Merge pull request #2898 from samuelgarcia/rem_verbose_from_job_kwargs

remove verbose from job_kwargs

src/spikeinterface/core/job_tools.py

@@ -47,7 +47,6 @@
     "chunk_duration",
     "progress_bar",
     "mp_context",
-    "verbose",
     "max_threads_per_process",
 )
 

src/spikeinterface/core/recording_tools.py

@@ -73,6 +73,7 @@ def write_binary_recording(
     add_file_extension: bool = True,
     byte_offset: int = 0,
     auto_cast_uint: bool = True,
+    verbose: bool = True,
     **job_kwargs,
 ):
     """
@@ -98,6 +99,8 @@ def write_binary_recording(
     auto_cast_uint: bool, default: True
         If True, unsigned integers are automatically cast to int if the specified dtype is signed
         .. deprecated:: 0.103, use the `unsigned_to_signed` function instead.
+    verbose: bool
+        If True, output is verbose
     {}
     """
     job_kwargs = fix_job_kwargs(job_kwargs)
@@ -138,7 +141,7 @@ def write_binary_recording(
     init_func = _init_binary_worker
     init_args = (recording, file_path_dict, dtype, byte_offset, cast_unsigned)
     executor = ChunkRecordingExecutor(
-        recording, func, init_func, init_args, job_name="write_binary_recording", **job_kwargs
+        recording, func, init_func, init_args, job_name="write_binary_recording", verbose=verbose, **job_kwargs
     )
     executor.run()
 

src/spikeinterface/core/tests/test_recording_tools.py

@@ -37,8 +37,8 @@ def test_write_binary_recording(tmp_path):
     file_paths = [tmp_path / "binary01.raw"]
 
     # Write binary recording
-    job_kwargs = dict(verbose=False, n_jobs=1)
-    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, **job_kwargs)
+    job_kwargs = dict(n_jobs=1)
+    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, verbose=False, **job_kwargs)
 
     # Check if written data matches original data
     recorder_binary = BinaryRecordingExtractor(
@@ -64,9 +64,11 @@ def test_write_binary_recording_offset(tmp_path):
     file_paths = [tmp_path / "binary01.raw"]
 
     # Write binary recording
-    job_kwargs = dict(verbose=False, n_jobs=1)
+    job_kwargs = dict(n_jobs=1)
     byte_offset = 125
-    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, byte_offset=byte_offset, **job_kwargs)
+    write_binary_recording(
+        recording, file_paths=file_paths, dtype=dtype, byte_offset=byte_offset, verbose=False, **job_kwargs
+    )
 
     # Check if written data matches original data
     recorder_binary = BinaryRecordingExtractor(
@@ -97,8 +99,8 @@ def test_write_binary_recording_parallel(tmp_path):
     file_paths = [tmp_path / "binary01.raw", tmp_path / "binary02.raw"]
 
     # Write binary recording
-    job_kwargs = dict(verbose=False, n_jobs=2, chunk_memory="100k", mp_context="spawn")
-    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, **job_kwargs)
+    job_kwargs = dict(n_jobs=2, chunk_memory="100k", mp_context="spawn")
+    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, verbose=False, **job_kwargs)
 
     # Check if written data matches original data
     recorder_binary = BinaryRecordingExtractor(
@@ -127,8 +129,8 @@ def test_write_binary_recording_multiple_segment(tmp_path):
     file_paths = [tmp_path / "binary01.raw", tmp_path / "binary02.raw"]
 
     # Write binary recording
-    job_kwargs = dict(verbose=False, n_jobs=2, chunk_memory="100k", mp_context="spawn")
-    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, **job_kwargs)
+    job_kwargs = dict(n_jobs=2, chunk_memory="100k", mp_context="spawn")
+    write_binary_recording(recording, file_paths=file_paths, dtype=dtype, verbose=False, **job_kwargs)
 
