deprecate copy behavior

zm711 · zm711 · commit bfb502dad090 · 2024-09-13T11:32:20.000-04:00
diff --git a/neo/core/analogsignal.py b/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)
@@ -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.
diff --git a/neo/core/imagesequence.py b/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,
diff --git a/neo/core/irregularlysampledsignal.py b/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"):
diff --git a/neo/core/spiketrain.py b/neo/core/spiketrain.py
@@ -138,7 +138,7 @@ def _new_spiketrain(
     t_stop,
     units=None,
     dtype=None,
-    copy=True,
+    copy=None,
     sampling_rate=1.0 * pq.Hz,
     t_start=0.0 * pq.s,
     waveforms=None,
@@ -158,19 +158,19 @@ def _new_spiketrain(
     if annotations is None:
         annotations = {}
     obj = SpikeTrain(
-        signal,
-        t_stop,
-        units,
-        dtype,
-        copy,
-        sampling_rate,
-        t_start,
-        waveforms,
-        left_sweep,
-        name,
-        file_origin,
-        description,
-        array_annotations,
+        signal=signal,
+        t_stop=t_stop,
+        units=units,
+        dtype=dtype,
+        copy=copy,
+        sampling_rate=sampling_rate,
+        t_start=t_start,
+        waveforms=waveforms,
+        left_sweep=left_sweep,
+        name=name,
+        file_origin=file_origin,
+        description=description,
+        array_annotations=array_annotations,
         **annotations,
     )
     obj.segment = segment
@@ -246,11 +246,9 @@ class SpikeTrain(DataObject):
         Required if `times` is a list or numpy.ndarray`
         Not required if times is a quantities.Quantity
     dtype: numpy dtype | str | None, default: None
-        Overrides the dtype of the times array if given.
-        If None, the dtype of the times is used
-    copy: bool, default: True
-        Whether to copy the times array.
-        Must be True when you request a change of units or dtype.
+        Due to change in `copy` behavior this argument is also deprecated during construction
+    copy: bool, default: None
+        Deprecated in order to support NumPy 2.0 and will be removed.
     sampling_rate: quantity scalar, default: 1.0 pq.Hz
         Number of samples per unit time for the waveforms.
     t_start: quantity scalar | numpy scalar | float
@@ -330,7 +328,7 @@ def __new__(
         t_stop,
         units=None,
         dtype=None,
-        copy=True,
+        copy=None,
         sampling_rate=1.0 * pq.Hz,
         t_start=0.0 * pq.s,
         waveforms=None,
@@ -347,13 +345,17 @@ def __new__(
         This is called whenever a new :class:`SpikeTrain` 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."
+            )
+
         if len(times) != 0 and waveforms is not None and len(times) != waveforms.shape[0]:
             # len(times)!=0 has been used to workaround a bug occurring during neo import
             raise ValueError("the number of waveforms should be equal to the number of spikes")
 
         if dtype is not None and hasattr(times, "dtype") and times.dtype != dtype:
-            if not copy:
-                raise ValueError("cannot change dtype and return view")
+            raise ValueError("cannot change dtype during construction due to change in copy behavior")
 
             # if t_start.dtype or t_stop.dtype != times.dtype != dtype,
             # _check_time_in_range can have problems, so we set the t_start
@@ -420,7 +422,7 @@ def __init__(
         t_stop,
         units=None,
         dtype=None,
-        copy=True,
+        copy=None,
         sampling_rate=1.0 * pq.Hz,
         t_start=0.0 * pq.s,
         waveforms=None,
diff --git a/neo/test/coretest/test_analogsignal.py b/neo/test/coretest/test_analogsignal.py
@@ -131,30 +131,31 @@ def test__create_inconsistent_sampling_rate_and_period_ValueError(self):
         data = np.arange(10.0) * pq.mV
         self.assertRaises(ValueError, AnalogSignal, data, sampling_rate=1 * pq.kHz, sampling_period=5 * pq.s)
 
