Merge branch 'master' into patch-1

.github/workflows/core-test.yml

@@ -7,6 +7,7 @@ on:
     paths:
       - 'neo/core/**'
       - 'pyproject.toml'
+      - '.github/workflows/*.yml'
 
   # run checks on any change of master, including merge of PRs
   push:
@@ -26,14 +27,12 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.8', '3.9', '3.10', '3.11']
-        numpy-version: ['1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1']
+        numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1']
         exclude:
-           - python-version: '3.10'
-             numpy-version: '1.19.5'
+           - python-version: '3.8'
+             numpy-version: '1.25.1'
            - python-version: '3.10'
              numpy-version: '1.20.3'
-           - python-version: '3.11'
-             numpy-version: '1.19.5'
            - python-version: '3.11'
              numpy-version: '1.20.3'
            - python-version: '3.11'

.github/workflows/io-test.yml

@@ -103,6 +103,8 @@ jobs:
           sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
 
       - name: Test with pytest
+        env:
+          HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_local_plugin_path
         run: |
           # only neo.rawio and neo.io
           pytest --cov=neo neo/test/rawiotest

.readthedocs.yaml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.11"
 
 sphinx:
    configuration: doc/source/conf.py
@@ -14,4 +14,3 @@ python:
       path: .
       extra_requirements:
         - docs
-

CONTRIBUTING.md

@@ -1 +1 @@
-See http://neo.readthedocs.io/en/latest/developers_guide.html
+See https://neo.readthedocs.io/en/latest/contributing.html

doc/source/authors.rst

@@ -62,6 +62,7 @@ and may not be the current affiliation of a contributor.
 * Elodie Legouée [21]
 * Heberto Mayorquin [24]
 * Thomas Perret [25]
+* Kyle Johnsen [26, 27]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -88,6 +89,8 @@ and may not be the current affiliation of a contributor.
 23. Bio Engineering Laboratory, DBSSE, ETH, Basel, Switzerland
 24. CatalystNeuro
 25. Institut des Sciences Cognitives Marc Jeannerod, CNRS UMR5229, Lyon, France
+26. Georgia Institute of Technology
+27. Emory University
 
 If we've somehow missed you off the list we're very sorry - please let us know.
 

doc/source/governance.rst

@@ -37,6 +37,7 @@ The current maintainers are:
 - Samuel Garcia (`@samuelgarcia`_)
 - Julia Sprenger (`@JuliaSprenger`_)
 - Michael Denker (`@mdenker`_)
+- Alessio Buccino (`@alejoe91`_)
 
 
 .. _`Neo maintainers team`: https://github.com/orgs/NeuralEnsemble/teams/neo-maintainers
@@ -45,3 +46,4 @@ The current maintainers are:
 .. _`@samuelgarcia`: https://github.com/samuelgarcia
 .. _`@JuliaSprenger`: https://github.com/JuliaSprenger
 .. _`@mdenker`: https://github.com/mdenker
+.. _`@alejoe91`: https://github.com/alejoe91

neo/core/analogsignal.py

@@ -416,12 +416,9 @@ def _repr_pretty_(self, pp, cycle):
         '''
         Handle pretty-printing the :class:`AnalogSignal`.
         '''
-        pp.text("{cls} with {channels} channels of length {length}; "
-                "units {units}; datatype {dtype} ".format(cls=self.__class__.__name__,
-                                                          channels=self.shape[1],
-                                                          length=self.shape[0],
-                                                          units=self.units.dimensionality.string,
-                                                          dtype=self.dtype))
+        pp.text(f"{self.__class__.__name__} with {self.shape[1]} channels of length "
+                f"{self.shape[0]}; units {self.units.dimensionality.string}; datatype "
+                f"{self.dtype}")
         if self._has_repr_pretty_attrs_():
             pp.breakable()
             self._repr_pretty_attrs_(pp, cycle)
@@ -431,8 +428,8 @@ def _pp(line):
             with pp.group(indent=1):
                 pp.text(line)
 
