Update inspector for compliance with nwb schema 2.9.0 (#602)

* update pynwb minimum

* update electrodes table usage

* update device model usage

* fix warnings in tests

* fix message with pynwb 3.0 deprecations

* update CHANGELOG

Author: stephprince

CHANGELOG.md

@@ -9,6 +9,9 @@
 * Fixed error when checking for negative values in a time column with array data [#600](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/600)
 * Fixed issue where the io object remained open after inspection was completed. [#601](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/601)
 
+### Improvements
+* Added support for PyNWB 3.1 and NWB Schema 2.9 [#602](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/602)
+
 # v0.6.3 (March 13, 2025)
 
 ### Improvements

pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "pynwb>=3.0",   # NWB Inspector should always be used with most recent minor versions of PyNWB
+    "pynwb>=3.1",   # NWB Inspector should always be used with most recent minor versions of PyNWB
     "hdmf-zarr",
     "fsspec",
     "requests",

src/nwbinspector/_nwb_inspection.py

@@ -278,8 +278,7 @@ def inspect_nwbfile(
         in_memory_nwbfile, io = read_nwbfile_and_io(nwbfile_path=nwbfile_path)
 
         if not skip_validate:
-            # TODO - update validation call when pynwb 3.0 is the minimal
-            validation_result = pynwb.validate(paths=[nwbfile_path])
+            validation_result = pynwb.validate(path=nwbfile_path)
             if isinstance(validation_result, tuple):
                 validation_errors = validation_result[0]
             else:

src/nwbinspector/checks/_images.py

@@ -37,8 +37,8 @@ def check_order_of_images_len(images: Images) -> Optional[InspectorMessage]:
 def check_index_series_points_to_image(index_series: IndexSeries) -> Optional[InspectorMessage]:
     if index_series.indexed_timeseries is not None:
         return InspectorMessage(
-            message="Pointing an IndexSeries to a TimeSeries will be deprecated. Please point to an Images "
+            message="Pointing an IndexSeries to a TimeSeries is deprecated. Please point to an Images "
             "container instead."
-        )  # TODO - update when pynwb 3.0 is the minimum version
+        )
 
     return None

tests/unit_tests/test_general.py

@@ -86,9 +86,9 @@ def test_check_description_missing():
 def test_check_description_feature_extraction():
     import numpy as np
     from pynwb.ecephys import FeatureExtraction
-    from pynwb.testing.mock.ecephys import mock_ElectrodeTable
+    from pynwb.testing.mock.ecephys import mock_ElectrodesTable
 
-    electrodes = mock_ElectrodeTable()
+    electrodes = mock_ElectrodesTable()
 
     dynamic_table_region = DynamicTableRegion(
         name="electrodes", description="I am wrong", data=[0, 1, 2, 3, 4], table=electrodes

tests/unit_tests/test_images.py

@@ -106,8 +106,8 @@ def test_fail_check_index_series_points_to_image():
         object_name="stimuli",
         importance=Importance.BEST_PRACTICE_VIOLATION,
         object_type="IndexSeries",
-        message="Pointing an IndexSeries to a TimeSeries will be deprecated. Please point to an Images container "
-        "instead.",  # TODO - update message when PyNWB 3.0 is released
+        message="Pointing an IndexSeries to a TimeSeries is deprecated. Please point to an Images container "
+        "instead.",
         location="/",
         check_function_name="check_index_series_points_to_image",
     )

tests/unit_tests/test_nwb_containers.py

@@ -114,7 +114,9 @@ def test_no_error_raised_when_dataset_is_compressed():
 
 
 def test_hit_check_empty_string_for_optional_attribute():
-    nwbfile = NWBFile(session_description="aa", identifier="aa", session_start_time=datetime.now(), pharmacology="")
+    nwbfile = NWBFile(
+        session_description="aa", identifier="aa", session_start_time=datetime.now().astimezone(), pharmacology=""
+    )
 
     assert check_empty_string_for_optional_attribute(nwb_container=nwbfile)[0] == InspectorMessage(
         message='The attribute "pharmacology" is optional and you have supplied an empty string. Improve my omitting '
@@ -128,7 +130,7 @@ def test_hit_check_empty_string_for_optional_attribute():
 
 
 def test_miss_check_empty_string_for_optional_attribute():
-    nwbfile = NWBFile(session_description="aa", identifier="aa", session_start_time=datetime.now())
+    nwbfile = NWBFile(session_description="aa", identifier="aa", session_start_time=datetime.now().astimezone())
     assert check_empty_string_for_optional_attribute(nwb_container=nwbfile) is None
 
