diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 33e90770..a972bb66 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - run: pip install pandas && pip install -e ".[dev]"
+      - run: pip install pandas && pip install -e ".[dev,api,viz]"
       - name: Run tests with coverage
         run: |
           pytest tests/ -m "not slow and not benchmark" \
@@ -58,7 +58,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - run: pip install pandas && pip install -e ".[dev]"
+      - run: pip install pandas && pip install -e ".[dev,api,viz]"
       - name: CLI smoke
         run: omega --help
       - name: Import smoke
diff --git a/pyproject.toml b/pyproject.toml
index 1d270168..2b90211f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,6 +29,7 @@ viz = ["matplotlib~=3.7"]
 dev = [
   "pytest~=8.0",
   "pytest-cov~=5.0",
+  "pytest-timeout>=2.2",
   "ruff~=0.6",
   "mypy~=1.8",
   "types-PyYAML",
diff --git a/src/omega_pbpk/adapters/__init__.py b/src/omega_pbpk/adapters/__init__.py
index 6672166e..53a34816 100644
--- a/src/omega_pbpk/adapters/__init__.py
+++ b/src/omega_pbpk/adapters/__init__.py
@@ -1,3 +1,3 @@
-from omega_pbpk.adapters.yaml_loader import load_drug_spec, drug_to_spec, spec_to_drug
+from omega_pbpk.adapters.yaml_loader import drug_to_spec, load_drug_spec, spec_to_drug
 
 __all__ = ["load_drug_spec", "drug_to_spec", "spec_to_drug"]
diff --git a/src/omega_pbpk/adapters/population_adapter.py b/src/omega_pbpk/adapters/population_adapter.py
index c3d07d60..e67020d8 100644
--- a/src/omega_pbpk/adapters/population_adapter.py
+++ b/src/omega_pbpk/adapters/population_adapter.py
@@ -1,4 +1,5 @@
 """VirtualPopulation → PatientSpec 변환 어댑터."""
+
 from __future__ import annotations
 
 from omega_pbpk.contracts.patient_spec import PatientSpec
diff --git a/src/omega_pbpk/adapters/yaml_loader.py b/src/omega_pbpk/adapters/yaml_loader.py
index aea93a15..262487d3 100644
--- a/src/omega_pbpk/adapters/yaml_loader.py
+++ b/src/omega_pbpk/adapters/yaml_loader.py
@@ -8,9 +8,9 @@
     spec = load_drug_spec("compounds/caffeine.yaml")
     spec.validate()
 """
+
 from __future__ import annotations
 
-import warnings
 from pathlib import Path
 from typing import Literal
 
@@ -34,9 +34,7 @@
 
 def drug_to_spec(drug: Drug, param_source: str = "yaml") -> DrugSpec:
     """기존 Drug 객체 → DrugSpec 변환."""
-    compound_type = _DRUG_TYPE_MAP.get(
-        getattr(drug, "drug_type", "neutral"), "neutral"
-    )
+    compound_type = _DRUG_TYPE_MAP.get(getattr(drug, "drug_type", "neutral"), "neutral")
     return DrugSpec(
         name=drug.name,
         smiles=drug.smiles,
@@ -61,8 +59,12 @@ def drug_to_spec(drug: Drug, param_source: str = "yaml") -> DrugSpec:
 def spec_to_drug(spec: DrugSpec) -> Drug:
     """DrugSpec → 기존 Drug 객체 역변환 (ODE 엔진 호환용)."""
     # compound_type → drug_type 역매핑
-    _reverse_map = {"neutral": "neutral", "acid": "monoprotic_acid",
-                    "base": "monoprotic_base", "zwitterion": "diprotic"}
+    _reverse_map = {
+        "neutral": "neutral",
+        "acid": "monoprotic_acid",
+        "base": "monoprotic_base",
+        "zwitterion": "diprotic",
+    }
     return Drug(
         name=spec.name,
         smiles=spec.smiles,
@@ -96,6 +98,7 @@ def load_drug_spec(path: str | Path) -> DrugSpec:
         FileNotFoundError: YAML 파일 없음
     """
     from omega_pbpk.config import load_compound
+
     drug = load_compound(path)
     return drug_to_spec(drug, param_source="yaml")
 
diff --git a/src/omega_pbpk/api/app.py b/src/omega_pbpk/api/app.py
index f6327e2e..324d6af9 100644
--- a/src/omega_pbpk/api/app.py
+++ b/src/omega_pbpk/api/app.py
@@ -24,6 +24,7 @@
 try:
     from fastapi import FastAPI, HTTPException
     from fastapi.responses import RedirectResponse
+
     HAS_FASTAPI = True
 except ImportError:
     HAS_FASTAPI = False
@@ -37,8 +38,7 @@
 
 if not HAS_FASTAPI:
     raise ImportError(
-        "FastAPI is required to use the API server. "
-        "Install with: pip install omega-pbpk[api]"
+        "FastAPI is required to use the API server. Install with: pip install omega-pbpk[api]"
     )
 
 app = FastAPI(
@@ -653,13 +653,14 @@ def train_surrogate(req: TrainSurrogateRequest) -> TrainSurrogateResponse:
     if req.n_samples < 10 or req.n_samples > 10000:
         raise HTTPException(status_code=422, detail="n_samples must be 10–10000")
     try:
-        from omega_pbpk.surrogate.data_generator import generate_training_data
         from omega_pbpk.surrogate import PKSurrogate
+        from omega_pbpk.surrogate.data_generator import generate_training_data
 
         data = generate_training_data(n_samples=min(req.n_samples, 100))  # MVP: 100으로 제한
         model = PKSurrogate(n_input=data.n_params)
         model.train(data.X, data.y, epochs=min(req.epochs, 20))
         import os
+
         os.makedirs(req.output_dir, exist_ok=True)
         model.save(req.output_dir)
         return TrainSurrogateResponse(
@@ -695,6 +696,8 @@ def validate(req: ValidateRequest) -> ValidateResponse:
         except Exception as exc:
             return ValidateResponse(mode="benchmark", passed=False, results={"error": str(exc)})
     elif req.mode == "sanity":
-        return ValidateResponse(mode="sanity", passed=True, results={"message": "Sanity checks passed"})
+        return ValidateResponse(
+            mode="sanity", passed=True, results={"message": "Sanity checks passed"}
+        )
     else:
         raise HTTPException(status_code=422, detail=f"Unknown mode: {req.mode}")
diff --git a/src/omega_pbpk/api/server.py b/src/omega_pbpk/api/server.py
index b7bdba06..69e703fd 100644
--- a/src/omega_pbpk/api/server.py
+++ b/src/omega_pbpk/api/server.py
@@ -2,6 +2,7 @@
 
 This module is kept for backward compatibility.
 """
+
 import warnings
 
 warnings.warn(
diff --git a/src/omega_pbpk/cli.py b/src/omega_pbpk/cli.py
index 6f0ce945..f4de3432 100644
--- a/src/omega_pbpk/cli.py
+++ b/src/omega_pbpk/cli.py
@@ -42,14 +42,14 @@
 # 4-verb sub-apps (M3 CLI restructure)
 # ---------------------------------------------------------------------------
 simulate_app = typer.Typer(help="Run PBPK simulations.")
-train_app    = typer.Typer(help="Train ML surrogate or calibrate models.")
+train_app = typer.Typer(help="Train ML surrogate or calibrate models.")
 validate_app = typer.Typer(help="Validate, benchmark, and QA.")
-serve_app    = typer.Typer(help="Start API server.")
+serve_app = typer.Typer(help="Start API server.")
 
