Fix warnings (#1571)

* Fix warnings * Make sure unittest CI runs test_mock * Update changelog * Cut number of tests run on CI
NeurodataWithoutBorders · Oct 19, 2022 · 4f8f7eb · 4f8f7eb
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diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -20,13 +20,10 @@ jobs:
       matrix:
         include:
           - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
           - { name: linux-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest , upload-wheels: true }
           - { name: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: windows-latest }
           - { name: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
-          - { name: macos-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: macos-latest }
     steps:
       - name: Cancel any previous incomplete runs
         uses: styfle/[email protected]
@@ -81,11 +78,11 @@ jobs:
       matrix:
         include:
           - { name: linux-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.8-upgraded  , test-tox-env: gallery-py38-upgraded, python-ver: "3.8", os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-upgraded   , test-tox-env: gallery-py38-upgraded , python-ver: "3.8" , os: ubuntu-latest }
           # allensdk is not compatible with python 3.9+, so run gallery tests only on python <=3.8
           # - { name: linux-gallery-python3.10-upgraded  , test-tox-env: gallery-py310-upgraded, python-ver: "3.10", os: ubuntu-latest }
           - { name: windows-gallery-python3.7-minimum  , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-gallery-python3.8-upgraded, test-tox-env: gallery-py38-upgraded, python-ver: "3.8", os: windows-latest }
+          - { name: windows-gallery-python3.8-upgraded , test-tox-env: gallery-py38-upgraded , python-ver: "3.8" , os: windows-latest }
           # - { name: windows-gallery-python3.10-upgraded, test-tox-env: gallery-py310-upgraded, python-ver: "3.10", os: windows-latest }
     steps:
       - name: Cancel any previous incomplete runs

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,8 @@
 ### Bug fixes
 - Fixed bug in ``pynwb.testing.mock.file.mock_NWBFile`` to identifier UUID to string. @oruebel
   [#1557](https://github.com/NeurodataWithoutBorders/pynwb/pull/1557)
+- Minor fixes to test suite to prevent warnings. @rly
+  [#1571](https://github.com/NeurodataWithoutBorders/pynwb/pull/1571)
 
 ## PyNWB 2.1.1 (September 1, 2022)
 

diff --git a/src/pynwb/testing/mock/ecephys.py b/src/pynwb/testing/mock/ecephys.py
@@ -38,7 +38,10 @@ def mock_ElectrodeTable(n_rows=5, group=None):
 
 def mock_electrodes(n_electrodes=5, table=mock_ElectrodeTable(n_rows=5)):
     return DynamicTableRegion(
-        "electrodes", list(range(n_electrodes)), "the first and third electrodes", table
+        name="electrodes",
+        data=list(range(n_electrodes)),
+        description="the first and third electrodes",
+        table=table,
     )
 
 

diff --git a/src/pynwb/testing/mock/file.py b/src/pynwb/testing/mock/file.py
@@ -1,5 +1,6 @@
 from uuid import uuid4
 from datetime import datetime
+from dateutil.tz import tzlocal
 
 from ...file import NWBFile, Subject
 from .utils import name_generator
@@ -8,7 +9,7 @@
 def mock_NWBFile(
     session_description='session_description',
     identifier=None,
-    session_start_time=datetime(1970, 1, 1),
+    session_start_time=datetime(1970, 1, 1, tzinfo=tzlocal()),
     subject=None,
     **kwargs
 ):

diff --git a/tests/back_compat/2.1.0_imageseries_no_data.nwb b/tests/back_compat/2.1.0_imageseries_no_data.nwb
diff --git a/tests/back_compat/2.1.0_imageseries_non_external_format.nwb b/tests/back_compat/2.1.0_imageseries_non_external_format.nwb
diff --git a/tests/back_compat/2.1.0_imageseries_nonmatch_starting_frame.nwb b/tests/back_compat/2.1.0_imageseries_nonmatch_starting_frame.nwb
diff --git a/tests/back_compat/test_read.py b/tests/back_compat/test_read.py
@@ -42,6 +42,7 @@ def test_read(self):
         for f in nwb_files:
             with self.subTest(file=f.name):
                 with warnings.catch_warnings(record=True) as warnings_on_read:
+                    warnings.simplefilter("always")
                     with NWBHDF5IO(str(f), 'r', load_namespaces=True) as io:
                         errors = validate(io)
                         io.read()

diff --git a/tests/unit/test_mock.py b/tests/unit/test_mock.py
@@ -29,30 +29,33 @@
     mock_SpikeEventSeries,
 )
 
+from pynwb.testing import TestCase
 import pytest
 
 
-@pytest.mark.parametrize(
-    "mock_function", [
-        mock_ImagingPlane,
-        mock_TwoPhotonSeries,
-        mock_RoiResponseSeries,
-        mock_PlaneSegmentation,
-        mock_OpticalChannel,
-        mock_OptogeneticStimulusSite,
-        mock_OptogeneticSeries,
-        mock_Device,
-        mock_Position,
-        mock_PupilTracking,
-        mock_CompassDirection,
-        mock_SpatialSeries,
-        mock_ElectrodeGroup,
-        mock_ElectrodeTable,
-        mock_ElectricalSeries,
-        mock_SpikeEventSeries,
-        mock_Subject,
-        mock_NWBFile,
-    ],
-)
-def test_mock(mock_function):
-    mock_function()
+class TestMock(TestCase):
+
+    @pytest.mark.parametrize(
+        "mock_function", [
+            mock_ImagingPlane,
+            mock_TwoPhotonSeries,
+            mock_RoiResponseSeries,
+            mock_PlaneSegmentation,
+            mock_OpticalChannel,
+            mock_OptogeneticStimulusSite,
+            mock_OptogeneticSeries,
+            mock_Device,
+            mock_Position,
+            mock_PupilTracking,
+            mock_CompassDirection,
+            mock_SpatialSeries,
+            mock_ElectrodeGroup,
+            mock_ElectrodeTable,
+            mock_ElectricalSeries,
+            mock_SpikeEventSeries,
+            mock_Subject,
+            mock_NWBFile,
+        ],
+    )
+    def test_mock(mock_function):
+        mock_function()