Fix warnings from tests

.github/workflows/run_all_tests.yml

@@ -196,9 +196,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-python3.11-ros3, python-ver: "3.11", os: windows-latest }
-          - { name: macos-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
+          - { name: conda-linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-windows-python3.11-ros3, python-ver: "3.11", os: windows-latest }
+          - { name: conda-macos-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/cancel-workflow-action@0.11.0
@@ -243,9 +243,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-gallery-python3.11-ros3, python-ver: "3.11", os: windows-latest }
-          - { name: macos-gallery-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
+          - { name: conda-linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-windows-gallery-python3.11-ros3, python-ver: "3.11", os: windows-latest }
+          - { name: conda-macos-gallery-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/cancel-workflow-action@0.11.0

.github/workflows/run_dandi_read_tests.yml

@@ -47,4 +47,4 @@ jobs:
 
       - name: Run DANDI read tests
         run: |
-          pytest -rP tests/read_dandi/
+          python tests/read_dandi/test_read_dandi.py

.github/workflows/run_tests.yml

@@ -174,7 +174,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/cancel-workflow-action@0.11.0
@@ -219,7 +219,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/cancel-workflow-action@0.11.0

docs/notebooks/convert-crcns-ret-1-meisterlab.ipynb

@@ -1004,7 +1004,7 @@
    "source": [
     "## Step 5.2: Convert all files\n",
     "\n",
-    "Convert all the files by iteating over the files and calling `convert_single_file` function for each of the file"
+    "Convert all the files by iterating over the files and calling `convert_single_file` function for each of the file"
    ]
   },
   {

docs/notebooks/convert-crcns-ret-1-old/convert-crcns-ret-1-meisterlab-with-custom-extensions-and-external-stimulus.ipynb

@@ -1001,7 +1001,7 @@
    "source": [
     "## Step 5.3: Convert all files\n",
     "\n",
-    "Convert all the files by iteating over the files and calling `convert_single_file` function for each of the file"
+    "Convert all the files by iterating over the files and calling `convert_single_file` function for each of the file"
    ]
   },
   {

docs/notebooks/convert-crcns-ret-1-old/convert-crcns-ret-1-meisterlab-with-custom-extensions.ipynb

@@ -974,7 +974,7 @@
    "source": [
     "## Step 5.3: Convert all files\n",
     "\n",
-    "Convert all the files by iteating over the files and calling `convert_single_file` function for each of the file"
+    "Convert all the files by iterating over the files and calling `convert_single_file` function for each of the file"
    ]
   },
   {

docs/notebooks/convert-crcns-ret-1-old/convert-crcns-ret-1-meisterlab-without-custom-extensions.ipynb

@@ -649,7 +649,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Convert all the files by iteating over the files and calling `convert_single_file` function for each of the file"
+    "Convert all the files by iterating over the files and calling `convert_single_file` function for each of the file"
    ]
   },
   {

setup.cfg

@@ -28,6 +28,7 @@ per-file-ignores =
   tests/integration/__init__.py:F401
   src/pynwb/testing/__init__.py:F401
   src/pynwb/validate.py:T201
+  tests/read_dandi/test_read_dandi.py:T201
   setup.py:T201
   test.py:T201
   scripts/*:T201

src/pynwb/testing/mock/ophys.py

@@ -4,7 +4,7 @@
 
 from hdmf.common.table import DynamicTableRegion
 
-from ... import NWBFile
+from ... import NWBFile, ProcessingModule
 from ...device import Device
 from ...ophys import (
     RoiResponseSeries,
@@ -272,6 +272,8 @@ def mock_RoiResponseSeries(
     else:
         n_rois = 5
 
