Add comments to io/file.py (#1925)

* Add comments to io/file.py

* Update changelog

Author: rly

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Documentation and tutorial enhancements
 - Simplified the introduction to NWB tutorial. @rly [#1914](https://github.com/NeurodataWithoutBorders/pynwb/pull/1914)
 - Simplified the ecephys and ophys tutorials. [#1915](https://github.com/NeurodataWithoutBorders/pynwb/pull/1915)
+- Add comments to `src/pynwb/io/file.py` to improve developer documentation. @rly [#1925](https://github.com/NeurodataWithoutBorders/pynwb/pull/1925)
 
 ### Bug fixes
 - Fixed use of `channel_conversion` in `TimeSeries` `get_data_in_units`. @rohanshah [1923](https://github.com/NeurodataWithoutBorders/pynwb/pull/1923)

src/pynwb/io/file.py

@@ -127,6 +127,15 @@ def __init__(self, spec):
 
     @ObjectMapper.object_attr('scratch_datas')
     def scratch_datas(self, container, manager):
+        """Set the value for the 'scratch_datas' spec on NWBFile to a list of ScratchData objects.
+
+        Used when writing (building) the NWBFile container to a file.
+
+        The 'scratch' group can contain both groups and datasets. This mapping function
+        is used when writing the value for the 'scratch_datas' spec (ScratchData type
+        -- see __init__ above). The value is set to a list of all ScratchData
+        objects in the 'scratch' field of the NWBFile container.
+        """
         scratch = container.scratch
         ret = list()
         for s in scratch.values():
@@ -136,6 +145,15 @@ def scratch_datas(self, container, manager):
 
     @ObjectMapper.object_attr('scratch_containers')
     def scratch_containers(self, container, manager):
+        """Set the value for the 'scratch_containers' spec on NWBFile to a list of non-ScratchData objects.
+
+        Used when writing (building) the NWBFile container to a file.
+
+        The 'scratch' group can contain both groups and datasets. This mapping function
+        is used when writing the value for the 'scratch_containers' spec (NWBContainers
+        and DynamicTable type -- see __init__ above). The value is set to a list of all non-ScratchData
+        objects in the 'scratch' field of the NWBFile container.
+        """
         scratch = container.scratch
         ret = list()
         for s in scratch.values():
@@ -145,6 +163,14 @@ def scratch_containers(self, container, manager):
 
     @ObjectMapper.constructor_arg('scratch')
     def scratch(self, builder, manager):
+        """Set the constructor arg for 'scratch' to a tuple of objects.
+
+        Used when constructing the NWBFile container from a written file.
+
+        The 'scratch' group can contain both groups and datasets. This mapping function
+        is used to construct the contained groups and datasets and put them into a single
+        field 'scratch' on the NWBFile container for user convenience.
+        """
         scratch = builder.get('scratch')
         ret = list()
         if scratch is not None:
@@ -156,28 +182,54 @@ def scratch(self, builder, manager):
 
     @ObjectMapper.constructor_arg('session_start_time')
     def dateconversion(self, builder, manager):
+        """Set the constructor arg for 'session_start_time' to a datetime object.
+
+        Used when constructing the NWBFile container from a written file.
+
+        Dates are read into builders as strings and are parsed into datetime objects
+        for user convenience and consistency with how they are written.
+        """
         datestr = builder.get('session_start_time').data
         date = dateutil_parse(datestr)
         return date
 
     @ObjectMapper.constructor_arg('timestamps_reference_time')
     def dateconversion_trt(self, builder, manager):
+        """Set the constructor arg for 'timestamps_reference_time' to a datetime object.
+
+        Used when constructing the NWBFile container from a written file.
+
+        Dates are read into builders as strings and are parsed into datetime objects
+        for user convenience and consistency with how they are written.
+        """
         datestr = builder.get('timestamps_reference_time').data
         date = dateutil_parse(datestr)
         return date
 
     @ObjectMapper.constructor_arg('file_create_date')
     def dateconversion_list(self, builder, manager):
+        """Set the constructor arg for 'file_create_date' to a datetime object.
+
+        Used when constructing the NWBFile container from a written file.
+
+        Dates are read into builders as strings and are parsed into datetime objects
+        for user convenience and consistency with how they are written.
+        """
         datestr = builder.get('file_create_date').data
         dates = list(map(dateutil_parse, datestr))
         return dates
 
