Set verbose = False as default on all the interfaces (#1153)

Co-authored-by: Paul Adkisson <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -8,6 +8,8 @@
 * Added `metadata` and `conversion_options` as arguments to `NWBConverter.temporally_align_data_interfaces` [PR #1162](https://github.com/catalystneuro/neuroconv/pull/1162)
 
 ## Improvements
+* Interfaces and converters now have `verbose=False` by default [PR #1153](https://github.com/catalystneuro/neuroconv/pull/1153)
+
 
 # v0.6.7 (January 20, 2024)
 
@@ -29,8 +31,9 @@
 
 # v0.6.6 (December 20, 2024)
 
-## Deprecations
+## Deprecations and Changes
 * Removed use of `jsonschema.RefResolver` as it will be deprecated from the jsonschema library [PR #1133](https://github.com/catalystneuro/neuroconv/pull/1133)
+* Completely removed compression settings from most places[PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126)
 * Completely removed compression settings from most places [PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126)
 * Soft deprecation for `file_path` as an argument of  `SpikeGLXNIDQInterface` and `SpikeGLXRecordingInterface` [PR #1155](https://github.com/catalystneuro/neuroconv/pull/1155)
 * `starting_time` in RecordingInterfaces has given a soft deprecation in favor of time alignment methods [PR #1158](https://github.com/catalystneuro/neuroconv/pull/1158)

docs/conversion_examples_gallery/recording/openephys.rst

@@ -30,4 +30,3 @@ Convert OpenEphys data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys
     >>> # Choose a path for saving the nwb file and run the conversion
     >>> nwbfile_path = f"{path_to_save_nwbfile}"  # This should be something like: "./saved_file.nwb"
     >>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
-    NWB file saved at ...

src/neuroconv/datainterfaces/behavior/audio/audiointerface.py

@@ -170,8 +170,6 @@ def add_to_nwbfile(
         stub_frames: int = 1000,
         write_as: Literal["stimulus", "acquisition"] = "stimulus",
         iterator_options: Optional[dict] = None,
-        overwrite: bool = False,
-        verbose: bool = True,
     ):
         """
         Parameters
@@ -186,8 +184,6 @@ def add_to_nwbfile(
             "stimulus" or as "acquisition".
         iterator_options : dict, optional
             Dictionary of options for the SliceableDataChunkIterator.
-        overwrite : bool, default: False
-        verbose : bool, default: True
 
         Returns
         -------

src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py

@@ -31,7 +31,7 @@ def __init__(
         file_path: FilePath,
         config_file_path: Optional[FilePath] = None,
         subject_name: str = "ind1",
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """
         Interface for writing DLC's output files to nwb using dlc2nwb.

src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py

@@ -159,7 +159,7 @@ def __init__(
         file_path: FilePath,
         radius: Optional[float] = None,
         configuration_file_path: Optional[FilePath] = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """
         Interface for writing FicTrac files to nwb.
@@ -173,7 +173,7 @@ def __init__(
             and the units are set to meters. If not provided the units are set to radians.
         configuration_file_path : FilePath, optional
             Path to the .txt file with the configuration metadata. Usually called config.txt
-        verbose : bool, default: True
+        verbose : bool, default: False
             controls verbosity. ``True`` by default.
         """
         self.file_path = Path(file_path)

src/neuroconv/datainterfaces/behavior/lightningpose/lightningposeconverter.py

@@ -34,7 +34,7 @@ def __init__(
         labeled_video_file_path: Optional[FilePath] = None,
         image_series_original_video_name: Optional[str] = None,
         image_series_labeled_video_name: Optional[str] = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """
         The converter for Lightning Pose format to convert the pose estimation data
@@ -52,7 +52,7 @@ def __init__(
             The name of the ImageSeries to add for the original video.
         image_series_labeled_video_name: string, optional
             The name of the ImageSeries to add for the labeled video.
-        verbose : bool, default: True
+        verbose : bool, default: False
             controls verbosity. ``True`` by default.
         """
         self.verbose = verbose

src/neuroconv/datainterfaces/behavior/lightningpose/lightningposedatainterface.py

@@ -64,7 +64,7 @@ def __init__(
         file_path: FilePath,
         original_video_file_path: FilePath,
         labeled_video_file_path: Optional[FilePath] = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """
         Interface for writing pose estimation data from the Lightning Pose algorithm.
@@ -77,7 +77,7 @@ def __init__(
             Path to the original video file (.mp4).
         labeled_video_file_path : a string or a path, optional
             Path to the labeled video file (.mp4).
-        verbose : bool, default: True
+        verbose : bool, default: False
             controls verbosity. ``True`` by default.
         """
         # This import is to assure that the ndx_pose is in the global namespace when an pynwb.io object is created

src/neuroconv/datainterfaces/behavior/medpc/medpcdatainterface.py

@@ -49,7 +49,7 @@ def __init__(
         start_variable: str,
         metadata_medpc_name_to_info_dict: dict,
         aligned_timestamp_names: Optional[list[str]] = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """
         Initialize MedpcInterface.

src/neuroconv/datainterfaces/behavior/neuralynx/neuralynx_nvt_interface.py

@@ -22,15 +22,15 @@ class NeuralynxNvtInterface(BaseTemporalAlignmentInterface):
     info = "Interface for writing Neuralynx position tracking .nvt files to NWB."
 
     @validate_call
-    def __init__(self, file_path: FilePath, verbose: bool = True):
+    def __init__(self, file_path: FilePath, verbose: bool = False):
         """
         Interface for writing Neuralynx .nvt files to nwb.
 
         Parameters
         ----------
         file_path : FilePath
             Path to the .nvt file
-        verbose : bool, default: True
+        verbose : bool, default: Falsee
             controls verbosity.
         """
 

src/neuroconv/datainterfaces/behavior/sleap/sleapdatainterface.py

@@ -32,7 +32,7 @@ def __init__(
         self,
         file_path: FilePath,
         video_file_path: Optional[FilePath] = None,
-        verbose: bool = True,
+        verbose: bool = False,
         frames_per_second: Optional[float] = None,
     ):
         """
@@ -42,7 +42,7 @@ def __init__(
         ----------
         file_path : FilePath
             Path to the .slp file (the output of sleap)
-        verbose : bool, default: True
+        verbose : bool, default: Falsee
             controls verbosity. ``True`` by default.
         video_file_path : FilePath, optional
             The file path of the video for extracting timestamps.

src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py

@@ -26,7 +26,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict:
         extractor_kwargs["stream_id"] = self.stream_id
         return extractor_kwargs
 
-    def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: str = "ElectricalSeries"):
         """
         Load and prepare data for AlphaOmega.
 
@@ -36,7 +36,7 @@ def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str
             Path to the folder of .mpx files.
         verbose: boolean
             Allows verbose.
-            Default is True.
+            Default is False.
         es_key: str, default: "ElectricalSeries"
         """
         super().__init__(folder_path=folder_path, verbose=verbose, es_key=es_key)

src/neuroconv/datainterfaces/ecephys/axona/axonadatainterface.py

@@ -36,7 +36,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict:
 
         return extractor_kwargs
 
-    def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"):
         """
 
         Parameters

src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py

@@ -15,7 +15,7 @@ class BaseLFPExtractorInterface(BaseRecordingExtractorInterface):
         "LF",
     )
 
-    def __init__(self, verbose: bool = True, es_key: str = "ElectricalSeriesLFP", **source_data):
+    def __init__(self, verbose: bool = False, es_key: str = "ElectricalSeriesLFP", **source_data):
         super().__init__(verbose=verbose, es_key=es_key, **source_data)
 
     def add_to_nwbfile(

src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py

@@ -20,11 +20,11 @@ class BaseRecordingExtractorInterface(BaseExtractorInterface):
 
     ExtractorModuleName = "spikeinterface.extractors"
 
