Sonarqube cleanup 3

backend/openmlr/routes/agent.py

@@ -60,7 +60,7 @@ async def _stream():
                 except TimeoutError:
                     yield ":ping\n\n"
         except asyncio.CancelledError:
-            pass
+            raise
         except GeneratorExit:
             pass
         finally:
@@ -150,7 +150,7 @@ async def get_conversation(
     # Re-generate title if still "New conversation" and has messages
     if conv.title == "New conversation" and msgs:
         msg_dicts = [_msg_dict(m) for m in msgs]
-        asyncio.create_task(
+        _task = asyncio.create_task(
             _auto_title(_sm(request), _bus(request), db, conv.id, conv.uuid, msg_dicts)
         )
 
@@ -408,7 +408,9 @@ async def send_message(
         # Title generation (still async in web process for now)
         if user_count in (1, 3):
             msg_dicts = await _load_messages(db, conv.id)
-            asyncio.create_task(_auto_title(sm, event_bus, db, conv.id, conv.uuid, msg_dicts))
+            _task = asyncio.create_task(
+                _auto_title(sm, event_bus, db, conv.id, conv.uuid, msg_dicts)
+            )
 
         return {"ok": True, "job_id": job.job_id if job else None, "background": True}
 
@@ -443,11 +445,11 @@ async def send_message(
         _wire_persistence(active, db, conv.id)
         active._persist_wired = True
 
-    asyncio.create_task(sm.process_message(conv.id, body.message, mode=body.mode))
+    _task = asyncio.create_task(sm.process_message(conv.id, body.message, mode=body.mode))
 
     if user_count in (1, 3):
         msg_dicts = await _load_messages(db, conv.id)
-        asyncio.create_task(_auto_title(sm, event_bus, db, conv.id, conv.uuid, msg_dicts))
+        _task = asyncio.create_task(_auto_title(sm, event_bus, db, conv.id, conv.uuid, msg_dicts))
 
     return {"ok": True, "background": False}
 
@@ -601,7 +603,9 @@ async def submit_approval(
     if active and active.session.pending_approval:
         from ..agent.loop import _handle_approval
 
-        asyncio.create_task(_handle_approval(active.session, active.tool_router, body.approvals))
+        _task = asyncio.create_task(
+            _handle_approval(active.session, active.tool_router, body.approvals)
+        )
     return {"ok": True}
 
 

backend/openmlr/routes/terminal.py

@@ -92,9 +92,11 @@ async def _authenticate_ws(token: str | None) -> User | None:
 
 async def _cleanup_process(pid: int, master_fd: int) -> None:
     """Clean up PTY process with SIGKILL escalation to prevent zombies."""
+    loop = asyncio.get_event_loop()
+
     # Close the master fd first
     try:
-        os.close(master_fd)
+        await loop.run_in_executor(None, os.close, master_fd)
     except OSError:
         pass
 
@@ -103,14 +105,14 @@ async def _cleanup_process(pid: int, master_fd: int) -> None:
 
     # Send SIGTERM and wait with timeout
     try:
-        os.kill(pid, signal.SIGTERM)
+        await loop.run_in_executor(None, os.kill, pid, signal.SIGTERM)
     except ProcessLookupError:
         return
 
     # Poll up to 2 seconds for graceful exit
     for _ in range(20):
         try:
-            result, _ = os.waitpid(pid, os.WNOHANG)
+            result, _ = await loop.run_in_executor(None, os.waitpid, pid, os.WNOHANG)
             if result != 0:
                 return  # Process exited
         except ChildProcessError:
@@ -119,8 +121,8 @@ async def _cleanup_process(pid: int, master_fd: int) -> None:
 
