Update tests

src/pynwb/io/file.py

@@ -16,8 +16,6 @@ def parse_datetime(datestr):
     :param datestr: str
     :return: datetime.datetime or datetime.date
     """
-    if datestr is None:
-        return None
     if isinstance(datestr, bytes):
         datestr = datestr.decode("utf-8")
     dt = datetime.datetime.fromisoformat(datestr)

src/pynwb/testing/mock/file.py

@@ -10,7 +10,7 @@
 def mock_NWBFile(
     session_description: str = 'session_description',
     identifier: Optional[str] = None,
-    session_start_time: datetime = datetime(1970, 1, 1, tzinfo=tzlocal()),
+    session_start_time: datetime = datetime(1970, 1, 1),
     **kwargs
 ):
     return NWBFile(

src/pynwb/testing/testh5io.py

@@ -33,8 +33,8 @@ def getContainer(self, nwbfile):
 
     def setUp(self):
         self.container = self.setUpContainer()
-        self.start_time = datetime(1971, 1, 1, 12, tzinfo=tzutc())
-        self.create_date = datetime(2018, 4, 15, 12, tzinfo=tzlocal())
+        self.start_time = datetime(1971, 1, 1, 12)
+        self.create_date = datetime(2018, 4, 15, 12)
         self.container_type = self.container.__class__.__name__
         self.filename = 'test_%s.nwb' % self.container_type
         self.export_filename = 'test_export_%s.nwb' % self.container_type
@@ -226,7 +226,7 @@ def setUp(self):
         container_type = self.getContainerType().replace(" ", "_")
         session_description = 'A file to test writing and reading a %s' % container_type
         identifier = 'TEST_%s' % container_type
-        session_start_time = datetime(1971, 1, 1, 12, tzinfo=tzutc())
+        session_start_time = datetime(1971, 1, 1, 12)
         self.nwbfile = NWBFile(
             session_description=session_description,
             identifier=identifier,

tests/integration/hdf5/test_base.py

@@ -34,7 +34,7 @@ def test_timestamps_linking(self):
         tsa = TimeSeries(name='a', data=np.linspace(0, 1, 1000), timestamps=np.arange(1000.), unit='m')
         tsb = TimeSeries(name='b', data=np.linspace(0, 1, 1000), timestamps=tsa, unit='m')
         nwbfile = NWBFile(identifier='foo',
-                          session_start_time=datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()),
+                          session_start_time=datetime(2017, 5, 1, 12, 0, 0),
                           session_description='bar')
         nwbfile.add_acquisition(tsa)
         nwbfile.add_acquisition(tsb)
@@ -52,7 +52,7 @@ def test_data_linking(self):
         tsb = TimeSeries(name='b', data=tsa, timestamps=np.arange(1000.), unit='m')
         tsc = TimeSeries(name='c', data=tsb, timestamps=np.arange(1000.), unit='m')
         nwbfile = NWBFile(identifier='foo',
-                          session_start_time=datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()),
+                          session_start_time=datetime(2017, 5, 1, 12, 0, 0),
                           session_description='bar')
         nwbfile.add_acquisition(tsa)
         nwbfile.add_acquisition(tsb)

tests/integration/hdf5/test_io.py

@@ -245,7 +245,7 @@ class TestAppend(TestCase):
     def setUp(self):
         self.nwbfile = NWBFile(session_description='hi',
                                identifier='hi',
-                               session_start_time=datetime(1970, 1, 1, 12, tzinfo=tzutc()))
+                               session_start_time=datetime(1970, 1, 1, 12))
         self.path = "test_append.nwb"
 
     def tearDown(self):
@@ -312,7 +312,7 @@ class TestH5DataIO(TestCase):
     def setUp(self):
         self.nwbfile = NWBFile(session_description='a',
                                identifier='b',
-                               session_start_time=datetime(1970, 1, 1, 12, tzinfo=tzutc()))
+                               session_start_time=datetime(1970, 1, 1, 12))
         self.path = "test_pynwb_io_hdf5_h5dataIO.h5"
 
     def tearDown(self):

tests/integration/hdf5/test_modular_storage.py

@@ -19,7 +19,7 @@ def setUp(self):
         self.link_filename = os.path.join(os.getcwd(), 'test_time_series_modular_link.nwb')
 
