Merge branch 'dev' into add_dandi_inspector

docs/api/checks.rst

@@ -6,40 +6,40 @@ Check Functions
 
 NWBFile Metadata
 ----------------
-.. automodule:: nwbinspector.checks.nwbfile_metadata
+.. automodule:: nwbinspector.checks._nwbfile_metadata
 
 NWB Containers
 --------------
-.. automodule:: nwbinspector.checks.nwb_containers
+.. automodule:: nwbinspector.checks._nwb_containers
 
 Time Series
 -----------
-.. automodule:: nwbinspector.checks.time_series
+.. automodule:: nwbinspector.checks._time_series
 
 Tables
 ------
-.. automodule:: nwbinspector.checks.tables
+.. automodule:: nwbinspector.checks._tables
 
 Behavior
 --------
-.. automodule:: nwbinspector.checks.behavior
+.. automodule:: nwbinspector.checks._behavior
 
 Intracellular Electrophysiology (icephys)
 -----------------------------------------
-.. automodule:: nwbinspector.checks.icephys
+.. automodule:: nwbinspector.checks._icephys
 
 Extracellular Electrophysiology (ecephys)
 -----------------------------------------
-.. automodule:: nwbinspector.checks.ecephys
+.. automodule:: nwbinspector.checks._ecephys
 
 Optical Electrophysiology (ophys)
 ---------------------------------
-.. automodule:: nwbinspector.checks.ophys
+.. automodule:: nwbinspector.checks._ophys
 
 Optogenetics (ogen)
 -------------------
-.. automodule:: nwbinspector.checks.ogen
+.. automodule:: nwbinspector.checks._ogen
 
 ImageSeries
 -----------
-.. automodule:: nwbinspector.checks.image_series
+.. automodule:: nwbinspector.checks._image_series

docs/best_practices/behavior.rst

@@ -14,7 +14,7 @@ SpatialSeries Dimensionality
 
 :ref:`nwb-schema:sec-SpatialSeries` should have 1 column (x), 2 columns (x, y), or 3 columns (x, y, z).
 
-Check function: :py:meth:`~nwbinspector.checks.behavior.check_spatial_series_dims`
+Check function: :py:meth:`~nwbinspector.checks._behavior.check_spatial_series_dims`
 
 
 .. _best_practice_spatial_series_units:
@@ -25,7 +25,7 @@ SpatialSeries Units
 When a :ref:`nwb-schema:sec-SpatialSeries` is in a :ref:`nwb-schema:sec-CompassDirection`, the units should either be
 "degrees" or "radians".
 
-Check function: :py:meth:`~nwbinspector.checks.behavior.check_compass_direction_unit`
+Check function: :py:meth:`~nwbinspector.checks._behavior.check_compass_direction_unit`
 
 
 .. _best_practice_spatial_series_values:
@@ -37,4 +37,4 @@ When a :ref:`nwb-schema:sec-SpatialSeries` has units "radians", it should have d
 :ref:`nwb-schema:sec-SpatialSeries` has units "degrees", it should have data values between -360 and 360.
 
 Check functions: :py:meth:`~nwbinspector.checks.behavior.check_spatial_series_radians_magnitude`,
-:py:meth:`~nwbinspector.checks.behavior.check_spatial_series_degrees_magnitude`
+:py:meth:`~nwbinspector.checks._behavior.check_spatial_series_degrees_magnitude`

docs/best_practices/ecephys.rst

@@ -77,7 +77,7 @@ All spike times should be greater than zero. Being less than zero implies the sp
 should therefore be aligned to the ``timestamps_reference_time`` of the :ref:`nwb-schema:sec-NWBFile`) or the
 ``timestamps_reference_time`` itself is not set to the earliest recording time during the session.
 