-        _pp("sampling rate: {}".format(self.sampling_rate))
-        _pp("time: {} to {}".format(self.t_start, self.t_stop))
+        _pp(f"sampling rate: {self.sampling_rate}")
+        _pp(f"time: {self.t_start} to {self.t_stop}")
 
     def time_index(self, t):
         """Return the array index (or indices) corresponding to the time (or times) `t`"""
@@ -716,9 +713,9 @@ def concatenate(self, *signals, overwrite=False, padding=False):
             raise MergeError(f'Signals are not continuous. Can not concatenate signals with gaps. '
                              f'Please provide a padding value.')
         if padding is not False:
-            logger.warning('Signals will be padded using {}.'.format(padding))
+            logger.warning(f'Signals will be padded using {padding}.')
             if padding is True:
-                padding = np.NaN * units
+                padding = np.nan * units
             if isinstance(padding, pq.Quantity):
                 padding = padding.rescale(units).magnitude
             else:

neo/core/baseneo.py

@@ -33,17 +33,17 @@ def _check_annotations(value):
     """
     if isinstance(value, np.ndarray):
         if not issubclass(value.dtype.type, ALLOWED_ANNOTATION_TYPES):
-            raise ValueError("Invalid annotation. NumPy arrays with dtype %s"
-                             "are not allowed" % value.dtype.type)
+            raise ValueError(f"Invalid annotation. NumPy arrays with dtype {value.dtype.type}"
+                             f"are not allowed")
     elif isinstance(value, dict):
         for element in value.values():
             _check_annotations(element)
     elif isinstance(value, (list, tuple)):
         for element in value:
             _check_annotations(element)
     elif not isinstance(value, ALLOWED_ANNOTATION_TYPES):
-        raise ValueError("Invalid annotation. Annotations of type %s are not"
-                         "allowed" % type(value))
+        raise ValueError(f"Invalid annotation. Annotations of type {type(value)} are not"
+                         f"allowed")
 
 
 def merge_annotation(a, b):
@@ -58,8 +58,7 @@ def merge_annotation(a, b):
         For strings: concatenate with ';'
         Otherwise: fail if the annotations are not equal
     """
-    assert type(a) == type(b), 'type({}) {} != type({}) {}'.format(a, type(a),
-                                                               b, type(b))
+    assert type(a) == type(b), f'type({a})) {type(a)} != type({b}) {type(b)}'
     if isinstance(a, dict):
         return merge_annotations(a, b)
     elif isinstance(a, np.ndarray):  # concatenate b to a
@@ -72,7 +71,7 @@ def merge_annotation(a, b):
         else:
             return a + ";" + b
     else:
-        assert a == b, '{} != {}'.format(a, b)
+        assert a == b, f'{a} != {b}'
         return a
 
 
@@ -100,7 +99,7 @@ def merge_annotations(A, *Bs):
                     # exc.args += ('key %s' % name,)
                     # raise
                     merged[name] = "MERGE CONFLICT"  # temporary hack
-    logger.debug("Merging annotations: A=%s Bs=%s merged=%s", A, Bs, merged)
+    logger.debug(f"Merging annotations: A={A} Bs={Bs} merged={merged}")
     return merged
 
 
@@ -122,8 +121,7 @@ def intersect_annotations(A, B):
 
     for key in set(A.keys()) & set(B.keys()):
         v1, v2 = A[key], B[key]
-        assert type(v1) == type(v2), 'type({}) {} != type({}) {}'.format(v1, type(v1),
-                                                                         v2, type(v2))
+        assert type(v1) == type(v2), f'type({v1}) {type(v1)} != type({v2}) {type(v2)}'
         if isinstance(v1, dict) and v1 == v2:
             result[key] = deepcopy(v1)
         elif isinstance(v1, str) and v1 == v2:
@@ -299,7 +297,7 @@ def _repr_pretty_attrs_(self, pp, cycle):
                 else:
                     pp.breakable()
                 with pp.group(indent=1):
-                    pp.text("{}: ".format(key))
+                    pp.text(f"{key}: ")
                     pp.pretty(value)
 