     # Escalate to SIGKILL
     try:
-        os.kill(pid, signal.SIGKILL)
-        os.waitpid(pid, 0)  # Blocking wait after SIGKILL
+        await loop.run_in_executor(None, os.kill, pid, signal.SIGKILL)
+        await loop.run_in_executor(None, os.waitpid, pid, 0)  # Blocking wait after SIGKILL
     except (ProcessLookupError, ChildProcessError):
         pass
 

backend/openmlr/services/event_bus.py

@@ -110,9 +110,8 @@ async def stop_redis_bridge(self) -> None:
             self._redis_bridge_task.cancel()
             try:
                 await self._redis_bridge_task
-            except asyncio.CancelledError:
-                pass
-            self._redis_bridge_task = None
+            finally:
+                self._redis_bridge_task = None
 
     @property
     def subscriber_count(self) -> int:
@@ -130,6 +129,6 @@ async def sse_generator(queue: asyncio.Queue) -> AsyncGenerator[str, None]:
             except TimeoutError:
                 yield ":ping\n\n"
     except asyncio.CancelledError:
-        pass
+        raise
     except GeneratorExit:
         pass

backend/openmlr/services/redis_pubsub.py

@@ -94,8 +94,8 @@
             self._task.cancel()
             try:
                 await self._task
-            except asyncio.CancelledError:
+            finally:
                 pass
         logger.info("Redis event bridge stopped")
 
     def subscribe(self) -> asyncio.Queue:

backend/openmlr/tasks/agent_tasks.py

@@ -189,7 +189,7 @@
                     await clear_interrupt(conversation_id)
                     break
         except asyncio.CancelledError:
-            pass
+            raise
         except Exception as e:
             logger.warning(f"Interrupt poll error: {e}")
 
@@ -234,8 +234,8 @@
         interrupt_task.cancel()
         try:
             await interrupt_task
-        except asyncio.CancelledError:
+        finally:
             pass
 
         # Cleanup
         try:

backend/openmlr/tools/local.py

@@ -373,6 +373,11 @@ async def _direct_exec(command: str, timeout: int, cwd: str) -> tuple[str, bool]
 # ── File tools (host filesystem) ─────────────────────────
 
 
+def _read_file_lines(path: Path) -> list[str]:
+    with open(path, encoding="utf-8", errors="replace") as f:
+        return f.readlines()
+
+
 async def _handle_read(path: str, offset: int = 1, limit: int = 2000, **kwargs) -> tuple[str, bool]:
     try:
         target = Path(path).expanduser()
@@ -393,8 +398,8 @@ async def _handle_read(path: str, offset: int = 1, limit: int = 2000, **kwargs)
         if not target.exists():
             return f"File not found: {target}", False
 
-        with open(target, encoding="utf-8", errors="replace") as f:
-            all_lines = f.readlines()
+        loop = asyncio.get_event_loop()
+        all_lines = await loop.run_in_executor(None, _read_file_lines, target)
 
         start = max(0, offset - 1)
         end = start + limit

backend/openmlr/tools/papers.py

@@ -1019,8 +1019,7 @@ def _extract_arxiv_id(text: str) -> str | None:
 
 def _extract_arxiv_from_ids(ids: dict) -> str | None:
     """Extract arxiv ID from OpenAlex ids dict."""
-    ids.get("openalex", "")
-    doi = ids.get("doi", "")
+    doi = ids.get("openalex", "") or ids.get("doi", "")
     if "arXiv" in doi:
         return _extract_arxiv_id(doi)
     return None

backend/openmlr/tools/sandbox_tools.py

@@ -144,25 +144,29 @@ async def _local_probe() -> str:
     """Quick local environment probe."""
     import platform
     import shutil
-    import subprocess
 
     lines = [f"OS: {platform.system()} {platform.release()}"]
 
     try:
-        py = subprocess.run(["python3", "--version"], capture_output=True, text=True, timeout=5)
-        lines.append(f"Python: {py.stdout.strip()}")
+        py = await asyncio.create_subprocess_exec(
+            "python3", "--version", stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE
+        )
+        stdout, _ = await asyncio.wait_for(py.communicate(), timeout=5)
+        lines.append(f"Python: {stdout.decode().strip()}")
     except Exception:
         lines.append("Python: unknown")
 
