):
         objs = []