More cleanup of imports focused mostly on testing and utils around testing

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -3,10 +3,10 @@
 import subprocess
 import os
 from packaging import version
+import importlib.util
 
 import pytest
 
-from spikeinterface.core.testing import check_recordings_equal
 from spikeinterface import get_global_dataset_folder
 from spikeinterface.extractors import *
 
@@ -40,11 +40,10 @@ def has_plexon2_dependencies():
             return False
 
         # Check for 'zugbruecke' using pip
-        try:
-            import zugbruecke
-
+        zugbruecke_spec = importlib.util.find_spec("zugbruecke")
+        if zugbruecke_spec is not None:
             return True
-        except ImportError:
+        else:
             return False
     else:
         raise ValueError(f"Unsupported OS: {os_type}")

src/spikeinterface/generation/tests/test_drifing_generator.py

@@ -1,9 +1,4 @@
-import pytest
 import numpy as np
-from pathlib import Path
-import shutil
-
-import probeinterface
 
 from spikeinterface.generation import (
     make_one_displacement_vector,

src/spikeinterface/postprocessing/principal_component.py

@@ -43,6 +43,7 @@ class ComputePrincipalComponents(AnalyzerExtension):
         If True, waveforms are pre-whitened
     dtype : dtype, default: "float32"
         Dtype of the pc scores
+    {}
 
     Examples
     --------
@@ -522,8 +523,6 @@ def _transform_waveforms(self, spikes, waveforms, pca_model, progress_bar):
         # transform a waveforms buffer
         # used by _run() and project_new()
 
-        from sklearn.exceptions import NotFittedError
-
         mode = self.params["mode"]
 
         # prepare buffer
@@ -682,6 +681,7 @@ def _init_work_all_pc_extractor(recording, sorting, all_pcs_args, nbefore, nafte
     return worker_ctx
 
 
+ComputePrincipalComponents.__doc__.format(_shared_job_kwargs_doc)
 register_result_extension(ComputePrincipalComponents)
 compute_principal_components = ComputePrincipalComponents.function_factory()
 

src/spikeinterface/postprocessing/spike_amplitudes.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import numpy as np
-import warnings
 
 from spikeinterface.core.job_tools import fix_job_kwargs
 

src/spikeinterface/postprocessing/template_metrics.py

@@ -116,8 +116,6 @@ def _set_params(
         **other_kwargs,
     ):
 
-        import pandas as pd
-
         # TODO alessio can you check this : this used to be in the function but now we have ComputeTemplateMetrics.function_factory()
         if include_multi_channel_metrics or (
             metric_names is not None and any([m in get_multi_channel_template_metric_names() for m in metric_names])

src/spikeinterface/postprocessing/tests/test_correlograms.py

@@ -1,10 +1,11 @@
 import numpy as np
 
-try:
-    import numba
+import importlib.util
 
+numba_spec = importlib.util.find_spec("numba")
+if numba_spec is not None:
     HAVE_NUMBA = True
-except ModuleNotFoundError as err:
+else:
     HAVE_NUMBA = False
 
 from spikeinterface import NumpySorting, generate_sorting

src/spikeinterface/preprocessing/scale.py

@@ -1,8 +1,5 @@
 from __future__ import annotations
 
-import numpy as np
-
-from spikeinterface.core import BaseRecording
 from spikeinterface.preprocessing.basepreprocessor import BasePreprocessor
 
 

src/spikeinterface/preprocessing/tests/test_align_snippets.py

@@ -3,9 +3,6 @@
 but check only for BaseRecording general methods.
 """
 
-import pytest
-import numpy as np
-
 from spikeinterface.core import generate_snippets
 from spikeinterface.preprocessing.align_snippets import AlignSnippets
 

src/spikeinterface/preprocessing/tests/test_filter_gaussian.py

@@ -1,7 +1,6 @@
 import numpy as np
 import pytest
-from pathlib import Path
-from spikeinterface.core import load, set_global_tmp_folder
+from spikeinterface.core import load
 from spikeinterface.core.testing import check_recordings_equal
 from spikeinterface.core.generate import generate_recording
 from spikeinterface.preprocessing import gaussian_filter

src/spikeinterface/preprocessing/tests/test_highpass_spatial_filter.py

@@ -7,7 +7,6 @@
 import spikeinterface.preprocessing as spre
 import spikeinterface.extractors as se
 from spikeinterface.core import generate_recording
-import spikeinterface.widgets as sw
 import importlib.util
 
