Various bits of linting

src/ontogpt/clients/llm_client.py

@@ -37,7 +37,7 @@ def __post_init__(self):
         # Get appropriate API key for the model source
         # and other details if needed
         if self.model.startswith("ollama"):
-            self.api_key = "" # Don't need an API key
+            self.api_key = ""  # Don't need an API key
         if not self.api_key and not self.custom_llm_provider:
             self.api_key = get_apikey_value("openai")
         elif self.custom_llm_provider == "anthropic":

src/ontogpt/conf/synonymizer-conf.yaml

@@ -22,4 +22,3 @@ rules:
       match: "(.*) food product"
       match_scope: "FOODON"
       replacement: "\\1"
-

src/ontogpt/engines/generic_engine.py

@@ -1,4 +1,5 @@
-"""Synonym engine."""
+"""Generic engine."""
+
 import logging
 from copy import deepcopy
 from dataclasses import dataclass

src/ontogpt/engines/pheno_engine.py

@@ -1,4 +1,4 @@
-"""Reasoner engine."""
+"""Pheno engine."""
 
 import json
 import logging

src/ontogpt/io/json_wrapper.py

@@ -25,6 +25,7 @@ def eliminate_empty(obj: Any, preserve=False) -> Any:
     else:
         return obj
 
+
 def dump_minimal_json(obj: Any, minimize=True, file: Optional[TextIO] = None) -> str:
     """Dump a JSON string, but eliminate Nones and empty lists and dicts."""
     if not file: