Merge pull request #3076 from chrishalcrow/update-extractors-docstrings

Docstrings extractors update, fix PR01 and PR02 #3016

Author: alejoe91

doc/api.rst

@@ -117,7 +117,7 @@ Non-NEO-based
     .. autofunction:: read_bids
     .. autofunction:: read_cbin_ibl
     .. autofunction:: read_combinato
-    .. autofunction:: read_ibl_streaming_recording
+    .. autofunction:: read_ibl_recording
     .. autofunction:: read_hdsort
     .. autofunction:: read_herdingspikes
     .. autofunction:: read_kilosort

doc/modules/extractors.rst

@@ -125,7 +125,7 @@ For raw recording formats, we currently support:
 * **Biocam HDF5** :py:func:`~spikeinterface.extractors.read_biocam()`
 * **CED** :py:func:`~spikeinterface.extractors.read_ced()`
 * **EDF** :py:func:`~spikeinterface.extractors.read_edf()`
-* **IBL streaming** :py:func:`~spikeinterface.extractors.read_ibl_streaming_recording()`
+* **IBL streaming** :py:func:`~spikeinterface.extractors.read_ibl_recording()`
 * **Intan** :py:func:`~spikeinterface.extractors.read_intan()`
 * **MaxWell** :py:func:`~spikeinterface.extractors.read_maxwell()`
 * **MCS H5** :py:func:`~spikeinterface.extractors.read_mcsh5()`

src/spikeinterface/extractors/cbin_ibl.py

@@ -27,9 +27,11 @@ class CompressedBinaryIblExtractor(BaseRecording):
     load_sync_channel : bool, default: False
         Load or not the last channel (sync).
         If not then the probe is loaded.
-    stream_name : str, default: "ap".
+    stream_name : {"ap", "lp"}, default: "ap".
         Whether to load AP or LFP band, one
         of "ap" or "lp".
+    cbin_file : str or None, default None
+        The cbin file of the recording. If None, searches in `folder_path` for file.
 
     Returns
     -------

src/spikeinterface/extractors/herdingspikesextractors.py

@@ -20,7 +20,7 @@ class HerdingspikesSortingExtractor(BaseSorting):
 
     Parameters
     ----------
-    folder_path : str or Path
+    file_path : str or Path
         Path to the ALF folder.
     load_unit_info : bool, default: True
         Whether to load the unit info from the file.

src/spikeinterface/extractors/iblextractors.py

@@ -41,7 +41,7 @@ class IblRecordingExtractor(BaseRecording):
     stream_name : str
         The name of the stream to load for the session.
         These can be retrieved from calling `StreamingIblExtractor.get_stream_names(session="<your session ID>")`.
-    load_sync_channels : bool, default: false
+    load_sync_channel : bool, default: false
         Load or not the last channel (sync).
         If not then the probe is loaded.
     cache_folder : str or None, default: None

src/spikeinterface/extractors/neoextractors/alphaomega.py

@@ -50,6 +50,11 @@ def map_to_neo_kwargs(cls, folder_path, lsx_files=None):
 class AlphaOmegaEventExtractor(NeoBaseEventExtractor):
     """
     Class for reading events from AlphaOmega MPX file format
+
+    Parameters
+    ----------
+    folder_path : str or Path-like
+        The folder path to the AlphaOmega events.
     """
 
     mode = "folder"

src/spikeinterface/extractors/neoextractors/biocam.py

@@ -42,7 +42,6 @@ def __init__(
         electrode_width=None,
         stream_id=None,
         stream_name=None,
-        block_index=None,
         all_annotations=False,
     ):
         neo_kwargs = self.map_to_neo_kwargs(file_path)

src/spikeinterface/extractors/neoextractors/blackrock.py

@@ -26,6 +26,9 @@ class BlackrockRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        If False, use default IDs inherited from Neo. If True, use channel names as IDs.
+
     """
 
     mode = "file"
@@ -37,7 +40,6 @@ def __init__(
         file_path,
         stream_id=None,
         stream_name=None,
-        block_index=None,
         all_annotations=False,
         use_names_as_ids=False,
     ):

src/spikeinterface/extractors/neoextractors/ced.py

@@ -23,8 +23,6 @@ class CedRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream id you want to load.
     stream_name : str, default: None
         If there are several streams, specify the stream name you want to load.
-    block_index : int, default: None
-        If there are several blocks, specify the block index you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
     """

src/spikeinterface/extractors/neoextractors/intan.py

@@ -27,6 +27,10 @@ class IntanRecordingExtractor(NeoBaseRecordingExtractor):
         If True, data that violates integrity assumptions will be loaded. At the moment the only integrity
         check we perform is that timestamps are continuous. Setting this to True will ignore this check and set
         the attribute `discontinuous_timestamps` to True in the underlying neo object.
+    use_names_as_ids : bool, default: False
+        If False, use default IDs inherited from Neo. If True, use channel names as IDs.
+
+
     """
 
     mode = "file"