More deprecation updates for version 0.103.0

src/spikeinterface/benchmark/benchmark_plot_tools.py

@@ -374,55 +374,6 @@ def plot_agreement_matrix(study, ordered=True, case_keys=None, axs=None):
     return fig
 
 
-def plot_performances(study, mode="ordered", performance_names=("accuracy", "precision", "recall"), case_keys=None):
-    """
-    Plot performances over case for a study.
-
-    Parameters
-    ----------
-    study : BenchmarkStudy
-        A study object.
-    mode : "ordered" | "snr" | "swarm", default: "ordered"
-        Which plot mode to use:
-
-        * "ordered": plot performance metrics vs unit indices ordered by decreasing accuracy
-        * "snr": plot performance metrics vs snr
-        * "swarm": plot performance metrics as a swarm plot (see seaborn.swarmplot for details)
-    performance_names : list or tuple, default: ("accuracy", "precision", "recall")
-        Which performances to plot ("accuracy", "precision", "recall")
-    case_keys : list or None
-        A selection of cases to plot, if None, then all.
-
-    Returns
-    -------
-    fig : matplotlib.figure.Figure
-        The resulting figure containing the plots
-    """
-    if mode == "snr":
-        warnings.warn(
-            "Use study.plot_performances_vs_snr() instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        return plot_performances_vs_snr(study, case_keys=case_keys, performance_names=performance_names)
-    elif mode == "ordered":
-        warnings.warn(
-            "Use study.plot_performances_ordered() instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        return plot_performances_ordered(study, case_keys=case_keys, performance_names=performance_names)
-    elif mode == "swarm":
-        warnings.warn(
-            "Use study.plot_performances_swarm() instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        return plot_performances_swarm(study, case_keys=case_keys, performance_names=performance_names)
-    else:
-        raise ValueError("plot_performances() : wrong mode ")
-
-
 def plot_performances_vs_snr(
     study,
     case_keys=None,

src/spikeinterface/comparison/multicomparisons.py

@@ -190,63 +190,6 @@ def get_agreement_sorting(self, minimum_agreement_count=1, minimum_agreement_cou
         )
         return sorting
 
-    def save_to_folder(self, save_folder):
-        warnings.warn(
-            "save_to_folder() is deprecated. "
-            "You should save and load the multi sorting comparison object using pickle."
-            "\n>>> pickle.dump(mcmp, open('mcmp.pkl', 'wb'))\n>>> mcmp_loaded = pickle.load(open('mcmp.pkl', 'rb'))",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        for sorting in self.object_list:
-            assert sorting.check_serializability(
-                "json"
-            ), "MultiSortingComparison.save_to_folder() needs json serializable sortings"
-
-        save_folder = Path(save_folder)
-        save_folder.mkdir(parents=True, exist_ok=True)
-        filename = str(save_folder / "multicomparison.gpickle")
-        with open(filename, "wb") as f:
-            pickle.dump(self.graph, f, pickle.HIGHEST_PROTOCOL)
-        kwargs = {
-            "delta_time": float(self.delta_time),
-            "match_score": float(self.match_score),
-            "chance_score": float(self.chance_score),
-        }
-        with (save_folder / "kwargs.json").open("w") as f:
-            json.dump(kwargs, f)
-        sortings = {}
-        for name, sorting in zip(self.name_list, self.object_list):
-            sortings[name] = sorting.to_dict(recursive=True, relative_to=save_folder)
-        with (save_folder / "sortings.json").open("w") as f:
-            json.dump(sortings, f)
-
-    @staticmethod
-    def load_from_folder(folder_path):
-        warnings.warn(
-            "load_from_folder() is deprecated. "
-            "You should save and load the multi sorting comparison object using pickle."
-            "\n>>> pickle.dump(mcmp, open('mcmp.pkl', 'wb'))\n>>> mcmp_loaded = pickle.load(open('mcmp.pkl', 'rb'))",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        folder_path = Path(folder_path)
-        with (folder_path / "kwargs.json").open() as f:
-            kwargs = json.load(f)
-        with (folder_path / "sortings.json").open() as f:
-            dict_sortings = json.load(f)
-        name_list = list(dict_sortings.keys())
-        sorting_list = [load(v, base_folder=folder_path) for v in dict_sortings.values()]
-        mcmp = MultiSortingComparison(sorting_list=sorting_list, name_list=list(name_list), do_matching=False, **kwargs)
-        filename = str(folder_path / "multicomparison.gpickle")
-        with open(filename, "rb") as f:
-            mcmp.graph = pickle.load(f)
-        # do step 3 and 4
-        mcmp._clean_graph()
-        mcmp._do_agreement()
-        mcmp._populate_spiketrains()
-        return mcmp
-
 
