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

Author: rly

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/back_compat/1.1.2_nwbfile.nwb

@@ -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 """