updated based on merge NeurodataWithoutBorders#61 and NeurodataWithou…

…tBorders#62

src/form/utils.py

@@ -4,6 +4,7 @@
 from collections import Iterable
 from abc import ABCMeta
 import six
+from six import raise_from
 import numpy as np
 
 def __type_okay(value, argtype, allow_none=False):
@@ -266,15 +267,15 @@ def func_call(*args, **kwargs):
                 parse_err = parsed.get('errors')
                 if parse_err:
                     msg = ', '.join(parse_err)
-                    raise TypeError(msg) from None
+                    raise_from(TypeError(msg), None)
                 return func(self, **parsed['args'])
         else:
             def func_call(*args, **kwargs):
                 parsed = __parse_args(_copy.deepcopy(loc_val), args, kwargs, enforce_type=enforce_type)
                 parse_err = parsed.get('errors')
                 if parse_err:
                     msg = ', '.join(parse_err)
-                    raise TypeError(msg) from None
+                    raise_from(TypeError(msg), None)
                 return func(**parsed['args'])
         _rtype = rtype
         if isinstance(rtype, type):

src/pynwb/base.py

@@ -99,8 +99,8 @@ class TimeSeries(NWBContainer):
     def __init__(self, **kwargs):
         """Create a TimeSeries object
         """
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(TimeSeries, self).__init__, kwargs)
+        super(TimeSeries, self).__init__(*pargs, **pkwargs)
         keys = ("resolution",
                 "comments",
                 "description",

src/pynwb/core.py

@@ -34,7 +34,7 @@ class NWBContainer(with_metaclass(ExtenderMeta, Container)):
             {'name': 'container_source', 'type': object, 'doc': 'the source of this Container e.g. file name', 'default': None})
     def __init__(self, **kwargs):
         parent, container_source, source, help = getargs('parent', 'container_source', 'source', 'help', kwargs)
-        super().__init__()
+        super(NWBContainer, self).__init__()
 
         self.__fields = dict()
         self.__subcontainers = list()

src/pynwb/ecephys.py

@@ -19,7 +19,7 @@ class Device(NWBContainer):
             {'name': 'source', 'type': str, 'doc': 'the source of the data'},
             {'name': 'parent', 'type': 'NWBContainer', 'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
-        call_docval_func(super().__init__, kwargs)
+        call_docval_func(super(Device, self).__init__, kwargs)
 
 @register_class('ElectrodeGroup', CORE_NAMESPACE)
 class ElectrodeGroup(NWBContainer):
@@ -49,7 +49,7 @@ class ElectrodeGroup(NWBContainer):
             {'name': 'parent', 'type': 'NWBContainer', 'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
         channel_description, channel_location, channel_filtering, channel_coordinates, channel_impedance, description, location, device = popargs("channel_description", "channel_location", "channel_filtering", "channel_coordinates", "channel_impedance", "description", "location", "device", kwargs)
-        call_docval_func(super().__init__, kwargs)
+        call_docval_func(super(ElectrodeGroup, self).__init__, kwargs)
         self.channel_description = channel_description
         self.channel_location = channel_location
         self.channel_filtering = channel_filtering
@@ -363,4 +363,3 @@ def __init__(self, **kwargs):
         self.fields['description'] = description
         self.fields['times'] = list(times)
         self.fields['features'] = features
-

src/pynwb/epoch.py

@@ -41,7 +41,7 @@ class Epoch(NWBContainer):
     def __init__(self, **kwargs):
         start, stop, description, tags = getargs('start', 'stop', 'description', 'tags', kwargs)
         #super(Epoch, self).__init__(name=name, parent=parent)
-        call_docval_func(super().__init__, kwargs)
+        call_docval_func(super(Epoch, self).__init__, kwargs)
         # dict to keep track of which time series are linked to this epoch
         self._timeseries = dict()
         # start and stop time (in seconds)
@@ -194,6 +194,3 @@ def __init__(self, **kwargs):
         # and stop_time
         self.count = count
         self.idx_start = idx
-
-
-

