Move generate_ground_truth_recording to generation module

examples/forhowto/plot_extract_lfps.py

@@ -52,7 +52,7 @@
 import spikeinterface.extractors as se
 import spikeinterface.preprocessing as spre
 import spikeinterface.widgets as sw
-from spikeinterface.core import generate_ground_truth_recording
+from spikeinterface.generation import generate_ground_truth_recording
 
 ##############################################################################
 # 1. Generate simulated recording with low-frequency signals

examples/forhowto/plot_working_with_tetrodes.py

@@ -11,7 +11,7 @@
 
 import spikeinterface.preprocessing as spre
 from spikeinterface.widgets import plot_traces, plot_probe_map
-from spikeinterface import generate_ground_truth_recording
+from spikeinterface.generation import generate_ground_truth_recording
 
 from probeinterface import generate_tetrode, ProbeGroup
 

examples/tutorials/core/plot_4_sorting_analyzer.py

@@ -27,7 +27,8 @@
 
 import matplotlib.pyplot as plt
 
-from spikeinterface import create_sorting_analyzer, load_sorting_analyzer, generate_ground_truth_recording
+from spikeinterface import create_sorting_analyzer, load_sorting_analyzer
+from spikeinterface.generation import generate_ground_truth_recording
 
 ##############################################################################
 # First let's generate a simulated recording and sorting

examples/tutorials/curation/plot_1_automated_curation.py

@@ -28,6 +28,7 @@
 import spikeinterface.core as si
 import spikeinterface.curation as sc
 import spikeinterface.widgets as sw
+from spikeinterface.generation import generate_ground_truth_recording
 
 # note: you can use more cores using e.g.
 # si.set_global_jobs_kwargs(n_jobs = 8)
@@ -69,7 +70,7 @@
 # bunch of extensions. Follow these links for more info on `recordings <https://spikeinterface.readthedocs.io/en/latest/modules/extractors.html>`_, `sortings <https://spikeinterface.readthedocs.io/en/latest/modules/sorters.html>`_, `sorting analyzers <https://spikeinterface.readthedocs.io/en/latest/tutorials/core/plot_4_sorting_analyzer.html#sphx-glr-tutorials-core-plot-4-sorting-analyzer-py>`_
 # and `extensions <https://spikeinterface.readthedocs.io/en/latest/modules/postprocessing.html>`_.
 
-recording, sorting = si.generate_ground_truth_recording(num_channels=4, seed=4, num_units=10)
+recording, sorting = generate_ground_truth_recording(num_channels=4, seed=4, num_units=10)
 sorting_analyzer = si.create_sorting_analyzer(sorting=sorting, recording=recording)
 sorting_analyzer.compute(['noise_levels','random_spikes','waveforms','templates','spike_locations','spike_amplitudes','correlograms','principal_components','quality_metrics','template_metrics'])
 sorting_analyzer.compute('template_metrics', include_multi_channel_metrics=True)

examples/tutorials/curation/plot_2_train_a_model.py

@@ -21,6 +21,7 @@
 import spikeinterface.core as si
 import spikeinterface.curation as sc
 import spikeinterface.widgets as sw
+from spikeinterface.generation import generate_ground_truth_recording
 
 # Note, you can set the number of cores you use using e.g.
 # si.set_global_job_kwargs(n_jobs = 8)
@@ -37,8 +38,8 @@
 # `load your own recording <https://spikeinterface.readthedocs.io/en/latest/modules/extractors.html>`_
 # and `do a sorting <https://spikeinterface.readthedocs.io/en/latest/modules/sorters.html>`_ on your data.)
 
-recording, sorting_1 = si.generate_ground_truth_recording(num_channels=4, seed=1, num_units=5)
-_, sorting_2 =si.generate_ground_truth_recording(num_channels=4, seed=2, num_units=5)
+recording, sorting_1 = generate_ground_truth_recording(num_channels=4, seed=1, num_units=5)
+_, sorting_2 = generate_ground_truth_recording(num_channels=4, seed=2, num_units=5)
 
 both_sortings = si.aggregate_units([sorting_1, sorting_2])
 

examples/tutorials/metrics/plot_3_quality_metrics.py

@@ -8,6 +8,7 @@
 """
 
 import spikeinterface.core as si
+from spikeinterface.generation import generate_ground_truth_recording
 from spikeinterface.metrics import (
     compute_snrs,
     compute_presence_ratios,
@@ -17,7 +18,7 @@
 ##############################################################################
 # First, let's generate a simulated recording and sorting
 
-recording, sorting = si.generate_ground_truth_recording()
+recording, sorting = generate_ground_truth_recording()
 print(recording)
 print(sorting)
 

examples/tutorials/metrics/plot_4_curation.py

@@ -11,13 +11,14 @@
 # Import the modules and/or functions necessary from spikeinterface
 
 import spikeinterface.core as si
+from spikeinterface.generation import generate_ground_truth_recording
 
 
 ##############################################################################
 # Let's generate a simulated dataset, and imagine that the ground-truth
 # sorting is in fact the output of a sorter.
 
