Upgrade deps and python313 (#65)

* Upgrade deps and python 3.13

* fix moatless source

Author: aorwall

moatless/index/simple_faiss.py

@@ -14,7 +14,7 @@
 from fsspec.implementations.local import LocalFileSystem
 from llama_index.core.bridge.pydantic import PrivateAttr
 from llama_index.core.schema import BaseNode
-from llama_index.core.vector_stores.simple import _build_metadata_filter_fn
+from llama_index.core.vector_stores.simple import build_metadata_filter_fn
 from llama_index.core.vector_stores.types import (
     DEFAULT_PERSIST_DIR,
     BasePydanticVectorStore,
@@ -172,7 +172,7 @@ def query(
             similarity_top_k (int): top k most similar nodes
 
         """
-        query_filter_fn = _build_metadata_filter_fn(lambda node_id: self._data.metadata_dict[node_id], query.filters)
+        query_filter_fn = build_metadata_filter_fn(lambda node_id: self._data.metadata_dict[node_id], query.filters)
 
         query_embedding = cast(list[float], query.query_embedding)
         query_embedding_np = np.array(query_embedding, dtype="float32")[np.newaxis, :]

moatless/runner/docker_runner.py

@@ -271,6 +271,9 @@ async def start_job(
             elif effective_memory_limit:
                 # If memory limit is set but swap limit is not, default to twice the memory limit
                 cmd.extend(["--memory-swap", effective_memory_limit])
+            
+            # Add ulimit for file descriptors to prevent "Too many open files" errors
+            cmd.extend(["--ulimit", "nofile=65536:65536"])
 
             # Add Docker labels for easier container identification and querying
             job_labels = create_labels(project_id, trajectory_id)
@@ -292,6 +295,9 @@ async def start_job(
             if self.moatless_source_dir:
                 logger.info(f"Mounting {self.moatless_source_dir}:/opt/moatless/moatless")
                 cmd.extend(["-v", f"{self.moatless_source_dir}:/opt/moatless/moatless"])
+                # Also mount the lockfile to ensure dependency compatibility
+                cmd.extend(["-v", f"{self.moatless_source_dir}/uv.lock:/opt/moatless/uv.lock"])
+                cmd.extend(["-v", f"{self.moatless_source_dir}/pyproject.toml:/opt/moatless/pyproject.toml"])
                 cmd.extend(["-e", "PYTHONPATH=/opt/moatless/moatless:$PYTHONPATH"])
 
             args = create_job_args(project_id, trajectory_id, job_func, node_id)
@@ -311,6 +317,10 @@ async def start_job(
                 self.logger.info(f"Will run update-moatless.sh with branch {branch_to_use}")
                 run_command += f"/opt/moatless/docker/update-moatless.sh --branch {branch_to_use} && "
 
+            # If using local source, sync dependencies first (not frozen) to use local lockfile
+            if self.moatless_source_dir:
+                run_command += "cd /opt/moatless && uv sync --compile-bytecode --all-extras && "
+            
             # Add the main job command
             run_command += f"date '+%Y-%m-%d %H:%M:%S' && echo 'Starting job at ' $(date '+%Y-%m-%d %H:%M:%S') && uv run - <<EOF\n{args}\nEOF"
 

