Merge pull request #1554 from zm711/remove-copy

Deprecate Copy Behavior to support Quantities 16.0

Author: apdavison

.github/workflows/io-test.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.9', '3.11.9']
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

neo/core/analogsignal.py

@@ -52,7 +52,7 @@ def _new_AnalogSignalArray(
     signal,
     units=None,
     dtype=None,
-    copy=True,
+    copy=None,
     t_start=0 * pq.s,
     sampling_rate=None,
     sampling_period=None,
@@ -180,7 +180,7 @@ def __new__(
         signal,
         units=None,
         dtype=None,
-        copy=True,
+        copy=None,
         t_start=0 * pq.s,
         sampling_rate=None,
         sampling_period=None,
@@ -198,8 +198,13 @@ def __new__(
 
         __array_finalize__ is called on the new object.
         """
+        if copy is not None:
+            raise ValueError(
+                "`copy` is now deprecated in Neo due to removal in NumPy 2.0 and will be removed in 0.15.0."
+            )
+
         signal = cls._rescale(signal, units=units)
-        obj = pq.Quantity(signal, units=units, dtype=dtype, copy=copy).view(cls)
+        obj = pq.Quantity(signal, units=units, dtype=dtype).view(cls)
 
         if obj.ndim == 1:
             obj.shape = (-1, 1)
@@ -218,7 +223,7 @@ def __init__(
         signal,
         units=None,
         dtype=None,
-        copy=True,
+        copy=None,
         t_start=0 * pq.s,
         sampling_rate=None,
         sampling_period=None,
@@ -257,7 +262,7 @@ def __reduce__(self):
             np.array(self),
             self.units,
             self.dtype,
-            True,
+            None,
             self.t_start,
             self.sampling_rate,
             self.sampling_period,
@@ -547,6 +552,7 @@ def time_shift(self, t_shift):
 
         return new_sig
 
+    # copy in splice is a deepcopy not a numpy copy so we can keep
     def splice(self, signal, copy=False):
         """
         Replace part of the current signal by a new piece of signal.

neo/core/basesignal.py

@@ -267,7 +267,7 @@ def merge(self, other):
             stack,
             units=self.units,
             dtype=self.dtype,
-            copy=False,
+            copy=None,
             t_start=self.t_start,
             sampling_rate=self.sampling_rate,
             **kwargs,

neo/core/imagesequence.py

@@ -70,7 +70,7 @@ class ImageSequence(BaseSignal):
 
     *Optional attributes/properties*:
         :dtype: (numpy dtype or str) Override the dtype of the signal array.
-        :copy: (bool) True by default.
+        :copy: deprecated
 
     Note: Any other additional arguments are assumed to be user-specific
     metadata and stored in :attr:`annotations`.
@@ -103,7 +103,7 @@ def __new__(
         image_data,
         units=pq.dimensionless,
         dtype=None,
-        copy=True,
+        copy=None,
         t_start=0 * pq.s,
         spatial_scale=None,
         frame_duration=None,
@@ -121,14 +121,20 @@ def __new__(
 
         __array_finalize__ is called on the new object.
         """
+
+        if copy is not None:
+            raise ValueError(
+                "`copy` is now deprecated in Neo due to removal in NumPy 2.0 and will be removed in 0.15.0."
+            )
+
         if spatial_scale is None:
             raise ValueError("spatial_scale is required")
 
         image_data = np.stack(image_data)
         if len(image_data.shape) != 3:
             raise ValueError("list doesn't have the correct number of dimensions")
 
-        obj = pq.Quantity(image_data, units=units, dtype=dtype, copy=copy).view(cls)
+        obj = pq.Quantity(image_data, units=units, dtype=dtype).view(cls)
         obj.segment = None
         # function from analogsignal.py in neo/core directory
         obj.sampling_rate = _get_sampling_rate(sampling_rate, frame_duration)
@@ -144,7 +150,7 @@ def __init__(
         image_data,
         units=pq.dimensionless,
         dtype=None,
-        copy=True,
+        copy=None,
         t_start=0 * pq.s,
         spatial_scale=None,
         frame_duration=None,

neo/core/irregularlysampledsignal.py

@@ -38,7 +38,7 @@ def _new_IrregularlySampledSignal(
     units=None,
     time_units=None,
     dtype=None,
-    copy=True,
+    copy=None,
     name=None,
     file_origin=None,
     description=None,
@@ -93,8 +93,8 @@ class IrregularlySampledSignal(BaseSignal):
     dtype: numpy dtype | string | None, default: None
         Overrides the signal array dtype
         Does not affect the dtype of the times which must be floats
-    copy: bool, default: True
-        Whether copy should be set to True when making the quantity array
+    copy: bool | None, default: None
+        deprecated and no longer used (for NumPy 2.0 support). Will be removed.
     name: str | None, default: None
         An optional label for the dataset
     description: str | None, default: None
@@ -158,7 +158,7 @@ def __new__(
         units=None,
         time_units=None,
         dtype=None,
-        copy=True,
+        copy=None,
         name=None,
         file_origin=None,
         description=None,
@@ -171,6 +171,12 @@ def __new__(
         This is called whenever a new :class:`IrregularlySampledSignal` is
         created from the constructor, but not when slicing.
         """
+
+        if copy is not None:
+            raise ValueError(
+                "`copy` is now deprecated in Neo due to removal in NumPy 2.0 and will be removed in 0.15.0."
+            )
+
         signal = cls._rescale(signal, units=units)
         if time_units is None:
             if hasattr(times, "units"):
@@ -199,7 +205,7 @@ def __init__(
         units=None,
         time_units=None,
         dtype=None,
-        copy=True,
+        copy=None,
         name=None,
         file_origin=None,
         description=None,
@@ -231,7 +237,7 @@ def __reduce__(self):
             self.units,
             self.times.units,
             self.dtype,
-            True,
+            None,
             self.name,
             self.file_origin,
             self.description,
@@ -544,6 +550,9 @@ def time_shift(self, t_shift):
             (the original :class:`IrregularlySampledSignal` is not modified).
         """
         new_sig = deepcopy(self)
+        # As of numpy 2.0/quantities 0.16 we need to copy the array itself
+        # in order to be able to time_shift
+        new_sig.times = self.times.copy()
 
         new_sig.times += t_shift
 
@@ -588,7 +597,7 @@ def merge(self, other):
         merged_annotations = merge_annotations(self.annotations, other.annotations)
         kwargs.update(merged_annotations)
 
-        signal = self.__class__(self.times, stack, units=self.units, dtype=self.dtype, copy=False, **kwargs)
+        signal = self.__class__(self.times, stack, units=self.units, dtype=self.dtype, copy=None, **kwargs)
         signal.segment = self.segment
         signal.array_annotate(**self._merge_array_annotations(other))
 
@@ -681,7 +690,7 @@ def concatenate(self, other, allow_overlap=False):
             times=new_times[sorting],
             units=self.units,
             dtype=self.dtype,
-            copy=False,
+            copy=None,
             t_start=t_start,
             t_stop=t_stop,
             **kwargs,