Merge branch 'master' of https://github.com/NeuralEnsemble/python-neo into spikegadgets_implementation

Author: samuelgarcia

.github/workflows/full-test.yml

@@ -2,9 +2,13 @@ name: neo.io and neo.rawio tests
 
 on:
   pull_request:
-    branches: [master, gh_actions_and_datalad]
+    branches: [master]
     types: [synchronize, opened, reopened, ready_for_review]
 
+  # run checks on any change of master, including merge of PRs
+  push:
+    branches: [master]
+
 jobs:
   build-and-test:
     name: Test on (${{ matrix.os }})

README.rst

@@ -33,16 +33,13 @@ Code status
 
 .. image:: https://travis-ci.org/NeuralEnsemble/python-neo.png?branch=master
    :target: https://travis-ci.org/NeuralEnsemble/python-neo
-   :alt: Unit Test Status (TravisCI)
-.. image:: https://circleci.com/gh/NeuralEnsemble/python-neo.svg?style=svg
-    :target: https://circleci.com/gh/NeuralEnsemble/python-neo
-    :alt: Unit Test Status (CircleCI)
+   :alt: Core Unit Test Status (TravisCI)
+.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/full-test.yml/badge.svg?event=push&branch=master
+   :target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
+   :alt: IO Unit Test Status (Github Actions)
 .. image:: https://coveralls.io/repos/NeuralEnsemble/python-neo/badge.png
    :target: https://coveralls.io/r/NeuralEnsemble/python-neo
    :alt: Unit Test Coverage
-.. image:: https://requires.io/github/NeuralEnsemble/python-neo/requirements.png?branch=master
-   :target: https://requires.io/github/NeuralEnsemble/python-neo/requirements/?branch=master
-   :alt: Requirements Status
 
 More information
 ----------------

neo/converter.py

@@ -28,18 +28,10 @@
 .. autoclass:: CircularRegionOfInterest
 .. autoclass:: PolygonRegionOfInterest
 
-Deprecated classes:
-
-.. autoclass:: ChannelIndex
-.. autoclass:: Unit
-
 """
 
 from neo.core.block import Block
 from neo.core.segment import Segment
-from neo.core.channelindex import ChannelIndex
-from neo.core.unit import Unit
-
 from neo.core.analogsignal import AnalogSignal
 from neo.core.irregularlysampledsignal import IrregularlySampledSignal
 
@@ -55,9 +47,9 @@
 from neo.core.group import Group
 
 # Block should always be first in this list
-objectlist = [Block, Segment, ChannelIndex,
+objectlist = [Block, Segment,
               AnalogSignal, IrregularlySampledSignal,
-              Event, Epoch, Unit, SpikeTrain, ImageSequence,
+              Event, Epoch, SpikeTrain, ImageSequence,
               RectangularRegionOfInterest, CircularRegionOfInterest,
               PolygonRegionOfInterest, ChannelView, Group]
 

neo/core/__init__.py

@@ -58,7 +58,7 @@ def _get_sampling_rate(sampling_rate, sampling_period):
 def _new_AnalogSignalArray(cls, signal, units=None, dtype=None, copy=True, t_start=0 * pq.s,
                            sampling_rate=None, sampling_period=None, name=None, file_origin=None,
                            description=None, array_annotations=None, annotations=None,
-                           channel_index=None, segment=None):
+                           segment=None):
     '''
     A function to map AnalogSignal.__new__ to function that
         does not do the unit checking. This is needed for pickle to work.
@@ -68,7 +68,6 @@ def _new_AnalogSignalArray(cls, signal, units=None, dtype=None, copy=True, t_sta
               sampling_period=sampling_period, name=name,
               file_origin=file_origin, description=description,
               array_annotations=array_annotations, **annotations)
-    obj.channel_index = channel_index
     obj.segment = segment
     return obj
 
@@ -140,9 +139,6 @@ class AnalogSignal(BaseSignal):
         :times: (quantity 1D) The time points of each sample of the signal,
             read-only.
             (:attr:`t_start` + arange(:attr:`shape`[0])/:attr:`sampling_rate`)
-        :channel_index:
-            (deprecated) access to the channel_index attribute of the principal ChannelIndex
-            associated with this signal.
 