 ON_GITHUB = bool(os.getenv("GITHUB_ACTIONS"))
@@ -25,7 +24,7 @@
 
 
 @pytest.mark.skipif(
-    importlib.util.find_spec("neurodsp") is not None or importlib.util.find_spec("spikeglx") or ON_GITHUB,
+    importlib.util.find_spec("neurodsp") is None or importlib.util.find_spec("spikeglx") is None or ON_GITHUB,
     reason="Only local. Requires ibl-neuropixel install",
 )
 @pytest.mark.parametrize("lagc", [False, 1, 300])

src/spikeinterface/preprocessing/tests/test_normalize_scale.py

@@ -1,13 +1,9 @@
 import pytest
-from pathlib import Path
+import numpy as np
 
-from spikeinterface import set_global_tmp_folder
 from spikeinterface.core import generate_recording
-
 from spikeinterface.preprocessing import normalize_by_quantile, scale, center, zscore
 
-import numpy as np
-
 
 def test_normalize_by_quantile():
     rec = generate_recording()

src/spikeinterface/preprocessing/tests/test_rectify.py

@@ -1,13 +1,6 @@
-import pytest
-from pathlib import Path
-
-from spikeinterface import set_global_tmp_folder
 from spikeinterface.core import generate_recording
-
 from spikeinterface.preprocessing import rectify
 
-import numpy as np
-
 
 def test_rectify():
     rec = generate_recording()

src/spikeinterface/preprocessing/tests/test_unsigned_to_signed.py

@@ -1,14 +1,8 @@
-import pytest
-from pathlib import Path
-import shutil
-
-from spikeinterface import set_global_tmp_folder, NumpyRecording
-from spikeinterface.core import generate_recording
+import numpy as np
 
+from spikeinterface import NumpyRecording
 from spikeinterface.preprocessing import unsigned_to_signed
 
-import numpy as np
-
 
 def test_unsigned_to_signed():
     rng = np.random.RandomState(0)

src/spikeinterface/preprocessing/tests/test_whiten.py

@@ -1,17 +1,19 @@
+import importlib.util
+
 import pytest
 import numpy as np
 
 from spikeinterface.core import generate_recording
-from spikeinterface.core import BaseRecording, BaseRecordingSegment
 from spikeinterface.core.numpyextractors import NumpyRecording
 from spikeinterface.preprocessing import whiten, scale, compute_whitening_matrix
 from spikeinterface.preprocessing.whiten import compute_sklearn_covariance_matrix
 
-try:
+sklearn_spec = importlib.util.find_spec("sklearn")
+if sklearn_spec is not None:
     from sklearn import covariance as sklearn_covariance
 
     HAS_SKLEARN = True
-except ImportError:
+else:
     HAS_SKLEARN = False
 
 

src/spikeinterface/preprocessing/tests/test_zero_padding.py

@@ -1,8 +1,6 @@
 import pytest
-from pathlib import Path
 import numpy as np
 
-from spikeinterface import set_global_tmp_folder
 from spikeinterface.core import generate_recording
 from spikeinterface.core.numpyextractors import NumpyRecording
 

src/spikeinterface/sorters/external/tests/test_docker_containers.py

@@ -4,7 +4,6 @@
 
 from spikeinterface import generate_ground_truth_recording
 from spikeinterface.core.core_tools import is_editable_mode
-import spikeinterface.extractors as se
 import spikeinterface.sorters as ss
 
 

src/spikeinterface/sorters/external/tests/test_kilosort.py

@@ -1,6 +1,6 @@
 from spikeinterface.sorters import KilosortSorter
 
-import os, getpass
+import getpass
 
 if getpass.getuser() == "samuel":
     # kilosort_path = '/home/samuel/Documents/SpikeInterface/Kilosort1/'

src/spikeinterface/sorters/external/tests/test_kilosort2.py

@@ -1,6 +1,6 @@
 from spikeinterface.sorters import Kilosort2Sorter
 
-import os, getpass
+import getpass
 
 if getpass.getuser() == "samuel":
     kilosort2_path = "/home/samuel/Documents/SpikeInterface/Kilosort2"

