Revert "removed redundant module docstrings"

This reverts commit 9b33075.

src/roiextractors/__init__.py

@@ -1,3 +1,5 @@
+"""Python-based module for extracting from, converting between, and handling recorded and optical imaging data from several file formats."""
+
 from importlib.metadata import version
 
 __version__ = version("roiextractors")

src/roiextractors/example_datasets/__init__.py

@@ -1 +1,14 @@
+"""Toy example ImagingExtractor and SegmentationExtractor for testing.
+
+Modules
+-------
+toy_example
+    Create a toy example of an ImagingExtractor and a SegmentationExtractor.
+
+Functions
+---------
+toy_example
+    Create a toy example of an ImagingExtractor and a SegmentationExtractor.
+"""
+
 from .toy_example import toy_example

src/roiextractors/example_datasets/toy_example.py

@@ -1,4 +1,10 @@
-"""Toy example ImagingExtractor and SegmentationExtractor for testing."""
+"""Toy example ImagingExtractor and SegmentationExtractor for testing.
+
+Functions
+---------
+toy_example
+    Create a toy example of an ImagingExtractor and a SegmentationExtractor.
+"""
 
 import numpy as np
 

src/roiextractors/extraction_tools.py

@@ -1,4 +1,10 @@
-"""Various tools for extraction of ROIs from imaging data."""
+"""Various tools for extraction of ROIs from imaging data.
+
+Classes
+-------
+VideoStructure
+    A data class for specifying the structure of a video.
+"""
 
 import sys
 import importlib.util

src/roiextractors/extractors/__init__.py

@@ -0,0 +1 @@
+"""All specialized ImagingExtractors and SegmentationExtractors are defined here."""

src/roiextractors/extractors/caiman/__init__.py

@@ -1 +1,14 @@
+"""A Segmentation Extractor for Caiman.
+
+Modules
+-------
+caimansegmentationextractor
+    A Segmentation Extractor for Caiman.
+
+Classes
+-------
+CaimanSegmentationExtractor
+    A class for extracting segmentation from Caiman output.
+"""
+
 from .caimansegmentationextractor import CaimanSegmentationExtractor

src/roiextractors/extractors/caiman/caimansegmentationextractor.py

@@ -1,3 +1,11 @@
+"""A SegmentationExtractor for CaImAn.
+
+Classes
+-------
+CaimanSegmentationExtractor
+    A class for extracting segmentation from CaImAn output.
+"""
+
 from pathlib import Path
 
 try:

src/roiextractors/extractors/hdf5imagingextractor/__init__.py

@@ -1 +1,15 @@
+"""An imaging extractor for HDF5.
+
+Modules
+-------
+hdf5imagingextractor
+    An imaging extractor for HDF5.
+
+
+Classes
+-------
+Hdf5ImagingExtractor
+    An imaging extractor for HDF5.
+"""
+
 from .hdf5imagingextractor import Hdf5ImagingExtractor

src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py

@@ -1,3 +1,11 @@
+"""An imaging extractor for HDF5.
+
+Classes
+-------
+Hdf5ImagingExtractor
+    An imaging extractor for HDF5.
+"""
+
 from pathlib import Path
 from typing import Optional, Tuple
 from warnings import warn

src/roiextractors/extractors/inscopixextractors/__init__.py

@@ -1 +1,3 @@
+"""Defines extactors for Inscopix data."""
+
 from .inscopiximagingextractor import InscopixImagingExtractor

src/roiextractors/extractors/inscopixextractors/inscopiximagingextractor.py

@@ -1,3 +1,5 @@
+"""Inscopix Imaging Extractor."""
+
 import warnings
 from typing import Optional, Tuple
 

src/roiextractors/extractors/memmapextractors/__init__.py

@@ -1,4 +1,19 @@
-"""Defines memmap-based ImagingExtractors. Currently, only numpy.memmap is supported."""
+"""Defines memmap-based ImagingExtractors. Currently, only numpy.memmap is supported.
+
+Modules
+-------
+memmapextractors
+    The base class for memmapable imaging extractors.
+numpymemampextractor
+    The class for reading optical imaging data stored in a binary format with numpy.memmap.
+
+Classes
+-------
+MemmapImagingExtractor
+    The base class for memmapable imaging extractors.
+NumpyMemmapImagingExtractor
+    The class for reading optical imaging data stored in a binary format with numpy.memmap.
+"""
 