 app.add_typer(simulate_app, name="simulate")
-app.add_typer(train_app,    name="train")
+app.add_typer(train_app, name="train")
 app.add_typer(validate_app, name="validate")
-app.add_typer(serve_app,    name="serve")
+app.add_typer(serve_app, name="serve")
 
 logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
 logger = logging.getLogger("omega_pbpk")
@@ -1408,10 +1408,8 @@ def serve(
     try:
         import uvicorn
     except ImportError:
-        typer.echo(
-            "API server requires [api] extras. Install with: pip install omega-pbpk[api]"
-        )
-        raise SystemExit(1)
+        typer.echo("API server requires [api] extras. Install with: pip install omega-pbpk[api]")
+        raise SystemExit(1) from None
 
     typer.echo(f"Starting Omega PBPK API server on http://{host}:{port}")
     uvicorn.run("omega_pbpk.api.app:app", host=host, port=port, reload=reload)
@@ -1435,6 +1433,7 @@ def run_tests() -> None:
 
 # --- simulate group ----------------------------------------------------------
 
+
 @simulate_app.command("single")
 def simulate_single(
     compound: str = typer.Argument(..., help="Compound name or YAML path"),
@@ -1529,6 +1528,7 @@ def simulate_pgx(
 
 # --- train group -------------------------------------------------------------
 
+
 @train_app.command("surrogate")
 def train_surrogate_cmd(
     n_samples: int = typer.Option(500, help="Training samples"),
@@ -1572,6 +1572,7 @@ def train_calibrate_cmd(
 
 # --- validate group ----------------------------------------------------------
 
+
 @validate_app.command("benchmark")
 def validate_benchmark_cmd(
     suite_dir: str = typer.Option("benchmarks", help="Path to benchmark suite directory."),
@@ -1629,6 +1630,7 @@ def validate_sensitivity_cmd(
 
 # --- serve group -------------------------------------------------------------
 
+
 @serve_app.command("start")
 def serve_start(
     host: str = typer.Option("0.0.0.0", help="Host to bind the server to."),
@@ -1639,10 +1641,8 @@ def serve_start(
     try:
         import uvicorn
     except ImportError:
-        typer.echo(
-            "API server requires [api] extras: pip install omega-pbpk[api]", err=True
-        )
-        raise typer.Exit(1)
+        typer.echo("API server requires [api] extras: pip install omega-pbpk[api]", err=True)
+        raise typer.Exit(1) from None
 
     typer.echo(f"Starting Omega PBPK API server on http://{host}:{port}")
     uvicorn.run("omega_pbpk.api.app:app", host=host, port=port, reload=reload)
diff --git a/src/omega_pbpk/contracts/drug_spec.py b/src/omega_pbpk/contracts/drug_spec.py
index ef87e1b6..41500293 100644
--- a/src/omega_pbpk/contracts/drug_spec.py
+++ b/src/omega_pbpk/contracts/drug_spec.py
@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 from dataclasses import dataclass, field
 from typing import Literal
 
@@ -11,12 +12,12 @@ class DrugSpec:
     logP: float = 2.0
     pka: list[float] = field(default_factory=lambda: [7.0])
     compound_type: Literal["neutral", "acid", "base", "zwitterion"] = "neutral"
-    fup: float = 0.5          # fraction unbound in plasma
-    rbp: float = 1.0          # blood:plasma ratio
+    fup: float = 0.5  # fraction unbound in plasma
+    rbp: float = 1.0  # blood:plasma ratio
     clint_hepatic_L_per_h: float = 0.0
     clint_gut_L_per_h: float = 0.0
     clr_L_per_h: float = 0.0
-    peff: float = 1.0         # effective permeability (cm/s × 10^-4)
+    peff: float = 1.0  # effective permeability (cm/s × 10^-4)
     solubility_mg_mL: float = 1.0
     kp: dict[str, float] = field(default_factory=dict)
     permeability_limited: dict[str, dict[str, float]] = field(default_factory=dict)
@@ -32,7 +33,9 @@ def validate(self) -> None:
         if self.mw <= 0:
             raise ValueError(f"mw must be > 0, got {self.mw}")
         if self.clint_hepatic_L_per_h < 0:
-            raise ValueError(f"clint_hepatic_L_per_h must be >= 0, got {self.clint_hepatic_L_per_h}")
+            raise ValueError(
+                f"clint_hepatic_L_per_h must be >= 0, got {self.clint_hepatic_L_per_h}"
+            )
         if self.clr_L_per_h < 0:
             raise ValueError(f"clr_L_per_h must be >= 0, got {self.clr_L_per_h}")
         if self.peff < 0:
diff --git a/src/omega_pbpk/contracts/patient_spec.py b/src/omega_pbpk/contracts/patient_spec.py
index 65a84eb4..508b7974 100644
--- a/src/omega_pbpk/contracts/patient_spec.py
+++ b/src/omega_pbpk/contracts/patient_spec.py
@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 from dataclasses import dataclass
 from typing import Literal
 
@@ -12,7 +13,7 @@ class PatientSpec:
     gfr_mL_min: float = 125.0
     cardiac_output_L_h: float = 390.0
     child_pugh: Literal["normal", "A", "B", "C"] = "normal"
-    cyp3a4_activity: float = 1.0   # relative to EM
+    cyp3a4_activity: float = 1.0  # relative to EM
     cyp2d6_activity: float = 1.0
     cyp2c9_activity: float = 1.0
     hepatic_cl_factor: float = 1.0
diff --git a/src/omega_pbpk/contracts/simulation_io.py b/src/omega_pbpk/contracts/simulation_io.py
index ec981491..22d3df0a 100644
--- a/src/omega_pbpk/contracts/simulation_io.py
+++ b/src/omega_pbpk/contracts/simulation_io.py
@@ -1,6 +1,8 @@
 from __future__ import annotations
+
 from dataclasses import dataclass, field
 from typing import Literal
+
 import numpy as np
 from numpy.typing import NDArray
 
@@ -38,12 +40,12 @@ class PKMetrics:
 
 @dataclass(frozen=True)
 class ADMEOutput:
-    Fa: float = 1.0     # fraction absorbed
-    Fg: float = 1.0     # fraction surviving gut
-    Fh: float = 1.0     # fraction surviving liver
+    Fa: float = 1.0  # fraction absorbed
+    Fg: float = 1.0  # fraction surviving gut
+    Fh: float = 1.0  # fraction surviving liver
     CLint: float = 0.0  # intrinsic clearance L/h
-    fu: float = 0.5     # fraction unbound
-    Vd: float = 30.0    # volume of distribution L
+    fu: float = 0.5  # fraction unbound
+    Vd: float = 30.0  # volume of distribution L
     confidence: Literal["low", "medium", "high"] = "low"
 
 
diff --git a/src/omega_pbpk/engine/interface.py b/src/omega_pbpk/engine/interface.py
index 27f5b934..5fdd6a3b 100644
--- a/src/omega_pbpk/engine/interface.py
+++ b/src/omega_pbpk/engine/interface.py
@@ -15,7 +15,7 @@ class SimulationResult:
     """ODE 시뮬레이션 결과."""
 
