Update documentation

backend/src/monarch_py/solr_cli.py

@@ -213,6 +213,7 @@ def multi_entity_associations(
         typer.Option(
             "--counterpart-category",
             "-c",
+            help="A comma-separated list of counterpart categories"
         ),
     ] = None,
     limit: fields.LimitOption = 20,
@@ -305,24 +306,23 @@ def histopheno(
 
 @solr_app.command("association-counts")
 def association_counts(
-    entity: Annotated[str, typer.Argument(help="The entity to get association counts for")],
+    entity_id: Annotated[
+        str, typer.Argument(help="The entity to get association counts for")
+    ],
     fmt: fields.FormatOption = fields.OutputFormat.json,
     output: fields.OutputOption = None,
 ):
     """
     Retrieve the association counts for a given entity
     """
-    if not entity:
-        console.print("\n[bold red]Entity ID required.[/]\n")
-        raise typer.Exit(1)
     solr = get_solr(update=False)
-    response = solr.get_association_counts(entity)
+    response = solr.get_association_counts(entity_id)
     format_output(fmt, response, output)
 
 
 @solr_app.command("association-table")
 def association_table(
-    entity: Annotated[
+    entity_id: Annotated[
         str,
         typer.Argument(
             help="The entity to get associations for",
@@ -357,7 +357,7 @@ def association_table(
 ):
     solr = get_solr(update=False)
     response = solr.get_association_table(
-        entity=entity,
+        entity=entity_id,
         category=category,
         traverse_orthologs=traverse_orthologs,
         sort=sort,

backend/src/monarch_py/utils/cli_fields.py

@@ -51,7 +51,7 @@ class OutputFormat(str, Enum):
     Optional[str],
     typer.Option(
         "--output",
-        "-o",
-        help="The path to write command output (stdout if not specified)",
+        "-O",
+        help="Path to file to write command output (stdout if not specified)",
     ),
 ]