     def _repr_pretty_(self, pp, cycle):
@@ -366,8 +364,8 @@ def set_parent(self, obj):
         according to the type of "obj"
         """
         if obj.__class__.__name__ not in self._parent_objects:
-            raise TypeError("{} can only have parents of type {}, not {}".format(
-                self.__class__.__name__, self._parent_objects, obj.__class__.__name__))
+            raise TypeError((f"{self.__class__.__name__} can only have parents of "
+                             f"type {self._parwents_objects}, not {obj.__class__.__name__}"))
         loc = self._parent_objects.index(obj.__class__.__name__)
         parent_attr = self._parent_attrs[loc]
         setattr(self, parent_attr, obj)

neo/core/basesignal.py

@@ -259,7 +259,7 @@ def merge(self, other):
             if attr_self == attr_other:
                 kwargs[name] = attr_self
             else:
-                kwargs[name] = "merge({}, {})".format(attr_self, attr_other)
+                kwargs[name] = f"merge({attr_self}, {attr_other})"
         merged_annotations = merge_annotations(self.annotations, other.annotations)
         kwargs.update(merged_annotations)
 

neo/core/container.py

@@ -327,6 +327,39 @@ def size(self):
         return {name: len(getattr(self, name))
                     for name in self._child_containers}
 
+    @property
+    def _container_lookup(self):
+        return {
+            cls_name: getattr(self, container_name)
+            for cls_name, container_name in zip(self._child_objects, self._child_containers)
+        }
+
+    def _get_container(self, cls):
+        if hasattr(cls, "proxy_for"):
+            cls = cls.proxy_for
+        return self._container_lookup[cls.__name__]
+
+    def add(self, *objects):
+        """Add a new Neo object to the Container"""
+        for obj in objects:
+            if (
+                obj.__class__.__name__ in self._child_objects
+                or (
+                    hasattr(obj, "proxy_for")
+                    and obj.proxy_for.__name__ in self._child_objects
+                )
+            ):
+                container = self._get_container(obj.__class__)
+                container.append(obj)
+            else:
+                raise TypeError(
+                    f"Cannot add object of type {obj.__class__.__name__} "
+                    f"to a {self.__class__.__name__}, can only add objects of the "
+                    f"following types: {self._child_objects}"
+                )
+
+
+
     def filter(self, targdict=None, data=True, container=False, recursive=True,
                objects=None, **kwargs):
         """
@@ -530,7 +563,7 @@ def _repr_pretty_(self, pp, cycle):
         for container in self._child_containers:
             objs = getattr(self, container)
             if objs:
-                vals.append('{} {}'.format(len(objs), container))
+                vals.append(f'{objs} {container}')
         pp.text(', '.join(vals))
 
         if self._has_repr_pretty_attrs_():
@@ -540,7 +573,7 @@ def _repr_pretty_(self, pp, cycle):
         for container in self._repr_pretty_containers:
             pp.breakable()
             objs = getattr(self, container)
-            pp.text("# {} (N={})".format(container, len(objs)))
+            pp.text(f"# {container} (N={objs})")
             for (i, obj) in enumerate(objs):
                 pp.breakable()
                 pp.text("%s: " % i)

neo/core/dataobject.py

@@ -73,7 +73,7 @@ def _normalize_array_annotations(value, length):
 
         if not own_length == val_length:
             raise ValueError(
-                "Incorrect length of array annotation: {} != {}".format(val_length, own_length))
+                f"Incorrect length of array annotation: {val_length} != {own_length}")
 
         # Local function used to check single elements of a list or an array
         # They must not be lists or arrays and fit the usual annotation data types
@@ -264,10 +264,10 @@ def _merge_array_annotations(self, other):
 
