Incorporates recommendations for improving the docs

Author: erikhuck

docs/api.rst

@@ -1,3 +1,6 @@
+.. |Functionality| replace:: Provides API functionality
+.. |Interface for| replace:: Provides wrapper methods for
+
 API
 ===
 **Note:** Many KEGG entry IDs contain colons and ``kegg_pull`` saves KEGG entry files with their ID in the file name. When running on Windows, all file names with colons will have their colons replaced with underscores.

docs/cli.rst

@@ -1,3 +1,6 @@
+.. |Functionality| replace:: Provides commandline functionality
+.. |Interface for| replace:: Provides commandline functionality for accessing
+
 CLI
 ===
 **Note:** Many KEGG entry IDs contain colons and ``kegg_pull`` saves KEGG entry files with their ID in the file name. When running on Windows, all file names with colons will have their colons replaced with underscores.
@@ -15,7 +18,7 @@ Top-level commandline interface.
     :start-after: """
     :end-before: """
 
-A JSON file, called ``pull-results.json``, is saved describing the results of the pull. Below is the interpretation of each of the fields:
+A JSON file, called ``pull-results.json``, is saved, describing the results of the pull. Below is the interpretation of each of the fields:
 
 **percent-success:** The percentage of the requested entries that were successfully pulled and saved in a file.
 

docs/tutorial.rst

@@ -1,7 +1,7 @@
 """
 Pulling Lists of KEGG Entry IDs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Functionality for pulling lists of KEGG entry IDs from the KEGG REST API.
+|Functionality| for pulling lists of KEGG entry IDs from the KEGG REST API.
 """
 from . import rest as r
 from . import kegg_url as ku

src/kegg_pull/entry_ids.py

@@ -1,7 +1,7 @@
 """
 Constructing Mappings From KEGG "link" And "conv" Operations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Functionality for converting the output from the KEGG "link" or "conv" REST operations into mappings of the entry IDs from one database to the IDs of related entries.
+|Functionality| for converting the output from the KEGG "link" or "conv" REST operations into mappings of the entry IDs from one database to the IDs of related entries.
 """
 import typing as t
 import json
@@ -246,7 +246,7 @@ def indirect_link(
         raise ValueError(
             f'The source, intermediate, and target database must all be unique. Databases specified: {source_database}, '
             f'{intermediate_database}, {target_database}.')
-    source_to_target = dict()
+    source_to_target = KEGGmapping()
     source_to_intermediate = _to_dict(
         kegg_rest=kegg_rest, KEGGurl=ku.DatabaseLinkKEGGurl, source_database=source_database,
         target_database=intermediate_database)

src/kegg_pull/map.py

@@ -1,7 +1,7 @@
 """
 Flattening A Pathways Brite Hierarchy
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Functionality for flattening a pathways Brite hierarchy (ID: 'br:br08901') into a collection of its nodes, mapping a node ID to information about it, enabling combinations with other KEGG data.
+|Functionality| for flattening a pathways Brite hierarchy (ID: 'br:br08901') into a collection of its nodes, mapping a node ID to information about it, enabling combinations with other KEGG data.
 """
 from __future__ import annotations
 import json

src/kegg_pull/pathway_organizer.py

@@ -1,7 +1,7 @@
 """
 Pulling, Parsing, and Saving KEGG Entries
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Functionality for pulling KEGG entries from the KEGG REST API, parsing them, and saving the entries as files.
+|Functionality| for pulling KEGG entries from the KEGG REST API, parsing them, and saving the entries as files.
 """
 import multiprocessing as mp
 import os

src/kegg_pull/pull.py

@@ -1,7 +1,7 @@
 """
 KEGG REST API Operations
 ~~~~~~~~~~~~~~~~~~~~~~~~
-Interface for the KEGG REST API including all its operations.
+|Interface for| the KEGG REST API including all its operations.
 """
 import typing as t
 import enum as e