 from .memmapextractors import MemmapImagingExtractor
 from .numpymemampextractor import NumpyMemmapImagingExtractor

src/roiextractors/extractors/memmapextractors/memmapextractors.py

@@ -1,3 +1,11 @@
+"""Defines the base class for memmapable imaging extractors.
+
+Classes
+-------
+MemmapImagingExtractor
+    The base class for memmapable imaging extractors.
+"""
+
 from pathlib import Path
 
 import numpy as np

src/roiextractors/extractors/memmapextractors/numpymemampextractor.py

@@ -1,3 +1,11 @@
+"""NumpyMemmapImagingExtractor class.
+
+Classes
+-------
+NumpyMemmapImagingExtractor
+    The class for reading optical imaging data stored in a binary format with numpy.memmap.
+"""
+
 import os
 from pathlib import Path
 

src/roiextractors/extractors/miniscopeimagingextractor/__init__.py

@@ -1 +1,14 @@
+"""An ImagingExtractor for the Miniscope video (.avi) format.
+
+Modules
+-------
+miniscopeimagingextractor
+    An ImagingExtractor for the Miniscope video (.avi) format.
+
+Classes
+-------
+MiniscopeImagingExtractor
+    An ImagingExtractor for the Miniscope video (.avi) format.
+"""
+
 from .miniscopeimagingextractor import MiniscopeImagingExtractor

src/roiextractors/extractors/miniscopeimagingextractor/miniscopeimagingextractor.py

@@ -1,3 +1,11 @@
+"""MiniscopeImagingExtractor class.
+
+Classes
+-------
+MiniscopeImagingExtractor
+    An ImagingExtractor for the Miniscope video (.avi) format.
+"""
+
 import json
 import re
 from pathlib import Path

src/roiextractors/extractors/numpyextractors/__init__.py

@@ -1 +1,16 @@
+"""Imaging and Segmenation Extractors for .npy files.
+
+Modules
+-------
+numpyextractors
+    Imaging and Segmenation Extractors for .npy files.
+
+Classes
+-------
+NumpyImagingExtractor
+    An ImagingExtractor specified by timeseries .npy file, sampling frequency, and channel names.
+NumpySegmentationExtractor
+    A Segmentation extractor specified by image masks and traces .npy files.
+"""
+
 from .numpyextractors import NumpyImagingExtractor, NumpySegmentationExtractor

src/roiextractors/extractors/numpyextractors/numpyextractors.py

@@ -1,3 +1,13 @@
+"""Imaging and Segmenation Extractors for .npy files.
+
+Classes
+-------
+NumpyImagingExtractor
+    An ImagingExtractor specified by timeseries .npy file, sampling frequency, and channel names.
+NumpySegmentationExtractor
+    A Segmentation extractor specified by image masks and traces .npy files.
+"""
+
 from pathlib import Path
 from typing import Optional, Tuple
 

src/roiextractors/extractors/nwbextractors/__init__.py

@@ -1 +1,16 @@
+"""Imaging and segmentation extractors for NWB files.
+
+Modules
+-------
+nwbextractors
+    Imaging and segmentation extractors for NWB files.
+
+Classes
+-------
+NwbImagingExtractor
+    Extracts imaging data from NWB files.
+NwbSegmentationExtractor
+    Extracts segmentation data from NWB files.
+"""
+
 from .nwbextractors import NwbImagingExtractor, NwbSegmentationExtractor

src/roiextractors/extractors/nwbextractors/nwbextractors.py

@@ -1,3 +1,13 @@
+"""Imaging and segmentation extractors for NWB files.
+
+Classes
+-------
+NwbImagingExtractor
+    Extracts imaging data from NWB files.
+NwbSegmentationExtractor
+    Extracts segmentation data from NWB files.
+"""
+
 from pathlib import Path
 from typing import Union, Optional, Iterable, Tuple
 

src/roiextractors/extractors/sbximagingextractor/__init__.py

@@ -1 +1,14 @@
+"""A segmentation extractor for Scanbox imaging data.
+
+Modules
+-------
+sbximagingextractor
+    A segmentation extractor for Scanbox imaging data.
+
+Classes
+-------
+SbxImagingExtractor
+    An ImagingExtractor for Scanbox Image files.
+"""
+
 from .sbximagingextractor import SbxImagingExtractor