     *Slicing*:
         :class:`AnalogSignal` objects can be sliced. When taking a single
@@ -160,8 +156,8 @@ class AnalogSignal(BaseSignal):
 
     '''
 
-    _parent_objects = ('Segment', 'ChannelIndex')
-    _parent_attrs = ('segment', 'channel_index')
+    _parent_objects = ('Segment',)
+    _parent_attrs = ('segment',)
     _quantity_attr = 'signal'
     _necessary_attrs = (('signal', pq.Quantity, 2),
                         ('sampling_rate', pq.Quantity, 0),
@@ -192,7 +188,6 @@ def __new__(cls, signal, units=None, dtype=None, copy=True, t_start=0 * pq.s,
         obj._sampling_rate = _get_sampling_rate(sampling_rate, sampling_period)
 
         obj.segment = None
-        obj.channel_index = None
         return obj
 
     def __init__(self, signal, units=None, dtype=None, copy=True, t_start=0 * pq.s,
@@ -220,7 +215,7 @@ def __reduce__(self):
                                         True, self.t_start, self.sampling_rate,
                                         self.sampling_period, self.name, self.file_origin,
                                         self.description, self.array_annotations,
-                                        self.annotations, self.channel_index, self.segment)
+                                        self.annotations, self.segment)
 
     def _array_finalize_spec(self, obj):
         '''
@@ -244,14 +239,6 @@ def __repr__(self):
                                                            self.t_start, self.t_stop,
                                                            self.sampling_rate))
 
-    def get_channel_index(self):
-        """
-        """
-        if self.channel_index:
-            return self.channel_index.index
-        else:
-            return None
-
     def __getitem__(self, i):
         '''
         Get the item or slice :attr:`i`.
@@ -278,8 +265,6 @@ def __getitem__(self, i):
                     raise TypeError("%s not supported" % type(j))
                 if isinstance(k, (int, np.integer)):
                     obj = obj.reshape(-1, 1)
-                if self.channel_index:
-                    obj.channel_index = self.channel_index.__getitem__(k)
                 obj.array_annotate(**deepcopy(self.array_annotations_at_index(k)))
         elif isinstance(i, slice):
             obj = super().__getitem__(i)
@@ -448,7 +433,7 @@ def _pp(line):
     def time_index(self, t):
         """Return the array index (or indices) corresponding to the time (or times) `t`"""
         i = (t - self.t_start) * self.sampling_rate
-        i = np.rint(i.simplified.magnitude).astype(np.int)
+        i = np.rint(i.simplified.magnitude).astype(np.int64)
         return i
 
     def time_slice(self, t_start, t_stop):
@@ -534,7 +519,6 @@ def splice(self, signal, copy=False):
         if copy:
             new_signal = deepcopy(self)
             new_signal.segment = None
-            new_signal.channel_index = None
             new_signal[i:j, :] = signal
             return new_signal
         else:

neo/core/analogsignal.py

@@ -144,10 +144,7 @@ def _reference_name(class_name):
     `segment.block`. The attribute name `block` is obtained by calling
     `_container_name("Block")`.
     """
-    name_map = {
-        "ChannelIndex": "channel_index"
-    }
-    return name_map.get(class_name, class_name.lower())
+    return class_name.lower()
 
 
 def _container_name(class_name):
@@ -159,10 +156,7 @@ def _container_name(class_name):
     referenced by `block.segments`. The attribute name `segments` is
     obtained by calling `_container_name_plural("Segment")`.
     """
-    name_map = {
-        "ChannelIndex": "channel_indexes"
-    }
-    return name_map.get(class_name, _reference_name(class_name) + 's')
+    return _reference_name(class_name) + 's'
 
 
 class BaseNeo:

neo/core/baseneo.py

@@ -23,7 +23,6 @@
 
 from neo.core.baseneo import MergeError, merge_annotations
 from neo.core.dataobject import DataObject, ArrayDict
-from neo.core.channelindex import ChannelIndex
 
 logger = logging.getLogger("Neo")
 
