Remove Execution Wrapper (#905)

* Rm files readded by git

* Fix merge botch

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
 
       - id: black
         name: black
-        entry: bash -c 'cd py && poetry run black $(git diff --cached --name-only --diff-filter=ACM | grep ".py$" | xargs -I {} echo ../{})'
+        entry: bash -c 'cd py && poetry run black .'
         language: system
         types: [python]
         pass_filenames: false

py/cli/commands/ingestion.py

@@ -11,9 +11,15 @@
 
 
 @cli.command()
-@click.argument("file_paths", nargs=-1, required=True, type=click.Path(exists=True))
-@click.option("--document-ids", multiple=True, help="Document IDs for ingestion")
-@click.option("--metadatas", type=JSON, help="Metadatas for ingestion as a JSON string")
+@click.argument(
+    "file_paths", nargs=-1, required=True, type=click.Path(exists=True)
+)
+@click.option(
+    "--document-ids", multiple=True, help="Document IDs for ingestion"
+)
+@click.option(
+    "--metadatas", type=JSON, help="Metadatas for ingestion as a JSON string"
+)
 @click.option(
     "--versions",
     multiple=True,
@@ -27,18 +33,24 @@ def ingest_files(client, file_paths, document_ids, metadatas, versions):
         document_ids = list(document_ids) if document_ids else None
         versions = list(versions) if versions else None
 
-        response = client.ingest_files(file_paths, metadatas, document_ids, versions)
+        response = client.ingest_files(
+            file_paths, metadatas, document_ids, versions
+        )
     click.echo(json.dumps(response, indent=2))
 
 
 @cli.command()
-@click.argument("file-paths", nargs=-1, required=True, type=click.Path(exists=True))
+@click.argument(
+    "file-paths", nargs=-1, required=True, type=click.Path(exists=True)
+)
 @click.option(
     "--document-ids",
     required=True,
     help="Document IDs to update (comma-separated)",
 )
-@click.option("--metadatas", type=JSON, help="Metadatas for updating as a JSON string")
+@click.option(
+    "--metadatas", type=JSON, help="Metadatas for updating as a JSON string"
+)
 @click.pass_obj
 def update_files(client, file_paths, document_ids, metadatas):
     """Update existing files in R2R."""
@@ -77,7 +89,9 @@ def ingest_files_from_urls(client, urls):
 
         try:
             response = client.ingest_files([temp_file_path])
-            click.echo(f"File '{filename}' ingested successfully. Response: {response}")
+            click.echo(
+                f"File '{filename}' ingested successfully. Response: {response}"
+            )
             ingested_files.append(filename)
         finally:
             os.unlink(temp_file_path)

