Use HDMF 2.5.0

Legal.txt

@@ -1,4 +1,4 @@
-“pynwb” Copyright (c) 2017-2020, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+“pynwb” Copyright (c) 2017-2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 
 If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation & Partnerships Office at [email protected].
 

README.rst

@@ -77,7 +77,7 @@ For details on how to contribute to PyNWB see our `contribution guidelines <docs
 LICENSE
 =======
 
-"pynwb" Copyright (c) 2017-2019, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+"pynwb" Copyright (c) 2017-2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
 (1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
@@ -93,7 +93,7 @@ You are under no obligation whatsoever to provide any bug fixes, patches, or upg
 COPYRIGHT
 =========
 
-"pynwb" Copyright (c) 2017-2020, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+"pynwb" Copyright (c) 2017-2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation & Partnerships Office at [email protected].
 
 NOTICE.  This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.

docs/source/conf.py

@@ -93,7 +93,7 @@
 
 # General information about the project.
 project = u'PyNWB'
-copyright = u'2017-2020, Neurodata Without Borders'
+copyright = u'2017-2021, Neurodata Without Borders'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

license.txt

@@ -1,4 +1,4 @@
-“pynwb” Copyright (c) 2017-2020, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+“pynwb” Copyright (c) 2017-2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

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==2.4
+hdmf==2.5
 numpy==1.16
 pandas==0.23
 python-dateutil==2.7

requirements.txt

@@ -1,5 +1,5 @@
 h5py==2.10.0
-hdmf==2.4.0
+hdmf==2.5.0
 numpy==1.18.5
 pandas==0.25.3
 python-dateutil==2.8.1

src/pynwb/__init__.py

@@ -41,10 +41,8 @@ def _get_resources():
 __NS_CATALOG = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
 
 hdmf_typemap = hdmf.common.get_type_map()
-__NS_CATALOG.merge(hdmf_typemap.namespace_catalog)
-
 __TYPE_MAP = TypeMap(__NS_CATALOG)
-__TYPE_MAP.merge(hdmf_typemap)
+__TYPE_MAP.merge(hdmf_typemap, ns_catalog=True)
 
 
 @docval({'name': 'extensions', 'type': (str, TypeMap, list),
@@ -185,7 +183,7 @@ def get_sum(self, a, b):
 
     """
     neurodata_type, namespace = getargs('neurodata_type', 'namespace', kwargs)
-    return __TYPE_MAP.get_container_cls(namespace, neurodata_type)
+    return __TYPE_MAP.get_container_cls(neurodata_type, namespace)
 
 
 @docval({'name': 'io', 'type': HDMFIO, 'doc': 'the HDMFIO object to read from'},

tests/integration/test_io.py

@@ -275,8 +275,7 @@ def test_append(self):
             self.assertIs(nwb.processing['test_proc_mod']['LFP'].electrical_series['test_es'].electrodes,
                           nwb.acquisition['timeseries2'].electrodes)
             errors = validate(io)
-            for e in errors:
-                print('ERROR', e)
+            self.assertTrue(len(errors) == 0)
 
 
 class TestH5DataIO(TestCase):

tests/unit/test_core.py

@@ -81,4 +81,4 @@ def test_print_file(self):
 
 class TestAvailableNamespaces(TestCase):
     def test_available_namespaces(self):
-        self.assertEqual(available_namespaces(), ('hdmf-common', 'core'))
+        self.assertEqual(available_namespaces(), ('hdmf-common', 'hdmf-experimental', 'core'))

tests/unit/test_extension.py

@@ -49,7 +49,7 @@ def test_load_namespace(self):
     def test_get_class(self):
         self.test_export()
         type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
-        type_map.get_container_cls(self.prefix, 'TetrodeSeries')
+        type_map.get_container_cls('TetrodeSeries', self.prefix)
 
     def test_load_namespace_with_reftype_attribute(self):
         ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
@@ -74,7 +74,7 @@ def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
         ns_builder.add_spec(self.ext_source, test_ds_ext)
         ns_builder.export(self.ns_path, outdir=self.tempdir)
         type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
-        my_new_type = type_map.get_container_cls(self.prefix, 'my_new_type')
+        my_new_type = type_map.get_container_cls('my_new_type', self.prefix)
         docval = None
         for tmp in get_docval(my_new_type.__init__):
             if tmp['name'] == 'target_ds':
@@ -169,28 +169,3 @@ def test_catch_dup_name(self):
         ns_builder2.export(self.ns_path2, outdir=self.tempdir)
         type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path1))
         type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path2))
-
-
-class TestCatchDuplicateSpec(TestCase):
-
-    def setUp(self):
-        self.prefix = id_generator()
-        self.ext_source = '%s_extension3.yaml' % self.prefix
-
-    def tearDown(self):
-        pass
-
-    def test_catch_duplicate_spec(self):
-        spec1 = NWBGroupSpec("This is my new group 1",
-                             "Group1",
-                             neurodata_type_inc="NWBDataInterface",
-                             neurodata_type_def="Group1")
-        spec2 = NWBGroupSpec("This is my new group 2",
-                             "Group2",
-                             groups=[spec1],
-                             neurodata_type_inc="NWBDataInterface",
-                             neurodata_type_def="Group2")
-        ns_builder = NWBNamespaceBuilder("Example namespace", "pynwb_test_ext", version='0.1.0')
-        ns_builder.add_spec(self.ext_source, spec1)
-        with self.assertRaises(ValueError):
-            ns_builder.add_spec(self.ext_source, spec2)

tox.ini

@@ -136,22 +136,28 @@ basepython = python3.9
 deps = {[testenv:gallery]deps}
 commands = {[testenv:gallery]commands}
 
+
+# Test with python 3.8, pinned dev and doc reqs, and upgraded run requirements
 [testenv:gallery-py38-upgrade-dev]
 basepython = python3.8
 install_command =
     pip install -U -e . {opts} {packages}
 deps =
     -rrequirements-dev.txt
+    -rrequirements-doc.txt
 commands = {[testenv:gallery]commands}
 
+# Test with python 3.8, pinned dev and doc reqs, and pre-release run requirements
 [testenv:gallery-py38-upgrade-dev-pre]
 basepython = python3.8
 install_command =
     pip install -U --pre -e . {opts} {packages}
 deps =
     -rrequirements-dev.txt
+    -rrequirements-doc.txt
 commands = {[testenv:gallery]commands}
 
+# Test with python 3.6, pinned dev reqs, and minimum run requirements
 [testenv:gallery-py36-min-req]
 basepython = python3.6
 deps =
@@ -160,8 +166,8 @@ deps =
     -rrequirements-doc.txt
 commands = {[testenv:gallery]commands}
 
-[testenv:validation-py37]
-basepython = python3.7
+[testenv:validation-py38]
+basepython = python3.8
 install_command =
     pip install -U {opts} {packages}
 deps =