Make contact required, minor other fixes

catalystneuro · Jul 12, 2024 · 80dd349 · 80dd349
1 parent 4369cdc
commit 80dd349
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Showing 5 changed files with 33 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -106,7 +106,7 @@ classDiagram
         columns
         --------------------------------------
         id : VectorData[int]
-        contact : DynamicTableRegion, optional
+        contact : DynamicTableRegion
         --> target : ContactsTable
         reference_contact :  DynamicTableRegion, optional
         --> target : ContactsTable

diff --git a/spec/ndx-extracellular-channels.extensions.yaml b/spec/ndx-extracellular-channels.extensions.yaml
@@ -71,6 +71,7 @@ groups:
     neurodata_type_inc: VectorData
     dtype: text
     doc: Shape of the contact; e.g. 'circle'
+    quantity: '?'
   - name: radius_in_um
     neurodata_type_inc: VectorData
     dtype: float
@@ -221,7 +222,6 @@ groups:
   - name: contact
     neurodata_type_inc: DynamicTableRegion
     doc: The row in a ContactsTable that represents the contact used as a channel.
-    quantity: '?'
   - name: reference_contact
     neurodata_type_inc: DynamicTableRegion
     doc: The row in a ContactsTable that represents the contact used as a reference.

diff --git a/src/pynwb/ndx_extracellular_channels/__init__.py b/src/pynwb/ndx_extracellular_channels/__init__.py
@@ -28,5 +28,16 @@
 
 from .io import from_probeinterface, to_probeinterface
 
+__all__ = (
+    "ProbeInsertion",
+    "ContactsTable",
+    "ProbeModel",
+    "Probe",
+    "ChannelsTable",
+    "ExtracellularSeries",
+    "from_probeinterface",
+    "to_probeinterface",
+)
+
 # Remove these functions from the package
 del load_namespaces, get_class
diff --git a/src/pynwb/tests/test_classes.py b/src/pynwb/tests/test_classes.py
@@ -457,12 +457,16 @@ def test_constructor_add_row_minimal(self):
         ct = ChannelsTable(
             description="Test channels table",
             probe=probe,
+            target_tables={
+                "contact": probe.probe_model.contacts_table,
+            },
         )
-        ct.add_row()
-        ct.add_row()
+        ct.add_row(contact=0)
+        ct.add_row(contact=1)
 
         assert len(ct) == 2
         assert ct.id.data == [0, 1]
+        assert ct["contact"].data == [0, 1]
 
     def test_constructor_add_row(self):
         """Test that the constructor for ChannelsTable sets values as expected."""
@@ -611,10 +615,13 @@ def test_constructor(self):
             name="Neuropixels1ChannelsTable",
             description="Test channels table",
             probe=probe,
+            target_tables={
+                "contact": probe.probe_model.contacts_table,
+            },
         )
-        ct.add_row()
-        ct.add_row()
-        ct.add_row()
+        ct.add_row(contact=0)
+        ct.add_row(contact=1)
+        ct.add_row(contact=2)
 
         channels = DynamicTableRegion(
             name="channels",  # NOTE: this must be named "channels" when used in ExtracellularSeries
@@ -661,10 +668,13 @@ def addContainer(self):
             name="Neuropixels1ChannelsTable",
             description="Test channels table",
             probe=probe,
+            target_tables={
+                "contact": probe.probe_model.contacts_table,
+            },
         )
-        ct.add_row()
-        ct.add_row()
-        ct.add_row()
+        ct.add_row(contact=0)
+        ct.add_row(contact=1)
+        ct.add_row(contact=2)
 
         # put this in nwbfile.acquisition for testing
         self.nwbfile.add_acquisition(ct)

diff --git a/src/spec/create_extension_spec.py b/src/spec/create_extension_spec.py
@@ -56,7 +56,7 @@ def main():
                             "(first element), which direction is positive in the y direction (second element), etc."
                         ),
                         dtype="text",
-                        required=False,  # TODO should this be required?
+                        required=False,
                     )
                 ],
             ),
@@ -108,6 +108,7 @@ def main():
                 neurodata_type_inc="VectorData",
                 doc="Shape of the contact; e.g. 'circle'",
                 dtype="text",
+                quantity="?",
             ),
             NWBDatasetSpec(
                 name="radius_in_um",
@@ -315,7 +316,6 @@ def main():
                 name="contact",
                 neurodata_type_inc="DynamicTableRegion",
                 doc="The row in a ContactsTable that represents the contact used as a channel.",
-                quantity="?",  # TODO should this be optional?
             ),
             NWBDatasetSpec(
                 name="reference_contact",