         # Make the data container file write
-        self.start_time = datetime(1971, 1, 1, 12, tzinfo=tzutc())
+        self.start_time = datetime(1971, 1, 1, 12)
         self.data = np.arange(2000).reshape((1000, 2))
         self.timestamps = np.linspace(0, 1, 1000)
         # The container before roundtrip

tests/integration/hdf5/test_nwbfile.py

@@ -21,7 +21,12 @@ def setUp(self):
         """ Set up an NWBFile object with an acquisition TimeSeries, analysis TimeSeries, and a processing module """
         self.start_time = datetime(1970, 1, 1, 12, tzinfo=tzutc())
         self.ref_time = datetime(1979, 1, 1, 0, tzinfo=tzutc())
-        self.create_date = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
+        # try some dates with/without timezone and time
+        self.create_date = [
+            datetime(2017, 5, 1, 12, tzinfo=tzlocal()),
+            datetime(2017, 5, 2, 13),
+            datetime(2017, 5, 2),
+        ]
         self.manager = get_manager()
         self.filename = 'test_nwbfileio.h5'
         self.nwbfile = NWBFile(session_description='a test NWB File',
@@ -327,6 +332,30 @@ def getContainer(self, nwbfile):
         return nwbfile.subject
 
 
+class TestSubjectMinimalSetIO(NWBH5IOMixin, TestCase):
+
+    def setUpContainer(self):
+        """ Return the test Subject """
+        return Subject(
+            age="P90D",
+            description="An unfortunate rat",
+            genotype="WT",
+            sex="M",
+            species="Rattus norvegicus",
+            subject_id="RAT123",
+            weight="2 kg",
+            strain="my_strain",
+        )
+
+    def addContainer(self, nwbfile):
+        """ Add the test Subject to the given NWBFile """
+        nwbfile.subject = self.container
+
+    def getContainer(self, nwbfile):
+        """ Return the test Subject from the given NWBFile """
+        return nwbfile.subject
+
+
 class TestEmptySubjectIO(TestSubjectIO):
 
     def setUpContainer(self):

tests/unit/test_epoch.py

@@ -67,7 +67,7 @@ def test_dataframe_roundtrip_drop_ts(self):
         self.assertEqual(obtained.loc[2, 'foo'], df.loc[2, 'foo'])
 
     def test_no_tags(self):
-        nwbfile = NWBFile("a file with header data", "NB123A", datetime(1970, 1, 1, tzinfo=tz.tzutc()))
+        nwbfile = NWBFile("a file with header data", "NB123A", datetime(1970, 1, 1))
         df = self.get_dataframe()
         for i, row in df.iterrows():
             nwbfile.add_epoch(start_time=row['start_time'], stop_time=row['stop_time'])

tests/unit/test_extension.py

@@ -108,7 +108,7 @@ def __init__(self, **kwargs):
                 super().__init__(**kwargs)
                 self.test_attr = test_attr
 
-        nwbfile = NWBFile("a file with header data", "NB123A",  datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))
+        nwbfile = NWBFile("a file with header data", "NB123A",  datetime(2017, 5, 1, 12, 0, 0))
 
         nwbfile.add_lab_meta_data(MyTestMetaData(name='test_name', test_attr=5.))
 
