Merge branch 'dev' into schema_2.2.3

docs/CONTRIBUTING.rst

@@ -6,7 +6,7 @@ How to contribute to NWB:N software and documents
 Code of Conduct
 ---------------
 
-This project and everyone participating in it is governed by our `code of conduct guidelines <https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/.github/CONTRIBUTING.rst>`_. By participating, you are expected to uphold this code. Please report unacceptable behavior.
+This project and everyone participating in it is governed by our `code of conduct guidelines <https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/.github/CODE_OF_CONDUCT.rst>`_. By participating, you are expected to uphold this code. Please report unacceptable behavior.
 
 .. _sec-contribution-types:
 

requirements-min.txt

@@ -1,6 +1,6 @@
 # these minimum requirements specify '==' for testing; setup.py replaces '==' with '>='
 h5py==2.9  # support for setting attrs to lists of utf-8 added in 2.9
-hdmf==1.6.1,<2
+hdmf==1.6.2,<2
 numpy==1.16
 pandas==0.23
 python-dateutil==2.7

requirements.txt

@@ -1,5 +1,5 @@
 h5py==2.10.0
-hdmf==1.6.1
+hdmf==1.6.2
 numpy==1.18.1
 pandas==0.25.3
 python-dateutil==2.8.1

src/pynwb/__init__.py

@@ -49,12 +49,12 @@ def _get_resources():
 @docval({'name': 'extensions', 'type': (str, TypeMap, list),
          'doc': 'a path to a namespace, a TypeMap, or a list consisting of paths to namespaces and TypeMaps',
          'default': None},
-        returns="the namespaces loaded from the given file", rtype=tuple,
+        returns="TypeMap loaded for the given extension or NWB core namespace", rtype=tuple,
         is_method=False)
 def get_type_map(**kwargs):
     '''
-    Get a BuildManager to use for I/O using the given extensions. If no extensions are provided,
-    return a BuildManager that uses the core namespace
+    Get the TypeMap for the given extensions. If no extensions are provided,
+    return the TypeMap for the core namespace
     '''
     extensions = getargs('extensions', kwargs)
     type_map = None
@@ -227,7 +227,7 @@ def __init__(self, **kwargs):
                 raise ValueError("cannot load namespaces from file when writing to it")
 
             tm = get_type_map()
-            super(NWBHDF5IO, self).load_namespaces(tm, path)
+            super(NWBHDF5IO, self).load_namespaces(tm, path, file=file_obj)
             manager = BuildManager(tm)
 
             # XXX: Leaving this here in case we want to revert to this strategy for

src/pynwb/legacy/__init__.py

@@ -38,4 +38,4 @@ def _dec(cls):
         _dec(mapper_cls)
 
 
-from . import io  # noqa: F401
+from . import io  # noqa: F401,E402

test.py

@@ -197,9 +197,9 @@ def main():
 
     # set up logger
     root = logging.getLogger()
-    root.setLevel(logging.DEBUG)
+    root.setLevel(logging.INFO)
     ch = logging.StreamHandler(sys.stdout)
-    ch.setLevel(logging.DEBUG)
+    ch.setLevel(logging.INFO)
     formatter = logging.Formatter('======================================================================\n'
                                   '%(asctime)s - %(levelname)s - %(message)s')
     ch.setFormatter(formatter)

tests/coloredtestrunner.py

@@ -91,7 +91,7 @@ def __len__(self, x):
         return len(re.sub(r"\033\[[0-9];[0-9];[0-9]{1,2}m", "", x))
 
     def addRow(self, row):
-        rows = [[''] for l in range(len(row))]
+        rows = [[''] for i in range(len(row))]
         maxrows = 0
         for i, x in enumerate(row):
             for j, y in enumerate(x.split("\n")):

tests/integration/hdf5/test_base.py

@@ -10,8 +10,13 @@ class TestTimeSeriesIO(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test TimeSeries to read/write """
-        return TimeSeries('test_timeseries', list(range(100, 200, 10)),
-                          'SIunit', timestamps=list(range(10)), resolution=0.1)
+        return TimeSeries(
+            name='test_timeseries',
+            data=list(range(1000)),
+            unit='SIunit',
+            timestamps=np.arange(1000.),
+            resolution=0.1
+        )
 
 
 class TestTimeSeriesLinking(TestCase):
@@ -24,7 +29,7 @@ def tearDown(self):
 