-Check function: :py:meth:`~nwbinspector.checks.ecephys.check_negative_spike_times`
+Check function: :py:meth:`~nwbinspector.checks._ecephys.check_negative_spike_times`
 
 
 
@@ -88,4 +88,4 @@ Observation Intervals
 
 The ``obs_intervals`` field of the :ref:`nwb-schema:sec-units-src` table is used to indicate periods of time where the underlying electrical signal(s) were not observed. This can happen if the recording site moves away from the unit, or if the recording is stopped. Since the channel is not observed, it is not determinable whether a spike occurred during this time. Therefore, there should not be any identified spike times for units matched to those electrical signal(s) occurring outside of the defined ``obs_intervals``. If this variable is not set, it is assumed that all time is observed.
 
-Check function: :py:meth:`~nwbinspector.checks.ecephys.check_spike_times_not_in_unobserved_interval`
+Check function: :py:meth:`~nwbinspector.checks._ecephys.check_spike_times_not_in_unobserved_interval`

docs/best_practices/general.rst

@@ -42,7 +42,7 @@ Slash characters ``'/'`` and ``'\'``  should not be used in the ``name`` of an o
 
 For mathematical expressions, instead of including the special character in the name, please use an English equivalent instead. *E.g.*, instead of "Df/f" use "DfOverF".
 
-Check function: :py:meth:`~nwbinspector.checks.general.check_name_slashes`
+Check function: :py:meth:`~nwbinspector.checks._general.check_name_slashes`
 
 
 
@@ -55,7 +55,7 @@ The :py:attr:`name` of an object is for identifying that object within the file;
 
 It is acceptable to name an object something like ``ElectricalSeriesFromProbe1`` as per the uniqueness requirement of :ref:`best_practice_object_names`, however the name alone is not sufficient documentation of the signal source. In this case, the source of the signal will be clear from the :ref:`nwb-schema:devices` linkage in the rows of the passed :ref:`hdmf-schema:sec-dynamictableregion` subsetting the full ``ElectrodeTable``, so you would not need to add any explicit metadata explaining these details.
 
-Check function: :py:meth:`~nwbinspector.checks.general.check_description`
+Check function: :py:meth:`~nwbinspector.checks._general.check_description`
 
 
 

docs/best_practices/image_series.rst

@@ -14,7 +14,7 @@ an external file. That is, the file should be packaged together with the nwb fil
 This can be accomplished by using  the ``external_file`` file option to store the path instead. This is preferred for
 videos because it allows the usage of video compression codecs that are lossy and highly optimized for such videos.
 
-Check function: :py:meth:`~nwbinspector.checks.image_series.check_image_series_data_size`
+Check function: :py:meth:`~nwbinspector.checks._image_series.check_image_series_data_size`
 
 
 Use internal dataset for videos of neurophysiological data
@@ -32,4 +32,4 @@ Use relative path for external mode
 
 When using ``external_file`` the paths passed in the ``external_file`` option should be relative to the location of the nwb file.
 
-Check function: :py:meth:`~nwbinspector.checks.image_series.check_image_series_external_file_relative`
+Check function: :py:meth:`~nwbinspector.checks._image_series.check_image_series_external_file_relative`

docs/best_practices/nwbfile_metadata.rst

@@ -30,10 +30,10 @@ value. Default values should generally not be used for this field. If the true d
 best guess. If the exact start time is unknown, then it is fine to simply set it to midnight on that date.
 
 
-Check functions: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_session_start_time_old_date`,
-:py:meth:`~nwbinspector.checks.nwbfile_metadata.check_session_start_time_future_date`,
-:py:meth:`~nwbinspector.checks.time_series.check_timestamp_of_the_first_sample_is_not_negative`
-:py:meth:`~nwbinspector.checks.tables.check_table_time_columns_are_not_negative`
+Check functions: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_session_start_time_old_date`,
+:py:meth:`~nwbinspector.checks._nwbfile_metadata.check_session_start_time_future_date`,
+:py:meth:`~nwbinspector.checks._time_series.check_timestamp_of_the_first_sample_is_not_negative`
+:py:meth:`~nwbinspector.checks._tables.check_table_time_columns_are_not_negative`
 