 class AgreementSortingExtractor(BaseSorting):
     def __init__(

src/spikeinterface/comparison/tests/test_multisortingcomparison.py

@@ -76,10 +76,6 @@ def test_compare_multiple_sorters(setup_module):
     agreement_2 = msc.get_agreement_sorting(minimum_agreement_count=2, minimum_agreement_count_only=True)
     assert np.all([agreement_2.get_unit_property(u, "agreement_number")] == 2 for u in agreement_2.get_unit_ids())
 
-    msc.save_to_folder(multicomparison_folder)
-
-    msc = MultiSortingComparison.load_from_folder(multicomparison_folder)
-
 
 def test_compare_multi_segment():
     num_segments = 3

src/spikeinterface/core/loading.py

@@ -130,7 +130,7 @@ def load(
 
 def load_extractor(file_or_folder_or_dict, base_folder=None) -> "BaseExtractor":
     warnings.warn(
-        "load_extractor() is deprecated and will be removed in the future. Please use load() instead.",
+        "load_extractor() is deprecated and will be removed in version 0.104.0. Please use load() instead.",
         DeprecationWarning,
         stacklevel=2,
     )

src/spikeinterface/core/waveforms_extractor_backwards_compatibility.py

@@ -30,7 +30,7 @@
 # extract_waveforms() and WaveformExtractor() have been replaced by the `SortingAnalyzer` since version 0.101.0.
 # You should use `spikeinterface.create_sorting_analyzer()` instead.
 # `spikeinterface.extract_waveforms()` is now mocking the old behavior for backwards compatibility only,
-# and will be removed with version 0.103.0
+# and may potentially be removed in a future version.
 ####"""
 
 

src/spikeinterface/curation/auto_merge.py

@@ -635,8 +635,9 @@ def get_potential_auto_merge(
     done by Aurelien Wyngaard and Victor Llobet.
     https://github.com/BarbourLab/lussac/blob/v1.0.0/postprocessing/merge_units.py
     """
+    # deprecation moved to 0.105.0 for @zm711
     warnings.warn(
-        "get_potential_auto_merge() is deprecated. Use compute_merge_unit_groups() instead",
+        "get_potential_auto_merge() is deprecated and will be removed in version 0.105.0. Use compute_merge_unit_groups() instead",
         DeprecationWarning,
         stacklevel=2,
     )

src/spikeinterface/extractors/cbin_ibl.py

@@ -55,7 +55,7 @@ def __init__(
             raise ImportError(self.installation_mesg)
         if cbin_file is not None:
             warnings.warn(
-                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead",
+                "The `cbin_file` argument is deprecated and will be removed in version 0.104.0, please use `cbin_file_path` instead",
                 DeprecationWarning,
                 stacklevel=2,
             )

src/spikeinterface/extractors/neoextractors/openephys.py

@@ -80,8 +80,9 @@ def __init__(
         ignore_timestamps_errors: bool = None,
     ):
         if ignore_timestamps_errors is not None:
+            dep_msg = "OpenEphysLegacyRecordingExtractor: `ignore_timestamps_errors` is deprecated. It will be removed in version 0.104.0 and is currently ignored"
             warnings.warn(
-                "OpenEphysLegacyRecordingExtractor: ignore_timestamps_errors is deprecated and is ignored",
+                dep_msg,
                 DeprecationWarning,
                 stacklevel=2,
             )
@@ -161,8 +162,8 @@ def __init__(
 
         if load_sync_channel:
             warning_message = (
-                "OpenEphysBinaryRecordingExtractor: load_sync_channel is deprecated and will"
-                "be removed in version 0.104, use the stream_name or stream_id to load the sync stream if needed"
+                "OpenEphysBinaryRecordingExtractor: `load_sync_channel` is deprecated and will"
+                "be removed in version 0.104, use the `stream_name` or `stream_id` to load the sync stream if needed"
             )
             warnings.warn(warning_message, DeprecationWarning, stacklevel=2)
 

