Use HDMF 1.5.4 (#1154)

* Use HDMF 1.5.4

* Rename mixin classes to not start with Test* (#1153)

* Rename mixin classes to not start with Test*

* flake8 fix

* Use hdmf 1.5.4

* Use hdmf 1.5.4

* Add version to NWBNamespaceBuilder tests

* Add version to NWBNamespaceBuilder in extensions tutorial

* Add version 1.1.2 files for backwards compatibility tests

docs/gallery/general/extensions.py

@@ -35,7 +35,7 @@
 ns_path = "mylab.namespace.yaml"
 ext_source = "mylab.extensions.yaml"
 
-ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', "mylab")
+ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', "mylab", version='0.1.0')
 
 ns_builder.include_type('ElectricalSeries', namespace='core')
 
@@ -252,7 +252,7 @@ def __init__(self, **kwargs):
 ns_path = name + ".namespace.yaml"
 ext_source = name + ".extensions.yaml"
 
-ns_builder = NWBNamespaceBuilder(name + ' extensions', name)
+ns_builder = NWBNamespaceBuilder(name + ' extensions', name, version='0.1.0')
 ns_builder.include_type('NWBDataInterface', namespace='core')
 
 potato = NWBGroupSpec(neurodata_type_def='Potato',
@@ -387,7 +387,7 @@ class PotatoSack(MultiContainerInterface):
 
 # Now we set up the builder and add this object
 
-ns_builder = NWBNamespaceBuilder(name + ' extensions', name)
+ns_builder = NWBNamespaceBuilder(name + ' extensions', name, version='0.1.0')
 ns_builder.add_spec(ext_source, surface)
 ns_builder.export(ns_path)
 

docs/source/extensions.rst

@@ -166,7 +166,7 @@ Create a new namespace with extensions
     from pynwb.spec import NWBGroupSpec, NWBNamespaceBuilder
 
     # create a builder for the namespace
-    ns_builder = NWBNamespaceBuilder("Extension for use in my laboratory", "mylab", ...)
+    ns_builder = NWBNamespaceBuilder("Extension for use in my laboratory", "mylab", version='0.1.0', ...)
 
     # create extensions
     ext1 = NWBGroupSpec('A custom SpikeEventSeries interface',

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==1.5.3,<2
+hdmf==1.5.4,<2
 numpy==1.16
 pandas==0.23
 python-dateutil==2.7

requirements.txt

@@ -1,5 +1,5 @@
 h5py==2.10.0
-hdmf==1.5.3
+hdmf==1.5.4
 numpy==1.18.1
 pandas==0.25.3
 python-dateutil==2.8.0

src/pynwb/testing/__init__.py

@@ -1,5 +1,5 @@
-from hdmf.testing import TestCase, TestH5RoundTripMixin
-from .testh5io import TestNWBH5IOMixin, TestAcquisitionH5IOMixin
+from hdmf.testing import TestCase, H5RoundTripMixin
+from .testh5io import NWBH5IOMixin, AcquisitionH5IOMixin
 from .utils import remove_test_file
 
 CORE_NAMESPACE = 'core'

src/pynwb/testing/testh5io.py

@@ -10,7 +10,7 @@
 from hdmf.build.warnings import MissingRequiredWarning, OrphanContainerWarning
 
 
-class TestNWBH5IOMixin(metaclass=ABCMeta):
+class NWBH5IOMixin(metaclass=ABCMeta):
     """
     Mixin class for methods to run a roundtrip test writing an NWB file with an Container and reading the Container
     from the NWB file. The setUp, test_roundtrip, and tearDown methods will be run by unittest.
@@ -19,15 +19,15 @@ class TestNWBH5IOMixin(metaclass=ABCMeta):
     this mixin.
 
     Example:
-    class TestMyContainerIO(TestNWBH5IOMixin, TestCase):
+    class TestMyContainerIO(NWBH5IOMixin, TestCase):
         def setUpContainer(self):
             # return a test Container to read/write
         def addContainer(self, nwbfile):
             # add the test Container to an NWB file
         def getContainer(self, nwbfile):
             # return the test Container from an NWB file
 
-    This code is adapted from hdmf.testing.TestH5RoundTripMixin.
+    This code is adapted from hdmf.testing.H5RoundTripMixin.
     """
 
     def setUp(self):
@@ -120,7 +120,7 @@ def validate(self):
                         raise Exception(err)
 
 
-class TestAcquisitionH5IOMixin(TestNWBH5IOMixin):
+class AcquisitionH5IOMixin(NWBH5IOMixin):
     """
     Mixin class for methods to run a roundtrip test writing an NWB file with an Container as an acquisition and reading
     the Container as an acquisition from the NWB file. The setUp, test_roundtrip, and tearDown methods will be run by
@@ -129,11 +129,11 @@ class TestAcquisitionH5IOMixin(TestNWBH5IOMixin):
     The abstract method setUpContainer needs to be implemented by classes that include this mixin.
 