py/cli/commands/retrieval.py

@@ -5,7 +5,9 @@
 
 
 @cli.command()
-@click.option("--query", prompt="Enter your search query", help="The search query")
+@click.option(
+    "--query", prompt="Enter your search query", help="The search query"
+)
 # VectorSearchSettings
 @click.option(
     "--use-vector-search",
@@ -18,21 +20,27 @@
     type=JSON,
     help="Filters to apply to the vector search as a JSON",
 )
-@click.option("--search-limit", default=None, help="Number of search results to return")
+@click.option(
+    "--search-limit", default=None, help="Number of search results to return"
+)
 @click.option("--do-hybrid-search", is_flag=True, help="Perform hybrid search")
 @click.option(
     "--selected-group-ids", type=JSON, help="Group IDs to search for as a JSON"
 )
 # KGSearchSettings
-@click.option("--use-kg-search", is_flag=True, help="Use knowledge graph search")
+@click.option(
+    "--use-kg-search", is_flag=True, help="Use knowledge graph search"
+)
 @click.option("--kg-search-type", default=None, help="Local or Global")
 @click.option("--kg-search-level", default=None, help="Level of KG search")
 @click.option(
     "--kg-search-generation-config",
     type=JSON,
     help="KG search generation config",
 )
-@click.option("--entity-types", type=JSON, help="Entity types to search for as a JSON")
+@click.option(
+    "--entity-types", type=JSON, help="Entity types to search for as a JSON"
+)
 @click.option(
     "--relationships", type=JSON, help="Relationships to search for as a JSON"
 )
@@ -111,21 +119,27 @@ def search(client, query, **kwargs):
     "--use-vector-search", is_flag=True, default=True, help="Use vector search"
 )
 @click.option("--filters", type=JSON, help="Search filters as JSON")
-@click.option("--search-limit", default=10, help="Number of search results to return")
+@click.option(
+    "--search-limit", default=10, help="Number of search results to return"
+)
 @click.option("--do-hybrid-search", is_flag=True, help="Perform hybrid search")
 @click.option(
     "--selected-group-ids", type=JSON, help="Group IDs to search for as a JSON"
 )
 # KG Search Settings
-@click.option("--use-kg-search", is_flag=True, help="Use knowledge graph search")
+@click.option(
+    "--use-kg-search", is_flag=True, help="Use knowledge graph search"
+)
 @click.option("--kg-search-type", default="global", help="Local or Global")
 @click.option(
     "--kg-search-level",
     default=None,
     help="Level of cluster to use for Global KG search",
 )
 @click.option("--kg-search-model", default=None, help="Model for KG agent")
-@click.option("--entity-types", type=JSON, help="Entity types to search for as a JSON")
+@click.option(
+    "--entity-types", type=JSON, help="Entity types to search for as a JSON"
+)
 @click.option(
     "--relationships", type=JSON, help="Relationships to search for as a JSON"
 )

py/core/base/providers/kg.py

@@ -37,7 +37,9 @@ class KGProvider(ABC):
 
     def __init__(self, config: KGConfig) -> None:
         if not isinstance(config, KGConfig):
-            raise ValueError("KGProvider must be initialized with a `KGConfig`.")
+            raise ValueError(
+                "KGProvider must be initialized with a `KGConfig`."
+            )
         logger.info(f"Initializing KG provider with config: {config}")
         self.config = config
         self.validate_config()
@@ -116,7 +118,9 @@ def structured_query(
             param_map = {}
 
     @abstractmethod
-    def vector_query(self, query, **kwargs: Any) -> Tuple[list[Entity], list[float]]:
+    def vector_query(
+        self, query, **kwargs: Any
+    ) -> Tuple[list[Entity], list[float]]:
         """Abstract method to query the graph store with a vector store query."""
 
     # TODO - Type this method.

py/core/configs/unstructured.toml

@@ -5,4 +5,4 @@ provider = "unstructured_api"
 provider = "unstructured"
 method = "recursive"
 chunk_size = 512
-chunk_overlap = 50
+chunk_overlap = 50

py/core/main/app_entry.py

@@ -38,7 +38,10 @@ def r2r_app(
             raise ValueError(f"Invalid config name: {config_name}")
         config = R2RConfig.from_toml(R2RBuilder.CONFIG_OPTIONS[config_name])
 
-    if config.embedding.provider == "openai" and "OPENAI_API_KEY" not in os.environ:
+    if (
+        config.embedding.provider == "openai"
+        and "OPENAI_API_KEY" not in os.environ
+    ):
         raise ValueError(
             "Must set OPENAI_API_KEY in order to initialize OpenAIEmbeddingProvider."
         )

py/core/main/services/retrieval_service.py

@@ -61,7 +61,10 @@ async def search(
         async with manage_run(self.run_manager, "search_app") as run_id:
             t0 = time.time()
 