src/spikeinterface/extractors/nwbextractors.py

@@ -442,8 +442,6 @@ class NwbRecordingExtractor(BaseRecording, _BaseNWBExtractor):
     file_path : str, Path, or None
         Path to the NWB file or an s3 URL. Use this parameter to specify the file location
         if not using the `file` parameter.
-    electrical_series_name : str or None, default: None
-        Deprecated, use `electrical_series_path` instead.
     electrical_series_path : str or None, default: None
         The name of the ElectricalSeries object within the NWB file. This parameter is crucial
         when the NWB file contains multiple ElectricalSeries objects. It helps in identifying
@@ -511,7 +509,6 @@ class NwbRecordingExtractor(BaseRecording, _BaseNWBExtractor):
     def __init__(
         self,
         file_path: str | Path | None = None,  # provide either this or file
-        electrical_series_name: str | None = None,  # deprecated
         load_time_vector: bool = False,
         samples_for_rate_estimation: int = 1_000,
         stream_mode: Optional[Literal["fsspec", "remfile", "zarr"]] = None,
@@ -530,18 +527,6 @@ def __init__(
         if file_path is None and file is None:
             raise ValueError("Provide either file_path or file")
 
-        if electrical_series_name is not None:
-            warning_msg = (
-                "The `electrical_series_name` parameter is deprecated and will be removed in version 0.101.0.\n"
-                "Use `electrical_series_path` instead."
-            )
-            if electrical_series_path is None:
-                warning_msg += f"\nSetting `electrical_series_path` to 'acquisition/{electrical_series_name}'."
-                electrical_series_path = f"acquisition/{electrical_series_name}"
-            else:
-                warning_msg += f"\nIgnoring `electrical_series_name` and using the provided `electrical_series_path`."
-            warnings.warn(warning_msg, DeprecationWarning, stacklevel=2)
-
         self.file_path = file_path
         self.stream_mode = stream_mode
         self.stream_cache_path = stream_cache_path

src/spikeinterface/extractors/tests/test_nwbextractors.py

@@ -207,24 +207,6 @@ def test_nwb_extractor_channel_ids_retrieval(generate_nwbfile, use_pynwb):
         assert np.array_equal(extracted_channel_ids, expected_channel_ids)
 
 
-@pytest.mark.parametrize("use_pynwb", [True, False])
-def test_electrical_series_name_backcompatibility(generate_nwbfile, use_pynwb):
-    """
-    Test that the channel_ids are retrieved from the electrodes table ONLY from the corresponding
-    region of the electrical series
-    """
-    path_to_nwbfile, nwbfile_with_ecephys_content = generate_nwbfile
-    electrical_series_name_list = ["ElectricalSeries1", "ElectricalSeries2"]
-    for electrical_series_name in electrical_series_name_list:
-        with pytest.deprecated_call():
-            recording_extractor = NwbRecordingExtractor(
-                path_to_nwbfile,
-                electrical_series_name=electrical_series_name,
-                use_pynwb=use_pynwb,
-            )
-            assert recording_extractor.electrical_series_path == f"acquisition/{electrical_series_name}"
-
-
 @pytest.mark.parametrize("use_pynwb", [True, False])
 def test_nwb_extractor_property_retrieval(generate_nwbfile, use_pynwb):
     """

src/spikeinterface/sorters/launcher.py

@@ -233,7 +233,6 @@ def run_sorter_by_property(
     recording,
     grouping_property,
     folder,
-    mode_if_folder_exists=None,
     engine="loop",
     engine_kwargs=None,
     verbose=False,
@@ -260,10 +259,6 @@ def run_sorter_by_property(
         Property to split by before sorting
     folder : str | Path
         The working directory.
-    mode_if_folder_exists : bool or None, default: None
-        Must be None. This is deprecated.
-        If not None then a warning is raise.
-        Will be removed in next release.
     engine : "loop" | "joblib" | "dask" | "slurm", default: "loop"
         Which engine to use to run sorter.
     engine_kwargs : dict
@@ -293,12 +288,6 @@ def run_sorter_by_property(
                                             engine_kwargs={"n_jobs": 4})
 
     """
-    if mode_if_folder_exists is not None:
-        warnings.warn(
-            "run_sorter_by_property(): mode_if_folder_exists is not used anymore and will be removed in 0.102.0",
-            DeprecationWarning,
-            stacklevel=2,
-        )
 
     working_folder = Path(folder).absolute()