-    def test__create_with_copy_true_should_return_copy(self):
-        data = np.arange(10.0) * pq.mV
-        rate = 5000 * pq.Hz
-        signal = AnalogSignal(data, copy=True, sampling_rate=rate)
-        data[3] = 99 * pq.mV
-        assert_neo_object_is_compliant(signal)
-        self.assertNotEqual(signal[3, 0], 99 * pq.mV)
-
-    def test__create_with_copy_false_should_return_view(self):
-        data = np.arange(10.0) * pq.mV
-        rate = 5000 * pq.Hz
-        signal = AnalogSignal(data, copy=False, sampling_rate=rate)
-        data[3] = 99 * pq.mV
-        assert_neo_object_is_compliant(signal)
-        self.assertEqual(signal[3, 0], 99 * pq.mV)
-
-    def test__create2D_with_copy_false_should_return_view(self):
-        data = np.arange(10.0) * pq.mV
-        data = data.reshape((5, 2))
-        rate = 5000 * pq.Hz
-        signal = AnalogSignal(data, copy=False, sampling_rate=rate)
-        data[3, 0] = 99 * pq.mV
-        assert_neo_object_is_compliant(signal)
-        self.assertEqual(signal[3, 0], 99 * pq.mV)
+    # to be removed after testing in CI
+    #def test__create_with_copy_true_should_return_copy(self):
+    #    data = np.arange(10.0) * pq.mV
+    #   rate = 5000 * pq.Hz
+    #    signal = AnalogSignal(data, copy=True, sampling_rate=rate)
+    #    data[3] = 99 * pq.mV
+    #    assert_neo_object_is_compliant(signal)
+    #    self.assertNotEqual(signal[3, 0], 99 * pq.mV)
+
+    #def test__create_with_copy_false_should_return_view(self):
+    #   data = np.arange(10.0) * pq.mV
+    #    rate = 5000 * pq.Hz
+    #    signal = AnalogSignal(data, copy=False, sampling_rate=rate)
+    #    data[3] = 99 * pq.mV
+    #    assert_neo_object_is_compliant(signal)
+    #    self.assertEqual(signal[3, 0], 99 * pq.mV)
+
+    #def test__create2D_with_copy_false_should_return_view(self):
+    #    data = np.arange(10.0) * pq.mV
+    #    data = data.reshape((5, 2))
+    #    rate = 5000 * pq.Hz
+    #    signal = AnalogSignal(data, copy=False, sampling_rate=rate)
+    #    data[3, 0] = 99 * pq.mV
+    #    assert_neo_object_is_compliant(signal)
+    #    self.assertEqual(signal[3, 0], 99 * pq.mV)
 
     def test__create_with_additional_argument(self):
         signal = AnalogSignal(
@@ -1048,6 +1049,7 @@ def test_splice_1channel_inplace(self):
         assert_array_equal(result.array_annotations["anno2"], np.array(["a"]))
         self.assertIsInstance(result.array_annotations, ArrayDict)
 
+    # splice copy is a deepcopy not a numpy copy still need to test for numpy 2.0
     def test_splice_1channel_with_copy(self):
         signal_for_splicing = AnalogSignal(
             [0.1, 0.1, 0.1],
@@ -1066,6 +1068,7 @@ def test_splice_1channel_with_copy(self):
         assert_array_equal(result.array_annotations["anno2"], np.array(["a"]))
         self.assertIsInstance(result.array_annotations, ArrayDict)
 
+    # splice is a deepcopy still need to test for numpy 2.0
     def test_splice_2channels_inplace(self):
         arr_ann1 = {"index": np.arange(10, 12)}
         arr_ann2 = {"index": np.arange(2), "test": ["a", "b"]}
diff --git a/neo/test/coretest/test_spiketrain.py b/neo/test/coretest/test_spiketrain.py
diff --git a/pyproject.toml b/pyproject.toml