     # Check if written data matches original data
     recorder_binary = BinaryRecordingExtractor(

src/spikeinterface/sorters/internal/simplesorter.py

@@ -71,7 +71,7 @@ def get_sorter_version(cls):
     def _run_from_folder(cls, sorter_output_folder, params, verbose):
         job_kwargs = params["job_kwargs"]
         job_kwargs = fix_job_kwargs(job_kwargs)
-        job_kwargs.update({"verbose": verbose, "progress_bar": verbose})
+        job_kwargs.update({"progress_bar": verbose})
 
         from spikeinterface.sortingcomponents.peak_detection import detect_peaks
         from spikeinterface.sortingcomponents.tools import extract_waveform_at_max_channel

src/spikeinterface/sorters/internal/spyking_circus2.py

@@ -113,7 +113,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
 
         job_kwargs = params["job_kwargs"]
         job_kwargs = fix_job_kwargs(job_kwargs)
-        job_kwargs.update({"verbose": verbose, "progress_bar": verbose})
+        job_kwargs.update({"progress_bar": verbose})
 
         recording = cls.load_recording_from_folder(sorter_output_folder.parent, with_warnings=False)
 

src/spikeinterface/sortingcomponents/clustering/circus.py

@@ -63,6 +63,7 @@ class CircusClustering:
         "noise_levels": None,
         "tmp_folder": None,
         "job_kwargs": {},
+        "verbose": True,
     }
 
     @classmethod
@@ -72,7 +73,7 @@ def main_function(cls, recording, peaks, params):
         job_kwargs = fix_job_kwargs(params["job_kwargs"])
 
         d = params
-        verbose = job_kwargs.get("verbose", True)
+        verbose = d["verbose"]
 
         fs = recording.get_sampling_frequency()
         ms_before = params["ms_before"]
@@ -250,7 +251,6 @@ def main_function(cls, recording, peaks, params):
                 cleaning_matching_params.pop(value)
         cleaning_matching_params["chunk_duration"] = "100ms"
         cleaning_matching_params["n_jobs"] = 1
-        cleaning_matching_params["verbose"] = False
         cleaning_matching_params["progress_bar"] = False
 
         cleaning_params = params["cleaning_kwargs"].copy()

src/spikeinterface/sortingcomponents/clustering/position_and_features.py

@@ -42,7 +42,7 @@ class PositionAndFeaturesClustering:
         "ms_before": 1.5,
         "ms_after": 1.5,
         "cleaning_method": "dip",
-        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "verbose": True, "progress_bar": True},
+        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "progress_bar": True},
     }
 
     @classmethod

src/spikeinterface/sortingcomponents/clustering/position_and_pca.py

@@ -38,7 +38,7 @@ class PositionAndPCAClustering:
         "ms_after": 2.5,
         "n_components_by_channel": 3,
         "n_components": 5,
-        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "verbose": True, "progress_bar": True},
+        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "progress_bar": True},
         "hdbscan_global_kwargs": {"min_cluster_size": 20, "allow_single_cluster": True, "core_dist_n_jobs": -1},
         "hdbscan_local_kwargs": {"min_cluster_size": 20, "allow_single_cluster": True, "core_dist_n_jobs": -1},
         "waveform_mode": "shared_memory",

src/spikeinterface/sortingcomponents/clustering/position_ptp_scaled.py

@@ -26,7 +26,7 @@ class PositionPTPScaledClustering:
         "ptps": None,
         "scales": (1, 1, 10),
         "peak_localization_kwargs": {"method": "center_of_mass"},
-        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "verbose": True, "progress_bar": True},
+        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "progress_bar": True},
         "hdbscan_kwargs": {
             "min_cluster_size": 20,
             "min_samples": 20,

src/spikeinterface/sortingcomponents/clustering/random_projections.py

@@ -56,6 +56,7 @@ class RandomProjectionClustering:
         "smoothing_kwargs": {"window_length_ms": 0.25},
         "tmp_folder": None,
         "job_kwargs": {},
+        "verbose": True,
     }
 
     @classmethod
@@ -65,7 +66,7 @@ def main_function(cls, recording, peaks, params):
         job_kwargs = fix_job_kwargs(params["job_kwargs"])
 
         d = params
-        verbose = job_kwargs.get("verbose", True)
+        verbose = d["verbose"]
 
         fs = recording.get_sampling_frequency()
         radius_um = params["radius_um"]
@@ -161,7 +162,6 @@ def main_function(cls, recording, peaks, params):
                 cleaning_matching_params[value] = None
         cleaning_matching_params["chunk_duration"] = "100ms"
         cleaning_matching_params["n_jobs"] = 1
-        cleaning_matching_params["verbose"] = False
         cleaning_matching_params["progress_bar"] = False
 
         cleaning_params = params["cleaning_kwargs"].copy()

src/spikeinterface/sortingcomponents/clustering/sliding_hdbscan.py

@@ -55,7 +55,7 @@ class SlidingHdbscanClustering:
         "auto_merge_quantile_limit": 0.8,
         "ratio_num_channel_intersect": 0.5,
         # ~ 'auto_trash_misalignment_shift' : 4,
-        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "verbose": True, "progress_bar": True},
+        "job_kwargs": {"n_jobs": -1, "chunk_memory": "10M", "progress_bar": True},
     }
 
