chore: remove stale TODO and legacy comments (#2316)

cognee/api/v1/cognify/cognify.py

@@ -245,7 +245,7 @@ class ScientificPaper(DataPoint):
     )
 
 
-async def get_default_tasks(  # TODO: Find out a better way to do this (Boris's comment)
+async def get_default_tasks(  # TODO(#2349): Find out a better way to do this
     user: User = None,
     graph_model: BaseModel = KnowledgeGraph,
     chunker=TextChunker,

cognee/context_global_variables.py

@@ -138,8 +138,8 @@ async def set_database_global_context_variables(dataset: Union[str, UUID], user_
     )
 
     # Set vector and graph database configuration based on dataset database information
-    # TODO: Add better handling of vector and graph config across Cognee.
-    #  LRU_CACHE takes into account order of inputs, if order of inputs is changed it will be registered as a new DB adapter
+    # TODO(#2357): Add better handling of vector and graph config across Cognee.
+    #              LRU_CACHE takes into account order of inputs, if order of inputs is changed it will be registered as a new DB adapter
     vector_config = {
         "vector_db_provider": dataset_database.vector_database_provider,
         "vector_db_url": dataset_database.vector_database_url,

cognee/infrastructure/databases/cache/cache_db_interface.py

@@ -53,7 +53,7 @@ async def add_qa(
         context: str,
         answer: str,
     ):
-        """Backward-compatibility: delegates to create_qa_entry with generated qa_id. :TODO: delete when retrievers are updated"""
+        """Backward-compatibility: delegates to create_qa_entry with generated qa_id."""
         return await self.create_qa_entry(
             user_id,
             session_id,
@@ -82,7 +82,7 @@ async def create_qa_entry(
         pass
 
     async def get_latest_qa(self, user_id: str, session_id: str, last_n: int = 5):
-        """Backward-compat: delegates to get_latest_qa_entries. :TODO: delete when retrievers are updated"""
+        """Backward-compat: delegates to get_latest_qa_entries."""
         return await self.get_latest_qa_entries(user_id, session_id, last_n)
 
     @abstractmethod
@@ -93,7 +93,7 @@ async def get_latest_qa_entries(self, user_id: str, session_id: str, last_n: int
         pass
 
     async def get_all_qas(self, user_id: str, session_id: str):
-        """Backward-compat: delegates to get_all_qa_entries. :TODO: delete when retrievers are updated"""
+        """Backward-compat: delegates to get_all_qa_entries."""
         return await self.get_all_qa_entries(user_id, session_id)
 
     @abstractmethod

cognee/infrastructure/databases/exceptions/exceptions.py

@@ -46,7 +46,6 @@ def __init__(
         self.message = message
         self.name = name
         self.status_code = status_code
-        # super().__init__(message, name, status_code) :TODO: This is not an error anymore with the dynamic exception handling therefore we shouldn't log error
 
 
 class EntityAlreadyExistsError(CogneeValidationError):

cognee/infrastructure/databases/graph/neo4j_driver/Neo4jAuraDevDatasetDatabaseHandler.py

@@ -75,15 +75,15 @@ async def create_dataset(cls, dataset_id: Optional[UUID], user: Optional[User])
             "Content-Type": "application/json",
         }
 
-        # TODO: Maybe we can allow **kwargs parameter forwarding for cases like these
+        # TODO(#2354): Maybe we can allow **kwargs parameter forwarding for cases like these
         #       Too allow different configurations between datasets
         payload = {
             "version": "5",
             "region": "europe-west1",
             "memory": "1GB",
             "name": graph_db_name[
                 0:29
-            ],  # TODO: Find better name to name Neo4j instance within 30 character limit
+            ],  # TODO(#2354): Find better name to name Neo4j instance within 30 character limit
             "type": "professional-db",
             "tenant_id": tenant_id,
             "cloud_provider": "gcp",

cognee/infrastructure/databases/hybrid/neptune_analytics/NeptuneAnalyticsAdapter.py