 

tests/unit_tests/test_nwbfile_metadata.py

@@ -52,7 +52,9 @@ def test_check_session_start_time_old_date_fail():
 
 
 def test_check_session_start_time_future_date_pass():
-    nwbfile = NWBFile(session_description="", identifier=str(uuid4()), session_start_time=datetime(2010, 1, 1))
+    nwbfile = NWBFile(
+        session_description="", identifier=str(uuid4()), session_start_time=datetime(2010, 1, 1).astimezone()
+    )
     assert check_session_start_time_future_date(nwbfile) is None
 
 
@@ -329,7 +331,7 @@ def test_check_subject_sex_c_elegans_xx_sex():
 
 
 def test_pass_check_subject_age_with_dob():
-    subject = Subject(subject_id="001", sex="F", date_of_birth=datetime.now())
+    subject = Subject(subject_id="001", sex="F", date_of_birth=datetime.now().astimezone())
     assert check_subject_age(subject) is None
 
 

tests/unit_tests/test_ogen.py

@@ -11,7 +11,9 @@
 class TestCheckOptogeneticStimulusSiteHasOptogeneticSeries(TestCase):
     def setUp(self) -> None:
         self.nwbfile = NWBFile(
-            session_description="session_description", identifier="identifier", session_start_time=datetime.now()
+            session_description="session_description",
+            identifier="identifier",
+            session_start_time=datetime.now().astimezone(),
         )
 
         device = Device(name="device_name")

tests/unit_tests/test_ophys.py

@@ -5,7 +5,7 @@
 import numpy as np
 from hdmf.common.table import DynamicTable, DynamicTableRegion
 from pynwb import NWBFile
-from pynwb.device import Device
+from pynwb.device import Device, DeviceModel
 from pynwb.ophys import (
     ImageSegmentation,
     ImagingPlane,
@@ -32,9 +32,12 @@ def setUp(self):
             session_description="", identifier=str(uuid4()), session_start_time=datetime.now().astimezone()
         )
 
-        device = nwbfile.create_device(
-            name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+        device_model = nwbfile.create_device_model(
+            name="My Microscope",
+            description="My two-photon microscope",
+            manufacturer="The best microscope manufacturer",
         )
+        device = nwbfile.create_device(name="Microscope", description="My two-photon microscope", model=device_model)
         optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
         imaging_plane = nwbfile.create_imaging_plane(
             name="ImagingPlane",
@@ -180,9 +183,10 @@ def test_pass_check_roi_response_series_link_to_plane_segmentation(self):
 
 
 def test_check_excitation_lambda_in_nm():
-    device = Device(
-        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    device_model = DeviceModel(
+        name="My Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
     )
+    device = Device(name="Microscope", description="My two-photon microscope", model=device_model)
     optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
     imaging_plane = ImagingPlane(
         name="ImagingPlane",
@@ -203,9 +207,10 @@ def test_check_excitation_lambda_in_nm():
 
 
 def test_pass_check_excitation_lambda_in_nm():
-    device = Device(
-        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    device_model = DeviceModel(
+        name="My Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
     )
+    device = Device(name="Microscope", description="My two-photon microscope", model=device_model)
     optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
     imaging_plane = ImagingPlane(
         name="ImagingPlane",
@@ -236,9 +241,10 @@ def test_pass_check_emission_lambda_in_nm():
 
 
 def test_pass_check_plane_segmentation_image_mask_dims_against_imageseries():
-    device = Device(
-        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    device_model = DeviceModel(
+        name="My Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
     )
+    device = Device(name="Microscope", description="My two-photon microscope", model=device_model)
     optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
     imaging_plane = ImagingPlane(
         name="ImagingPlane",
@@ -275,9 +281,10 @@ def test_pass_check_plane_segmentation_image_mask_dims_against_imageseries():
 
 
 def test_fail_check_plane_segmentation_image_mask_dims_against_imageseries():
-    device = Device(
-        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    device_model = DeviceModel(
+        name="My Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
     )
+    device = Device(name="Microscope", description="My two-photon microscope", model=device_model)
     optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
     imaging_plane = ImagingPlane(
         name="ImagingPlane",
@@ -323,9 +330,10 @@ def test_fail_check_plane_segmentation_image_mask_dims_against_imageseries():
 
 
 def test_false_positive_skip_check_image_series_data_size():
-    device = Device(
-        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    device_model = DeviceModel(
+        name="My Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
     )
+    device = Device(name="Microscope", description="My two-photon microscope", model=device_model)
     optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
     imaging_plane = ImagingPlane(
         name="ImagingPlane",