     t: NDArray[np.float64]
-    amounts: NDArray[np.float64]           # shape (n_states, n_timepoints)
+    amounts: NDArray[np.float64]  # shape (n_states, n_timepoints)
     plasma_concentration: NDArray[np.float64]  # shape (n_timepoints,)
     drug_name: str = ""
     route: str = "oral"
diff --git a/src/omega_pbpk/plugins/__init__.py b/src/omega_pbpk/plugins/__init__.py
index 3f4b4d92..0345b1e3 100644
--- a/src/omega_pbpk/plugins/__init__.py
+++ b/src/omega_pbpk/plugins/__init__.py
@@ -1,5 +1,5 @@
-from omega_pbpk.plugins.base import PluginBase, SurrogateModelPlugin
 from omega_pbpk.plugins.adme_plugin import ADMEPredictorPlugin
+from omega_pbpk.plugins.base import PluginBase, SurrogateModelPlugin
 from omega_pbpk.plugins.heuristic_kp import HeuristicKpPlugin
 from omega_pbpk.plugins.parameter_net import ParameterNetPlugin
 
diff --git a/src/omega_pbpk/plugins/adme_plugin.py b/src/omega_pbpk/plugins/adme_plugin.py
index cda11528..b6b20bfd 100644
--- a/src/omega_pbpk/plugins/adme_plugin.py
+++ b/src/omega_pbpk/plugins/adme_plugin.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 
-from omega_pbpk.plugins.base import PluginBase
 from omega_pbpk.contracts import DrugSpec
+from omega_pbpk.plugins.base import PluginBase
 
 
 class ADMEPredictorPlugin(PluginBase):
@@ -12,6 +12,7 @@ class ADMEPredictorPlugin(PluginBase):
 
     def __init__(self) -> None:
         from omega_pbpk.prediction.adme_predictor import ADMEPredictor
+
         self._predictor = ADMEPredictor()
 
     def predict(self, spec: DrugSpec) -> dict[str, float | dict]:
@@ -21,13 +22,15 @@ def predict(self, spec: DrugSpec) -> dict[str, float | dict]:
             props = self._predictor.predict(smiles)
         else:
             # SMILES 없을 때: DrugSpec의 physicochemical 값으로 fallback
-            props = self._predictor.predict_from_dict({
-                "mw": spec.mw,
-                "logP": spec.logP,
-                "fup": spec.fup,
-                "rbp": spec.rbp,
-                "peff": spec.peff,
-            })
+            props = self._predictor.predict_from_dict(
+                {
+                    "mw": spec.mw,
+                    "logP": spec.logP,
+                    "fup": spec.fup,
+                    "rbp": spec.rbp,
+                    "peff": spec.peff,
+                }
+            )
 
         return {
             "fup": float(props.fup),
diff --git a/src/omega_pbpk/plugins/heuristic_kp.py b/src/omega_pbpk/plugins/heuristic_kp.py
index d2374d4e..4556d80c 100644
--- a/src/omega_pbpk/plugins/heuristic_kp.py
+++ b/src/omega_pbpk/plugins/heuristic_kp.py
@@ -2,8 +2,8 @@
 
 from typing import Literal
 
-from omega_pbpk.plugins.base import PluginBase
 from omega_pbpk.contracts import DrugSpec
+from omega_pbpk.plugins.base import PluginBase
 
 
 class HeuristicKpPlugin(PluginBase):
@@ -12,16 +12,15 @@ class HeuristicKpPlugin(PluginBase):
     name = "heuristic_kp"
     provides = frozenset({"kp"})
 
-    def __init__(
-        self, method: Literal["poulin_theil", "rodgers_rowland"] = "poulin_theil"
-    ) -> None:
+    def __init__(self, method: Literal["poulin_theil", "rodgers_rowland"] = "poulin_theil") -> None:
         self.method = method
 
     def predict(self, spec: DrugSpec) -> dict[str, float | dict]:
         pka = spec.pka[0] if spec.pka else None
 
         if self.method == "rodgers_rowland":
-            from omega_pbpk.core.heuristics import rodgers_rowland_kp, _TISSUE_FACTORS
+            from omega_pbpk.core.heuristics import _TISSUE_FACTORS, rodgers_rowland_kp
+
             kp_dict: dict[str, float] = {
                 tissue: rodgers_rowland_kp(
                     logP=spec.logP,
@@ -35,6 +34,7 @@ def predict(self, spec: DrugSpec) -> dict[str, float | dict]:
         else:
             # poulin_theil (default)
             from omega_pbpk.core.heuristics import estimate_all_kp
+
             kp_dict = estimate_all_kp(
                 logP=spec.logP,
                 pka=pka,
diff --git a/src/omega_pbpk/plugins/parameter_net.py b/src/omega_pbpk/plugins/parameter_net.py
index 1bdbc843..f968a56a 100644
--- a/src/omega_pbpk/plugins/parameter_net.py
+++ b/src/omega_pbpk/plugins/parameter_net.py
@@ -3,6 +3,7 @@
 MVP 구현: PGx CYP scaling + 체중/연령 allometric scaling.
 추후 ML NN으로 교체 가능한 PluginBase 구조.
 """
+
 from __future__ import annotations
 
 from omega_pbpk.contracts.drug_spec import DrugSpec
diff --git a/src/omega_pbpk/surrogate/__init__.py b/src/omega_pbpk/surrogate/__init__.py
index c22e5651..b52422e4 100644
--- a/src/omega_pbpk/surrogate/__init__.py
+++ b/src/omega_pbpk/surrogate/__init__.py
@@ -59,21 +59,33 @@ class PKSurrogate:
 
     # 18D extended feature lists
     PATIENT_FEATURES: ClassVar[list[str]] = [
-        "body_weight_kg", "age_years", "sex_binary",
-        "gfr_mL_min", "cardiac_output_L_h",
-        "cyp3a4_activity", "cyp2d6_activity",
-        "hepatic_cl_factor", "renal_cl_factor",
+        "body_weight_kg",
+        "age_years",
+        "sex_binary",
+        "gfr_mL_min",
+        "cardiac_output_L_h",
+        "cyp3a4_activity",
+        "cyp2d6_activity",
+        "hepatic_cl_factor",
+        "renal_cl_factor",
     ]
     REGIMEN_FEATURES: ClassVar[list[str]] = [
-        "dose_mg", "route_binary", "n_doses",
+        "dose_mg",
+        "route_binary",
+        "n_doses",
     ]
     FULL_FEATURES: ClassVar[list[str]] = (
         ["logP", "fup", "clint_L_h", "mw", "rbp", "peff"]
         + [
-            "body_weight_kg", "age_years", "sex_binary",
-            "gfr_mL_min", "cardiac_output_L_h",
-            "cyp3a4_activity", "cyp2d6_activity",
-            "hepatic_cl_factor", "renal_cl_factor",
+            "body_weight_kg",
+            "age_years",
+            "sex_binary",
+            "gfr_mL_min",
+            "cardiac_output_L_h",
+            "cyp3a4_activity",
+            "cyp2d6_activity",
+            "hepatic_cl_factor",
+            "renal_cl_factor",
         ]
         + ["dose_mg", "route_binary", "n_doses"]
     )
diff --git a/src/omega_pbpk/surrogate/data_generator.py b/src/omega_pbpk/surrogate/data_generator.py
index 2e20d85a..f730d158 100644
--- a/src/omega_pbpk/surrogate/data_generator.py
+++ b/src/omega_pbpk/surrogate/data_generator.py
@@ -244,12 +244,12 @@ def _run_single_simulation(
 # Grid parameter ranges for generate_grid_dataset() — wider space, includes mw.
 # Feature order matches PKSurrogate.EXPECTED_FEATURES: [logP, fup, clint_L_h, mw, rbp, peff]
 GRID_PARAM_RANGES: dict[str, tuple[float, float]] = {
-    "logP": (-2.0, 6.0),        # linear (already in log scale)
-    "fup": (0.01, 1.0),         # log-uniform
+    "logP": (-2.0, 6.0),  # linear (already in log scale)
+    "fup": (0.01, 1.0),  # log-uniform
     "clint_L_h": (1.0, 500.0),  # log-uniform → clint_hepatic_L_per_h
-    "mw": (100.0, 800.0),       # log-uniform
-    "rbp": (0.5, 5.0),          # log-uniform
-    "peff": (0.5, 10.0),        # log-uniform
+    "mw": (100.0, 800.0),  # log-uniform
+    "rbp": (0.5, 5.0),  # log-uniform
+    "peff": (0.5, 10.0),  # log-uniform
 }
 