     def test_timestamps_linking(self):
         ''' Test that timestamps get linked to in TimeSeries '''
-        tsa = TimeSeries(name='a', data=np.linspace(0, 1, 1000), timestamps=np.arange(1000), unit='m')
+        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()),

tests/integration/hdf5/test_ecephys.py

@@ -11,8 +11,11 @@ class TestElectrodeGroupIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test ElectrodeGroup to read/write """
-        self.dev1 = Device('dev1')
-        eg = ElectrodeGroup('elec1', 'a test ElectrodeGroup', 'a nonexistent place', self.dev1)
+        self.dev1 = Device(name='dev1')
+        eg = ElectrodeGroup(name='elec1',
+                            description='a test ElectrodeGroup',
+                            location='a nonexistent place',
+                            device=self.dev1)
         return eg
 
     def addContainer(self, nwbfile):
@@ -31,20 +34,29 @@ class TestElectricalSeriesIO(AcquisitionH5IOMixin, TestCase):
     def make_electrode_table(self):
         """ Make an electrode table, electrode group, and device """
         self.table = get_electrode_table()
-        self.dev1 = Device('dev1')
-        self.group = ElectrodeGroup('tetrode1',
-                                    'tetrode description', 'tetrode location', self.dev1)
+        self.dev1 = Device(name='dev1')
+        self.group = ElectrodeGroup(name='tetrode1',
+                                    description='tetrode description',
+                                    location='tetrode location',
+                                    device=self.dev1)
         for i in range(4):
             self.table.add_row(x=i, y=2.0, z=3.0, imp=-1.0, location='CA1', filtering='none', group=self.group,
                                group_name='tetrode1')
 
     def setUpContainer(self):
         """ Return the test ElectricalSeries to read/write """
         self.make_electrode_table(self)
-        region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', self.table)
+        region = DynamicTableRegion(name='electrodes',
+                                    data=[0, 2],
+                                    description='the first and third electrodes',
+                                    table=self.table)
         data = list(zip(range(10), range(10, 20)))
-        timestamps = list(map(lambda x: x/10, range(10)))
-        es = ElectricalSeries('test_eS', data, region, channel_conversion=[4., .4], timestamps=timestamps)
+        timestamps = list(map(lambda x: x/10., range(10)))
+        es = ElectricalSeries(name='test_eS',
+                              data=data,
+                              electrodes=region,
+                              channel_conversion=[4., .4],
+                              timestamps=timestamps)
         return es
 
     def addContainer(self, nwbfile):
@@ -78,13 +90,20 @@ def setUpContainer(self):
     def setUpTwoElectricalSeries(self):
         """ Return two test ElectricalSeries to read/write """
         TestElectricalSeriesIO.make_electrode_table(self)
-        region1 = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', self.table)
-        region2 = DynamicTableRegion('electrodes', [1, 3], 'the second and fourth electrodes', self.table)
+        region1 = DynamicTableRegion(name='electrodes',
+                                     data=[0, 2],
+                                     description='the first and third electrodes',
+                                     table=self.table)
+        region2 = DynamicTableRegion(name='electrodes',
+                                     data=[1, 3],
+                                     description='the second and fourth electrodes',
+                                     table=self.table)
         data1 = list(zip(range(10), range(10, 20)))
         data2 = list(zip(reversed(range(10)), reversed(range(10, 20))))
-        timestamps = list(map(lambda x: x/10, range(10)))
-        es1 = ElectricalSeries('test_eS1', data1, region1, timestamps=timestamps)
-        es2 = ElectricalSeries('test_eS2', data2, region2, channel_conversion=[4., .4], timestamps=timestamps)
+        timestamps = list(map(lambda x: x/10., range(10)))
+        es1 = ElectricalSeries(name='test_eS1', data=data1, electrodes=region1, timestamps=timestamps)
+        es2 = ElectricalSeries(name='test_eS2', data=data2, electrodes=region2, channel_conversion=[4., .4],
+                               timestamps=timestamps)
         return es1, es2
 
     def addContainer(self, nwbfile):
@@ -132,8 +151,14 @@ class EventWaveformConstructor(AcquisitionH5IOMixin, TestCase):
     def setUpContainer(self):
         """ Return a test EventWaveform to read/write """
         TestElectricalSeriesIO.make_electrode_table(self)
-        region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', self.table)
-        sES = SpikeEventSeries('test_sES', ((1, 1, 1), (2, 2, 2)), list(range(2)), region)
+        region = DynamicTableRegion(name='electrodes',
+                                    data=[0, 2],
+                                    description='the first and third electrodes',
+                                    table=self.table)
+        sES = SpikeEventSeries(name='test_sES',
+                               data=((1, 1, 1), (2, 2, 2)),
+                               timestamps=[0., 1.],
+                               electrodes=region)
         ew = EventWaveform(sES)
         return ew
 
