Add distributed similarity search

scimesh/worker/daemon.py

@@ -9,6 +9,7 @@ from pathlib import Path
 import random
 import re
 import shutil
+import subprocess
 import threading
 import time
 from datetime import datetime, timezone
@@ -202,12 +203,23 @@ class WorkerDaemon:
     def _report_failure(self, task: ClaimedTask, error: Exception) -> None:
         message = self._sanitize_error_message(error)
         try:
-            self.coordinator.fail(task, {"worker_id": self._worker_id(), "attempt": task.attempt, "error_code": type(error).__name__, "error_message": message})
+            self.coordinator.fail(task, {
+                "worker_id": self._worker_id(),
+                "attempt": task.attempt,
+                "error_code": type(error).__name__,
+                "error_message": message,
+                "retryable": self._is_retryable(error),
+            })
         except CoordinatorTransientError:
             raise
         except Exception:
             self._log("failed", task, error_type="FailureReportError")
 
+    @staticmethod
+    def _is_retryable(error: Exception) -> bool:
+        """Retry transient worker/transport failures, never invalid scientific input."""
+        return not isinstance(error, (ValueError, FileNotFoundError, subprocess.CalledProcessError))
+
     def _sanitize_error_message(self, error: Exception) -> str:
         """Keep coordinator-visible failures useful without exposing local paths."""
         message = str(error).replace(str(self.config.work_dir), "<worker-dir>")

scimesh/worker/runners.py

@@ -7,6 +7,8 @@ import subprocess
 import sys
 from typing import Protocol
 
+from scimesh.distributed.similarity_search import run_similarity_search_shard
+
 from .models import ClaimedTask, ProducedArtifact, RunResult
 
 
@@ -34,6 +36,12 @@ class SciMeshRunner:
             query_id, query_smiles = params.get("query_id"), params.get("query_smiles")
             if (query_id is None) == (query_smiles is None):
                 raise ValueError("exactly one of query_id or query_smiles is required")
+            if query_smiles is not None and "max_rows" not in params:
+                metrics = run_similarity_search_shard(input_path, params, output_path)
+                return RunResult((ProducedArtifact(output_path, "text/csv"),), metrics)
+            # Legacy URI jobs may still use query_id or an explicitly task-local
+            # max_rows value. CTX-08 plans never create those payloads; retain
+            # CLI execution only for backwards compatibility at this boundary.
             top_k = self._positive_int(params, "top_k", default=20)
             command += ["--query-id", self._string(params, "query_id")] if query_id is not None else ["--query-smiles", self._string(params, "query_smiles")]
             command += ["--top-k", str(top_k)]