 GRID_PARAM_NAMES: list[str] = list(GRID_PARAM_RANGES.keys())
@@ -358,12 +358,10 @@ def generate_grid_dataset(
             X[:, j] = np.exp(np.log(lo) + X_unit[:, j] * (np.log(hi) - np.log(lo)))
 
     all_params = [
-        {name: float(X[i, j]) for j, name in enumerate(GRID_PARAM_NAMES)}
-        for i in range(n_samples)
+        {name: float(X[i, j]) for j, name in enumerate(GRID_PARAM_NAMES)} for i in range(n_samples)
     ]
     worker_args = [
-        (params, dose_mg, route, body_weight, t_end_h, i)
-        for i, params in enumerate(all_params)
+        (params, dose_mg, route, body_weight, t_end_h, i) for i, params in enumerate(all_params)
     ]
 
     pk_rows: list[list[float] | None] = [None] * n_samples
@@ -381,9 +379,7 @@ def generate_grid_dataset(
         max_workers = min(n_workers, n_samples)
         completed = 0
         with ProcessPoolExecutor(max_workers=max_workers) as pool:
-            future_to_idx = {
-                pool.submit(_grid_sim_worker, args): args[-1] for args in worker_args
-            }
+            future_to_idx = {pool.submit(_grid_sim_worker, args): args[-1] for args in worker_args}
             for future in as_completed(future_to_idx):
                 idx, row = future.result()
                 if row is not None:
diff --git a/src/omega_pbpk/surrogate/train.py b/src/omega_pbpk/surrogate/train.py
index 675beb85..efa34825 100644
--- a/src/omega_pbpk/surrogate/train.py
+++ b/src/omega_pbpk/surrogate/train.py
@@ -284,15 +284,14 @@ def _r2(y_true: NDArray, y_pred: NDArray) -> float:
         return 1.0 - ss_res / (ss_tot + 1e-12)
 
     y_pred_test = model.predict(X_test)
-    auc_r2 = _r2(y_test[:, 1], y_pred_test[:, 1])   # AUC column
+    auc_r2 = _r2(y_test[:, 1], y_pred_test[:, 1])  # AUC column
     cmax_r2 = _r2(y_test[:, 0], y_pred_test[:, 0])  # Cmax column
 
     _Path(output_dir).mkdir(parents=True, exist_ok=True)
     model.save(output_dir)
 
     logger.info(
-        "train_with_grid_data: n_train=%d n_val=%d n_test=%d "
-        "loss=%.4f auc_r2=%.3f cmax_r2=%.3f",
+        "train_with_grid_data: n_train=%d n_val=%d n_test=%d loss=%.4f auc_r2=%.3f cmax_r2=%.3f",
         n_train,
         n_val,
         len(X_test),
diff --git a/src/omega_pbpk/validation/__init__.py b/src/omega_pbpk/validation/__init__.py
index a86dbbac..2ed0eb36 100644
--- a/src/omega_pbpk/validation/__init__.py
+++ b/src/omega_pbpk/validation/__init__.py
@@ -183,7 +183,9 @@ def oral_mass_balance_check(
 
     total_mass = float(np.sum(amounts[check_idx]))
     deviation_frac = abs(total_mass - dose_mg) / dose_mg
-    t_val = float(time_h[check_idx]) if time_h is not None and len(time_h) > abs(check_idx) else None
+    t_val = (
+        float(time_h[check_idx]) if time_h is not None and len(time_h) > abs(check_idx) else None
+    )
 
     if deviation_frac > tolerance_frac:
         t_info = f" at t={t_val:.2f}h" if t_val is not None else ""
diff --git a/src/omega_pbpk/validation/_param_guard.py b/src/omega_pbpk/validation/_param_guard.py
index 5e36af1f..ae84e208 100644
--- a/src/omega_pbpk/validation/_param_guard.py
+++ b/src/omega_pbpk/validation/_param_guard.py
@@ -10,13 +10,13 @@
 
 # Physical plausibility bounds for PBPK parameters
 _BOUNDS: dict[str, tuple[float, float]] = {
-    "clint_hepatic_L_per_h": (0.0, 500.0),    # max ~hepatic blood flow ceiling
+    "clint_hepatic_L_per_h": (0.0, 500.0),  # max ~hepatic blood flow ceiling
     "clint_gut_L_per_h": (0.0, 200.0),
     "fup": (1e-4, 1.0),
     "rbp": (0.1, 20.0),
     "mw": (50.0, 2000.0),
     "logP": (-6.0, 12.0),
-    "peff": (1e-6, 50.0),                      # cm/s × 1e-4 scale typical range
+    "peff": (1e-6, 50.0),  # cm/s × 1e-4 scale typical range
     "ka_per_h": (1e-4, 100.0),
 }
 
@@ -35,9 +35,7 @@ class ParamViolation:
     upper: float
 
     def __str__(self) -> str:
-        return (
-            f"{self.param}={self.value:.4g} outside [{self.lower:.4g}, {self.upper:.4g}]"
-        )
+        return f"{self.param}={self.value:.4g} outside [{self.lower:.4g}, {self.upper:.4g}]"
 
 
 def check_drug_params(
@@ -119,12 +117,12 @@ def check_drug_params(
 # validate_drug_params — legacy-compatible gateway (positional-arg style)
 # ---------------------------------------------------------------------------
 
-CLR_MAX_L_H = 200.0        # Approximate maximum renal blood flow
-CLINT_MAX_L_H = 5000.0     # Realistic maximum CLint
+CLR_MAX_L_H = 200.0  # Approximate maximum renal blood flow
+CLINT_MAX_L_H = 5000.0  # Realistic maximum CLint
 KP_MIN = 1e-4
 KP_MAX = 1000.0
 KA_MIN = 0.0
-KA_MAX = 100.0             # 1/h
+KA_MAX = 100.0  # 1/h
 FUP_MIN = 1e-4
 FUP_MAX = 1.0
 RBP_MIN = 0.1
diff --git a/tests/conftest.py b/tests/conftest.py
index a90db654..f378735f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,3 @@
-import pytest
-
-
 def pytest_configure(config):
     config.addinivalue_line("markers", "slow: slow tests requiring training")
     config.addinivalue_line("markers", "benchmark: benchmark tests")
diff --git a/tests/integration/test_plugin_pipeline.py b/tests/integration/test_plugin_pipeline.py
index 8328e1cf..40196d17 100644
--- a/tests/integration/test_plugin_pipeline.py
+++ b/tests/integration/test_plugin_pipeline.py
@@ -1,10 +1,12 @@
 """Integration: Plugin → DrugSpec → SimulationEngine E2E."""
-import pytest
+
 import numpy as np
+import pytest
+
 from omega_pbpk.adapters.yaml_loader import load_drug_spec_by_name
-from omega_pbpk.plugins import HeuristicKpPlugin
-from omega_pbpk.engine import WholeBodyPBPKEngine
 from omega_pbpk.contracts import PatientSpec, Regimen
+from omega_pbpk.engine import WholeBodyPBPKEngine
+from omega_pbpk.plugins import HeuristicKpPlugin
 
 
 @pytest.fixture(scope="module")
diff --git a/tests/integration/test_surrogate_vs_ode.py b/tests/integration/test_surrogate_vs_ode.py
index ff6474a5..cb191627 100644
--- a/tests/integration/test_surrogate_vs_ode.py
+++ b/tests/integration/test_surrogate_vs_ode.py
@@ -23,15 +23,15 @@
 # Constants
 # ---------------------------------------------------------------------------
 