@@ -128,7 +128,7 @@ def test_lab_meta_auto(self):
 
         MyTestMetaData = get_class('MyTestMetaData', self.prefix)
 
-        nwbfile = NWBFile("a file with header data", "NB123A", datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))
+        nwbfile = NWBFile("a file with header data", "NB123A", datetime(2017, 5, 1, 12, 0, 0))
 
         nwbfile.add_lab_meta_data(MyTestMetaData(name='test_name', test_attr=5.))
 

tests/unit/test_file.py

@@ -19,9 +19,10 @@ class NWBFileTest(TestCase):
     def setUp(self):
         self.start = datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal())
         self.ref_time = datetime(1979, 1, 1, 0, tzinfo=tzutc())
+        # try some dates with/without timezone and time
         self.create = [datetime(2017, 5, 1, 12, tzinfo=tzlocal()),
-                       datetime(2017, 5, 2, 13, 0, 0, 1, tzinfo=tzutc()),
-                       datetime(2017, 5, 2, 14, tzinfo=tzutc())]
+                       datetime(2017, 5, 2, 13),
+                       datetime(2017, 5, 2)]
         self.path = 'nwbfile_test.h5'
         self.nwbfile = NWBFile(session_description='a test session description for a test NWBFile',
                                identifier='FILE123',
@@ -533,7 +534,7 @@ def setUp(self):
             date_of_birth=datetime(2017, 5, 1, 12, tzinfo=tzlocal()),
             strain='my_strain',
         )
-        self.start = datetime(2017, 5, 1, 12, tzinfo=tzlocal())
+        self.start = datetime(2017, 5, 1, 12)
         self.path = 'nwbfile_test.h5'
         self.nwbfile = NWBFile(
             'a test session description for a test NWBFile',

tests/unit/test_icephys.py

@@ -46,7 +46,7 @@ def test_sweep_table_depractation_warn(self):
             _ = NWBFile(
                 session_description='NWBFile icephys test',
                 identifier='NWB123',  # required
-                session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
+                session_start_time=datetime(2017, 4, 3, 11),
                 ic_electrodes=[self.icephys_electrode, ],
                 sweep_table=SweepTable())
 
@@ -57,14 +57,14 @@ def test_ic_electrodes_parameter_deprecation(self):
             _ = NWBFile(
                 session_description='NWBFile icephys test',
                 identifier='NWB123',  # required
-                session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
+                session_start_time=datetime(2017, 4, 3, 11),
                 ic_electrodes=[self.icephys_electrode, ])
 
     def test_icephys_electrodes_parameter(self):
         nwbfile = NWBFile(
                 session_description='NWBFile icephys test',
                 identifier='NWB123',  # required
-                session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
+                session_start_time=datetime(2017, 4, 3, 11),
                 icephys_electrodes=[self.icephys_electrode, ])
         self.assertEqual(nwbfile.get_icephys_electrode('test_iS'), self.icephys_electrode)
 
@@ -73,7 +73,7 @@ def test_add_ic_electrode_deprecation(self):
         nwbfile = NWBFile(
                 session_description='NWBFile icephys test',
                 identifier='NWB123',  # required
-                session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()))
+                session_start_time=datetime(2017, 4, 3, 11))
 
         msg = "NWBFile.add_ic_electrode has been replaced by NWBFile.add_icephys_electrode."
         with self.assertWarnsWith(DeprecationWarning, msg):
@@ -83,7 +83,7 @@ def test_ic_electrodes_attribute_deprecation(self):
         nwbfile = NWBFile(
             session_description='NWBFile icephys test',
             identifier='NWB123',  # required
-            session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
+            session_start_time=datetime(2017, 4, 3, 11),
             icephys_electrodes=[self.icephys_electrode, ])
         # make sure NWBFile.ic_electrodes property warns
 
@@ -100,7 +100,7 @@ def test_create_ic_electrode_deprecation(self):
         nwbfile = NWBFile(
             session_description='NWBFile icephys test',
             identifier='NWB123',  # required
-            session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()))
+            session_start_time=datetime(2017, 4, 3, 11))
         device = Device(name='device_name')
         msg = "NWBFile.create_ic_electrode has been replaced by NWBFile.create_icephys_electrode."
         with self.assertWarnsWith(DeprecationWarning, msg):

tests/unit/test_scratch.py

@@ -15,7 +15,7 @@ def setUp(self):
         self.nwbfile = NWBFile(
             session_description='a file to test writing and reading scratch data',
             identifier='TEST_scratch',
-            session_start_time=datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal())
+            session_start_time=datetime(2017, 5, 1, 12, 0, 0)
         )
 
     def test_constructor_list(self):