@@ -236,7 +236,7 @@ async def search(
         query_vector: Optional[List[float]] = None,
         limit: Optional[int] = None,
         with_vector: bool = False,
-        include_payload: bool = False,  # TODO: Add support for this parameter
+        include_payload: bool = False,  # TODO(#2352): Add support for this parameter
     ):
         """
         Perform a search in the specified collection using either a text query or a vector

cognee/infrastructure/databases/vector/chromadb/ChromaDBAdapter.py

@@ -361,8 +361,8 @@ async def search(
         limit: Optional[int] = 15,
         with_vector: bool = False,
         normalized: bool = True,
-        include_payload: bool = False,  # TODO: Add support for this parameter when set to False
-        node_name: Optional[List[str]] = None,  # TODO: Add support/functionality for this parameter
+        include_payload: bool = False,  # TODO(#2353): Add support for this parameter when set to False
+        node_name: Optional[List[str]] = None,  # TODO(#2353): Add support/functionality for this parameter
     ):
         """
         Search for items in a collection using either a text or a vector query.

cognee/infrastructure/llm/structured_output_framework/litellm_instructor/llm/openai/adapter.py

@@ -87,8 +87,8 @@ def __init__(
             fallback_endpoint=fallback_endpoint,
         )
         self.instructor_mode = instructor_mode if instructor_mode else self.default_instructor_mode
-        # TODO: With gpt5 series models OpenAI expects JSON_SCHEMA as a mode for structured outputs.
-        #       Make sure all new gpt models will work with this mode as well.
+        # TODO(#2355): With gpt5 series models OpenAI expects JSON_SCHEMA as a mode for structured outputs.
+        #              Make sure all new gpt models will work with this mode as well.
         if "gpt-5" in model:
             self.aclient = instructor.from_litellm(
                 litellm.acompletion, mode=instructor.Mode(self.instructor_mode)

cognee/tests/integration/retrieval/test_rag_completion_retriever.py

@@ -285,7 +285,7 @@ async def test_rag_completion_context_multiple_chunks(setup_test_environment_wit
 @pytest.mark.asyncio
 async def test_rag_completion_context_complex(setup_test_environment_with_chunks_complex):
     """Integration test: verify CompletionRetriever can retrieve context (complex)."""
-    # TODO: top_k doesn't affect the output, it should be fixed.
+    # TODO(#2351): top_k doesn't affect the output, it should be fixed.
     retriever = CompletionRetriever(top_k=20)
     query = "Christina"
 

cognee/tests/test_cognee_server_start.py

@@ -188,7 +188,7 @@ def test_server_is_running(self):
             len(ontology_nodes), 0, "No ontology nodes found - ontology was not integrated"
         )
 
-        # TODO: Add test to verify cognify pipeline is complete before testing search
+        # TODO(#2350): Add test to verify cognify pipeline is complete before testing search
 
         # Search request
         url = "http://127.0.0.1:8000/api/v1/search"

cognee/tests/unit/entity_extraction/regex_entity_extraction_test.py

@@ -83,7 +83,7 @@ async def test_extract_times(regex_extractor):
 @pytest.mark.asyncio
 async def test_extract_money(regex_extractor):
     """Test extraction of monetary amounts."""
-    # TODO: Lazar to fix regex for test, it's failing currently
+    # TODO(#2356): Lazar to fix regex for test, it's failing currently
     pass
     # text = "The product costs $1,299.99 or €1.045,00 depending on your region."
     # entities = await regex_extractor.extract_entities(text)

cognee/tests/unit/infrastructure/databases/cache/test_fs_adapter_crud.py

@@ -87,7 +87,6 @@ async def test_prune(adapter):
     assert await adapter.get_all_qa_entries("u1", "s1") == []
 
 
-# Backward-compatibility tests (add_qa, get_latest_qa, get_all_qas):TODO: Can be deleted after session manager integration into retrievers
 
 
 @pytest.mark.asyncio

cognee/tests/unit/infrastructure/databases/cache/test_redis_adapter_crud.py

@@ -119,7 +119,6 @@ async def test_prune(adapter):
     assert await adapter.get_all_qa_entries("u1", "s1") == []
 
 
-# Backward-compatibility tests (add_qa, get_latest_qa, get_all_qas) :TODO: Can be deleted after session manager integration into retrievers
 @pytest.mark.asyncio
 async def test_add_qa_backward_compat(adapter):
     """Legacy add_qa stores entry with auto-generated qa_id."""

examples/pocs/single_add_datapoints/single_add_datapoints_pipeline.py

@@ -247,7 +247,7 @@ class ScientificPaper(DataPoint):
     )
 
 
-async def get_default_tasks(  # TODO: Find out a better way to do this (Boris's comment)
+async def get_default_tasks(  # TODO(#2349): Find out a better way to do this
     user: User = None,
     graph_model: BaseModel = KnowledgeGraph,
     chunker=TextChunker,