Update for pynwb use of DeviceModel

environment.yml

@@ -7,7 +7,7 @@ dependencies:
 - numpy
 - scipy
 - pandas
-- pynwb<=3.0.0
+- pynwb>=3.1.0
 - nwbinspector>=0.5.0
 - dask
 - ipython

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
     "numpy",
     "scipy",
     "pandas",
-    "pynwb<=3.0.0",
+    "pynwb>=3.1.0",
     "nwbinspector>=0.5.0",
     "ndx_franklab_novela",
     "pyyaml",

src/trodes_to_nwb/convert_yaml.py

@@ -25,6 +25,12 @@
 from pynwb import NWBFile
 from pynwb.file import ProcessingModule, Subject
 
+try:
+    from pynwb.device import DeviceModel
+except ImportError:
+    # Temporary error message to ensure existing users have the correct version of pynwb
+    raise ImportError("Please upgrade pynwb to 3.1.0 or later")
+
 import trodes_to_nwb.metadata_validation
 from trodes_to_nwb import __version__
 
@@ -134,13 +140,20 @@ def add_cameras(nwbfile: NWBFile, metadata: dict) -> None:
         metadata from the yaml generator
     """
     # add each camera device to the nwb
+    camera_devices = {}
     for camera_metadata in metadata["cameras"]:
+        if (model_name := camera_metadata["model"]) not in camera_devices:
+            camera_devices[model_name] = nwbfile.create_device_model(
+                name=camera_metadata["model"],
+                manufacturer=camera_metadata["manufacturer"],
+                description="",
+            )
         nwbfile.add_device(
             CameraDevice(
                 name="camera_device " + str(camera_metadata["id"]),
                 meters_per_pixel=camera_metadata["meters_per_pixel"],
                 manufacturer=camera_metadata["manufacturer"],
-                model=camera_metadata["model"],
+                model=camera_devices[model_name],
                 lens=camera_metadata["lens"],
                 camera_name=camera_metadata["camera_name"],
             )

src/trodes_to_nwb/tests/test_convert_yaml.py

@@ -60,7 +60,8 @@ def test_camera_creation():
     assert len(cameras) == 2
     name = "camera_device " + str(metadata["cameras"][0]["id"])
     assert cameras[name].meters_per_pixel == 0.001
-    assert cameras[name].model == "model1"
+    assert cameras[name].model.name == "model1"
+    assert cameras[name].manufacturer == "Allied Vision"
     assert cameras[name].lens == "lens1"
     assert cameras[name].manufacturer == "Allied Vision"