Merge pull request #264 from NeurodataWithoutBorders/fix_pynwb_version_icephys

Fix attribute retrieval from version-dependent icephys

Author: CodyCBakerPhD

.github/workflows/version_gallery.yml

@@ -0,0 +1,32 @@
+name: Past PyNWB Version
+on:
+  schedule:
+    - cron: "0 0 * * *"  # daily
+  pull_request:
+
+jobs:
+  build-and-test:
+    name: Testing against past PyNWB versions
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        pynwb-version: ["2.1.0", "2.0.0"]
+    steps:
+      - uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: 3.9
+          conda-channels: conda-forge
+      - uses: actions/checkout@v2
+      - run: git fetch --prune --unshallow --tags
+      - name: Install pytest
+        run: |
+          pip install pytest
+          pip install pytest-cov
+      - name: Install package
+        run: |
+          pip install -e .
+          pip install pynwb==${{ matrix.pynwb-version }}
+      - name: Run pytest with coverage
+        run: pytest -rsx

nwbinspector/checks/icephys.py

@@ -6,5 +6,5 @@
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=IntracellularElectrode)
 def check_intracellular_electrode_cell_id_exists(intracellular_electrode: IntracellularElectrode):
     """Check if the IntracellularElectrode contains a cell_id."""
-    if intracellular_electrode.cell_id is None:
+    if hasattr(intracellular_electrode, "cell_id") and intracellular_electrode.cell_id is None:
         return InspectorMessage(message="Please include a unique cell_id associated with this IntracellularElectrode.")

tests/unit_tests/test_icephys.py

@@ -1,15 +1,23 @@
+import pytest
+from packaging.version import Version
 from pynwb.icephys import IntracellularElectrode
 from pynwb.device import Device
 
 from nwbinspector import InspectorMessage, Importance, check_intracellular_electrode_cell_id_exists
+from nwbinspector.utils import get_package_version
 
+PYNWB_VERSION_LOWER_2_1_0 = get_package_version(name="pynwb") < Version("2.1.0")
+PYNWB_VERSION_LOWER_SKIP_REASON = "This test requires PyNWB>=2.1.0"
 
+
+@pytest.mark.skipif(PYNWB_VERSION_LOWER_2_1_0, reason=PYNWB_VERSION_LOWER_SKIP_REASON)
 def test_pass_check_intracellular_electrode_cell_id_exists():
     device = Device(name="device")
     ielec = IntracellularElectrode(name="ielec", cell_id="123", device=device, description="an intracellular electrode")
     assert check_intracellular_electrode_cell_id_exists(ielec) is None
 
 
+@pytest.mark.skipif(PYNWB_VERSION_LOWER_2_1_0, reason=PYNWB_VERSION_LOWER_SKIP_REASON)
 def test_fail_check_intracellular_electrode_cell_id_exists():
     device = Device(name="device")
     ielec = IntracellularElectrode(name="ielec", device=device, description="an intracellular electrode")
@@ -21,3 +29,10 @@ def test_fail_check_intracellular_electrode_cell_id_exists():
         object_name="ielec",
         location="/",
     )
+
+
+@pytest.mark.skipif(not PYNWB_VERSION_LOWER_2_1_0, reason="This test requires PyNWB<2.1.0")
+def test_skip_check_for_lower_versions():
+    device = Device(name="device")
+    ielec = IntracellularElectrode(name="ielec", device=device, description="an intracellular electrode")
+    assert check_intracellular_electrode_cell_id_exists(ielec) is None