Add "in_mm", add example usage, update tests

pyproject.toml

@@ -17,17 +17,16 @@ authors = [
 ]
 description = "NWB extension for storing extracellular probe and channels metadata"
 readme = "README.md"
-# requires-python = ">=3.8"
+requires-python = ">=3.8"
 license = {text = "BSD-3"}
 classifiers = [
-    # TODO: add classifiers before release
-    # "Programming Language :: Python",
-    # "Programming Language :: Python :: 3.8",
-    # "Programming Language :: Python :: 3.9",
-    # "Programming Language :: Python :: 3.10",
-    # "Programming Language :: Python :: 3.11",
-    # "Programming Language :: Python :: 3.12",
-    # "Development Status :: 4 - Beta",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: BSD License",
@@ -44,12 +43,12 @@ dependencies = [
 ]
 
 # TODO: add URLs before release
-# [project.urls]
-# "Homepage" = "https://github.com/organization/package"
+[project.urls]
+"Homepage" = "https://github.com/catalystneuro/ndx-extracellular-channels"
 # "Documentation" = "https://package.readthedocs.io/"
-# "Bug Tracker" = "https://github.com/organization/package/issues"
+"Bug Tracker" = "https://github.com/catalystneuro/ndx-extracellular-channels/issues"
 # "Discussions" = "https://github.com/organization/package/discussions"
-# "Changelog" = "https://github.com/organization/package/blob/main/CHANGELOG.md"
+"Changelog" = "https://github.com/catalystneuro/ndx-extracellular-channels/blob/main/CHANGELOG.md"
 
 [tool.hatch.build]
 include = [
@@ -116,6 +115,7 @@ line-length = 120
 [tool.ruff.per-file-ignores]
 "src/pynwb/ndx_extracellular_channels/__init__.py" = ["E402", "F401"]
 "src/spec/create_extension_spec.py" = ["T201"]
+"src/pynwb/tests/test_example_usage_all.py" = ["T201"]
 
 [tool.ruff.mccabe]
 max-complexity = 17

spec/ndx-extracellular-channels.extensions.yaml

@@ -5,7 +5,7 @@ groups:
   doc: Metadata about the contacts of a probe, compatible with the ProbeInterface
     specification.
   datasets:
-  - name: relative_position
+  - name: relative_position_in_mm
     neurodata_type_inc: VectorData
     dtype: float
     dims:
@@ -18,7 +18,7 @@ groups:
       - 2
     - - null
       - 3
-    doc: Relative position of the contact
+    doc: Relative position of the contact in millimeters, relative to `reference`.
     attributes:
     - name: reference
       dtype: text
@@ -179,7 +179,7 @@ groups:
     doc: The filter used on the raw (wideband) voltage data from this contact, including
       the filter name and frequency cutoffs, e.g., 'High-pass filter at 300 Hz.'
     quantity: '?'
-  - name: estimated_position
+  - name: estimated_position_in_mm
     neurodata_type_inc: VectorData
     dtype:
     - name: ap
@@ -207,7 +207,7 @@ groups:
     dtype: text
     doc: The brain area of the estimated contact position, e.g., 'CA1'.
     quantity: '?'
-  - name: actual_position
+  - name: actual_position_in_mm
     neurodata_type_inc: VectorData
     dtype:
     - name: ap

src/pynwb/tests/test_classes.py

@@ -34,7 +34,7 @@ def test_constructor_add_row(self):
 
         # for testing, mix and match different shapes. np.nan means the radius/width/height does not apply
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
             contact_id="C1",
             shank_id="shank0",
@@ -46,7 +46,7 @@ def test_constructor_add_row(self):
         )
 
         ct.add_row(
-            relative_position=[20.0, 10.0],
+            relative_position_in_mm=[20.0, 10.0],
             shape="square",
             contact_id="C2",
             shank_id="shank0",
@@ -59,13 +59,13 @@ def test_constructor_add_row(self):
 
         # TODO might be nice to put this on the constructor of ContactsTable as relative_position__reference
         # without using a custom mapper
-        ct["relative_position"].reference = "The bottom tip of the probe"
+        ct["relative_position_in_mm"].reference = "The bottom tip of the probe"
 
         assert ct.name == "ContactsTable"
         assert ct.description == "Test contacts table"
-        assert ct["relative_position"].reference == "The bottom tip of the probe"
+        assert ct["relative_position_in_mm"].reference == "The bottom tip of the probe"
 
-        assert ct["relative_position"].data == [[10.0, 10.0], [20.0, 10.0]]
+        assert ct["relative_position_in_mm"].data == [[10.0, 10.0], [20.0, 10.0]]
         assert ct["shape"].data == ["circle", "square"]
         assert ct["contact_id"].data == ["C1", "C2"]
         assert ct["shank_id"].data == ["shank0", "shank0"]
@@ -89,7 +89,7 @@ def addContainer(self):
 
