From ba9417a64e9da1f1462aae2f2a4fa7dcd69c0013 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Thu, 2 May 2024 19:18:56 -0600
Subject: [PATCH 1/2] move towards making set_probe in place

---
 .../core/baserecordingsnippets.py             | 34 +++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/baserecordingsnippets.py b/src/spikeinterface/core/baserecordingsnippets.py
index c2386d0af0..464e261bd1 100644
--- a/src/spikeinterface/core/baserecordingsnippets.py
+++ b/src/spikeinterface/core/baserecordingsnippets.py
@@ -76,7 +76,7 @@ def set_probe(self, probe, group_mode="by_probe", in_place=False):
 
         Parameters
         ----------
-        probe_or_probegroup: Probe, list of Probe, or ProbeGroup
+        probe: a Probe object
             The probe(s) to be attached to the recording
         group_mode: "by_probe" | "by_shank", default: "by_probe
             "by_probe" or "by_shank". Adds grouping property to the recording based on the probes ("by_probe")
@@ -90,6 +90,7 @@ def set_probe(self, probe, group_mode="by_probe", in_place=False):
         sub_recording: BaseRecording
             A view of the recording (ChannelSlice or clone or itself)
         """
+
         assert isinstance(probe, Probe), "must give Probe"
         probegroup = ProbeGroup()
         probegroup.add_probe(probe)
@@ -173,7 +174,15 @@ def set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False)
         probe_as_numpy_array = probe_as_numpy_array[order]
         probe_as_numpy_array["device_channel_indices"] = np.arange(probe_as_numpy_array.size, dtype="int64")
 
-        # create recording : channel slice or clone or self
+        deprecation_msg = (
+            "in_place will change its default to True in version 0.103 and stop returning a recording"
+            " use recording.create_with_probes(probe_or_probegroup) instead to replicate the old functionality"
+        )
+        warn.warn(
+            deprecation_msg,
+            DeprecationWarning,
+            stacklevel=2,
+        )
         if in_place:
             if not np.array_equal(new_channel_ids, self.get_channel_ids()):
                 raise Exception("set_probe(inplace=True) must have all channel indices")
@@ -225,6 +234,27 @@ def set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False)
 
         return sub_recording
 
+    def create_with_probes(self, probe_or_probegroup, group_mode="by_probe"):
+        """
+        Creates a new recording with a probe attached.
+
+        Parameters
+        ----------
+        probe_or_probegroup: Probe, list of Probes, or ProbeGroup
+            The probe(s) to be attached to the recording
+        group_mode: "by_probe" | "by_shank", default: "by_probe"
+            "by_probe" or "by_shank". Adds grouping property to the recording based on the probes ("by_probe")
+            or  shanks ("by_shank")
+
+        Returns
+        -------
+        new_recording: BaseRecording
+            A new recording object with the probe attached
+        """
+
+        # TODO: Once in_place is True by default in set_probes, we might re-organize the code
+        return self.set_probegroup(probe_or_probegroup, in_place=False)
+
     def get_probe(self):
         probes = self.get_probes()
         assert len(probes) == 1, "there are several probe use .get_probes() or get_probegroup()"

From 5f2d22712b0e9171364faa2679f1bb31a90f6308 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Thu, 2 May 2024 19:44:24 -0600
Subject: [PATCH 2/2] fix warning

---
 src/spikeinterface/core/baserecordingsnippets.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/baserecordingsnippets.py b/src/spikeinterface/core/baserecordingsnippets.py
index 464e261bd1..48595be0c3 100644
--- a/src/spikeinterface/core/baserecordingsnippets.py
+++ b/src/spikeinterface/core/baserecordingsnippets.py
@@ -2,11 +2,11 @@
 from pathlib import Path
 
 import numpy as np
+import warnings
 
 from probeinterface import Probe, ProbeGroup, write_probeinterface, read_probeinterface, select_axes
 
 from .base import BaseExtractor
-from .core_tools import check_json
 from .recording_tools import check_probe_do_not_overlap
 
 from warnings import warn
@@ -178,7 +178,7 @@ def set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False)
             "in_place will change its default to True in version 0.103 and stop returning a recording"
             " use recording.create_with_probes(probe_or_probegroup) instead to replicate the old functionality"
         )
-        warn.warn(
+        warnings.warn(
             deprecation_msg,
             DeprecationWarning,
             stacklevel=2,