From 123ca040b11a5961643c4de080df89af9b1fcd24 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:58:28 +0100
Subject: [PATCH] [Fix] neo v0.13.4 deprecated copy (#646)

* remove copy from conversion

* remove copy from spike_train_correlation

* fix surrogates

* fix statistics
---
 elephant/conversion.py              | 2 +-
 elephant/spike_train_correlation.py | 2 +-
 elephant/spike_train_surrogates.py  | 7 ++-----
 elephant/statistics.py              | 2 +-
 4 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/elephant/conversion.py b/elephant/conversion.py
index f3686d643..a80b51ee0 100644
--- a/elephant/conversion.py
+++ b/elephant/conversion.py
@@ -854,7 +854,7 @@ def to_spike_trains(self, spikes="random", as_array=False,
                     array_ants = dict(bins=bin_indices)
                 spiketrain = neo.SpikeTrain(spiketrain, t_start=self._t_start,
                                             t_stop=self._t_stop,
-                                            units=self.units, copy=False,
+                                            units=self.units,
                                             description=description,
                                             array_annotations=array_ants,
                                             bin_size=self.bin_size)
diff --git a/elephant/spike_train_correlation.py b/elephant/spike_train_correlation.py
index 65ccf6800..1d7cf0656 100644
--- a/elephant/spike_train_correlation.py
+++ b/elephant/spike_train_correlation.py
@@ -809,7 +809,7 @@ def cross_correlation_histogram(
         signal=np.expand_dims(cross_corr, axis=1),
         units=pq.dimensionless,
         t_start=t_start,
-        sampling_period=binned_spiketrain_i.bin_size, copy=False,
+        sampling_period=binned_spiketrain_i.bin_size,
         **annotations)
     return cch_result, lags
 
diff --git a/elephant/spike_train_surrogates.py b/elephant/spike_train_surrogates.py
index 5d6cd4300..962596423 100644
--- a/elephant/spike_train_surrogates.py
+++ b/elephant/spike_train_surrogates.py
@@ -736,7 +736,6 @@ def _continuous_time_bin_shuffling(spiketrain, max_displacement, bin_size,
             units=units,
             t_start=t_start,
             t_stop=t_stop,
-            copy=False,
         )
 
         surrogate_spiketrains.append(surrogate_spiketrain)
@@ -1252,8 +1251,7 @@ def trial_shifting(spiketrains, dither, n_surrogates=1):
             surrogate_spiketrain[trial_id] * pq.s,
             t_start=t_starts[trial_id] * pq.s,
             t_stop=t_stops[trial_id] * pq.s,
-            units=units,
-            sampling_rate=sampling_rates[trial_id])
+            sampling_rate=sampling_rates[trial_id]).rescale(units)
           for trial_id in range(len(surrogate_spiketrain))]
          for surrogate_spiketrain in surrogate_spiketrains]
 
@@ -1337,8 +1335,7 @@ def _trial_shifting_of_concatenated_spiketrain(
         np.hstack(surrogate_spiketrain) * pq.s,
         t_start=t_start * pq.s,
         t_stop=t_stop * pq.s,
-        units=units,
-        sampling_rate=spiketrain.sampling_rate)
+        sampling_rate=spiketrain.sampling_rate).rescale(units)
         for surrogate_spiketrain in surrogate_spiketrains]
     return surrogate_spiketrains
 
diff --git a/elephant/statistics.py b/elephant/statistics.py
index 0ab389572..45d9cd283 100644
--- a/elephant/statistics.py
+++ b/elephant/statistics.py
@@ -1201,7 +1201,7 @@ def _rate() -> pq.Quantity:
                             sampling_period=bin_size,
                             units=normalised_bin_hist.units,
                             t_start=binned_spiketrain.t_start,
-                            normalization=output, copy=False)
+                            normalization=output)
 
 
 @deprecated_alias(binsize='bin_size')