Fix relative worker work directory

scimesh/worker/config.py

@@ -68,6 +68,10 @@ class WorkerConfig:
             _positive_number(self.cleanup_after_seconds, "cleanup_after_seconds", allow_zero=True)
         if not self.capabilities:
             raise ValueError("capabilities cannot be empty")
+        # Runner subprocesses use a task directory as their cwd. Keep the
+        # configured root absolute so input/output paths remain valid there
+        # even when the CLI received a convenient relative --work-dir value.
+        object.__setattr__(self, "work_dir", self.work_dir.expanduser().resolve())
 
     @classmethod
     def from_environment(

scimesh/worker/runners.py

@@ -18,6 +18,9 @@ class SciMeshRunner:
     """Allowlisted adapter from coordinator workloads to the local SciMesh CLI."""
 
     def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
+        # The subprocess changes cwd to task_dir. Absolute paths keep a caller
+        # supplied relative work directory from being resolved twice.
+        task_dir = task_dir.resolve()
         input_path = task_dir / "input"
         output_path = task_dir / "result.csv"
         # The coordinator contract historically used underscores while the

tests/test_worker_daemon.py

@@ -314,6 +314,32 @@ def test_environment_overrides_allow_cli_only_configuration(monkeypatch: pytest.
     assert "similarity_search" in config.capabilities
 
 
+def test_relative_work_dir_is_normalized_for_runner_subprocesses(
+    monkeypatch: pytest.MonkeyPatch, tmp_path: Path
+) -> None:
+    monkeypatch.chdir(tmp_path)
+    config = WorkerConfig("https://coordinator.example", None, Path("./worker-data"))
+    assert config.work_dir == tmp_path / "worker-data"
+
+    task_dir = config.work_dir / "task" / "1"
+    task_dir.mkdir(parents=True)
+    (task_dir / "input").write_text("fixture", encoding="utf-8")
+    command: list[str] = []
+
+    def fake_run(args: list[str], **_: object) -> None:
+        command.extend(args)
+        output = Path(args[args.index("--output") + 1])
+        output.write_text("id,score\n", encoding="utf-8")
+
+    monkeypatch.setattr("scimesh.worker.runners.subprocess.run", fake_run)
+    task = ClaimedTask(
+        "task", 1, "2026-07-30T00:00:00Z", "similarity-search",
+        InputArtifact("https://example.test/input", "a" * 64), {"query_smiles": "CCO"},
+    )
+    SciMeshRunner().run(task, task_dir)
+    assert command[4] == str(task_dir / "input")
+
+
 def test_worker_registration_sets_returned_identity(tmp_path: Path) -> None:
     worker, _, _, _, _ = daemon(tmp_path, None, b"")
     worker._register_worker()