fix: #936 Extract hardcoded PRAGMA busy_timeout=5000

Automated salvage commit — agent session ended (exit 124).
Work in progress, may need continuation.

src/infrastructure/events/bus.py

@@ -16,6 +16,8 @@ from datetime import UTC, datetime
 from pathlib import Path
 from typing import Any
 
+from src.config import settings
+
 logger = logging.getLogger(__name__)
 
 
@@ -102,7 +104,7 @@ class EventBus:
         self._persistence_db_path.parent.mkdir(parents=True, exist_ok=True)
         with closing(sqlite3.connect(str(self._persistence_db_path))) as conn:
             conn.execute("PRAGMA journal_mode=WAL")
-            conn.execute("PRAGMA busy_timeout=5000")
+            conn.execute(f"PRAGMA busy_timeout={settings.db_busy_timeout_ms}")
             conn.executescript(_EVENTS_SCHEMA)
             conn.commit()
 
@@ -114,7 +116,7 @@ class EventBus:
             return
         with closing(sqlite3.connect(str(self._persistence_db_path))) as conn:
             conn.row_factory = sqlite3.Row
-            conn.execute("PRAGMA busy_timeout=5000")
+            conn.execute(f"PRAGMA busy_timeout={settings.db_busy_timeout_ms}")
             yield conn
 
     def _persist_event(self, event: Event) -> None:

src/infrastructure/models/registry.py

@@ -18,6 +18,8 @@ from datetime import UTC, datetime
 from enum import StrEnum
 from pathlib import Path
 
+from src.config import settings
+
 logger = logging.getLogger(__name__)
 
 DB_PATH = Path("data/swarm.db")
@@ -68,7 +70,7 @@ def _get_conn() -> Generator[sqlite3.Connection, None, None]:
     with closing(sqlite3.connect(str(DB_PATH))) as conn:
         conn.row_factory = sqlite3.Row
         conn.execute("PRAGMA journal_mode=WAL")
-        conn.execute("PRAGMA busy_timeout=5000")
+        conn.execute(f"PRAGMA busy_timeout={settings.db_busy_timeout_ms}")
         conn.execute("""
             CREATE TABLE IF NOT EXISTS custom_models (
                 name            TEXT PRIMARY KEY,

src/spark/eidos.py

@@ -22,6 +22,8 @@ from dataclasses import dataclass
 from datetime import UTC, datetime
 from pathlib import Path
 
+from src.config import settings
+
 logger = logging.getLogger(__name__)
 
 DB_PATH = Path("data/spark.db")
@@ -47,7 +49,7 @@ def _get_conn() -> Generator[sqlite3.Connection, None, None]:
     with closing(sqlite3.connect(str(DB_PATH))) as conn:
         conn.row_factory = sqlite3.Row
         conn.execute("PRAGMA journal_mode=WAL")
-        conn.execute("PRAGMA busy_timeout=5000")
+        conn.execute(f"PRAGMA busy_timeout={settings.db_busy_timeout_ms}")
         conn.execute("""
             CREATE TABLE IF NOT EXISTS spark_predictions (
                 id               TEXT PRIMARY KEY,

src/spark/memory.py

@@ -19,6 +19,8 @@ from dataclasses import dataclass
 from datetime import UTC, datetime
 from pathlib import Path
 
+from src.config import settings
+
 logger = logging.getLogger(__name__)
 
 DB_PATH = Path("data/spark.db")
@@ -63,7 +65,7 @@ def _get_conn() -> Generator[sqlite3.Connection, None, None]:
     with closing(sqlite3.connect(str(DB_PATH))) as conn:
         conn.row_factory = sqlite3.Row
         conn.execute("PRAGMA journal_mode=WAL")
-        conn.execute("PRAGMA busy_timeout=5000")
+        conn.execute(f"PRAGMA busy_timeout={settings.db_busy_timeout_ms}")
         conn.execute("""
             CREATE TABLE IF NOT EXISTS spark_events (
                 id          TEXT PRIMARY KEY,

src/timmy/paperclip.py

@@ -13,8 +13,8 @@ from dataclasses import dataclass
 import httpx
 
 from config import settings
+from timmy.research_tools import get_llm_client, google_web_search
 from timmy.research_triage import triage_research_report
-from timmy.research_tools import google_web_search, get_llm_client
 
 logger = logging.getLogger(__name__)
 

src/timmy/research_tools.py

@@ -6,7 +6,6 @@ import logging
 import os
 from typing import Any
 
-from config import settings
 from serpapi import GoogleSearch
 
 logger = logging.getLogger(__name__)

tests/infrastructure/test_db_pool.py

@@ -6,8 +6,8 @@ import time
 from pathlib import Path
 
 import pytest
-
+from src.config import settings
-from infrastructure.db_pool import ConnectionPool
+from src.infrastructure.db_pool import ConnectionPool
 
 
 class TestConnectionPoolInit:
@@ -330,9 +330,9 @@ class TestPragmaApplication:
         """busy_timeout pragma set on a pooled connection persists."""
         pool = ConnectionPool(tmp_path / "test.db")
         conn = pool.get_connection()
-        conn.execute("PRAGMA busy_timeout=5000")
+        conn.execute(f"PRAGMA busy_timeout={settings.db_busy_timeout_ms}")
         timeout = conn.execute("PRAGMA busy_timeout").fetchone()[0]
-        assert timeout == 5000
+        assert timeout == settings.db_busy_timeout_ms
         pool.close_connection()
 
     def test_pragmas_apply_per_connection(self, tmp_path):

tests/scripts/test_export_trajectories.py

@@ -9,10 +9,8 @@ import json
 from pathlib import Path
 
 import pytest
-
 import scripts.export_trajectories as et
 
-
 # ── Fixtures ──────────────────────────────────────────────────────────────────
 
 
@@ -236,7 +234,9 @@ def test_export_training_data_writes_jsonl(simple_session: Path, tmp_path: Path)
     count = et.export_training_data(logs_dir=simple_session, output_path=output)
     assert count == 2
     assert output.exists()
-    lines = [json.loads(l) for l in output.read_text().splitlines() if l.strip()]
+    lines = [
+        json.loads(line) for line in output.read_text().splitlines() if line.strip()
+    ]
     assert len(lines) == 2
     for line in lines:
         assert "messages" in line

tests/unit/test_retrain_loop.py

@@ -9,19 +9,15 @@ Refs: #1105
 from __future__ import annotations
 
 import json
-import tempfile
 from datetime import UTC, datetime, timedelta
 from pathlib import Path
 
-import pytest
-
 from timmy_automations.retrain.quality_filter import QualityFilter, TrajectoryQuality
 from timmy_automations.retrain.retrain import RetrainOrchestrator
 from timmy_automations.retrain.training_dataset import TrainingDataset
 from timmy_automations.retrain.training_log import CycleMetrics, TrainingLog
 from timmy_automations.retrain.trajectory_exporter import Trajectory, TrajectoryExporter
 
-
 # ── Fixtures ─────────────────────────────────────────────────────────────────
 
 
@@ -382,7 +378,7 @@ class TestTrainingDataset:
         ds = TrainingDataset(repo_root=tmp_path)
         ds.append([self._make_result()], "2026-W12")
         with open(ds.dataset_path) as f:
-            lines = [l.strip() for l in f if l.strip()]
+            lines = [line.strip() for line in f if line.strip()]
         assert len(lines) == 1
         record = json.loads(lines[0])
         assert "messages" in record