Implement scope control over check submodule (#486)

* implement scope control over check submodule

* remove hallucinated names and fix test imports

* adjust imports for deprecated submodules

---------

Co-authored-by: CodyCBakerPhD <[email protected]>

src/nwbinspector/__init__.py

@@ -18,7 +18,7 @@
     InspectorOutputJSONEncoder,
 )
 from ._organization import organize_messages
-from .checks import *
+from .checks import *  # These need to be imported to trigger registration with 'available_checks', but are not exposed
 
 default_check_registry = {check.__name__: check for check in available_checks}
 

src/nwbinspector/checks/__init__.py

@@ -1,12 +1,149 @@
-from .ecephys import *
-from .general import *
-from .image_series import *
-from .images import *
-from .nwb_containers import *
-from .nwbfile_metadata import *
-from .ogen import *
-from .ophys import *
-from .tables import *
-from .time_series import *
-from .icephys import *
-from .behavior import *
+from ._ecephys import (
+    check_negative_spike_times,
+    check_electrical_series_dims,
+    check_electrical_series_reference_electrodes_table,
+    check_spike_times_not_in_unobserved_interval,
+)
+from ._general import (
+    check_description,
+    check_name_slashes,
+)
+from ._image_series import (
+    check_image_series_data_size,
+    check_image_series_external_file_relative,
+    check_image_series_external_file_valid,
+)
+from ._images import (
+    check_order_of_images_unique,
+    check_order_of_images_len,
+    check_index_series_points_to_image,
+)
+from ._nwb_containers import (
+    check_empty_string_for_optional_attribute,
+    check_small_dataset_compression,
+    check_large_dataset_compression,
+)
+from ._nwbfile_metadata import (
+    check_keywords,
+    check_institution,
+    check_subject_age,
+    check_subject_sex,
+    check_subject_exists,
+    check_doi_publications,
+    check_experimenter_form,
+    check_experimenter_exists,
+    check_experiment_description,
+    check_subject_id_exists,
+    check_subject_species_exists,
+    check_subject_species_form,
+    check_subject_proper_age_range,
+    check_session_start_time_future_date,
+    check_processing_module_name,
+    check_session_start_time_old_date,
+)
+from ._ogen import (
+    check_optogenetic_stimulus_site_has_optogenetic_series,
+)
+from ._ophys import (
+    check_excitation_lambda_in_nm,
+    check_plane_segmentation_image_mask_shape_against_ref_images,
+    check_roi_response_series_dims,
+    check_emission_lambda_in_nm,
+    check_roi_response_series_link_to_plane_segmentation,
+)
+from ._tables import (
+    check_single_row,
+    check_ids_unique,
+    check_empty_table,
+    check_col_not_nan,
+    check_column_binary_capability,
+    check_dynamic_table_region_data_validity,
+    check_time_interval_time_columns,
+    check_time_intervals_stop_after_start,
+    check_table_values_for_dict,
+    check_table_time_columns_are_not_negative,
+)
+from ._time_series import (
+    check_resolution,
+    check_missing_unit,
+    check_regular_timestamps,
+    check_timestamps_ascending,
+    check_data_orientation,
+    check_timestamps_without_nans,
+    check_timestamps_match_first_dimension,
+    check_timestamp_of_the_first_sample_is_not_negative,
+    check_rate_is_not_zero,
+)
+from ._icephys import (
+    check_intracellular_electrode_cell_id_exists,
+)
+from ._behavior import (
+    check_compass_direction_unit,
+    check_spatial_series_radians_magnitude,
+    check_spatial_series_dims,
+    check_spatial_series_degrees_magnitude,
+)
+
+__all__ = [
+    "check_negative_spike_times",
+    "check_electrical_series_dims",
+    "check_electrical_series_reference_electrodes_table",
+    "check_spike_times_not_in_unobserved_interval",
+    "check_description",
+    "check_name_slashes",
+    "check_image_series_data_size",
+    "check_image_series_external_file_relative",
+    "check_image_series_external_file_valid",
+    "check_order_of_images_unique",
+    "check_order_of_images_len",
+    "check_index_series_points_to_image",
+    "check_empty_string_for_optional_attribute",
+    "check_small_dataset_compression",
+    "check_large_dataset_compression",
+    "check_keywords",
+    "check_institution",
+    "check_subject_age",
+    "check_subject_sex",
+    "check_subject_exists",
+    "check_doi_publications",
+    "check_experimenter_form",
+    "check_experimenter_exists",
+    "check_experiment_description",
+    "check_subject_id_exists",
+    "check_subject_species_exists",
+    "check_subject_species_form",
+    "check_subject_proper_age_range",
+    "check_session_start_time_future_date",
+    "check_processing_module_name",
+    "check_session_start_time_old_date",
+    "check_optogenetic_stimulus_site_has_optogenetic_series",
+    "check_excitation_lambda_in_nm",
+    "check_plane_segmentation_image_mask_shape_against_ref_images",
+    "check_roi_response_series_dims",
+    "check_emission_lambda_in_nm",
+    "check_roi_response_series_link_to_plane_segmentation",
+    "check_single_row",
+    "check_ids_unique",
+    "check_empty_table",
+    "check_col_not_nan",
+    "check_column_binary_capability",
+    "check_dynamic_table_region_data_validity",
+    "check_time_interval_time_columns",
+    "check_time_intervals_stop_after_start",
+    "check_table_values_for_dict",
+    "check_table_time_columns_are_not_negative",
+    "check_resolution",
+    "check_missing_unit",
+    "check_regular_timestamps",
+    "check_timestamps_ascending",
+    "check_data_orientation",
+    "check_timestamps_without_nans",
+    "check_timestamps_match_first_dimension",
+    "check_timestamp_of_the_first_sample_is_not_negative",
+    "check_rate_is_not_zero",
+    "check_intracellular_electrode_cell_id_exists",
+    "check_compass_direction_unit",
+    "check_spatial_series_radians_magnitude",
+    "check_spatial_series_dims",
+    "check_spatial_series_degrees_magnitude",
+]