-    @ObjectMapper.constructor_arg('file_name')
-    def name(self, builder, manager):
-        return builder.name
-
     @ObjectMapper.constructor_arg('experimenter')
     def experimenter_carg(self, builder, manager):
+        """Set the constructor arg for 'experimenter' to a tuple if the builder value is a string.
+
+        Used when constructing the NWBFile container from a written file.
+
+        In early versions of the NWB 2 schema, 'experimenter' was specified as a string.
+        Then it was changed to be a 1-D array of strings. This mapping function is necessary
+        to allow reading of both data where 'experimenter' was specified as a string and data
+        where 'experimenter' was specified as an array.
+        """
         ret = None
         exp_bldr = builder['general'].get('experimenter')
         if exp_bldr is not None:
@@ -189,13 +241,30 @@ def experimenter_carg(self, builder, manager):
 
     @ObjectMapper.object_attr('experimenter')
     def experimenter_obj_attr(self, container, manager):
+        """Change the value for the field 'experimenter' on NWBFile to a tuple if it is a string.
+
+        Used when writing (building) the NWBFile container to a file.
+
+        In early versions of the NWB 2 schema, 'experimenter' was specified as a string.
+        Then it was changed to be a 1-D array of strings. This mapping function is necessary
+        for writing a valid 'experimenter' array if it is a string in the NWBFile container.
+        """
         ret = None
         if isinstance(container.experimenter, str):
             ret = (container.experimenter,)
         return ret
 
     @ObjectMapper.constructor_arg('related_publications')
     def publications_carg(self, builder, manager):
+        """Set the constructor arg for 'related_publications' to a tuple if the builder value is a string.
+
+        Used when constructing the NWBFile container from a written file.
+
+        In early versions of the NWB 2 schema, 'related_publications' was specified as a string.
+        Then it was changed to be a 1-D array of strings. This mapping function is necessary
+        to allow reading of both data where 'related_publications' was specified as a string and data
+        where 'related_publications' was specified as an array.
+        """
         ret = None
         pubs_bldr = builder['general'].get('related_publications')
         if pubs_bldr is not None:
@@ -207,6 +276,14 @@ def publications_carg(self, builder, manager):
 
     @ObjectMapper.object_attr('related_publications')
     def publication_obj_attr(self, container, manager):
+        """Change the value for the field 'related_publications' on NWBFile to a tuple if it is a string.
+
+        Used when writing (building) the NWBFile container to a file.
+
+        In early versions of the NWB 2 schema, 'related_publications' was specified as a string.
+        Then it was changed to be a 1-D array of strings. This mapping function is necessary
+        for writing a valid 'related_publications' array if it is a string in the NWBFile container.
+        """
         ret = None
         if isinstance(container.related_publications, str):
             ret = (container.related_publications,)
@@ -218,6 +295,13 @@ class SubjectMap(ObjectMapper):
 
     @ObjectMapper.constructor_arg('date_of_birth')
     def dateconversion(self, builder, manager):
+        """Set the constructor arg for 'date_of_birth' to a datetime object.
+
+        Used when constructing the Subject container from a written file.
+
+        Dates are read into builders as strings and are parsed into datetime objects
+        for user convenience and consistency with how they are written.
+        """
         dob_builder = builder.get('date_of_birth')
         if dob_builder is None:
             return
@@ -228,6 +312,18 @@ def dateconversion(self, builder, manager):
 
     @ObjectMapper.constructor_arg("age__reference")
     def age_reference_none(self, builder, manager):
+        """Set the constructor arg for 'age__reference' to "unspecified" for NWB files < 2.6, else "birth".
+
+        Used when constructing the Subject container from a written file.
+
+        NWB schema 2.6.0 introduced a new optional attribute 'reference' on the 'age' dataset with a default
+        value of "birth". When data written with NWB versions < 2.6 are read, 'age__reference' is set to
+        "unspecified" in the Subject constructor. "unspecified" is a special non-None placeholder value
+        that is handled specially in Subject.__init__ to distinguish it from no value being provided by the
+        user. When data written with NWB versions >= 2.6 are read, 'age__reference' is set to the default
+        value, "birth", in the Subject constructor (this is not strictly necessary because Subject.__init__
+        has default value "birth" for 'age__reference').
+        """
         age_builder = builder.get("age")
         age_reference = None
         if age_builder is not None: