Merge branch 'master' into numpy-2-0

Author: zm711

neo/core/spiketrain.py

@@ -194,10 +194,8 @@ def normalize_times_array(times, units=None, dtype=None, copy=None):
     """
 
     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."
-            )
-    
+        raise ValueError("`copy` is now deprecated in Neo due to removal in NumPy 2.0 and will be removed in 0.15.0.")
+
     if dtype is None:
         if not hasattr(times, "dtype"):
             dtype = float
@@ -218,14 +216,20 @@ def normalize_times_array(times, units=None, dtype=None, copy=None):
                 units = None  # units will be taken from times, avoids copying
             else:
                 raise ValueError("cannot rescale and return view")
-                
 
     # check to make sure the units are time
     # this approach is orders of magnitude faster than comparing the
     # reference dimensionality
     if len(dim) != 1 or list(dim.values())[0] != 1 or not isinstance(list(dim.keys())[0], pq.UnitTime):
         ValueError(f"Units have dimensions {dim.simplified}, not [time]")
-    return pq.Quantity(times, units=units, dtype=dtype,), dim
+    return (
+        pq.Quantity(
+            times,
+            units=units,
+            dtype=dtype,
+        ),
+        dim,
+    )
 
 
 class SpikeTrain(DataObject):
@@ -807,19 +811,19 @@ def time_shift(self, t_shift):
         t_stop = self.t_stop + t_shift
         t_start = self.t_start + t_shift
         new_st = SpikeTrain(
-                times=times,
-                t_stop=t_stop,
-                units=self.unit,
-                sampling_rate=self.sampling_rate,
-                t_start=t_start,
-                waveforms=self.waveforms,
-                left_sweep=self.left_sweep,
-                name=self.name,
-                file_origin=self.file_origin,
-                description=self.description,
-                array_annotations=deepcopy(self.array_annotations),
-                **self.annotations,
-            )
+            times=times,
+            t_stop=t_stop,
+            units=self.unit,
+            sampling_rate=self.sampling_rate,
+            t_start=t_start,
+            waveforms=self.waveforms,
+            left_sweep=self.left_sweep,
+            name=self.name,
+            file_origin=self.file_origin,
+            description=self.description,
+            array_annotations=deepcopy(self.array_annotations),
+            **self.annotations,
+        )
 
         # Here we can safely copy the array annotations since we know that
         # the length of the SpikeTrain does not change.

neo/rawio/plexonrawio.py

@@ -157,7 +157,7 @@ def _parse_header(self):
 
         upper_byte_of_5_byte_timestamp = int(bl_header["UpperByteOf5ByteTimestamp"])
         bl_header_timestamp = int(bl_header["TimeStamp"])
-        self._last_timestamps =  upper_byte_of_5_byte_timestamp * 2**32 + bl_header_timestamp
+        self._last_timestamps = upper_byte_of_5_byte_timestamp * 2**32 + bl_header_timestamp
 
         # ... and finalize them in self._data_blocks
         # for a faster access depending on type (1, 4, 5)

neo/test/coretest/test_analogsignal.py

@@ -131,7 +131,6 @@ 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_additional_argument(self):
         signal = AnalogSignal(
             [1, 2, 3], units="mV", sampling_rate=1 * pq.kHz, file_origin="crack.txt", ratname="Nicolas"
@@ -1762,6 +1761,7 @@ def test__pickle_2d(self):
         fobj.close()
         os.remove("./pickle")
 
+
 class TestAnalogSignalSampling(unittest.TestCase):
     def test___get_sampling_rate__period_none_rate_none_ValueError(self):
         sampling_rate = None

neo/test/coretest/test_spiketrain.py

@@ -236,7 +236,6 @@ def test__create_from_list_no_start_stop_units(self):
         self.result_spike_check(train1, st_out, t_start_out, t_stop_out, dtype, units)
         self.result_spike_check(train2, st_out, t_start_out, t_stop_out, dtype, units)
 
-
     def test__create_from_array(self):
         times = np.arange(10)
         t_start = 0.0 * pq.s
@@ -297,7 +296,6 @@ def test__create_from_array_no_start_stop_units_with_dtype(self):
         self.result_spike_check(train1, st_out, t_start_out, t_stop_out, dtype, units)
         self.result_spike_check(train2, st_out, t_start_out, t_stop_out, dtype, units)
 
-
     def test__create_from_quantity_array(self):
         times = np.arange(10) * pq.ms
         t_start = 0.0 * pq.s
@@ -332,7 +330,6 @@ def test__create_from_quantity_array_with_dtype(self):
         self.result_spike_check(train1, st_out, t_start_out, t_stop_out, dtype, units)
         self.result_spike_check(train2, st_out, t_start_out, t_stop_out, dtype, units)
 
-
     def test__create_from_quantity_array_no_start_stop_units(self):
         times = np.arange(10) * pq.ms
         t_start = 0.0
@@ -367,7 +364,6 @@ def test__create_from_quantity_array_no_start_stop_units_with_dtype(self):
         self.result_spike_check(train1, st_out, t_start_out, t_stop_out, dtype, units)
         self.result_spike_check(train2, st_out, t_start_out, t_stop_out, dtype, units)
 
-
     def test__create_from_list_without_units_should_raise_ValueError(self):
         times = range(10)
         t_start = 0.0 * pq.s
@@ -1237,7 +1233,7 @@ def test_correct_times(self):
         self.assertIsInstance(result.array_annotations, ArrayDict)
 
     def test_rescaling_units(self):
-        train3 = self.train1.duplicate_with_new_data(signal=(self.train1.times.magnitude/1000) * pq.millisecond)
+        train3 = self.train1.duplicate_with_new_data(signal=(self.train1.times.magnitude / 1000) * pq.millisecond)
         train3.segment = self.train1.segment
         train3.array_annotate(**self.arr_ann1)
         # Array annotations merge warning was already tested, can be ignored now
@@ -1503,7 +1499,6 @@ def test_array_annotations(self):
 
 class TestChanging(unittest.TestCase):
 
-
     # now we test default behavior here so change false to None
     def test_change_with_default(self):
         # Changing spike train also changes data, because it is a view
@@ -1532,7 +1527,6 @@ def test_change_and_rescale_true(self):
         data = [3, 4, 5] * pq.s
         self.assertRaises(ValueError, SpikeTrain, data, units="ms", t_stop=10000)
 
-
     def test_change_and_data_not_quantity(self):
         # Changing spike train also changes data, because it is a view
         # Data source is array
@@ -1550,7 +1544,6 @@ def test__dtype_change(self):
         data = np.array([3, 4, 5])
         self.assertRaises(ValueError, SpikeTrain, data, units="sec", t_stop=101, dtype=np.float64)
 
-
     def test_changing_slice_changes_original_spiketrain(self):
         # If we slice a spiketrain and then change the slice, the
         # original spiketrain should change.
@@ -1856,7 +1849,7 @@ def test__pretty(self):
 
 
 class TestMiscellaneous(unittest.TestCase):
-    
+
     def test_as_array(self):
         data = np.arange(10.0)
         st = SpikeTrain(data, t_stop=10.0, units="ms")