@@ -80,7 +79,6 @@ def __array_finalize__(self, obj):
 
         # Parent objects
         self.segment = getattr(obj, 'segment', None)
-        self.channel_index = getattr(obj, 'channel_index', None)
 
     @classmethod
     def _rescale(self, signal, units=None):
@@ -100,11 +98,6 @@ def _rescale(self, signal, units=None):
                 signal = signal.rescale(units)
         return signal
 
-    def rescale(self, units):
-        obj = super().rescale(units)
-        obj.channel_index = self.channel_index
-        return obj
-
     def __getslice__(self, i, j):
         '''
         Get a slice from :attr:`i` to :attr:`j`.attr[0]
@@ -279,18 +272,6 @@ def merge(self, other):
         if hasattr(self, "lazy_shape"):
             signal.lazy_shape = merged_lazy_shape
 
-        # merge channel_index (move to ChannelIndex.merge()?)
-        if self.channel_index and other.channel_index:
-            signal.channel_index = ChannelIndex(index=np.arange(signal.shape[1]),
-                                                channel_ids=np.hstack(
-                                                    [self.channel_index.channel_ids,
-                                                     other.channel_index.channel_ids]),
-                                                channel_names=np.hstack(
-                                                    [self.channel_index.channel_names,
-                                                     other.channel_index.channel_names]))
-        else:
-            signal.channel_index = ChannelIndex(index=np.arange(signal.shape[1]))
-
         return signal
 
     def time_slice(self, t_start, t_stop):

neo/core/basesignal.py

@@ -54,24 +54,17 @@ class Block(Container):
             data file.
         :rec_datetime: (datetime) The date and time of the original recording.
 
-    *Properties available on this object*:
-        :list_units: (deprecated) descends through hierarchy and returns a list of
-            :class:`Unit` objects existing in the block. This shortcut exists
-            because a common analysis case is analyzing all neurons that
-            you recorded in a session.
-
     Note: Any other additional arguments are assumed to be user-specific
     metadata and stored in :attr:`annotations`.
 
     *Container of*:
         :class:`Segment`
         :class:`Group`
-        :class:`ChannelIndex` (deprecated)
 
     '''
 
-    _container_child_objects = ('Segment', 'ChannelIndex', 'Group')
-    _child_properties = ('Unit',)
+    _container_child_objects = ('Segment', 'Group')
+    _child_properties = ()
     _recommended_attrs = ((('file_datetime', datetime),
                            ('rec_datetime', datetime),
                            ('index', int)) +
@@ -104,7 +97,7 @@ def data_children_recur(self):
         obtained recursively.
         '''
         # subclassing this to remove duplicate objects such as SpikeTrain
-        # objects in both Segment and Unit
+        # objects in both Segment and Group
         # Only Block can have duplicate items right now, so implement
         # this here for performance reasons.
         return tuple(unique_objs(super().data_children_recur))
@@ -117,14 +110,7 @@ def list_children_by_class(self, cls):
         or the name of the container storing the class.
         '''
         # subclassing this to remove duplicate objects such as SpikeTrain
-        # objects in both Segment and Unit
+        # objects in both Segment and Group
         # Only Block can have duplicate items right now, so implement
         # this here for performance reasons.
         return unique_objs(super().list_children_by_class(cls))
-
-    @property
-    def list_units(self):
-        '''
-        Return a list of all :class:`Unit` objects in the :class:`Block`.
-        '''
-        return self.list_children_by_class('unit')