Merge branch 'nwb_schema_2.8.0' into deprecate_image_mask_series

CHANGELOG.md

@@ -1,5 +1,11 @@
 # PyNWB Changelog
 
+## PyNWB 3.0.0 (Upcoming)
+
+### Enhancements and minor changes
+- Added support for NWB schema 2.8.0:
+  - Fixed support for `data__bounds` field to `SpatialSeries` to set optional boundary range (min, max) for each dimension of data. Removed `SpatialSeries.bounds` field that was not functional. @rly [#1907](https://github.com/NeurodataWithoutBorders/pynwb/pull/1907)
+
 ## PyNWB 2.8.3 (Upcoming)
 
 ### Performance
@@ -43,7 +49,7 @@
 ## PyNWB 2.7.0 (May 2, 2024)
 
 ### Enhancements and minor changes
-- Added `bounds` field to `SpatialSeries` to set optional boundary range (min, max) for each dimension of data. @mavaylon1 [#1869](https://github.com/NeurodataWithoutBorders/pynwb/pull/1869/files)
+- Added `bounds` field to `SpatialSeries` to set optional boundary range (min, max) for each dimension of data. @mavaylon1 [#1869](https://github.com/NeurodataWithoutBorders/pynwb/pull/1869)
 - Added support for NWB schema 2.7.0. See [2.7.0 release notes](https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html) for details
 - Deprecated `ImagingRetinotopy` neurodata type. @rly [#1813](https://github.com/NeurodataWithoutBorders/pynwb/pull/1813)
 - Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. @rly [#1812](https://github.com/NeurodataWithoutBorders/pynwb/pull/1812)

docs/gallery/domain/plot_behavior.py

@@ -105,7 +105,7 @@
 #
 # For position data ``reference_frame`` indicates the zero-position, e.g.
 # the 0,0 point might be the bottom-left corner of an enclosure, as viewed from the tracking camera.
-# In :py:class:`~pynwb.behavior.SpatialSeries`, the ``bounds`` field allows the user to set
+# In :py:class:`~pynwb.behavior.SpatialSeries`, the ``data__bounds`` field allows the user to set
 # the boundary range, i.e.,  (min, max), for each dimension of ``data``. The units are the same as in ``data``.
 # This field does not enforce a boundary on the dataset itself.
 
@@ -115,7 +115,7 @@
     name="SpatialSeries",
     description="Position (x, y) in an open field.",
     data=position_data,
-    bounds=[(0,50), (0,50)],
+    data__bounds=[(0,50), (0,50)],
     timestamps=timestamps,
     reference_frame="(0,0) is bottom left corner",
 )

src/pynwb/behavior.py

@@ -20,13 +20,13 @@ class SpatialSeries(TimeSeries):
     tracking camera. The unit of data will indicate how to interpret SpatialSeries values.
     """
 
-    __nwbfields__ = ('reference_frame',)
+    __nwbfields__ = ('data__bounds', 'reference_frame',)
 
     @docval(*get_docval(TimeSeries.__init__, 'name'),  # required
             {'name': 'data', 'type': ('array_data', 'data', TimeSeries), 'shape': ((None, ), (None, None)), # required
              'doc': ('The data values. Can be 1D or 2D. The first dimension must be time. If 2D, there can be 1, 2, '
                      'or 3 columns, which represent x, y, and z.')},
-            {'name': 'bounds', 'type': list, 'shape': ((1, 2), (2, 2), (3, 2)), 'default': None,
+            {'name': 'data__bounds', 'type': ('data', 'array_data'), 'shape': ((1, 2), (2, 2), (3, 2)), 'default': None,
              'doc': 'The boundary range (min, max) for each dimension of data.'},
             {'name': 'reference_frame', 'type': str,   # required
              'doc': 'description defining what the zero-position is'},
@@ -38,7 +38,9 @@ def __init__(self, **kwargs):
         """
         Create a SpatialSeries TimeSeries dataset
         """
-        name, data, bounds, reference_frame, unit = popargs('name', 'data', 'bounds', 'reference_frame', 'unit', kwargs)
+        name, data, data__bounds, reference_frame, unit = popargs(
+            'name', 'data', 'data__bounds', 'reference_frame', 'unit', kwargs
+        )
         super().__init__(name, data, unit, **kwargs)
 
         # NWB 2.5 restricts length of second dimension to be <= 3
@@ -49,7 +51,7 @@ def __init__(self, **kwargs):
                           "The second dimension should have length <= 3 to represent at most x, y, z." %
                           (name, str(data_shape)))
 
-        self.bounds = bounds
+        self.data__bounds = data__bounds
         self.reference_frame = reference_frame
 
     @staticmethod

tests/integration/hdf5/test_behavior.py

@@ -11,7 +11,7 @@ def setUpContainer(self):
         return SpatialSeries(
             name='test_sS',
             data=np.ones((3, 2)),
-            bounds=[(-1,1),(-1,1),(-1,1)],
+            data__bounds=[(-1,1),(-1,1),(-1,1)],
             reference_frame='reference_frame',
             timestamps=[1., 2., 3.]
         )

tests/unit/test_behavior.py

@@ -12,13 +12,13 @@ def test_init(self):
         sS = SpatialSeries(
             name='test_sS',
             data=np.ones((3, 2)),
-            bounds=[(-1,1),(-1,1),(-1,1)],
+            data__bounds=[(-1,1),(-1,1),(-1,1)],
             reference_frame='reference_frame',
             timestamps=[1., 2., 3.]
         )
         self.assertEqual(sS.name, 'test_sS')
         self.assertEqual(sS.unit, 'meters')
-        self.assertEqual(sS.bounds, [(-1,1),(-1,1),(-1,1)])
+        self.assertEqual(sS.data__bounds, [(-1,1),(-1,1),(-1,1)])
         self.assertEqual(sS.reference_frame, 'reference_frame')
 
     def test_set_unit(self):