src/pynwb/file.py

@@ -58,8 +58,8 @@ class NWBFile(NWBContainer):
             {'name': 'devices', 'type': (list, tuple), 'doc': 'Device objects belonging to this NWBFile', 'default': None},
     )
     def __init__(self, **kwargs):
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(NWBFile, self).__init__, kwargs)
+        super(NWBFile, self).__init__(*pargs, **pkwargs)
         self.__filename = getargs('file_name', kwargs)
         self.__start_time = datetime.utcnow()
         self.__file_id = '%s %s' % (self.__filename, self.__start_time.strftime('%Y-%m-%dT%H:%M:%SZ'))

src/pynwb/icephys.py

@@ -33,8 +33,8 @@ class IntracellularElectrode(NWBContainer):
             {'name': 'device', 'type': str, 'doc': 'Name(s) of devices in general/devices.'})
     def __init__(self, **kwargs):
         slice, seal, description, location, resistance, filtering, initial_access_resistance, device = popargs('slice', 'seal', 'description', 'location', 'resistance', 'filtering', 'initial_access_resistance', 'device', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(IntracellularElectrode, self).__init__, kwargs)
+        super(IntracellularElectrode, self).__init__(*pargs, **pkwargs)
         self.slice = slice
         self.seal = seal
         self.description = description

src/pynwb/io/epoch.py

@@ -7,7 +7,7 @@
 class EpochMap(ObjectMapper):
 
     def __init__(self, spec):
-        super().__init__(spec)
+        super(EpochMap, self).__init__(spec)
         start_spec = self.spec.get_dataset('start_time')
         stop_spec = self.spec.get_dataset('stop_time')
         self.map_const_arg('start', start_spec)
@@ -23,6 +23,6 @@ def name(self, builder):
 class EpochTimeSeriesMap(ObjectMapper):
 
     def __init__(self, spec):
-        super().__init__(spec)
+        super(EpochTimeSeriesMap, self).__init__(spec)
         ts_spec = self.spec.get_link('timeseries')
         self.map_const_arg('ts', ts_spec)

src/pynwb/misc.py

@@ -180,7 +180,7 @@ class SpikeUnit(NWBContainer):
             {'name': 'source', 'type': str, 'doc': 'Name, path or description of where unit times originated. This is necessary only if the info here differs from or is more fine-grained than the interfaces source field.', 'default': None})
     def __init__(self, **kwargs):
         times, unit_description = popargs('times', 'unit_description', kwargs)
-        call_docval_func(super().__init__, kwargs)
+        call_docval_func(super(SpikeUnit, self).__init__, kwargs)
         self.times = times
         self.unit_description = unit_description
 
@@ -209,4 +209,3 @@ def __init__(self, **kwargs):
     @property
     def unit_list(self):
         return [si.name for si in self.spike_units]
-

src/pynwb/ogen.py

@@ -24,8 +24,8 @@ class OptogeneticStimulusSite(NWBContainer):
             {'name': 'location', 'type': str, 'doc': 'Location of stimulation site.'})
     def __init__(self, **kwargs):
         device, description, excitation_lambda, location = popargs('device', 'description', 'excitation_lambda', 'location', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(OptogeneticStimulusSite, self).__init__, kwargs)
+        super(OptogeneticStimulusSite, self).__init__(*pargs, **pkwargs)
         self.device = device
         self.description = description
         self.excitation_lambda = excitation_lambda
@@ -65,6 +65,6 @@ class OptogeneticSeries(TimeSeries):
             {'name': 'parent', 'type': 'NWBContainer', 'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
         site = popargs('site', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(OptogeneticSeries, self).__init__, kwargs)
+        super(OptogeneticSeries, self).__init__(*pargs, **pkwargs)
         self.site = site

src/pynwb/ophys.py

@@ -23,8 +23,8 @@ class OpticalChannel(NWBContainer):
             {'name': 'parent', 'type': 'NWBContainer', 'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
         description, emission_lambda, parent = popargs("description", "emission_lambda", "parent", kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(OpticalChannel, self).__init__, kwargs)
+        super(OpticalChannel, self).__init__(*pargs, **pkwargs)
         self.description = description
         self.emission_lambda = emission_lambda
 