-AUC_RE_MAX = 0.20   # surrogate AUC must be within 20% of ODE AUC
+AUC_RE_MAX = 0.20  # surrogate AUC must be within 20% of ODE AUC
 CMAX_RE_MAX = 0.25  # surrogate Cmax must be within 25% of ODE Cmax
 
 # Canonical parameter set for test drugs (input feature order matches EXPECTED_FEATURES)
 # [logP, fup, clint_L_h, mw, rbp, peff]
 TEST_DRUGS = {
-    "caffeine":   [0.07, 0.65, 2.0,  194.19, 0.8,  4.0],
-    "midazolam":  [3.89, 0.03, 60.0, 325.77, 0.53, 2.0],
-    "propranolol":[3.48, 0.13, 70.0, 259.34, 0.81, 3.0],
+    "caffeine": [0.07, 0.65, 2.0, 194.19, 0.8, 4.0],
+    "midazolam": [3.89, 0.03, 60.0, 325.77, 0.53, 2.0],
+    "propranolol": [3.48, 0.13, 70.0, 259.34, 0.81, 3.0],
 }
 
 
@@ -39,6 +39,7 @@
 # Helpers
 # ---------------------------------------------------------------------------
 
+
 def _run_ode(params: list[float], dose_mg: float = 100.0) -> tuple[float, float]:
     """Run ODE simulation for given params, return (Cmax, AUC)."""
     from omega_pbpk._compat import np_trapz
@@ -65,7 +66,7 @@ def _run_ode(params: list[float], dose_mg: float = 100.0) -> tuple[float, float]
     return cmax, auc
 
 
-def _train_surrogate_on_drugs(drug_params: list[list[float]], n_aug: int = 15) -> "PKSurrogate":  # noqa: F821
+def _train_surrogate_on_drugs(drug_params: list[list[float]], n_aug: int = 15) -> PKSurrogate:  # noqa: F821
     """Train a minimal surrogate on the test drugs with augmentation."""
     from omega_pbpk.surrogate import PKSurrogate
     from omega_pbpk.surrogate.train import build_training_dataset
@@ -82,6 +83,7 @@ def _train_surrogate_on_drugs(drug_params: list[list[float]], n_aug: int = 15) -
 # Contract: surrogate EXPECTED_FEATURES matches ODE input convention
 # ---------------------------------------------------------------------------
 
+
 class TestFeatureOrderContract:
     def test_surrogate_feature_order_matches_train_order(self):
         """EXPECTED_FEATURES must match the column order in train._params_to_array."""
@@ -90,8 +92,12 @@ def test_surrogate_feature_order_matches_train_order(self):
 
         expected = PKSurrogate.EXPECTED_FEATURES
         ref_drug = {
-            "logP": 2.0, "fup": 0.5, "clint": 10.0,
-            "mw": 300.0, "rbp": 1.0, "peff": 2.0,
+            "logP": 2.0,
+            "fup": 0.5,
+            "clint": 10.0,
+            "mw": 300.0,
+            "rbp": 1.0,
+            "peff": 2.0,
         }
         arr = _params_to_array(ref_drug)
         for i, feat_name in enumerate(expected):
@@ -106,10 +112,12 @@ def test_surrogate_feature_order_matches_train_order(self):
 
     def test_expected_features_count_matches_default_n_input(self):
         from omega_pbpk.surrogate import PKSurrogate
+
         assert len(PKSurrogate.EXPECTED_FEATURES) == PKSurrogate().n_input
 
     def test_expected_outputs_count_matches_default_n_output(self):
         from omega_pbpk.surrogate import PKSurrogate
+
         assert len(PKSurrogate.EXPECTED_OUTPUTS) == PKSurrogate().n_output
 
 
@@ -117,6 +125,7 @@ def test_expected_outputs_count_matches_default_n_output(self):
 # ODE: baseline outputs for reference drugs
 # ---------------------------------------------------------------------------
 
+
 class TestODEBaseline:
     def test_ode_caffeine_positive_cmax_auc(self):
         cmax, auc = _run_ode(TEST_DRUGS["caffeine"])
@@ -139,6 +148,7 @@ def test_ode_outputs_finite(self):
 # Surrogate vs ODE agreement (slow — requires training)
 # ---------------------------------------------------------------------------
 
+
 @pytest.mark.slow
 class TestSurrogateVsODE:
     @pytest.fixture(scope="class")
diff --git a/tests/regression/test_golden_snapshot.py b/tests/regression/test_golden_snapshot.py
index 8df68022..432b63f1 100644
--- a/tests/regression/test_golden_snapshot.py
+++ b/tests/regression/test_golden_snapshot.py
@@ -1,4 +1,5 @@
 """Regression: ODE output must not drift from golden snapshot > ±10%."""
+
 from __future__ import annotations
 
 import json
diff --git a/tests/test_adme_plugin.py b/tests/test_adme_plugin.py
index 282ecfbf..c30eaf97 100644
--- a/tests/test_adme_plugin.py
+++ b/tests/test_adme_plugin.py
@@ -2,8 +2,6 @@
 
 from __future__ import annotations
 
-import pytest
-
 from omega_pbpk.contracts.drug_spec import DrugSpec
 from omega_pbpk.plugins.adme_plugin import ADMEPredictorPlugin
 from omega_pbpk.plugins.heuristic_kp import HeuristicKpPlugin
@@ -34,9 +32,11 @@
 # Import guard (works without torch)
 # ---------------------------------------------------------------------------
 
+
 def test_import_plugins():
     """플러그인이 torch 없이도 import 성공해야 한다."""
     from omega_pbpk.plugins import ADMEPredictorPlugin, HeuristicKpPlugin  # noqa: F401
+
     assert ADMEPredictorPlugin is not None
     assert HeuristicKpPlugin is not None
 
@@ -45,6 +45,7 @@ def test_import_plugins():
 # ADMEPredictorPlugin
 # ---------------------------------------------------------------------------
 
+
 class TestADMEPredictorPlugin:
     def setup_method(self):
         self.plugin = ADMEPredictorPlugin()
@@ -96,6 +97,7 @@ def test_confidence_without_smiles(self):
 # HeuristicKpPlugin
 # ---------------------------------------------------------------------------
 
+
 class TestHeuristicKpPlugin:
     def setup_method(self):
         self.plugin = HeuristicKpPlugin()
diff --git a/tests/test_api_m3.py b/tests/test_api_m3.py
index 02ab7c79..5aae91b8 100644
--- a/tests/test_api_m3.py
+++ b/tests/test_api_m3.py
@@ -1,10 +1,12 @@
 """Tests for M3-2 FastAPI integration — new endpoints and validators."""
+
 from __future__ import annotations
 
 import pytest
 
 try:
     from omega_pbpk.api.app import app
+
     HAS_FASTAPI = True
 except ImportError:
     HAS_FASTAPI = False
@@ -13,6 +15,7 @@
 
 if HAS_FASTAPI:
     from fastapi.testclient import TestClient
+
     client = TestClient(app)
 else:
     client = None  # type: ignore[assignment]
diff --git a/tests/test_cli_m3.py b/tests/test_cli_m3.py
index 1eb7caeb..00c6c5c4 100644
--- a/tests/test_cli_m3.py
+++ b/tests/test_cli_m3.py
@@ -36,9 +36,7 @@ def test_simulate_single_help():
 
 
 def test_simulate_single_json():
-    result = runner.invoke(
-        app, ["simulate", "single", "compounds/caffeine.yaml", "--json"]
-    )
+    result = runner.invoke(app, ["simulate", "single", "compounds/caffeine.yaml", "--json"])
     assert result.exit_code == 0, result.output
     data = json.loads(result.output)
     assert "Cmax" in data or "cmax" in data or len(data) > 0
diff --git a/tests/test_contracts.py b/tests/test_contracts.py
index f6f06229..d976c47c 100644
--- a/tests/test_contracts.py
+++ b/tests/test_contracts.py
@@ -1,13 +1,14 @@
 """Unit tests for omega_pbpk.contracts module."""
+
 import pytest
 
 from omega_pbpk.contracts import DrugSpec, PatientSpec, Regimen
 
-
 # ---------------------------------------------------------------------------
 # DrugSpec.validate()
 # ---------------------------------------------------------------------------
 
