Add __all__ declarations to multiple modules for improved API clarity

src/pynwb/__init__.py

@@ -613,6 +613,32 @@ def read_nwb(**kwargs):
 from hdmf.data_utils import DataChunkIterator  # noqa: F401,E402
 from hdmf.backends.hdf5 import H5DataIO  # noqa: F401,E402
 
+__all__ = [
+    # Functions
+    'get_type_map',
+    'get_manager',
+    'load_namespaces', 
+    'available_namespaces',
+    'register_class',
+    'register_map',
+    'get_class',
+    'load_type_config',
+    'get_loaded_type_config',
+    'unload_type_config',
+    'read_nwb',
+    'get_nwbfile_version',
+
+    # Classes
+    'NWBHDF5IO',
+    'NWBContainer',
+    'NWBData', 
+    'TimeSeries',
+    'ProcessingModule',
+    'NWBFile',
+    'DataChunkIterator',
+    'H5DataIO'
+]
+
 
 
 from ._due import due, BibTeX  # noqa: E402

src/pynwb/base.py

@@ -12,6 +12,17 @@
 from .core import NWBDataInterface, MultiContainerInterface, NWBData
 
 
+__all__ = [
+    'ProcessingModule',
+    'TimeSeries',
+    'Image',
+    'ImageReferences',
+    'Images',
+    'TimeSeriesReferenceVectorData',
+    'TimeSeriesReference'
+]
+
+
 @register_class('ProcessingModule', CORE_NAMESPACE)
 class ProcessingModule(MultiContainerInterface):
     """ Processing module. This is a container for one or more containers

src/pynwb/behavior.py

@@ -7,6 +7,17 @@
 from .misc import IntervalSeries
 from .base import TimeSeries
 
+__all__ = [
+    'SpatialSeries',
+    'BehavioralEpochs',
+    'BehavioralEvents',
+    'BehavioralTimeSeries',
+    'PupilTracking',
+    'EyeTracking',
+    'CompassDirection',
+    'Position'
+]
+
 
 @register_class('SpatialSeries', CORE_NAMESPACE)
 class SpatialSeries(TimeSeries):

src/pynwb/core.py

@@ -13,6 +13,17 @@
 from pynwb import get_type_map
 
 
+__all__ = [
+    'NWBMixin',
+    'NWBContainer',
+    'NWBDataInterface',
+    'NWBData',
+    'ScratchData',
+    'NWBTable',
+    'MultiContainerInterface'
+]
+
+
 def _not_parent(arg):
     return arg['name'] != 'parent'
 

src/pynwb/device.py

@@ -3,6 +3,7 @@
 from . import register_class, CORE_NAMESPACE
 from .core import NWBContainer
 
+__all__ = ['Device']
 
 @register_class('Device', CORE_NAMESPACE)
 class Device(NWBContainer):

src/pynwb/ecephys.py

@@ -11,6 +11,16 @@
 from .core import NWBContainer, NWBDataInterface, MultiContainerInterface
 from .device import Device
 
+__all__ = [
+    'ElectrodeGroup',
+    'ElectricalSeries',
+    'SpikeEventSeries',
+    'EventDetection',
+    'LFP',
+    'FilteredEphys',
+    'FeatureExtraction'
+]
+
 
 @register_class('ElectrodeGroup', CORE_NAMESPACE)
 class ElectrodeGroup(NWBContainer):

src/pynwb/epoch.py

@@ -7,6 +7,7 @@
 from . import register_class, CORE_NAMESPACE
 from .base import TimeSeries, TimeSeriesReferenceVectorData, TimeSeriesReference
 
+__all__ = ['TimeIntervals']
 
 @register_class('TimeIntervals', CORE_NAMESPACE)
 class TimeIntervals(DynamicTable):

src/pynwb/file.py

@@ -26,6 +26,16 @@
 from .core import NWBContainer, NWBDataInterface, MultiContainerInterface, ScratchData, LabelledDict
 