 
 
@@ -65,7 +65,7 @@ The name of any given processing module should be chosen from the following type
 modalities. It also helps distinguish components of a given experiment, such as decoupling the intermediate data from
 neural acquisition systems from behavioral ones.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_processing_module_name`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_processing_module_name`
 
 
 
@@ -103,7 +103,7 @@ Experimenter
 
 The ``experimenter`` field of an :ref:`nwb-schema:sec-NWBFile` should be specified as any of the accepted forms: 'LastName, Firstname', 'LastName, FirstName MiddleInitial.' or 'LastName, FirstName MiddleName'.
 
-Check functions: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_experimenter_exists` and :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_experimenter_form`
+Check functions: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_experimenter_exists` and :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_experimenter_form`
 
 
 
@@ -115,7 +115,7 @@ Experiment Description
 The ``experiment_description`` field of an :ref:`nwb-schema:sec-NWBFile` should be specified. This helps provide
 context for understanding the contents of the file.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_experiment_description`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_experiment_description`
 
 
 
@@ -127,7 +127,7 @@ Institution
 The ``institution`` field should be specified. This allows metadata collection programs, such as those on the
 :dandi-archive:`DANDI archive <>` to easily scan NWBFiles to deliver summary statistics.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_institution`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_institution`
 
 
 
@@ -159,7 +159,7 @@ of the form ``'doi: ###'`` or as an external link of the form ``'http://dx.doi.o
 This allows metadata collection programs, such as those on the :dandi-archive:`DANDI archive <>` to easily form direct
 hyperlinks to the publications.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_doi_publications`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_doi_publications`
 
 
 
@@ -171,7 +171,7 @@ Subject
 It is recommended to always include as many details about the experimental subject as possible. If the data is
 simulated, a simple ID of "simulated_subject" would be sufficient.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_subject_exists`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_exists`
 
 
 
@@ -186,7 +186,7 @@ not intended for DANDI upload, if the :ref:`nwb-schema:sec-Subject` is specified
 
 In the special case of *in vitro* studies where the 'subject' of scientific interest was not a tissue sample obtained from a living subject but was instead a purified protein, this will be annotated by prepending the keyphrase "protein" to the subject ID; *e.g*, "proteinCaMPARI3". In the case where the *in vitro* experiment is performed on an extracted or cultured biological sample, the other subject attributes (such as age and sex) should be specified as their values at the time the sample was collected.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_subject_id_exists`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_id_exists`
 
 
 
@@ -200,7 +200,7 @@ following four possibilities: "M" (male), "F" (female), "U" (unknown), or "O" (o
 
 C. elegans are an exception to this rule. For C. elegans, the sex should either be "XO" (male) or "XX" (hermaphrodite).
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_subject_sex`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_sex`
 
 
 
@@ -211,7 +211,7 @@ Subject Species
 
 The ``species`` of a :ref:`nwb-schema:sec-Subject` should be set to the proper :wikipedia:`Latin binomial <Binomial_nomenclature>` or otherwise a full link to the Term IRI for the :ncbi:`NCBI Taxonomy <>`, which can be easily found at the :ontobee:`Ontobee  <>` database. *E.g.*, a rat would be "Rattus norvegicus" or "http://purl.obolibrary.org/obo/NCBITaxon_10116".
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_subject_species_form`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_species_form`
 
 
 
@@ -235,7 +235,7 @@ If the precise age is unknown, an age range can be given by "[lower bound]/[uppe
 that the age is in between 10 and 20 days. If only the lower bound is known, then including only the slash after that lower bound can be used to indicate a
 missing bound. For instance, "P90Y/" would indicate that the age is 90 years or older.
 
-Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_subject_age`
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_age`
 
 
 

docs/best_practices/ogen.rst

@@ -9,4 +9,4 @@ OptogeneticSeries
 Each :ref:`nwb-schema:sec-OptogeneticStimulusSite` object should be referenced by at least one
 :ref:`nwb-schema:sec-OptogeneticSeries` in the same file.
 
-Check function: :py:meth:`~nwbinspector.checks.ogen.check_optogenetic_stimulus_site_has_optogenetic_series`
+Check function: :py:meth:`~nwbinspector.checks._ogen.check_optogenetic_stimulus_site_has_optogenetic_series`

docs/best_practices/tables.rst

@@ -12,7 +12,7 @@ Table Values
 
 String-valued table entries should not contain :wikipedia:`JSON <JSON>`. Instead, these values should be unpacked and used as additional columns of that table.
 
-Check function: :py:meth:`~nwbinspector.checks.tables.check_table_values_for_dict`
+Check function: :py:meth:`~nwbinspector.checks._tables.check_table_values_for_dict`
 
 
 
@@ -32,7 +32,7 @@ Tables With Only a Single Row
 
 It is not common to save a table with only a single row entry. Consider other ``neurodata_types``, such as a one-dimensional :ref:`nwb-schema:sec-TimeSeries`.
 
-Check function: :py:meth:`~nwbinspector.checks.tables.check_single_row`
+Check function: :py:meth:`~nwbinspector.checks._tables.check_single_row`
 
 
 
@@ -44,7 +44,7 @@ Tables With an Entire Column as ``NaN``
 If an entire column of a :ref:`hdmf-schema:sec-dynamictable` would be filled with ``NaN`` values, then it should not be written.
 
 
-Check function: :py:meth:`~nwbinspector.checks.tables.check_col_not_nan`
+Check function: :py:meth:`~nwbinspector.checks._tables.check_col_not_nan`
 
 
 
@@ -56,7 +56,7 @@ Table Region Data
 Store data with long columns rather than long rows. When constructing dynamic tables, keep in mind that the data is
 stored by column, so it will be less efficient to store data in a table that has many more columns than rows.
 
-Check function :py:meth:`~nwbinspector.checks.tables.check_dynamic_table_region_data_validity`
+Check function :py:meth:`~nwbinspector.checks._tables.check_dynamic_table_region_data_validity`
 
 
 

docs/best_practices/time_series.rst

@@ -19,8 +19,8 @@ Keep in mind that the dimensions are reversed in MatNWB, so in memory in MatNWB
 
 In PyNWB the order of the dimensions is the same in memory as on disk, so the time index should be first.
 
-Check functions: :py:meth:`~nwbinspector.checks.time_series.check_data_orientation` and
-:py:meth:`~nwbinspector.checks.time_series.check_timestamps_match_first_dimension`
+Check functions: :py:meth:`~nwbinspector.checks._time_series.check_data_orientation` and
+:py:meth:`~nwbinspector.checks._time_series.check_timestamps_match_first_dimension`
 
 
 
@@ -35,7 +35,7 @@ Every :ref:`nwb-schema:sec-TimeSeries` instance has ``unit`` as an attribute, wh
 measurement for that data, using the appropriate type from the
 :wikipedia:`International System of Units (SI) <International_System_of_Units>`.
 
-Check function: :py:meth:`~nwbinspector.checks.time_series.check_missing_unit`
+Check function: :py:meth:`~nwbinspector.checks._time_series.check_missing_unit`
 
 
 
@@ -82,7 +82,7 @@ A primary implication is that the values in :ref:`nwb-schema:TimeSeries.timestam
 corresponding ordering of their indices in the :ref:`nwb-schema:TimeSeries.data <sec-TimeSeries>` array, should always
 be strictly increasing.
 
-Check function: :py:meth:`~nwbinspector.checks.time_series.check_timestamps_ascending`
+Check function: :py:meth:`~nwbinspector.checks._time_series.check_timestamps_ascending`
 
 
 
@@ -98,7 +98,7 @@ Ensure that all timestamps are valid numerical values. If gaps in time need to b
 data into separate :ref:`nwb-schema:sec-TimeSeries` objects with appropriate ``starting_time`` or use the ``timestamps``
 vector to explicitly represent time gaps.
 