     Example:
-    class TestMyContainerIO(TestNWBH5IOMixin, TestCase):
+    class TestMyContainerIO(NWBH5IOMixin, TestCase):
         def setUpContainer(self):
             # return a test Container to read/write
 
-    This code is adapted from hdmf.testing.TestH5RoundTripMixin.
+    This code is adapted from hdmf.testing.H5RoundTripMixin.
     """
 
     def addContainer(self, nwbfile):

tests/integration/hdf5/test_base.py

@@ -3,10 +3,10 @@
 from dateutil.tz import tzlocal
 
 from pynwb import TimeSeries, NWBFile, NWBHDF5IO
-from pynwb.testing import TestAcquisitionH5IOMixin, TestCase
+from pynwb.testing import AcquisitionH5IOMixin, TestCase
 
 
-class TestTimeSeriesIO(TestAcquisitionH5IOMixin, TestCase):
+class TestTimeSeriesIO(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test TimeSeries to read/write """

tests/integration/hdf5/test_device.py

@@ -1,8 +1,8 @@
 from pynwb.device import Device
-from pynwb.testing import TestNWBH5IOMixin, TestCase
+from pynwb.testing import NWBH5IOMixin, TestCase
 
 
-class TestDeviceIO(TestNWBH5IOMixin, TestCase):
+class TestDeviceIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test Device to read/write """

tests/integration/hdf5/test_ecephys.py

@@ -4,10 +4,10 @@
                           SpikeEventSeries, EventWaveform, EventDetection, FeatureExtraction
 from pynwb.device import Device
 from pynwb.file import ElectrodeTable as get_electrode_table
-from pynwb.testing import TestNWBH5IOMixin, TestAcquisitionH5IOMixin, TestCase
+from pynwb.testing import NWBH5IOMixin, AcquisitionH5IOMixin, TestCase
 
 
-class TestElectrodeGroupIO(TestNWBH5IOMixin, TestCase):
+class TestElectrodeGroupIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test ElectrodeGroup to read/write """
@@ -25,7 +25,7 @@ def getContainer(self, nwbfile):
         return nwbfile.get_electrode_group(self.container.name)
 
 
-class TestElectricalSeriesIO(TestAcquisitionH5IOMixin, TestCase):
+class TestElectricalSeriesIO(AcquisitionH5IOMixin, TestCase):
 
     @staticmethod
     def make_electrode_table(self):
@@ -66,7 +66,7 @@ def test_eg_ref(self):
         self.assertIsInstance(row2.iloc[0]['group'], ElectrodeGroup)
 
 
-class TestMultiElectricalSeriesIOMixin(TestAcquisitionH5IOMixin):
+class MultiElectricalSeriesIOMixin(AcquisitionH5IOMixin):
     """
     Mixin class for methods to run a roundtrip test writing an NWB file with multiple ElectricalSeries.
 
@@ -95,7 +95,7 @@ def addContainer(self, nwbfile):
         nwbfile.add_acquisition(self.container)
 
 
-class TestLFPIO(TestMultiElectricalSeriesIOMixin, TestCase):
+class TestLFPIO(MultiElectricalSeriesIOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test LFP to read/write """
@@ -104,7 +104,7 @@ def setUpContainer(self):
         return lfp
 
 
-class TestFilteredEphysIO(TestMultiElectricalSeriesIOMixin, TestCase):
+class TestFilteredEphysIO(MultiElectricalSeriesIOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test FilteredEphys to read/write """
@@ -113,7 +113,7 @@ def setUpContainer(self):
         return fe
 
 
-class TestClusteringIO(TestAcquisitionH5IOMixin, TestCase):
+class TestClusteringIO(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test Clustering to read/write """
@@ -127,7 +127,7 @@ def roundtripContainer(self, cache_spec=False):
             return super().roundtripContainer(cache_spec)
 
 
-class EventWaveformConstructor(TestAcquisitionH5IOMixin, TestCase):
+class EventWaveformConstructor(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test EventWaveform to read/write """
@@ -145,7 +145,7 @@ def addContainer(self, nwbfile):
         nwbfile.add_acquisition(self.container)
 