     @classmethod

src/spikeinterface/sortingcomponents/tests/test_clustering.py

@@ -13,7 +13,7 @@
 
 
 def job_kwargs():
-    return dict(n_jobs=1, chunk_size=10000, progress_bar=True, verbose=True, mp_context="spawn")
+    return dict(n_jobs=1, chunk_size=10000, progress_bar=True, mp_context="spawn")
 
 
 @pytest.fixture(name="job_kwargs", scope="module")
@@ -78,6 +78,7 @@ def test_find_cluster_from_peaks(clustering_method, recording, peaks, peak_locat
     peak_locations = run_peak_locations(recording, peaks, job_kwargs)
     # method = "position_and_pca"
     # method = "circus"
-    method = "tdc_clustering"
+    # method = "tdc_clustering"
+    method = "random_projections"
 
     test_find_cluster_from_peaks(method, recording, peaks, peak_locations)

src/spikeinterface/sortingcomponents/tests/test_motion_estimation.py

@@ -47,7 +47,6 @@ def setup_module():
         detect_threshold=5,
         exclude_sweep_ms=0.1,
         chunk_size=10000,
-        verbose=1,
         progress_bar=True,
         pipeline_nodes=pipeline_nodes,
     )
@@ -156,12 +155,14 @@ def test_estimate_motion():
             bin_um=10.0,
             margin_um=5,
             output_extra_check=True,
-            progress_bar=False,
-            verbose=False,
         )
         kwargs.update(cases_kwargs)
 
-        motion, temporal_bins, spatial_bins, extra_check = estimate_motion(recording, peaks, peak_locations, **kwargs)
+        job_kwargs = dict(progress_bar=False)
+
+        motion, temporal_bins, spatial_bins, extra_check = estimate_motion(
+            recording, peaks, peak_locations, **kwargs, **job_kwargs
+        )
 
         motions[name] = motion
 

src/spikeinterface/sortingcomponents/tests/test_peak_detection.py

@@ -60,7 +60,7 @@ def sorting(dataset):
 
 
 def job_kwargs():
-    return dict(n_jobs=1, chunk_size=10000, progress_bar=True, verbose=True, mp_context="spawn")
+    return dict(n_jobs=1, chunk_size=10000, progress_bar=True, mp_context="spawn")
 
 
 @pytest.fixture(name="job_kwargs", scope="module")

src/spikeinterface/sortingcomponents/tests/test_peak_localization.py

@@ -10,8 +10,8 @@
 def test_localize_peaks():
     recording, _ = make_dataset()
 
-    # job_kwargs = dict(n_jobs=2, chunk_size=10000, verbose=False, progress_bar=True)
-    job_kwargs = dict(n_jobs=1, chunk_size=10000, verbose=False, progress_bar=True)
+    # job_kwargs = dict(n_jobs=2, chunk_size=10000, progress_bar=True)
+    job_kwargs = dict(n_jobs=1, chunk_size=10000, progress_bar=True)
 
     peaks = detect_peaks(
         recording, method="locally_exclusive", peak_sign="neg", detect_threshold=5, exclude_sweep_ms=0.1, **job_kwargs

src/spikeinterface/sortingcomponents/tests/test_peak_selection.py

@@ -23,13 +23,12 @@ def test_select_peaks():
         detect_threshold=5,
         exclude_sweep_ms=0.1,
         chunk_size=10000,
-        verbose=1,
         progress_bar=False,
         noise_levels=noise_levels,
     )
 
     peak_locations = localize_peaks(
-        recording, peaks, method="center_of_mass", n_jobs=2, chunk_size=10000, verbose=True, progress_bar=True
+        recording, peaks, method="center_of_mass", n_jobs=2, chunk_size=10000, progress_bar=True
     )
 
     n_peaks = 100