-recording, sorting = si.generate_ground_truth_recording()
+recording, sorting = generate_ground_truth_recording()
 print(recording)
 print(sorting)
 

examples/tutorials/widgets/plot_3_waveforms_gallery.py

@@ -10,11 +10,12 @@
 import spikeinterface as si
 import spikeinterface.extractors as se
 import spikeinterface.widgets as sw
+from spikeinterface.generation import generate_ground_truth_recording
 
 ##############################################################################
 # First, let's generate a simulated dataset
 
-recording, sorting = si.generate_ground_truth_recording()
+recording, sorting = generate_ground_truth_recording()
 print(recording)
 print(sorting)
 

src/spikeinterface/__init__.py

@@ -6,6 +6,25 @@
 
 from .core import *
 
+
+def __getattr__(name):
+    if name == "generate_ground_truth_recording":
+        import warnings
+
+        warnings.warn(
+            "Importing generate_ground_truth_recording from spikeinterface is deprecated. "
+            "Import from spikeinterface.generation instead: "
+            "`from spikeinterface.generation import generate_ground_truth_recording`. "
+            "This will be removed in version 0.106.0.",
+            FutureWarning,
+            stacklevel=2,
+        )
+        from .generation.ground_truth_generator import generate_ground_truth_recording
+
+        return generate_ground_truth_recording
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
 import warnings
 
 warnings.filterwarnings("ignore", message="distutils Version classes are deprecated")

src/spikeinterface/benchmark/tests/common_benchmark_testing.py

@@ -12,13 +12,12 @@
 import numpy as np
 
 from spikeinterface.core import (
-    generate_ground_truth_recording,
     estimate_templates,
     Templates,
     create_sorting_analyzer,
     ms_to_samples,
 )
-from spikeinterface.generation import generate_drifting_recording
+from spikeinterface.generation import generate_drifting_recording, generate_ground_truth_recording
 
 ON_GITHUB = bool(os.getenv("GITHUB_ACTIONS"))
 
@@ -39,7 +38,7 @@ def make_dataset(job_kwargs={}):
             contact_shape_params={"radius": 6},
         ),
         generate_sorting_kwargs=dict(firing_rates=6.0, refractory_period_ms=4.0),
-        noise_kwargs=dict(noise_levels=5.0, strategy="on_the_fly"),
+        noise_kwargs=dict(noise_levels=5.0),
         seed=2205,
     )
 

src/spikeinterface/benchmark/tests/test_benchmark_sorter.py

@@ -2,7 +2,7 @@
 import pytest
 from pathlib import Path
 
-from spikeinterface import generate_ground_truth_recording
+from spikeinterface.generation import generate_ground_truth_recording
 from spikeinterface.preprocessing import bandpass_filter
 from spikeinterface.benchmark import SorterStudy
 

src/spikeinterface/benchmark/tests/test_benchmark_sorter_without_gt.py

@@ -2,7 +2,7 @@
 import pytest
 from pathlib import Path
 
-from spikeinterface import generate_ground_truth_recording
+from spikeinterface.generation import generate_ground_truth_recording
 from spikeinterface.preprocessing import bandpass_filter
 from spikeinterface.benchmark import SorterStudyWithoutGroundTruth
 

src/spikeinterface/comparison/tests/test_templatecomparison.py

@@ -2,7 +2,8 @@
 import pytest
 import numpy as np
 
-from spikeinterface.core import create_sorting_analyzer, generate_ground_truth_recording
+from spikeinterface.core import create_sorting_analyzer
+from spikeinterface.generation import generate_ground_truth_recording
 from spikeinterface.comparison import compare_templates, compare_multiple_templates
 
 # def setup_module():

src/spikeinterface/core/__init__.py

@@ -48,7 +48,6 @@
     generate_recording_by_size,
     InjectTemplatesRecording,
     inject_templates,
-    generate_ground_truth_recording,
 )
 
 # utils to append and concatenate segment (equivalent to OLD MultiRecordingTimeExtractor)
@@ -213,4 +212,18 @@ def __getattr__(name):
             "noise_generator_recording": noise_generator_recording,
         }
         return _map[name]
+    if name == "generate_ground_truth_recording":
+        import warnings
+
+        warnings.warn(
+            "Importing generate_ground_truth_recording from spikeinterface.core is deprecated. "
+            "Import from spikeinterface.generation instead: "
+            "`from spikeinterface.generation import generate_ground_truth_recording`. "
+            "This will be removed in version 0.106.0.",
+            FutureWarning,
+            stacklevel=2,
+        )
+        from spikeinterface.generation.ground_truth_generator import generate_ground_truth_recording
+
+        return generate_ground_truth_recording
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")