         # for testing, mix and match different shapes. np.nan means the radius/width/height does not apply
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
             contact_id="C1",
             shank_id="shank0",
@@ -101,7 +101,7 @@ def addContainer(self):
         )
 
         ct.add_row(
-            relative_position=[20.0, 10.0],
+            relative_position_in_mm=[20.0, 10.0],
             shape="square",
             contact_id="C2",
             shank_id="shank0",
@@ -129,7 +129,7 @@ def test_constructor(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
         )
 
@@ -162,7 +162,7 @@ def addContainer(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
         )
 
@@ -191,7 +191,7 @@ def test_constructor_minimal(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
         )
 
@@ -219,7 +219,7 @@ def test_constructor(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
         )
 
@@ -252,7 +252,7 @@ def addContainer(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position=[10.0, 10.0],
+            relative_position_in_mm=[10.0, 10.0],
             shape="circle",
         )
 
@@ -283,15 +283,15 @@ def _create_test_probe():
         description="Test contacts table",
     )
     ct.add_row(
-        relative_position=[10.0, 10.0],
+        relative_position_in_mm=[10.0, 10.0],
         shape="circle",
     )
     ct.add_row(
-        relative_position=[10.0, 10.0],
+        relative_position_in_mm=[10.0, 10.0],
         shape="circle",
     )
     ct.add_row(
-        relative_position=[10.0, 10.0],
+        relative_position_in_mm=[10.0, 10.0],
         shape="circle",
     )
 
@@ -419,26 +419,26 @@ def test_constructor_add_row(self):
             contact=0,
             reference_contact=2,
             filter="High-pass at 300 Hz",
-            estimated_position=[-1.5, 2.5, -2.5],
+            estimated_position_in_mm=[-1.5, 2.5, -2.5],
             estimated_brain_area="CA3",
-            actual_position=[-1.5, 2.4, -2.4],
+            actual_position_in_mm=[-1.5, 2.4, -2.4],
             actual_brain_area="CA3",
         )
 
         ct.add_row(
             contact=1,
             reference_contact=2,
             filter="High-pass at 300 Hz",
-            estimated_position=[-1.5, 2.5, -2.4],
+            estimated_position_in_mm=[-1.5, 2.5, -2.4],
             estimated_brain_area="CA3",
-            actual_position=[-1.5, 2.4, -2.3],
+            actual_position_in_mm=[-1.5, 2.4, -2.3],
             actual_brain_area="CA3",
         )
 
         # TODO might be nice to put this on the constructor of ContactsTable as relative_position__reference
         # without using a custom mapper
-        ct["estimated_position"].reference = "Bregma at the cortical surface"
-        ct["actual_position"].reference = "Bregma at the cortical surface"
+        ct["estimated_position_in_mm"].reference = "Bregma at the cortical surface"
+        ct["actual_position_in_mm"].reference = "Bregma at the cortical surface"
 
         # TODO
         assert ct.name == "Neuropixels1ChannelsTable"
@@ -477,27 +477,27 @@ def addContainer(self):
             contact=0,
             reference_contact=2,
             filter="High-pass at 300 Hz",
-            estimated_position=[-1.5, 2.5, -2.5],
+            estimated_position_in_mm=[-1.5, 2.5, -2.5],
             estimated_brain_area="CA3",
-            actual_position=[-1.5, 2.4, -2.4],
+            actual_position_in_mm=[-1.5, 2.4, -2.4],
             actual_brain_area="CA3",
         )
 
         ct.add_row(
             contact=1,
             reference_contact=2,
             filter="High-pass at 300 Hz",
-            estimated_position=[-1.5, 2.5, -2.4],
+            estimated_position_in_mm=[-1.5, 2.5, -2.4],
             estimated_brain_area="CA3",
-            actual_position=[-1.5, 2.4, -2.3],
+            actual_position_in_mm=[-1.5, 2.4, -2.3],
             actual_brain_area="CA3",
         )
 
         # TODO might be nice to put this on the constructor of ContactsTable as relative_position__reference
         # without using a custom mapper
         # TODO does matching this happen in the container equals roundtrip test?
-        ct["estimated_position"].reference = "Bregma at the cortical surface"
-        ct["actual_position"].reference = "Bregma at the cortical surface"
+        ct["estimated_position_in_mm"].reference = "Bregma at the cortical surface"
+        ct["actual_position_in_mm"].reference = "Bregma at the cortical surface"
 
         # put this in nwbfile.acquisition for testing
         self.nwbfile.add_acquisition(ct)