 
+__all__ = [
+    'LabMetaData',
+    'Subject',
+    'NWBFile',
+    'ElectrodeTable',
+    'TrialTable',
+    'InvalidTimesTable'
+]
+
+
 def _not_parent(arg):
     return arg['name'] != 'parent'
 

src/pynwb/icephys.py

@@ -11,6 +11,24 @@
 from .core import NWBContainer
 from .device import Device
 
+__all__ = [
+    'IntracellularElectrode',
+    'PatchClampSeries',
+    'CurrentClampSeries',
+    'IZeroClampSeries',
+    'CurrentClampStimulusSeries',
+    'VoltageClampSeries',
+    'VoltageClampStimulusSeries',
+    'IntracellularElectrodesTable',
+    'IntracellularStimuliTable',
+    'IntracellularResponsesTable',
+    'IntracellularRecordingsTable',
+    'SimultaneousRecordingsTable',
+    'SequentialRecordingsTable',
+    'RepetitionsTable',
+    'ExperimentalConditionsTable'
+]
+
 
 def ensure_unit(self, name, current_unit, unit, nwb_version):
     """A helper to ensure correct unit used.

src/pynwb/image.py

@@ -17,6 +17,16 @@
 from .device import Device
 
 
+__all__ = [
+    'ImageSeries',
+    'IndexSeries',
+    'OpticalSeries',
+    'GrayscaleImage',
+    'RGBImage',
+    'RGBAImage'
+]
+
+
 @register_class('ImageSeries', CORE_NAMESPACE)
 class ImageSeries(TimeSeries):
     '''

src/pynwb/misc.py

@@ -11,6 +11,13 @@
 from .ecephys import ElectrodeGroup
 from hdmf.common import DynamicTable, DynamicTableRegion
 
+__all__ = [
+    'AnnotationSeries',
+    'AbstractFeatureSeries',
+    'IntervalSeries',
+    'Units',
+    'DecompositionSeries'
+]
 
 @register_class('AnnotationSeries', CORE_NAMESPACE)
 class AnnotationSeries(TimeSeries):

src/pynwb/ogen.py

@@ -5,6 +5,10 @@
 from .core import NWBContainer
 from .device import Device
 
+__all__ = [
+    'OptogeneticStimulusSite',
+    'OptogeneticSeries'
+]
 
 @register_class('OptogeneticStimulusSite', CORE_NAMESPACE)
 class OptogeneticStimulusSite(NWBContainer):

src/pynwb/ophys.py

@@ -11,6 +11,20 @@
 from .core import NWBContainer, MultiContainerInterface, NWBDataInterface
 from .device import Device
 
+__all__ = [
+    'OpticalChannel',
+    'ImagingPlane',
+    'OnePhotonSeries',
+    'TwoPhotonSeries',
+    'CorrectedImageStack',
+    'MotionCorrection',
+    'PlaneSegmentation',
+    'ImageSegmentation',
+    'RoiResponseSeries',
+    'DfOverF',
+    'Fluorescence'
+]
+
 
 @register_class('OpticalChannel', CORE_NAMESPACE)
 class OpticalChannel(NWBContainer):

src/pynwb/resources.py

@@ -2,6 +2,7 @@
 from . import get_type_map as tm
 from hdmf.utils import docval, get_docval
 
+__all__ = ['HERD']
 
 class HERD(hdmf_HERD):
     """

src/pynwb/spec.py

@@ -8,6 +8,19 @@
 from . import CORE_NAMESPACE
 
 
+__all__ = [
+    'NWBRefSpec',
+    'NWBAttributeSpec',
+    'NWBLinkSpec',
+    'NWBDtypeSpec',
+    'NWBDatasetSpec',
+    'NWBGroupSpec',
+    'NWBNamespace',
+    'NWBNamespaceBuilder',
+    'export_spec'  # Re-exported from hdmf.spec.write
+]
+
+
 def __swap_inc_def(cls):
     args = get_docval(cls.__init__)
     clsname = 'NWB%s' % cls.__name__

src/pynwb/validate.py

@@ -14,6 +14,12 @@
 from pynwb.spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace
 
 
+__all__ = [
+    'validate',
+    'get_cached_namespaces_to_validate'
+]
+
+
 def _print_errors(validation_errors: list):
     if validation_errors:
         print(" - found the following errors:", file=sys.stderr)