pyproject.toml

@@ -11,50 +11,50 @@ readme = "README.md"
 authors = [
     {name = "Albert Örwall", email = "[email protected]"},
 ]
-requires-python = "<3.13,>=3.10"
+requires-python = "<3.14,>=3.10"
 dependencies = [
-    "pydantic<3.0.0,>=2.8.2",
-    "tiktoken<1.0.0,>=0.8.0",
-    "networkx<4.0,>=3.3",
+    "pydantic<3.0.0,>=2.11.7",
+    "tiktoken<2.0.0,>=0.11.0",
+    "networkx<4.0,>=3.4",
     "tree-sitter==0.24.0",
     "tree-sitter-python==0.23.6",
     "tree-sitter-java==0.23.5",
-    "rapidfuzz<4.0.0,>=3.9.5",
-    "gitpython<4.0.0,>=3.1.43",
+    "rapidfuzz<4.0.0,>=3.13.0",
+    "gitpython<4.0.0,>=3.1.45",
     "unidiff<1.0.0,>=0.7.5",
     "python-dotenv==1.0.1",
-    "docstring-parser<1.0,>=0.16",
-    "litellm<2.0.0,>=1.67.0",
-    "openai<2.0.0,>=1.41.0",
-    "anthropic<1.0.0,>=0.49.0",
-    "llama-index<1.0.0,>=0.12.11",
-    "llama-index-embeddings-openai<1.0.0,>=0.3.1",
-    "llama-index-embeddings-voyageai<1.0.0,>=0.3.4",
-    "llama-index-readers-file<1.0.0,>=0.4.3",
-    "faiss-cpu<2.0.0.0,>=1.8.0.post1",
-    "voyageai<1.0.0,>=0.3.2",
-    "filelock<4.0.0,>=3.16.1",
+    "docstring-parser<1.0,>=0.17.0",
+    "litellm<2.0.0,>=1.75.5",
+    "openai<2.0.0,>=1.99.9",
+    "anthropic<1.0.0,>=0.62.0",
+    "llama-index<2.0.0,>=0.13.1",
+    "llama-index-embeddings-openai<1.0.0,>=0.5.0",
+    "llama-index-embeddings-voyageai<1.0.0,>=0.4.1",
+    "llama-index-readers-file<1.0.0,>=0.5.0",
+    "faiss-cpu<2.0.0.0,>=1.11.0.post1",
+    "voyageai<1.0.0,>=0.3.4",
+    "filelock<4.0.0,>=3.18.0",
     "aiofiles<25.0.0,>=24.1.0",
-    "swebench<4.0.0,>=3.0.15",
-    "opentelemetry-sdk<2.0.0,>=1.30.0",
-    "sqlalchemy>=2.0.41",
+    "swebench<4.0.0,>=3.0.17",
+    "opentelemetry-sdk<2.0.0,>=1.36.0",
+    "sqlalchemy>=2.0.43",
     "psycopg2-binary>=2.9.10",
-    "redis<6.0.0,>=5.2.1",
+    "redis<6.0.0,>=5.3.1",
     "gunicorn>=23.0.0",
-    "opentelemetry-api<2.0.0,>=1.30.0",
-    "opentelemetry-exporter-otlp<2.0.0,>=1.30.0",
-    "opentelemetry-instrumentation<1.0,>=0.51b0",
-    "opentelemetry-instrumentation-fastapi<1.0,>=0.51b0",
-    "fastapi>=0.115.12",
-    "uvicorn>=0.34.2",
+    "opentelemetry-api<2.0.0,>=1.36.0",
+    "opentelemetry-exporter-otlp<2.0.0,>=1.36.0",
+    "opentelemetry-instrumentation<1.0,>=0.57b0",
+    "opentelemetry-instrumentation-fastapi<1.0,>=0.57b0",
+    "fastapi>=0.116.1",
+    "uvicorn>=0.35.0",
     "dotenv>=0.9.9",
-    "botocore<2.0.0,>=1.35.54",
-    "boto3<2.0.0,>=1.35.54",
-    "aioboto3<15.0.0,>=14.1.0",
-    "kubernetes<33.0.0,>=32.0.0",
-    "kubernetes-asyncio<33.0.0,>=32.0.0",
-    "azure-storage-blob<13.0.0,>=12.25.0",
-    "azure-monitor-opentelemetry<2.0.0,>=1.6.5",
+    "botocore<2.0.0,>=1.37.3",
+    "boto3<2.0.0,>=1.37.3",
+    "aioboto3<15.0.0,>=14.3.0",
+    "kubernetes<33.0.0,>=32.0.1",
+    "kubernetes-asyncio<33.0.0,>=32.3.2",
+    "azure-storage-blob<13.0.0,>=12.26.0",
+    "azure-monitor-opentelemetry<2.0.0,>=1.6.13",
 ]
 
 [dependency-groups]