+    plane_seg = plane_segmentation or mock_PlaneSegmentation(n_rois=n_rois, nwbfile=nwbfile)
+
     roi_response_series = RoiResponseSeries(
         name=name if name is not None else name_generator("RoiResponseSeries"),
         data=data if data is not None else np.ones((30, n_rois)),
@@ -280,7 +282,7 @@ def mock_RoiResponseSeries(
         or DynamicTableRegion(
             name="rois",
             description="rois",
-            table=plane_segmentation or mock_PlaneSegmentation(n_rois=n_rois, nwbfile=nwbfile),
+            table=plane_seg,
             data=list(range(n_rois)),
         ),
         resolution=resolution,
@@ -298,6 +300,9 @@ def mock_RoiResponseSeries(
         if "ophys" not in nwbfile.processing:
             nwbfile.create_processing_module("ophys", "ophys")
 
+        if plane_seg.name not in nwbfile.processing["ophys"].data_interfaces:
+            nwbfile.processing["ophys"].add(plane_seg)
+
         nwbfile.processing["ophys"].add(roi_response_series)
 
     return roi_response_series
@@ -309,16 +314,24 @@ def mock_DfOverF(
     nwbfile: Optional[NWBFile] = None
 ) -> DfOverF:
     df_over_f = DfOverF(
-        roi_response_series=roi_response_series or [mock_RoiResponseSeries(nwbfile=nwbfile)],
         name=name if name is not None else name_generator("DfOverF"),
     )
+    plane_seg = mock_PlaneSegmentation(nwbfile=nwbfile)
 
     if nwbfile is not None:
         if "ophys" not in nwbfile.processing:
             nwbfile.create_processing_module("ophys", "ophys")
 
         nwbfile.processing["ophys"].add(df_over_f)
 
+    else:
+        pm = ProcessingModule(name="ophys", description="ophys")
+        pm.add(plane_seg)
+        pm.add(df_over_f)
+
+    df_over_f.add_roi_response_series(
+        roi_response_series or mock_RoiResponseSeries(nwbfile=nwbfile, plane_segmentation=plane_seg)
+    )
     return df_over_f
 
 
@@ -328,13 +341,22 @@ def mock_Fluorescence(
     nwbfile: Optional[NWBFile] = None,
 ) -> Fluorescence:
     fluorescence = Fluorescence(
-        roi_response_series=roi_response_series or [mock_RoiResponseSeries(nwbfile=nwbfile)],
         name=name if name is not None else name_generator("Fluorescence"),
     )
+    plane_seg = mock_PlaneSegmentation(nwbfile=nwbfile)
 
     if nwbfile is not None:
         if "ophys" not in nwbfile.processing:
             nwbfile.create_processing_module("ophys", "ophys")
+
         nwbfile.processing["ophys"].add(fluorescence)
+    else:
+        pm = ProcessingModule(name="ophys", description="ophys")
+        pm.add(plane_seg)
+        pm.add(fluorescence)
+
+    fluorescence.add_roi_response_series(
+        roi_response_series or mock_RoiResponseSeries(nwbfile=nwbfile, plane_segmentation=plane_seg)
+    )
 
     return fluorescence

test.py

@@ -163,7 +163,7 @@ def validate_nwbs():
 
                 def get_namespaces(nwbfile):
                     comp = run(["python", "-m", "pynwb.validate",
-                               "--list-namespaces", "--cached-namespace", nwb],
+                               "--list-namespaces", nwbfile],
                                stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=30)
 
                     if comp.returncode != 0:
@@ -179,14 +179,13 @@ def get_namespaces(nwbfile):
 
                 cmds = []
                 cmds += [["python", "-m", "pynwb.validate", nwb]]
-                cmds += [["python", "-m", "pynwb.validate", "--cached-namespace", nwb]]
                 cmds += [["python", "-m", "pynwb.validate", "--no-cached-namespace", nwb]]
 
                 for ns in namespaces:
                     # for some reason, this logging command is necessary to correctly printing the namespace in the
                     # next logging command
                     logging.info("Namespace found: %s" % ns)
-                    cmds += [["python", "-m", "pynwb.validate", "--cached-namespace", "--ns", ns, nwb]]
+                    cmds += [["python", "-m", "pynwb.validate", "--ns", ns, nwb]]
 
                 for cmd in cmds:
                     logging.info("Validating with \"%s\"." % (" ".join(cmd[:-1])))