Merge branch 'dev' into add/missing_tutorial_icons

CHANGELOG.md

@@ -7,6 +7,10 @@
 
 ### Bug fixes
 - Fixed bug in how `ElectrodeGroup.__init__` validates its `position` argument. @oruebel [#1770](https://github.com/NeurodataWithoutBorders/pynwb/pull/1770)
+- Changed `SpatialSeries.reference_frame` from required to optional as specified in the schema. @rly [#1986](https://github.com/NeurodataWithoutBorders/pynwb/pull/1986)
+
+### Enhancements and minor changes`
+- Added warning when writing files with `NWBHDF5IO` without the `.nwb` extension. @stephprince [#1978](https://github.com/NeurodataWithoutBorders/pynwb/pull/1978)
 
 ## PyNWB 2.8.2 (September 9, 2024)
 

src/pynwb/__init__.py

@@ -397,6 +397,10 @@ def __init__(self, **kwargs):
         if mode in io_modes_that_create_file or manager is not None or extensions is not None:
             load_namespaces = False
 
+        if mode in io_modes_that_create_file and not str(path).endswith('.nwb'):
+            warn(f"The file path provided: {path} does not end in '.nwb'. "
+                 "It is recommended that NWB files using the HDF5 backend use the '.nwb' extension.", UserWarning)
+
         if load_namespaces:
             tm = get_type_map()
             super().load_namespaces(tm, path, file=file_obj, driver=driver, aws_region=aws_region)

src/pynwb/behavior.py

@@ -28,8 +28,8 @@ class SpatialSeries(TimeSeries):
                      'or 3 columns, which represent x, y, and z.')},
             {'name': 'bounds', 'type': list, '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'},
+            {'name': 'reference_frame', 'type': str,
+             'doc': 'description defining what the zero-position is', 'default': None},
             {'name': 'unit', 'type': str, 'doc': 'The base unit of measurement (should be SI unit)',
              'default': 'meters'},
             *get_docval(TimeSeries.__init__, 'conversion', 'resolution', 'timestamps', 'starting_time', 'rate',

tests/integration/hdf5/test_behavior.py

@@ -15,3 +15,14 @@ def setUpContainer(self):
             reference_frame='reference_frame',
             timestamps=[1., 2., 3.]
         )
+
+
+class TestSpatialSeriesMinIO(AcquisitionH5IOMixin, TestCase):
+
+    def setUpContainer(self):
+        """ Return the test TimeSeries to read/write """
+        return SpatialSeries(
+            name='test_sS',
+            data=np.ones((3, 2)),
+            timestamps=[1., 2., 3.]
+        )

tests/integration/hdf5/test_file_copy.py

@@ -9,8 +9,8 @@
 class TestFileCopy(TestCase):
 
     def setUp(self):
-        self.path1 = "test_a.h5"
-        self.path2 = "test_b.h5"
+        self.path1 = "test_a.nwb"
+        self.path2 = "test_b.nwb"
 
     def tearDown(self):
         if os.path.exists(self.path1):

tests/integration/hdf5/test_io.py

@@ -313,7 +313,7 @@ def setUp(self):
         self.nwbfile = NWBFile(session_description='a',
                                identifier='b',
                                session_start_time=datetime(1970, 1, 1, 12, tzinfo=tzutc()))
-        self.path = "test_pynwb_io_hdf5_h5dataIO.h5"
+        self.path = "test_pynwb_io_hdf5_h5dataIO.nwb"
 
     def tearDown(self):
         remove_test_file(self.path)
@@ -428,7 +428,7 @@ def setUp(self):
         self.nwbfile = NWBFile(session_description='a test NWB File',
                                identifier='TEST123',
                                session_start_time=datetime(1970, 1, 1, 12, tzinfo=tzutc()))
-        self.path = "test_pynwb_io_nwbhdf5.h5"
+        self.path = "test_pynwb_io_nwbhdf5.nwb"
 
     def tearDown(self):
         remove_test_file(self.path)
@@ -532,6 +532,23 @@ def test_round_trip_with_pathlib_path(self):
             read_file = io.read()
             self.assertContainerEqual(read_file, self.nwbfile)
 
+    def test_warn_for_nwb_extension(self):
+        """Creating a file with an extension other than .nwb should raise a warning"""
+        pathlib_path = Path(self.path).with_suffix('.h5')
+
+        with self.assertWarns(UserWarning):
+            with NWBHDF5IO(pathlib_path, 'w') as io:
+                io.write(self.nwbfile)
+        with self.assertWarns(UserWarning):
+            with NWBHDF5IO(str(pathlib_path), 'w') as io:
+                io.write(self.nwbfile)
+
+        # should not warn on read or append
+        with NWBHDF5IO(str(pathlib_path), 'r') as io:
+            io.read()
+        with NWBHDF5IO(str(pathlib_path), 'a') as io:
+            io.read()
+
     def test_can_read_current_nwb_file(self):
         with NWBHDF5IO(self.path, 'w') as io:
             io.write(self.nwbfile)

tests/unit/test_behavior.py

@@ -21,6 +21,15 @@ def test_init(self):
         self.assertEqual(sS.bounds, [(-1,1),(-1,1),(-1,1)])
         self.assertEqual(sS.reference_frame, 'reference_frame')
 
+    def test_init_minimum(self):
+        sS = SpatialSeries(
+            name='test_sS',
+            data=np.ones((3, 2)),
+            timestamps=[1., 2., 3.]
+        )
+        assert sS.bounds is None
+        assert sS.reference_frame is None
+
     def test_set_unit(self):
         sS = SpatialSeries(
             name='test_sS',

tests/unit/test_icephys_metadata_tables.py

@@ -82,7 +82,7 @@ def setUp(self):
             sweep_number=np.uint64(15)
         )
         self.nwbfile.add_acquisition(self.response)
-        self.path = 'test_icephys_meta_intracellularrecording.h5'
+        self.path = 'test_icephys_meta_intracellularrecording.nwb'
 
     def tearDown(self):
         remove_test_file(self.path)
@@ -1037,7 +1037,7 @@ class NWBFileTests(TestCase):
     """
     def setUp(self):
         warnings.simplefilter("always")  # Trigger all warnings
-        self.path = 'test_icephys_meta_intracellularrecording.h5'
+        self.path = 'test_icephys_meta_intracellularrecording.nwb'
 
     def tearDown(self):
         remove_test_file(self.path)