         # Warn if keys were omitted
         if omitted_keys_other or omitted_keys_self:
-            warnings.warn("The following array annotations were omitted, because they were only "
-                          "present in one of the merged objects: {} from the one that was merged "
-                          "into and {} from the one that was merged into the other"
-                          "".format(omitted_keys_self, omitted_keys_other), UserWarning)
+            warnings.warn(f"The following array annotations were omitted, because they were only "
+                          f"present in one of the merged objects: {omitted_keys_self} from the "
+                          f"one that was merged into and {omitted_keys_other} from the one that "
+                          f"was merged into the other", UserWarning)
 
         # Return the merged array_annotations
         return merged_array_annotations

neo/core/epoch.py

@@ -263,7 +263,7 @@ def merge(self, other):
             if attr_self == attr_other:
                 kwargs[name] = attr_self
             else:
-                kwargs[name] = "merge({}, {})".format(attr_self, attr_other)
+                kwargs[name] = f"merge({attr_self}, {attr_other})"
 
         merged_annotations = merge_annotations(self.annotations, other.annotations)
         kwargs.update(merged_annotations)
@@ -354,8 +354,8 @@ def time_shift(self, t_shift):
 
     def set_labels(self, labels):
         if self.labels is not None and self.labels.size > 0 and len(labels) != self.size:
-            raise ValueError("Labels array has different length to times ({} != {})"
-                             .format(len(labels), self.size))
+            raise ValueError(f"Labels array has different length to times "
+                             f"({len(labels)} != {self.size})")
         self._labels = np.array(labels)
 
     def get_labels(self):
@@ -365,8 +365,8 @@ def get_labels(self):
 
     def set_durations(self, durations):
         if self.durations is not None and self.durations.size > 0 and len(durations) != self.size:
-            raise ValueError("Durations array has different length to times ({} != {})"
-                             .format(len(durations), self.size))
+            raise ValueError("Durations array has different length to times "
+                             f"({len(durations)} != {self.size})")
         self._durations = durations
 
     def get_durations(self):

neo/core/event.py

@@ -101,7 +101,7 @@ def __new__(cls, times=None, labels=None, units=None, name=None, description=Non
         # reference dimensionality
         if (len(dim) != 1 or list(dim.values())[0] != 1 or not isinstance(list(dim.keys())[0],
                                                                           pq.UnitTime)):
-            ValueError("Unit {} has dimensions {}, not [time]".format(units, dim.simplified))
+            ValueError(f"Unit {units} has dimensions {dim.simplified}, not [time].")
 
         obj = pq.Quantity(times, units=dim).view(cls)
         obj._labels = labels
@@ -204,7 +204,7 @@ def merge(self, other):
             if attr_self == attr_other:
                 kwargs[name] = attr_self
             else:
-                kwargs[name] = "merge({}, {})".format(attr_self, attr_other)
+                kwargs[name] = f"merge({attr_self}, {attr_other})"
 
         print('Event: merge annotations')
         merged_annotations = merge_annotations(self.annotations, other.annotations)
@@ -244,8 +244,8 @@ def __getitem__(self, i):
 
     def set_labels(self, labels):
         if self.labels is not None and self.labels.size > 0 and len(labels) != self.size:
-            raise ValueError("Labels array has different length to times ({} != {})"
-                            .format(len(labels), self.size))
+            raise ValueError(f"Labels array has different length to times "
+                             f"({len(labels)} != {self.size})")
         self._labels = np.array(labels)
 
     def get_labels(self):
@@ -353,13 +353,13 @@ def to_epoch(self, pairwise=False, durations=None):
             times = self.times[::2]
             durations = self.times[1::2] - times
             labels = np.array(
-                ["{}-{}".format(a, b) for a, b in zip(self.labels[::2], self.labels[1::2])])
+                [f"{a}-{b}" for a, b in zip(self.labels[::2], self.labels[1::2])])
         elif durations is None:
             # Mode 1
             times = self.times[:-1]
             durations = np.diff(self.times)
             labels = np.array(
-                ["{}-{}".format(a, b) for a, b in zip(self.labels[:-1], self.labels[1:])])
+                [f"{a}-{b}" for a, b in zip(self.labels[:-1], self.labels[1:])])
         else:
             # Mode 3
             times = self.times