+
 class TestDrugSpecValidate:
     def test_valid_default(self):
         DrugSpec(name="test").validate()
@@ -71,6 +72,7 @@ def test_rbp_negative_raises(self):
 # PatientSpec.validate()
 # ---------------------------------------------------------------------------
 
+
 class TestPatientSpecValidate:
     def test_valid_default(self):
         PatientSpec().validate()
@@ -106,6 +108,7 @@ def test_cardiac_output_zero_raises(self):
 # Regimen.validate()
 # ---------------------------------------------------------------------------
 
+
 class TestRegimenValidate:
     def test_valid(self):
         Regimen(dose_mg=100).validate()
diff --git a/tests/test_param_guard.py b/tests/test_param_guard.py
index ecc8e9ea..21aa5b1f 100644
--- a/tests/test_param_guard.py
+++ b/tests/test_param_guard.py
@@ -1,4 +1,5 @@
 import pytest
+
 from omega_pbpk.validation._param_guard import validate_drug_params
 
 
@@ -24,13 +25,21 @@ def test_fup_above_one_raises():
 
 def test_negative_kp_raises():
     with pytest.raises(ValueError, match="kp"):
-        validate_drug_params(clint_hepatic=0, clint_gut=0, clr=0, fup=0.5, rbp=1.0,
-                             kp={"liver": -0.1})
+        validate_drug_params(
+            clint_hepatic=0, clint_gut=0, clr=0, fup=0.5, rbp=1.0, kp={"liver": -0.1}
+        )
 
 
 def test_valid_params_pass():
-    validate_drug_params(clint_hepatic=10.0, clint_gut=5.0, clr=2.0,
-                         fup=0.1, rbp=0.9, kp={"liver": 2.0, "muscle": 0.5}, ka=1.5)
+    validate_drug_params(
+        clint_hepatic=10.0,
+        clint_gut=5.0,
+        clr=2.0,
+        fup=0.1,
+        rbp=0.9,
+        kp={"liver": 2.0, "muscle": 0.5},
+        ka=1.5,
+    )
 
 
 def test_extreme_clint_raises():
diff --git a/tests/test_plugins_base.py b/tests/test_plugins_base.py
index 22620b76..e5beb4d8 100644
--- a/tests/test_plugins_base.py
+++ b/tests/test_plugins_base.py
@@ -8,11 +8,11 @@
 from omega_pbpk.engine import SimulationEngine, SimulationResult, WholeBodyPBPKEngine
 from omega_pbpk.plugins import PluginBase, SurrogateModelPlugin
 
-
 # ---------------------------------------------------------------------------
 # Helpers
 # ---------------------------------------------------------------------------
 
+
 def _caffeine_spec() -> DrugSpec:
     return DrugSpec(
         name="caffeine",
@@ -37,6 +37,7 @@ def _oral_regimen(dose_mg: float = 200.0) -> Regimen:
 # PluginBase tests
 # ---------------------------------------------------------------------------
 
+
 class _GoodPlugin(PluginBase):
     @property
     def name(self) -> str:
@@ -94,6 +95,7 @@ def test_surrogate_model_plugin_is_protocol():
 # SimulationEngine ABC tests
 # ---------------------------------------------------------------------------
 
+
 def test_simulation_engine_cannot_be_instantiated():
     with pytest.raises(TypeError):
         SimulationEngine()  # type: ignore[abstract]
@@ -108,18 +110,24 @@ def test_whole_body_pbpk_engine_is_instance_of_simulation_engine():
 # Import tests
 # ---------------------------------------------------------------------------
 
+
 def test_import_plugins():
     from omega_pbpk.plugins import PluginBase, SurrogateModelPlugin  # noqa: F401
 
 
 def test_import_engine():
-    from omega_pbpk.engine import SimulationEngine, SimulationResult, WholeBodyPBPKEngine  # noqa: F401
+    from omega_pbpk.engine import (  # noqa: F401
+        SimulationEngine,
+        SimulationResult,
+        WholeBodyPBPKEngine,
+    )
 
 
 # ---------------------------------------------------------------------------
 # WholeBodyPBPKEngine functional test
 # ---------------------------------------------------------------------------
 
+
 def test_engine_run_caffeine_oral():
     engine = WholeBodyPBPKEngine()
     drug = _caffeine_spec()
diff --git a/tests/test_population_adapter.py b/tests/test_population_adapter.py
index c1112465..100f14f3 100644
--- a/tests/test_population_adapter.py
+++ b/tests/test_population_adapter.py
@@ -1,4 +1,5 @@
 """Tests for population_adapter and ParameterNetPlugin."""
+
 from __future__ import annotations
 
 import pytest
@@ -11,11 +12,11 @@
 from omega_pbpk.contracts.patient_spec import PatientSpec
 from omega_pbpk.plugins import ParameterNetPlugin
 
-
 # ---------------------------------------------------------------------------
 # Fixtures
 # ---------------------------------------------------------------------------
 
+
 @pytest.fixture
 def base_drug() -> DrugSpec:
     return DrugSpec(
@@ -41,6 +42,7 @@ def pm_patient() -> PatientSpec:
 # sample_patient_spec
 # ---------------------------------------------------------------------------
 
+
 def test_sample_patient_spec_count():
     specs = sample_patient_spec(n=5, seed=0)
     assert len(specs) == 5
@@ -74,6 +76,7 @@ def test_sample_patient_spec_positive_bw():
 # subject_covariates_to_patient_spec field mapping
 # ---------------------------------------------------------------------------
 
+
 def test_sex_mapping_male():
     from omega_pbpk.population.physiology import SubjectCovariates
 
@@ -150,6 +153,7 @@ def test_renal_cl_factor_normal_gfr():
 # ParameterNetPlugin.predict()
 # ---------------------------------------------------------------------------
 
+
 def test_parameter_net_plugin_provides_keys(em_patient, base_drug):
     plugin = ParameterNetPlugin(patient=em_patient)
     result = plugin.predict(base_drug)
@@ -180,15 +184,14 @@ def test_parameter_net_apply_updates_drug(em_patient, base_drug):
     updated = plugin.apply(base_drug)
     assert isinstance(updated, DrugSpec)
     # Reference patient at 70 kg + EM: scales should be ~1.0
-    assert updated.clint_hepatic_L_per_h == pytest.approx(
-        base_drug.clint_hepatic_L_per_h, rel=0.05
-    )
+    assert updated.clint_hepatic_L_per_h == pytest.approx(base_drug.clint_hepatic_L_per_h, rel=0.05)
 
 
 # ---------------------------------------------------------------------------
 # ParameterNetPlugin.apply_pgx()
 # ---------------------------------------------------------------------------
 
+
 def test_apply_pgx_pm_em_um_differ(base_drug):
     plugin = ParameterNetPlugin()
 
@@ -218,6 +221,8 @@ def test_apply_pgx_em_full_clint(base_drug):
 # Import check
 # ---------------------------------------------------------------------------
 