-            if kg_search_settings.use_kg_search and self.config.kg.provider is None:
+            if (
+                kg_search_settings.use_kg_search
+                and self.config.kg.provider is None
+            ):
                 raise R2RException(
                     status_code=400,
                     message="Knowledge Graph search is not enabled in the configuration.",
@@ -164,17 +167,23 @@ async def rag(
                 )
 
                 if len(results) == 0:
-                    raise R2RException(status_code=404, message="No results found")
+                    raise R2RException(
+                        status_code=404, message="No results found"
+                    )
                 if len(results) > 1:
-                    logger.warning(f"Multiple results found for query: {query}")
+                    logger.warning(
+                        f"Multiple results found for query: {query}"
+                    )
 
                 completion_record.search_results = (
                     results[0].search_results
                     if hasattr(results[0], "search_results")
                     else None
                 )
                 completion_record.llm_response = (
-                    results[0].completion if hasattr(results[0], "completion") else None
+                    results[0].completion
+                    if hasattr(results[0], "completion")
+                    else None
                 )
                 completion_record.completion_end_time = datetime.now()
 
@@ -210,7 +219,9 @@ async def stream_rag_response(
     ):
         async def stream_response():
             async with manage_run(self.run_manager, "arag"):
-                async for chunk in await self.pipelines.streaming_rag_pipeline.run(
+                async for (
+                    chunk
+                ) in await self.pipelines.streaming_rag_pipeline.run(
                     input=to_async_generator([query]),
                     run_manager=self.run_manager,
                     vector_search_settings=vector_search_settings,
@@ -260,7 +271,9 @@ async def agent(
 
                     async def stream_response():
                         async with manage_run(self.run_manager, "arag_agent"):
-                            async for chunk in self.agents.streaming_rag_agent.arun(
+                            async for (
+                                chunk
+                            ) in self.agents.streaming_rag_agent.arun(
                                 messages=messages,
                                 system_instruction=task_prompt_override,
                                 vector_search_settings=vector_search_settings,
@@ -300,4 +313,6 @@ async def stream_response():
                         status_code=502,
                         message="Ollama server not reachable or returned an invalid response",
                     )
-                raise R2RException(status_code=500, message="Internal Server Error")
+                raise R2RException(
+                    status_code=500, message="Internal Server Error"
+                )

py/pyproject.toml

@@ -24,10 +24,10 @@ python = ">=3.9,<3.13"
 httpx = "^0.27.0"
 nest-asyncio = "^1.6.0"
 fastapi = "^0.109.2"
+click = "^8.1.7"
 
 # Core dependencies (optional)
 openai = { version = "^1.11.1" }
-
 pydantic = { extras = ["email"], version = "^2.8.2", optional = true }
 python-multipart = { version = "^0.0.9", optional = true }
 gunicorn = { version = "^21.2.0", optional = true }

py/sdk/client.py

@@ -105,7 +105,9 @@ def __init__(
             self._retrieval,
             self._server,
         ]:
-            for name, method in inspect.getmembers(group, predicate=inspect.isfunction):
+            for name, method in inspect.getmembers(
+                group, predicate=inspect.isfunction
+            ):
                 if not name.startswith("_"):
                     self._methods[name] = method
 
@@ -181,7 +183,9 @@ async def __aexit__(self, exc_type, exc_val, exc_tb):
 
     def __getattr__(self, name):
         if name in self._methods:
-            return lambda *args, **kwargs: self._methods[name](self, *args, **kwargs)
+            return lambda *args, **kwargs: self._methods[name](
+                self, *args, **kwargs
+            )
         raise AttributeError(f"'R2RClient' object has no attribute '{name}'")
 
     def __dir__(self):

py/sdk/ingestion.py

@@ -34,7 +34,9 @@ async def ingest_files(
         for path in file_paths:
             if os.path.isdir(path):
                 for root, _, files in os.walk(path):
-                    all_file_paths.extend(os.path.join(root, file) for file in files)
+                    all_file_paths.extend(
+                        os.path.join(root, file) for file in files
+                    )
             else:
                 all_file_paths.append(path)
 
@@ -94,7 +96,9 @@ async def update_files(
             dict: Update results containing processed, failed, and skipped documents.
         """
         if len(file_paths) != len(document_ids):
-            raise ValueError("Number of file paths must match number of document IDs.")
+            raise ValueError(
+                "Number of file paths must match number of document IDs."
+            )
 
         with ExitStack() as stack:
             files = [