-    def __init__(self, verbose: bool = True, es_key: str = "ElectricalSeries", **source_data):
+    def __init__(self, verbose: bool = False, es_key: str = "ElectricalSeries", **source_data):
         """
         Parameters
         ----------
-        verbose : bool, default: True
+        verbose : bool, default: False
             If True, will print out additional information.
         es_key : str, default: "ElectricalSeries"
             The key of this ElectricalSeries in the metadata dictionary.

src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py

@@ -18,7 +18,8 @@ class BaseSortingExtractorInterface(BaseExtractorInterface):
 
     ExtractorModuleName = "spikeinterface.extractors"
 
-    def __init__(self, verbose: bool = True, **source_data):
+    def __init__(self, verbose: bool = False, **source_data):
+
         super().__init__(**source_data)
         self.sorting_extractor = self.get_extractor()(**source_data)
         self.verbose = verbose

src/neuroconv/datainterfaces/ecephys/biocam/biocamdatainterface.py

@@ -20,15 +20,15 @@ def get_source_schema(cls) -> dict:
         schema["properties"]["file_path"]["description"] = "Path to the .bwr file."
         return schema
 
-    def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"):
         """
         Load and prepare data for Biocam.
 
         Parameters
         ----------
         file_path : string or Path
             Path to the .bwr file.
-        verbose : bool, default: True
+        verbose : bool, default: False
             Allows verbose.
         es_key: str, default: "ElectricalSeries"
         """

src/neuroconv/datainterfaces/ecephys/blackrock/blackrockdatainterface.py

@@ -35,7 +35,7 @@ def __init__(
         self,
         file_path: FilePath,
         nsx_override: Optional[FilePath] = None,
-        verbose: bool = True,
+        verbose: bool = False,
         es_key: str = "ElectricalSeries",
     ):
         """
@@ -90,7 +90,7 @@ def get_source_schema(cls) -> dict:
         metadata_schema["properties"]["file_path"].update(description="Path to Blackrock .nev file.")
         return metadata_schema
 
-    def __init__(self, file_path: FilePath, sampling_frequency: Optional[float] = None, verbose: bool = True):
+    def __init__(self, file_path: FilePath, sampling_frequency: Optional[float] = None, verbose: bool = False):
         """
         Parameters
         ----------
@@ -100,7 +100,7 @@ def __init__(self, file_path: FilePath, sampling_frequency: Optional[float] = No
             The sampling frequency for the sorting extractor. When the signal data is available (.ncs) those files will be
             used to extract the frequency automatically. Otherwise, the sampling frequency needs to be specified for
             this extractor to be initialized.
-        verbose : bool, default: True
+        verbose : bool, default: False
             Enables verbosity
         """
         super().__init__(file_path=file_path, sampling_frequency=sampling_frequency, verbose=verbose)

src/neuroconv/datainterfaces/ecephys/cellexplorer/cellexplorerdatainterface.py

@@ -254,7 +254,7 @@ class CellExplorerRecordingInterface(BaseRecordingExtractorInterface):
         The folder where the session data is located. It should contain a
         `{folder.name}.session.mat` file and the binary files `{folder.name}.dat`
         or `{folder.name}.lfp` for the LFP interface.
-    verbose : bool, default: True
+    verbose : bool, default: Falsee
             Whether to output verbose text.
     es_key : str, default: "ElectricalSeries" and "ElectricalSeriesLFP" for the LFP interface
 
@@ -294,7 +294,7 @@ def get_source_schema(cls) -> dict:
         source_schema["properties"]["folder_path"]["description"] = "Folder containing the .session.mat file"
         return source_schema
 
-    def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: str = "ElectricalSeries"):
         """
 
         Parameters
@@ -382,7 +382,7 @@ class CellExplorerLFPInterface(CellExplorerRecordingInterface):
     sampling_frequency_key = "srLfp"
     binary_file_extension = "lfp"
 