+
 def test_parameter_net_plugin_importable():
     from omega_pbpk.plugins import ParameterNetPlugin as PNP  # noqa: F401
+
     assert PNP is ParameterNetPlugin
diff --git a/tests/test_surrogate_extensions.py b/tests/test_surrogate_extensions.py
index 039b9c10..cd34f5a4 100644
--- a/tests/test_surrogate_extensions.py
+++ b/tests/test_surrogate_extensions.py
@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 from omega_pbpk.surrogate import PKSurrogate
 from omega_pbpk.surrogate.data_generator import generate_training_data
 
@@ -41,7 +42,7 @@ def test_conformal_calibration_coverage():
 
     # test coverage on calibration set (should be ~90%)
     covered = 0
-    for x, y_true_norm in zip(X_cal, y_cal):
+    for x, y_true_norm in zip(X_cal, y_cal, strict=False):
         y_true_orig = y_true_norm * model.y_std + model.y_mean
         y_pred, ci_lo, ci_hi = model.predict_conformal(x, alpha=0.10)
         if np.all(ci_lo <= y_true_orig) and np.all(y_true_orig <= ci_hi):
diff --git a/tests/test_yaml_loader.py b/tests/test_yaml_loader.py
index c1e6357b..61cb8f9d 100644
--- a/tests/test_yaml_loader.py
+++ b/tests/test_yaml_loader.py
@@ -1,17 +1,18 @@
 """Tests for YAML → DrugSpec adapter (M0-3)."""
+
 from __future__ import annotations
 
-import pytest
 from pathlib import Path
 
+import pytest
+
 from omega_pbpk.adapters.yaml_loader import (
-    load_drug_spec_by_name,
-    load_drug_spec,
     drug_to_spec,
+    load_drug_spec,
+    load_drug_spec_by_name,
     spec_to_drug,
 )
 from omega_pbpk.contracts import DrugSpec
-from omega_pbpk.drugs.drug import Drug
 
 REPO_ROOT = Path(__file__).parent.parent
 COMPOUNDS_DIR = REPO_ROOT / "compounds"
diff --git a/tests/unit/plugins/test_param_plugin.py b/tests/unit/plugins/test_param_plugin.py
index a69560c9..09e96088 100644
--- a/tests/unit/plugins/test_param_plugin.py
+++ b/tests/unit/plugins/test_param_plugin.py
@@ -10,7 +10,6 @@
 
 from omega_pbpk.validation._param_guard import ParamViolation, check_drug_params
 
-
 # ---------------------------------------------------------------------------
 # Fixtures: valid & invalid param sets
 # ---------------------------------------------------------------------------
@@ -32,6 +31,7 @@
 # Happy-path: all valid params pass without exception
 # ---------------------------------------------------------------------------
 
+
 class TestValidParams:
     def test_valid_params_no_violations(self):
         violations = check_drug_params(**VALID_PARAMS, raise_on_violation=False)
@@ -58,6 +58,7 @@ def test_no_params_no_violations(self):
 # fup boundary cases
 # ---------------------------------------------------------------------------
 
+
 class TestFupBounds:
     def test_fup_zero_raises(self):
         with pytest.raises(ValueError, match="fup"):
@@ -82,6 +83,7 @@ def test_fup_minimum_boundary_valid(self):
 # CLint boundary cases
 # ---------------------------------------------------------------------------
 
+
 class TestClintBounds:
     def test_negative_clint_hepatic_raises(self):
         with pytest.raises(ValueError, match="clint_hepatic_L_per_h"):
@@ -102,6 +104,7 @@ def test_clint_at_max_boundary_valid(self):
 # Kp boundary cases
 # ---------------------------------------------------------------------------
 
+
 class TestKpBounds:
     def test_negative_kp_raises(self):
         with pytest.raises(ValueError, match="kp\\[liver\\]"):
@@ -126,6 +129,7 @@ def test_kp_at_max_boundary_valid(self):
 # Multiple violations reported together
 # ---------------------------------------------------------------------------
 
+
 class TestMultipleViolations:
     def test_multiple_violations_all_reported(self):
         violations = check_drug_params(
@@ -156,6 +160,7 @@ def test_violation_str_format(self):
 # MW, logP, rbp bounds
 # ---------------------------------------------------------------------------
 
+
 class TestOtherBounds:
     def test_low_mw_raises(self):
         with pytest.raises(ValueError, match="mw"):
diff --git a/tests/unit/plugins/test_plugin_contracts.py b/tests/unit/plugins/test_plugin_contracts.py
index c94ac54d..b4b6dd9f 100644
--- a/tests/unit/plugins/test_plugin_contracts.py
+++ b/tests/unit/plugins/test_plugin_contracts.py
@@ -1,8 +1,10 @@
 """Plugin 공통 계약 단위 테스트."""
+
 import pytest
+
+from omega_pbpk.adapters.yaml_loader import load_drug_spec_by_name
 from omega_pbpk.plugins import ADMEPredictorPlugin, HeuristicKpPlugin
 from omega_pbpk.plugins.base import PluginBase
-from omega_pbpk.adapters.yaml_loader import load_drug_spec_by_name
 
 
 @pytest.fixture(scope="module")
@@ -60,6 +62,7 @@ def test_rodgers_rowland(self, caffeine_spec):
 class TestPluginBaseContract:
     def test_provides_mismatch_raises(self, caffeine_spec):
         """predict()가 provides와 다른 키 반환 시 TypeError."""
+
         class BrokenPlugin(PluginBase):
             name = "broken"
             provides = frozenset({"nonexistent_field"})
diff --git a/tests/unit/plugins/test_surrogate_plugin.py b/tests/unit/plugins/test_surrogate_plugin.py
index 902a7fb2..f4dce44c 100644
--- a/tests/unit/plugins/test_surrogate_plugin.py
+++ b/tests/unit/plugins/test_surrogate_plugin.py
@@ -12,11 +12,11 @@
 
 from omega_pbpk.surrogate import PKSurrogate
 
-
 # ---------------------------------------------------------------------------
 # Fixtures
 # ---------------------------------------------------------------------------
 
+
 @pytest.fixture
 def untrained_surrogate() -> PKSurrogate:
     """Default PKSurrogate with He-initialized (random) weights."""
@@ -30,12 +30,14 @@ def trained_surrogate() -> PKSurrogate:
     n = 80
     X = rng.uniform([[-2, 0.01, 0.1, 100, 0.5, 0.5]], [[6, 1.0, 200, 800, 5.0, 10.0]], (n, 6))
     # Synthetic PK outputs: Cmax, AUC, Tmax, t_half (all positive)
-    y = np.column_stack([
-        rng.uniform(0.01, 10, n),   # Cmax
-        rng.uniform(0.1, 100, n),   # AUC
-        rng.uniform(0.25, 6, n),    # Tmax
-        rng.uniform(1, 20, n),      # t_half
-    ])
+    y = np.column_stack(
+        [
+            rng.uniform(0.01, 10, n),  # Cmax
+            rng.uniform(0.1, 100, n),  # AUC
+            rng.uniform(0.25, 6, n),  # Tmax
+            rng.uniform(1, 20, n),  # t_half
+        ]
+    )
     s = PKSurrogate(n_input=6, n_output=4)
     s.param_names = PKSurrogate.EXPECTED_FEATURES
     s.output_names = PKSurrogate.EXPECTED_OUTPUTS
@@ -47,6 +49,7 @@ def trained_surrogate() -> PKSurrogate:
 # T04a: EXPECTED_FEATURES class constant
 # ---------------------------------------------------------------------------
 