     try:
-        gpu = subprocess.run(
-            ["nvidia-smi", "--query-gpu=name,memory.total", "--format=csv,noheader"],
-            capture_output=True,
-            text=True,
-            timeout=5,
+        gpu = await asyncio.create_subprocess_exec(
+            "nvidia-smi",
+            "--query-gpu=name,memory.total",
+            "--format=csv,noheader",
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
         )
+        stdout, _ = await asyncio.wait_for(gpu.communicate(), timeout=5)
         if gpu.returncode == 0:
-            lines.append(f"GPU: {gpu.stdout.strip()}")
+            lines.append(f"GPU: {stdout.decode().strip()}")
         else:
             lines.append("GPU: not available")
     except Exception:

backend/openmlr/tools/workspace_tools.py

@@ -8,6 +8,7 @@
 - Log tool failures
 """
 
+import asyncio
 import json
 import logging
 from contextvars import ContextVar
@@ -185,8 +186,13 @@ async def _workspace_search(query: str) -> tuple[str, bool]:
             try:
                 if os.path.getsize(fpath) > 500_000:
                     continue
-                with open(fpath, encoding="utf-8", errors="ignore") as f:
-                    content = f.read(10000)
+
+                def read_file(path: str = fpath) -> str:
+                    with open(path, encoding="utf-8", errors="ignore") as f:
+                        return f.read(10000)
+
+                loop = asyncio.get_event_loop()
+                content = await loop.run_in_executor(None, read_file)
                 if query_lower in content.lower():
                     results.append(f"- **{rel_path}** (content match)")
             except Exception:

backend/tests/test_compute.py

@@ -280,7 +280,7 @@ def test_roundtrip(self):
         restored = ComputeCapabilities.from_dict(d)
         assert restored.platform == "test"
         assert restored.cpu_cores == 16
-        assert restored.available_ram_gb == 32.5
+        assert restored.available_ram_gb == pytest.approx(32.5)
         assert len(restored.gpu_info) == 2
         assert restored.docker_available is True
 

backend/tests/test_config.py

@@ -25,7 +25,7 @@ def test_yolo_mode_default(self):
         assert AgentConfig().yolo_mode is False
 
     def test_compact_threshold_ratio_default(self):
-        assert AgentConfig().compact_threshold_ratio == 0.90
+        assert AgentConfig().compact_threshold_ratio == pytest.approx(0.90)
 
     def test_untouched_messages_default(self):
         assert AgentConfig().untouched_messages == 5

backend/tests/test_db_operations.py

@@ -261,7 +261,7 @@ async def test_set_user_setting_int_value(self, db_session: AsyncSession, test_u
     async def test_set_user_setting_float_value(self, db_session: AsyncSession, test_user):
         await ops.set_user_setting(db_session, test_user.id, "agent", "threshold", 0.85)
         val = await ops.get_user_setting(db_session, test_user.id, "agent", "threshold")
-        assert val == 0.85
+        assert val == pytest.approx(0.85)
 
     async def test_get_user_agent_settings(self, db_session: AsyncSession, test_user):
         await ops.set_user_setting(db_session, test_user.id, "agent", "default_model", "claude")

backend/tests/test_prompts.py

@@ -13,7 +13,7 @@ def test_renders_with_tools(self):
         prompt = build_system_prompt(tool_specs=tools, mode="general", username="tester")
         assert isinstance(prompt, str)
         assert len(prompt) > 0
-        assert "read_file" in prompt or "read_file" in prompt
+        assert "read_file" in prompt
 
     def test_renders_with_username(self):
         tools = [ToolSpec(name="test_tool", description="Test", parameters={"type": "object"})]

backend/tests/test_sandbox_types.py

@@ -15,8 +15,8 @@ def test_defaults(self):
         assert caps.gpu_available is False
         assert caps.gpu_info == []
         assert caps.installed_packages == []
-        assert caps.available_disk_gb == 0.0
-        assert caps.available_ram_gb == 0.0
+        assert caps.available_disk_gb == pytest.approx(0.0)
+        assert caps.available_ram_gb == pytest.approx(0.0)
 