 
-class ClusterWaveformsConstructor(TestAcquisitionH5IOMixin, TestCase):
+class ClusterWaveformsConstructor(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test ClusterWaveforms to read/write """
@@ -171,7 +171,7 @@ def roundtripContainer(self, cache_spec=False):
             return super().roundtripContainer(cache_spec)
 
 
-class FeatureExtractionConstructor(TestAcquisitionH5IOMixin, TestCase):
+class FeatureExtractionConstructor(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test FeatureExtraction to read/write """
@@ -191,7 +191,7 @@ def addContainer(self, nwbfile):
         nwbfile.add_acquisition(self.container)
 
 
-class EventDetectionConstructor(TestAcquisitionH5IOMixin, TestCase):
+class EventDetectionConstructor(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test EventDetection to read/write """

tests/integration/hdf5/test_icephys.py

@@ -1,14 +1,12 @@
-from abc import ABCMeta
-
 from pynwb import NWBFile
 from pynwb.icephys import (IntracellularElectrode, PatchClampSeries, CurrentClampStimulusSeries,
                            SweepTable, VoltageClampStimulusSeries, CurrentClampSeries,
                            VoltageClampSeries, IZeroClampSeries)
 from pynwb.device import Device
-from pynwb.testing import TestNWBH5IOMixin, TestAcquisitionH5IOMixin, TestCase
+from pynwb.testing import NWBH5IOMixin, AcquisitionH5IOMixin, TestCase
 
 
-class TestIntracellularElectrode(TestNWBH5IOMixin, TestCase):
+class TestIntracellularElectrode(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test IntracellularElectrode to read/write """
@@ -32,7 +30,7 @@ def getContainer(self, nwbfile):
         return nwbfile.get_ic_electrode(self.container.name)
 
 
-class TestPatchClampSeries(TestAcquisitionH5IOMixin, metaclass=ABCMeta):
+class TestPatchClampSeries(AcquisitionH5IOMixin, TestCase):
 
     def setUpElectrode(self):
         """ Set up the test IntracellularElectrode """
@@ -111,7 +109,7 @@ def setUpContainer(self):
                                 starting_time=123.6, rate=10e3, electrode=self.elec, gain=0.126)
 
 
-class TestSweepTableRoundTripEasy(TestNWBH5IOMixin, TestCase):
+class TestSweepTableRoundTripEasy(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test SweepTable to read/write """
@@ -154,7 +152,7 @@ def test_container(self):
         self.assertEqual(sweep_table['sweep_number'].data[0], 4711)
 
 
-class TestSweepTableRoundTripComplicated(TestNWBH5IOMixin, TestCase):
+class TestSweepTableRoundTripComplicated(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test SweepTable to read/write """

tests/integration/hdf5/test_image.py

@@ -1,10 +1,10 @@
 import numpy as np
 
 from pynwb.image import OpticalSeries
-from pynwb.testing import TestNWBH5IOMixin, TestCase
+from pynwb.testing import NWBH5IOMixin, TestCase
 
 
-class TestOpticalSeriesIO(TestNWBH5IOMixin, TestCase):
+class TestOpticalSeriesIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test OpticalSeries to read/write """

tests/integration/hdf5/test_misc.py

@@ -3,10 +3,10 @@
 from hdmf.common import DynamicTable, VectorData
 from pynwb import TimeSeries
 from pynwb.misc import Units, DecompositionSeries
-from pynwb.testing import TestNWBH5IOMixin, TestAcquisitionH5IOMixin, TestCase
+from pynwb.testing import NWBH5IOMixin, AcquisitionH5IOMixin, TestCase
 
 
-class TestUnitsIO(TestAcquisitionH5IOMixin, TestCase):
+class TestUnitsIO(AcquisitionH5IOMixin, TestCase):
     """ Test adding Units into acquisition and accessing Units after read """
 
     def setUpContainer(self):
@@ -35,7 +35,7 @@ def test_get_obs_intervals(self):
         self.assertTrue(np.array_equal(ut['obs_intervals'][:], [[[0, 1], [2, 3]], [[2, 5], [6, 7]]]))
 
 
-class TestUnitsFileIO(TestNWBH5IOMixin, TestCase):
+class TestUnitsFileIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return placeholder Units object. Tested units are added directly to the NWBFile in addContainer """
@@ -71,7 +71,7 @@ def test_to_dataframe(self):
         units.to_dataframe()
 
 
-class TestDecompositionSeriesIO(TestNWBH5IOMixin, TestCase):
+class TestDecompositionSeriesIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test DecompositionSeries to read/write """