src/nwbinspector/checks/behavior/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._behavior import *

src/nwbinspector/checks/ecephys/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._ecephys import *

src/nwbinspector/checks/general/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._general import *

src/nwbinspector/checks/icephys/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._icephys import *

src/nwbinspector/checks/image_series/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._image_series import *

src/nwbinspector/checks/images/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._images import *

src/nwbinspector/checks/nwb_containers/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._nwb_containers import *

src/nwbinspector/checks/nwbfile_metadata/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._nwbfile_metadata import *

src/nwbinspector/checks/ogen/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._ogen import *

src/nwbinspector/checks/ophys/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._ophys import *

src/nwbinspector/checks/tables/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._tables import *

src/nwbinspector/checks/time_series/__init__.py

@@ -0,0 +1,13 @@
+import warnings
+
+message = (
+    "All submodules below the level 'nwbinspector.checks'  have been deprecated. "
+    "Please retrieve the specific check function(s) you wish to use from the `available_checks` registry "
+    "at the top-level or import directly from 'nwbinspector.checks'."
+)
+
+warnings.warn(message=message, category=DeprecationWarning, stacklevel=2)
+
+# Still keep imports functional with warning for soft deprecation cycle
+# TODO: remove after 9/15/2024
+from .._time_series import *

tests/test_check_configuration.py

@@ -3,16 +3,18 @@
 
 from nwbinspector import (
     Importance,
-    check_small_dataset_compression,
-    check_regular_timestamps,
-    check_data_orientation,
-    check_timestamps_match_first_dimension,
     available_checks,
     default_check_registry,
     validate_config,
     configure_checks,
     load_config,
 )
+from nwbinspector.checks import (
+    check_small_dataset_compression,
+    check_regular_timestamps,
+    check_data_orientation,
+    check_timestamps_match_first_dimension,
+)
 from nwbinspector._configuration import _copy_function
 
 

tests/unit_tests/test_nwbfile_metadata.py

@@ -22,9 +22,9 @@
     check_processing_module_name,
     check_session_start_time_old_date,
     check_session_start_time_future_date,
-    PROCESSING_MODULE_CONFIG,
 )
 from nwbinspector.testing import make_minimal_nwbfile
+from nwbinspector.checks._nwbfile_metadata import PROCESSING_MODULE_CONFIG
 
 
 minimal_nwbfile = make_minimal_nwbfile()