src/roiextractors/extractors/sbximagingextractor/sbximagingextractor.py

@@ -1,3 +1,11 @@
+"""Imaging Extractors for Scanbox files.
+
+Classes
+-------
+SbxImagingExtractor
+    An ImagingExtractor for Scanbox Image files.
+"""
+
 from multiprocessing.sharedctypes import Value
 import os
 from pathlib import Path

src/roiextractors/extractors/schnitzerextractor/__init__.py

@@ -1,3 +1,24 @@
+"""Segmentation extractors for CNMF-E and EXTRACT ROI segmentation method.
+
+Modules
+-------
+cnmfesegmentationextractor
+    A segmentation extractor for CNMF-E ROI segmentation method.
+extractsegmentationextractor
+    A segmentation extractor for EXTRACT segmentation method.
+
+Classes
+-------
+CnmfeSegmentationExtractor
+    A segmentation extractor for CNMF-E ROI segmentation method.
+ExtractSegmentationExtractor
+    Abstract class that defines which EXTRACT class to use for a given file (new vs old).
+NewExtractSegmentationExtractor
+    Extractor for reading the segmentation data that results from calls to newer versions of EXTRACT.
+LegacyExtractSegmentationExtractor
+    Extractor for reading the segmentation data that results from calls to older versions of EXTRACT.
+"""
+
 from .cnmfesegmentationextractor import CnmfeSegmentationExtractor
 from .extractsegmentationextractor import (
     LegacyExtractSegmentationExtractor,

src/roiextractors/extractors/schnitzerextractor/cnmfesegmentationextractor.py

@@ -1,3 +1,11 @@
+"""A segmentation extractor for CNMF-E ROI segmentation method.
+
+Classes
+-------
+CnmfeSegmentationExtractor
+    A segmentation extractor for CNMF-E ROI segmentation method.
+"""
+
 from pathlib import Path
 
 try:

src/roiextractors/extractors/schnitzerextractor/extractsegmentationextractor.py

@@ -1,3 +1,15 @@
+"""Extractor for reading the segmentation data that results from calls to EXTRACT.
+
+Classes
+-------
+ExtractSegmentationExtractor
+    Abstract class that defines which extractor class to use for a given file.
+NewExtractSegmentationExtractor
+    Extractor for reading the segmentation data that results from calls to newer versions of EXTRACT.
+LegacyExtractSegmentationExtractor
+    Extractor for reading the segmentation data that results from calls to older versions of EXTRACT.
+"""
+
 from abc import ABC
 from pathlib import Path
 from typing import Optional

src/roiextractors/extractors/simaextractor/__init__.py

@@ -1 +1,14 @@
+"""A segmentation extractor for Sima.
+
+Modules
+-------
+simasegmentationextractor
+    A segmentation extractor for Sima.
+
+Classes
+-------
+SimaSegmentationExtractor
+    A segmentation extractor for Sima.
+"""
+
 from .simasegmentationextractor import SimaSegmentationExtractor

src/roiextractors/extractors/simaextractor/simasegmentationextractor.py

@@ -1,3 +1,11 @@
+"""A segmentation extractor for Sima.
+
+Classes
+-------
+SimaSegmentationExtractor
+    A segmentation extractor for Sima.
+"""
+
 import os
 import pickle
 import re

src/roiextractors/extractors/suite2p/__init__.py

@@ -1 +1,14 @@
+"""A segmentation extractor for Suite2p.
+
+Modules
+-------
+suite2psegmentationextractor
+    A segmentation extractor for Suite2p.
+
+Classes
+-------
+Suite2pSegmentationExtractor
+    A segmentation extractor for Suite2p.
+"""
+
 from .suite2psegmentationextractor import Suite2pSegmentationExtractor

src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py

@@ -1,3 +1,11 @@
+"""A segmentation extractor for Suite2p.
+
+Classes
+-------
+Suite2pSegmentationExtractor
+    A segmentation extractor for Suite2p.
+"""
+
 import shutil
 from pathlib import Path
 from typing import Optional