src/spikeinterface/sorters/external/tests/test_kilosort3.py

@@ -1,6 +1,6 @@
 from spikeinterface.sorters import Kilosort3Sorter
 
-import os, getpass
+import getpass
 
 if getpass.getuser() == "samuel":
     kilosort3_path = "/home/samuel/Documents/SpikeInterface/Kilosort3"

src/spikeinterface/sorters/external/tests/test_kilosort4.py

@@ -1,6 +1,5 @@
 import unittest
 import pytest
-from pathlib import Path
 
 from spikeinterface import load, generate_ground_truth_recording
 from spikeinterface.sorters import Kilosort4Sorter, run_sorter

src/spikeinterface/sorters/external/waveclus.py

@@ -6,6 +6,7 @@
 import shutil
 import sys
 import json
+import importlib.util
 
 
 from spikeinterface.sorters.basesorter import BaseSorter
@@ -14,15 +15,15 @@
 from spikeinterface.core import write_to_h5_dataset_format
 from spikeinterface.extractors import WaveClusSortingExtractor
 from spikeinterface.core.channelslice import ChannelSliceRecording
-from spikeinterface.preprocessing import ScaleRecording
 
 PathType = Union[str, Path]
 
-try:
+h5py_spec = importlib.util.find_spec("h5py")
+if h5py_spec is not None:
     import h5py
 
     HAVE_H5PY = True
-except ImportError:
+else:
     HAVE_H5PY = False
 
 

src/spikeinterface/sorters/runsorter.py

@@ -27,7 +27,6 @@
     has_singularity,
     has_spython,
     has_docker_nvidia_installed,
-    get_nvidia_docker_dependecies,
 )
 from .container_tools import (
     find_recording_folders,

src/spikeinterface/sorters/tests/test_runsorter_dependency_checks.py

@@ -1,14 +1,9 @@
-import os
 import pytest
-from pathlib import Path
-import shutil
 import platform
 from spikeinterface import generate_ground_truth_recording
 from spikeinterface.sorters.utils import has_spython, has_docker_python, has_docker, has_singularity
 from spikeinterface.sorters import run_sorter
-import subprocess
 import sys
-import copy
 
 
 def _monkeypatch_return_false():

src/spikeinterface/sorters/utils/__init__.py

@@ -10,5 +10,5 @@
     has_singularity,
     has_spython,
     has_docker_nvidia_installed,
-    get_nvidia_docker_dependecies,
+    get_nvidia_docker_dependencies,
 )

src/spikeinterface/sorters/utils/misc.py

@@ -1,11 +1,8 @@
 from __future__ import annotations
 
-from pathlib import Path
 import subprocess  # TODO: decide best format for this
 from subprocess import check_output, CalledProcessError
-from typing import List, Union
-
-import numpy as np
+import importlib.util
 
 
 class SpikeSortingError(RuntimeError):
@@ -66,13 +63,13 @@ def has_nvidia():
     """
     Checks if the machine has nvidia capability.
     """
-
-    try:
+    cuda_spec = importlib.util.find_spec("cuda")
+    if cuda_spec is not None:
         from cuda import cuda
-    except ModuleNotFoundError as err:
+    else:
         raise Exception(
             "This sorter requires cuda, but the package 'cuda-python' is not installed. You can install it with:\npip install cuda-python"
-        ) from err
+        )
 
     try:
         (cu_result_init,) = cuda.cuInit(0)
@@ -118,14 +115,14 @@ def has_docker_nvidia_installed():
     Whether at least one of the dependencies listed in
     `get_nvidia_docker_dependecies()` is installed.
     """
-    all_dependencies = get_nvidia_docker_dependecies()
+    all_dependencies = get_nvidia_docker_dependencies()
     has_dep = []
     for dep in all_dependencies:
         has_dep.append(_run_subprocess_silently(f"{dep} --version").returncode == 0)
     return any(has_dep)
 
 
-def get_nvidia_docker_dependecies():
+def get_nvidia_docker_dependencies():
     """
     See `has_docker_nvidia_installed()`
     """
@@ -137,18 +134,16 @@ def get_nvidia_docker_dependecies():
 
 
 def has_docker_python():
-    try:
-        import docker
-
+    docker_spec = importlib.util.find_spec("docker")
+    if docker_spec is not None:
         return True
-    except ImportError:
+    else:
         return False
 
 
 def has_spython():
-    try:
-        import spython
-
+    spython_spec = importlib.util.find_spec("spython")
+    if spython_spec is not None:
         return True
-    except ImportError:
+    else:
         return False