@@ -61,8 +61,8 @@ class ImagingPlane(NWBContainer):
             {'name': 'parent', 'type': 'NWBContainer', 'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
         optical_channel, description, device, excitation_lambda, imaging_rate, indicator, location, manifold, conversion, unit, reference_frame, parent = popargs('optical_channel', 'description', 'device', 'excitation_lambda', 'imaging_rate', 'indicator', 'location', 'manifold', 'conversion', 'unit', 'reference_frame', 'parent', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(ImagingPlane, self).__init__, kwargs)
+        super(ImagingPlane, self).__init__(*pargs, **pkwargs)
         self.optical_channel = optical_channel if isinstance(optical_channel, list) else [optical_channel]
         self.description = description
         self.device = device
@@ -120,8 +120,8 @@ class TwoPhotonSeries(ImageSeries):
     )
     def __init__(self, **kwargs):
         field_of_view, imaging_plane, pmt_gain, scan_line_rate = popargs('field_of_view', 'imaging_plane', 'pmt_gain', 'scan_line_rate', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(TwoPhotonSeries, self).__init__, kwargs)
+        super(TwoPhotonSeries, self).__init__(*pargs, **pkwargs)
         self.field_of_view = field_of_view
         self.imaging_plane = imaging_plane
         self.pmt_gain = pmt_gain
@@ -147,8 +147,8 @@ class ROI(NWBContainer):
             {'name': 'reference_images', 'type': ImageSeries, 'doc': 'One or more image stacks that the masks apply to (can be oneelement stack).'})
     def __init__(self, **kwargs):
         name, roi_description, pix_mask, pix_mask_weight, img_mask = popargs('name', 'roi_description', 'pix_mask', 'pix_mask_weight', 'img_mask', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(ROI, self).__init__, kwargs)
+        super(ROI, self).__init__(*pargs, **pkwargs)
         self.roi_description = roi_description
         self.pix_mask = pix_mask
         self.pix_mask_weight = pix_mask_weight
@@ -173,8 +173,8 @@ class PlaneSegmentation(NWBContainer):
             {'name': 'reference_images', 'type': ImageSeries, 'doc': 'One or more image stacks that the masks apply to (can be oneelement stack).'})
     def __init__(self, **kwargs):
         name, description, roi_list, imaging_plane, reference_images = popargs('name', 'description', 'roi_list', 'imaging_plane', 'reference_images', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(PlaneSegmentation, self).__init__, kwargs)
+        super(PlaneSegmentation, self).__init__(*pargs, **pkwargs)
         self.description = description
         self.roi_list = roi_list
         self.imaging_plane = imaging_plane
@@ -200,8 +200,8 @@ class ImageSegmentation(NWBContainer):
             {'name': 'plane_segmentation', 'type': PlaneSegmentation, 'doc': 'ImagePlane class.'})
     def __init__(self, **kwargs):
         plane_segmentation = popargs('plane_segmentation', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(ImageSegmentation, self).__init__, kwargs)
+        super(ImageSegmentation, self).__init__(*pargs, **pkwargs)
         self.plane_segmentation = plane_segmentation
 
 @register_class('RoiResponseSeries', CORE_NAMESPACE)
@@ -241,8 +241,8 @@ class RoiResponseSeries(TimeSeries):
     )
     def __init__(self, **kwargs):
         roi_names, segmenttation_interface = popargs('roi_names', 'segmenttation_interface', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(RoiResponseSeries, self).__init__, kwargs)
+        super(RoiResponseSeries, self).__init__(*pargs, **pkwargs)
         self.roi_names = roi_names
         self.segmenttation_interface = segmenttation_interface
 