@@ -177,10 +202,13 @@ def setUpContainer(self):
         """ Return a test FeatureExtraction to read/write """
         event_times = [1.9, 3.5]
         TestElectricalSeriesIO.make_electrode_table(self)
-        region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', self.table)
+        region = DynamicTableRegion(name='electrodes',
+                                    data=[0, 2],
+                                    description='the first and third electrodes',
+                                    table=self.table)
         description = ['desc1', 'desc2', 'desc3']
         features = [[[0., 1., 2.], [3., 4., 5.]], [[6., 7., 8.], [9., 10., 11.]]]
-        fe = FeatureExtraction(region, description, event_times, features)
+        fe = FeatureExtraction(electrodes=region, description=description, times=event_times, features=features)
         return fe
 
     def addContainer(self, nwbfile):
@@ -196,11 +224,17 @@ class EventDetectionConstructor(AcquisitionH5IOMixin, TestCase):
     def setUpContainer(self):
         """ Return a test EventDetection to read/write """
         TestElectricalSeriesIO.make_electrode_table(self)
-        region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', self.table)
+        region = DynamicTableRegion(name='electrodes',
+                                    data=[0, 2],
+                                    description='the first and third electrodes',
+                                    table=self.table)
         data = list(range(10))
         ts = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
-        self.eS = ElectricalSeries('test_eS', data, region, timestamps=ts)
-        eD = EventDetection('detection_method', self.eS, (1, 2, 3), (0.1, 0.2, 0.3))
+        self.eS = ElectricalSeries(name='test_eS', data=data, electrodes=region, timestamps=ts)
+        eD = EventDetection(detection_method='detection_method',
+                            source_electricalseries=self.eS,
+                            source_idx=(1, 2, 3),
+                            times=(0.1, 0.2, 0.3))
         return eD
 
     def addContainer(self, nwbfile):

tests/integration/hdf5/test_icephys.py

@@ -13,13 +13,15 @@ class TestIntracellularElectrode(NWBH5IOMixin, TestCase):
     def setUpContainer(self):
         """ Return the test IntracellularElectrode to read/write """
         self.device = Device(name='device_name')
-        elec = IntracellularElectrode(name="elec0", slice='tissue slice',
-                                           resistance='something measured in ohms',
-                                           seal='sealing method', description='a fake electrode object',
-                                           location='Springfield Elementary School',
-                                           filtering='a meaningless free-form text field',
-                                           initial_access_resistance='I guess this changes',
-                                           device=self.device)
+        elec = IntracellularElectrode(name="elec0",
+                                      slice='tissue slice',
+                                      resistance='something measured in ohms',
+                                      seal='sealing method',
+                                      description='a fake electrode object',
+                                      location='Springfield Elementary School',
+                                      filtering='a meaningless free-form text field',
+                                      initial_access_resistance='I guess this changes',
+                                      device=self.device)
         return elec
 
     def addContainer(self, nwbfile):
@@ -50,7 +52,7 @@ def setUpContainer(self):
         self.setUpElectrode()
         return PatchClampSeries(name="pcs", data=[1, 2, 3, 4, 5], unit='A',
                                 starting_time=123.6, rate=10e3, electrode=self.elec, gain=0.126,
-                                stimulus_description="gotcha ya!", sweep_number=4711)
+                                stimulus_description="gotcha ya!", sweep_number=np.uint(4711))
 
     def addContainer(self, nwbfile):
         """

tests/integration/hdf5/test_image.py

@@ -15,7 +15,7 @@ def setUpContainer(self):
                                             data=np.ones((10, 3, 3)),
                                             unit='m',
                                             format='raw',
-                                            timestamps=np.arange(10))
+                                            timestamps=np.arange(10.))
         return self.optical_series
 
     def addContainer(self, nwbfile):