-    def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str = "ElectricalSeriesLFP"):
+    def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: str = "ElectricalSeriesLFP"):
         super().__init__(folder_path, verbose, es_key)
 
     def add_to_nwbfile(
@@ -425,7 +425,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict:
 
         return extractor_kwargs
 
-    def __init__(self, file_path: FilePath, verbose: bool = True):
+    def __init__(self, file_path: FilePath, verbose: bool = False):
         """
         Initialize read of Cell Explorer file.
 

src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py

@@ -37,7 +37,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict:
     def __init__(
         self,
         file_path: FilePath,
-        verbose: bool = True,
+        verbose: bool = False,
         es_key: str = "ElectricalSeries",
         channels_to_skip: Optional[list] = None,
     ):
@@ -50,7 +50,7 @@ def __init__(
         ----------
         file_path : str or Path
             Path to the edf file
-        verbose : bool, default: True
+        verbose : bool, default: Falseeeeee
             Allows verbose.
         es_key : str, default: "ElectricalSeries"
             Key for the ElectricalSeries metadata

src/neuroconv/datainterfaces/ecephys/intan/intandatainterface.py

@@ -35,7 +35,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict:
     def __init__(
         self,
         file_path: FilePath,
-        verbose: bool = True,
+        verbose: bool = False,
         es_key: str = "ElectricalSeries",
         ignore_integrity_checks: bool = False,
     ):
@@ -47,7 +47,7 @@ def __init__(
         file_path : FilePathType
             Path to either a rhd or a rhs file
 
-        verbose : bool, default: True
+        verbose : bool, default: False
             Verbose
         es_key : str, default: "ElectricalSeries"
         ignore_integrity_checks, bool, default: False.

src/neuroconv/datainterfaces/ecephys/kilosort/kilosortdatainterface.py

@@ -22,7 +22,7 @@ def __init__(
         self,
         folder_path: DirectoryPath,
         keep_good_only: bool = False,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """
         Load and prepare sorting data for kilosort

src/neuroconv/datainterfaces/ecephys/maxwell/maxonedatainterface.py

@@ -47,7 +47,7 @@ def __init__(
         file_path: FilePath,
         hdf5_plugin_path: Optional[DirectoryPath] = None,
         download_plugin: bool = True,
-        verbose: bool = True,
+        verbose: bool = False,
         es_key: str = "ElectricalSeries",
     ) -> None:
         """

src/neuroconv/datainterfaces/ecephys/mcsraw/mcsrawdatainterface.py

@@ -20,7 +20,7 @@ def get_source_schema(cls) -> dict:
         source_schema["properties"]["file_path"]["description"] = "Path to the .raw file."
         return source_schema
 
-    def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"):
         """
         Load and prepare data for MCSRaw.
 

src/neuroconv/datainterfaces/ecephys/mearec/mearecdatainterface.py

@@ -23,15 +23,15 @@ def get_source_schema(cls) -> dict:
         source_schema["properties"]["file_path"]["description"] = "Path to the MEArec .h5 file."
         return source_schema
 
-    def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"):
         """
         Load and prepare data for MEArec.
 
         Parameters
         ----------
         folder_path : str or Path
             Path to the MEArec .h5 file.
-        verbose : bool, default: True
+        verbose : bool, default: Falsee
             Allows verbose.
         es_key : str, default: "ElectricalSeries"
         """

src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py

@@ -116,7 +116,7 @@ def __init__(
         self,
         folder_path: DirectoryPath,
         sampling_frequency: Optional[float] = None,
-        verbose: bool = True,
+        verbose: bool = False,
         stream_id: Optional[str] = None,
     ):
         """_summary_
@@ -127,7 +127,7 @@ def __init__(
             The path to the folder/directory containing the data files for the session (nse, ntt, nse, nev)
         sampling_frequency : float, optional
             If a specific sampling_frequency is desired it can be set with this argument.
-        verbose : bool, default: True
+        verbose : bool, default: False
             Enables verbosity
         stream_id: str, optional
             Used by Spikeinterface and neo to calculate the t_start, if not provided and the stream is unique