@@ -261,8 +261,8 @@ class DfOverF(NWBContainer):
             {'name': 'roi_response_series', 'type': RoiResponseSeries, 'doc': 'RoiResponseSeries or any subtype.'})
     def __init__(self, **kwargs):
         roi_response_series = popargs('roi_response_series', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(DfOverF, self).__init__, kwargs)
+        super(DfOverF, self).__init__(*pargs, **pkwargs)
         self.roi_response_series = roi_response_series
 
 @register_class('Fluorescence', CORE_NAMESPACE)
@@ -280,6 +280,6 @@ class Fluorescence(NWBContainer):
             {'name': 'roi_response_series', 'type': RoiResponseSeries, 'doc': 'RoiResponseSeries or any subtype.'})
     def __init__(self, **kwargs):
         roi_response_series = popargs('roi_response_series', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(Fluorescence, self).__init__, kwargs)
+        super(Fluorescence, self).__init__(*pargs, **pkwargs)
         self.roi_response_series = roi_response_series

src/pynwb/retinotopy.py

@@ -26,8 +26,8 @@ class aimage(NWBContainer):
             {'name': 'focal_depth', 'type': float, 'doc': 'Focal depth offset, in meters.'})
     def __init__(self, **kwargs):
         data, bits_per_pixel, dimension, format, field_of_view = popargs('data', 'bits_per_pixel', 'dimension', 'format', 'field_of_view', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(aimage, self).__init__, kwargs)
+        super(aimage, self).__init__(*pargs, **pkwargs)
         self.data = data
         self.bits_per_pixel = bits_per_pixel
         self.dimension = format
@@ -49,8 +49,8 @@ class amap(NWBContainer):
             {'name': 'dimension', 'type': Iterable, 'doc': 'Number of rows and columns in the image'})
     def __init__(self, **kwargs):
         data, field_of_view, unit, dimension = popargs('data', 'field_of_view', 'unit', 'dimension', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(amap, self).__init__, kwargs)
+        super(amap, self).__init__(*pargs, **pkwargs)
         self.data = data
         self.field_of_view = field_of_view
         self.unit = unit
@@ -88,8 +88,8 @@ class ImagingRetinotopy(NWBContainer):
             {'name': 'vasculature_image', 'type': aimage, 'doc': 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns].'})
     def __init__(self, **kwargs):
         axis_1_phase_map, axis_1_power_map, axis_2_phase_map, axis_2_power_map, axis_descriptions, focal_depth_image, sign_map, vasculature_image = popargs('axis_1_phase_map', 'axis_1_power_map', 'axis_2_phase_map', 'axis_2_power_map', 'axis_descriptions', 'focal_depth_image', 'sign_map', 'vasculature_image', kwargs)
-        pargs, pkwargs = fmt_docval_args(super().__init__, kwargs)
-        super().__init__(*pargs, **pkwargs)
+        pargs, pkwargs = fmt_docval_args(super(ImagingRetinotopy, self).__init__, kwargs)
+        super(ImagingRetinotopy, self).__init__(*pargs, **pkwargs)
         self.axis_1_phase_map = axis_1_phase_map
         self.axis_1_power_map = axis_1_power_map
         self.axis_2_phase_map = axis_2_phase_map
@@ -98,4 +98,3 @@ def __init__(self, **kwargs):
         self.focal_depth_image = focal_depth_image
         self.sign_map = sign_map
         self.vasculature_image = vasculature_image
-

tests/unit/form_tests/utils_test/test_core_NWBContainer.py

@@ -5,7 +5,7 @@
 class MyTestClass(NWBContainer):
 
     def __init__(self, src, parent=None):
-        super().__init__(src, parent=parent)
+        super(MyTestClass, self).__init__(src, parent=parent)
 
     def basic_add(self, **kwargs):
         return kwargs