-Check function: :py:meth:`~nwbinspector.checks.time_series.check_timestamps_without_nans`
+Check function: :py:meth:`~nwbinspector.checks._time_series.check_timestamps_without_nans`
 
 
 
@@ -120,7 +120,7 @@ For segmented data, refer to the section covering :ref:`best_practice_timestamps
     2. Even if the sampling rate is constant within each segment, a single :ref:`nwb-schema:sec-TimeSeries` can be
     written using the ``timestamps`` vector to appropriately indicate the gaps between segments.
 
-Check function: :py:meth:`~nwbinspector.checks.time_series.check_regular_timestamps`
+Check function: :py:meth:`~nwbinspector.checks._time_series.check_regular_timestamps`
 
 
 
@@ -161,8 +161,8 @@ chunk individually. This is especially important when writing NWBFiles that are
 :pynwb-docs:`PyNWB tutorial <tutorials/advanced_io/h5dataio.html#compression-and-other-i-o-filters>` or the
 `MatNWB instructions <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dataPipe.html#2>`_
 
-Check functions: :py::meth:`~nwbinspector.checks.nwb_containers.check_large_dataset_compression`,
-:py::meth:`~nwbinspector.checks.nwb_containers.check_small_dataset_compression`
+Check functions: :py::meth:`~nwbinspector.checks._nwb_containers.check_large_dataset_compression`,
+:py::meth:`~nwbinspector.checks._nwb_containers.check_small_dataset_compression`
 
 
 
@@ -173,7 +173,7 @@ Unknown Resolution
 
 If the ``resolution`` of a :ref:`nwb-schema:sec-TimeSeries` is unknown, use ``-1.0`` or ``NaN`` to indicate this.
 
-Check function: :py::meth:`~nwbinspector.checks.time_series.check_resolution`
+Check function: :py::meth:`~nwbinspector.checks._time_series.check_resolution`
 
 
 
@@ -184,4 +184,4 @@ Zero Rate
 
 If the ``data`` field of :ref:`nwb-schema:sec-TimeSeries` has more than one frame, and according to :ref:`best_practice_data_orientation` this axis ought to be time, then the ``rate`` field should not be ``0.0``.
 
-Check function: :py::meth:`~nwbinspector.checks.time_series.check_rate_is_not_zero`
+Check function: :py::meth:`~nwbinspector.checks._time_series.check_rate_is_not_zero`

src/nwbinspector/checks/_ecephys.py

@@ -50,7 +50,11 @@ def check_electrical_series_dims(electrical_series: ElectricalSeries):
 
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=ElectricalSeries)
 def check_electrical_series_reference_electrodes_table(electrical_series: ElectricalSeries):
-    """Check that the 'electrodes' of an ElectricalSeries references the ElectrodesTable."""
+    """
+    Check that the 'electrodes' of an ElectricalSeries references the ElectrodesTable.
+
+    Best Practice: TODO
+    """
     if electrical_series.electrodes.table.name != "electrodes":
         return InspectorMessage(message="electrodes does not  reference an electrodes table.")
 

src/nwbinspector/checks/_icephys.py

@@ -7,6 +7,10 @@
 
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=IntracellularElectrode)
 def check_intracellular_electrode_cell_id_exists(intracellular_electrode: IntracellularElectrode):
-    """Check if the IntracellularElectrode contains a cell_id."""
+    """
+    Check if the IntracellularElectrode contains a cell_id.
+
+    Best Practice: TODO
+    """
     if hasattr(intracellular_electrode, "cell_id") and intracellular_electrode.cell_id is None:
         return InspectorMessage(message="Please include a unique cell_id associated with this IntracellularElectrode.")