     def test_custom_values(self):
         caps = ComputeCapabilities(
@@ -47,7 +47,7 @@ def test_defaults(self):
         assert r.output == "done"
         assert r.success is True
         assert r.exit_code == 0
-        assert r.duration_seconds == 0.0
+        assert r.duration_seconds == pytest.approx(0.0)
 
     def test_failure(self):
         r = ExecutionResult(output="error", success=False, exit_code=1, duration_seconds=2.5)

backend/tests/test_workspace.py

@@ -289,7 +289,7 @@ def test_log_experiment(self, workspace_dir):
         assert filepath.exists()
         data = json.loads(filepath.read_text())
         assert data["name"] == "train-bert"
-        assert data["result"]["accuracy"] == 0.95
+        assert data["result"]["accuracy"] == pytest.approx(0.95)
 
     def test_state_persistence(self, workspace_dir):
         wp = WorkspacePersistence(workspace_dir)

frontend/src/components/ModelModal.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect, useMemo, useCallback } from 'react';
 import { Search, ChevronDown, Check, X, Filter, Save } from 'lucide-react';
 import { api } from '../api';

frontend/src/components/ProjectManageModal.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useRef, useEffect } from 'react';
 import { X, FolderOpen, Pencil, Trash2, Check, Layers } from 'lucide-react';
 import { api } from '../api';

frontend/src/components/ProjectModal.tsx

@@ -1,3 +1,4 @@
+
 import { useState } from 'react';
 import { X, FolderPlus } from 'lucide-react';
 import { api } from '../api';

frontend/src/components/RightPanel.tsx

@@ -1,3 +1,4 @@
+
 import { useState } from 'react';
 import { 
   Circle, 
@@ -42,8 +43,8 @@ function SearchBudgetDialog({ currentMax, onSave, onClose }: { currentMax: numbe
   const [saving, setSaving] = useState(false);
 
   const handleSave = async () => {
-    const num = parseInt(value, 10);
-    if (isNaN(num) || num < 1) return;
+    const num = Number.parseInt(value, 10);
+    if (Number.isNaN(num) || num < 1) return;
     setSaving(true);
     try {
       await api.updateSetting('agent', 'paper_search_budget', num);

frontend/src/components/SettingsPage.tsx

@@ -1,3 +1,4 @@
+
 import { Link, Outlet, useLocation } from 'react-router-dom';
 import { ArrowLeft, Key, Bot, Server, Cpu, PenTool } from 'lucide-react';
 

frontend/src/components/Terminal.tsx

@@ -1,3 +1,4 @@
+
 import { useEffect, useRef, useState, useCallback } from 'react';
 import {
   Terminal as TerminalIcon,

frontend/src/components/TodoReviewDrawer.tsx

@@ -1,3 +1,4 @@
+
 import { useState } from 'react';
 import { Check, X, Plus, Trash2, GripVertical } from 'lucide-react';
 import { api } from '../api';

frontend/src/components/settings/AddKeyModal.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect } from 'react';
 import { X, Upload, KeyRound } from 'lucide-react';
 

frontend/src/components/settings/AddNodeModal.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect } from 'react';
 import { X, Server, Monitor, Cloud, TestTube } from 'lucide-react';
 import { api } from '../../api';

frontend/src/components/settings/AgentSettings.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect, useCallback } from 'react';
 import { api } from '../../api';
 

frontend/src/components/settings/McpSettings.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect, useCallback } from 'react';
 import { api } from '../../api';
 

frontend/src/components/settings/ProvidersSettings.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect, useCallback, useMemo } from 'react';
 import { api } from '../../api';
 import type { Provider } from '../../types';

frontend/src/components/settings/WritingSettings.tsx

@@ -1,3 +1,5 @@
+
+
 import { useState, useEffect, useCallback } from 'react';
 import { api } from '../../api';