+
 class TestExpectedFeaturesContract:
     def test_expected_features_is_class_attribute(self):
         assert hasattr(PKSurrogate, "EXPECTED_FEATURES")
@@ -55,17 +58,13 @@ def test_expected_features_length(self):
         assert len(PKSurrogate.EXPECTED_FEATURES) == 6
 
     def test_expected_features_names(self):
-        assert PKSurrogate.EXPECTED_FEATURES == [
-            "logP", "fup", "clint_L_h", "mw", "rbp", "peff"
-        ]
+        assert PKSurrogate.EXPECTED_FEATURES == ["logP", "fup", "clint_L_h", "mw", "rbp", "peff"]
 
     def test_expected_outputs_is_class_attribute(self):
         assert hasattr(PKSurrogate, "EXPECTED_OUTPUTS")
 
     def test_expected_outputs_names(self):
-        assert PKSurrogate.EXPECTED_OUTPUTS == [
-            "cmax_mg_L", "auc_mg_h_L", "tmax_h", "t_half_h"
-        ]
+        assert PKSurrogate.EXPECTED_OUTPUTS == ["cmax_mg_L", "auc_mg_h_L", "tmax_h", "t_half_h"]
 
     def test_expected_features_match_n_input_default(self):
         """Default n_input must equal len(EXPECTED_FEATURES)."""
@@ -81,6 +80,7 @@ def test_expected_outputs_match_n_output_default(self):
 # T04b: validate_feature_contract
 # ---------------------------------------------------------------------------
 
+
 class TestValidateFeatureContract:
     def test_valid_params_pass(self, untrained_surrogate):
         valid = {"logP": 2.0, "fup": 0.5, "clint_L_h": 10.0, "mw": 300.0, "rbp": 1.0, "peff": 2.0}
@@ -101,15 +101,27 @@ def test_missing_multiple_keys_listed_in_error(self, untrained_surrogate):
     def test_extra_keys_allowed(self, untrained_surrogate):
         """Extra keys from ADME plugin must not cause failures."""
         extra = {
-            "logP": 2.0, "fup": 0.5, "clint_L_h": 10.0,
-            "mw": 300.0, "rbp": 1.0, "peff": 2.0,
-            "logD": 1.5, "pka": 7.4,  # extra keys
+            "logP": 2.0,
+            "fup": 0.5,
+            "clint_L_h": 10.0,
+            "mw": 300.0,
+            "rbp": 1.0,
+            "peff": 2.0,
+            "logD": 1.5,
+            "pka": 7.4,  # extra keys
         }
         untrained_surrogate.validate_feature_contract(extra)  # no exception
 
     def test_wrong_feature_name_raises(self, untrained_surrogate):
         """logD instead of logP should raise (missing logP)."""
-        wrong_names = {"logD": 2.0, "fup": 0.5, "clint_L_h": 10.0, "mw": 300.0, "rbp": 1.0, "peff": 2.0}
+        wrong_names = {
+            "logD": 2.0,
+            "fup": 0.5,
+            "clint_L_h": 10.0,
+            "mw": 300.0,
+            "rbp": 1.0,
+            "peff": 2.0,
+        }
         with pytest.raises(ValueError, match="logP"):
             untrained_surrogate.validate_feature_contract(wrong_names)
 
@@ -118,6 +130,7 @@ def test_wrong_feature_name_raises(self, untrained_surrogate):
 # Non-negativity: outputs must always be ≥ 0
 # ---------------------------------------------------------------------------
 
+
 class TestNonNegativity:
     def test_predict_returns_nonnegative_single(self, trained_surrogate):
         x = np.array([2.0, 0.5, 10.0, 300.0, 1.0, 2.0])
@@ -132,10 +145,12 @@ def test_predict_returns_nonnegative_batch(self, trained_surrogate):
 
     def test_predict_with_extreme_inputs_nonnegative(self, trained_surrogate):
         """Even very extreme inputs must not produce negative outputs."""
-        extremes = np.array([
-            [10.0, 0.001, 0.001, 2000.0, 10.0, 0.001],   # extreme high logP
-            [-5.0, 1.0, 500.0, 50.0, 0.1, 50.0],          # extreme negative logP
-        ])
+        extremes = np.array(
+            [
+                [10.0, 0.001, 0.001, 2000.0, 10.0, 0.001],  # extreme high logP
+                [-5.0, 1.0, 500.0, 50.0, 0.1, 50.0],  # extreme negative logP
+            ]
+        )
         y = trained_surrogate.predict(extremes)
         assert np.all(y >= 0)
 
@@ -150,6 +165,7 @@ def test_untrained_predict_nonnegative(self, untrained_surrogate):
 # Reproducibility (determinism)
 # ---------------------------------------------------------------------------
 
+
 class TestReproducibility:
     def test_same_input_same_output_trained(self, trained_surrogate):
         x = np.array([2.0, 0.5, 10.0, 300.0, 1.0, 2.0])
@@ -191,6 +207,7 @@ def test_training_with_same_seed_reproducible(self):
 # Output shape & structure
 # ---------------------------------------------------------------------------
 
+
 class TestOutputShape:
     def test_predict_single_returns_1d_array(self, trained_surrogate):
         x = np.array([2.0, 0.5, 10.0, 300.0, 1.0, 2.0])
diff --git a/tests/unit/test_mass_balance.py b/tests/unit/test_mass_balance.py
index b503edcd..fa93923e 100644
--- a/tests/unit/test_mass_balance.py
+++ b/tests/unit/test_mass_balance.py
@@ -13,11 +13,11 @@
 
 from omega_pbpk.validation import mass_balance_check, oral_mass_balance_check
 
-
 # ---------------------------------------------------------------------------
 # Helpers
 # ---------------------------------------------------------------------------
 
+
 def _perfect_amounts(n_time: int, n_states: int, dose_mg: float) -> np.ndarray:
     """Create amounts array where mass is perfectly conserved (all in state 0)."""
     amounts = np.zeros((n_time, n_states))
@@ -40,6 +40,7 @@ def _depleting_amounts(n_time: int, n_states: int, dose_mg: float) -> np.ndarray
 # mass_balance_check (IV route)
 # ---------------------------------------------------------------------------
 
+
 class TestMassBalanceCheckIV:
     def test_perfect_conservation_no_warnings(self):
         amounts = _perfect_amounts(100, 35, 100.0)
@@ -126,6 +127,7 @@ def test_returns_list_type(self):
 # oral_mass_balance_check
 # ---------------------------------------------------------------------------
 
+
 class TestOralMassBalanceCheck:
     def test_perfect_conservation_no_warnings(self):
         n_time, n_states, dose = 200, 35, 100.0
@@ -139,7 +141,7 @@ def test_skip_when_gi_residual_too_high(self):
         n_time, dose = 100, 100.0
         time_h = np.linspace(0, 12, n_time)
         amounts = np.zeros((n_time, 35))
-        amounts[:, 0] = dose * 0.3   # only 30% absorbed
+        amounts[:, 0] = dose * 0.3  # only 30% absorbed
         # GI still holds 70% of dose
         gi_states = np.ones((n_time, 8)) * dose * 0.7 / 8.0
         result = oral_mass_balance_check(
@@ -154,7 +156,7 @@ def test_checks_when_gi_absorbed(self):
         amounts = _perfect_amounts(n_time, 35, dose)
         # Simulate complete absorption: GI residual drops to near 0
         gi_states = np.zeros((n_time, 8))
-        gi_states[:5, :] = dose / 8.0   # GI drains completely by t≈5
+        gi_states[:5, :] = dose / 8.0  # GI drains completely by t≈5
         result = oral_mass_balance_check(amounts, dose, time_h, gi_states=gi_states)
         assert result == []
 
@@ -201,6 +203,7 @@ def test_returns_list_type(self):
 # Integration: IV simulation with real ODE
 # ---------------------------------------------------------------------------
 
+
 class TestMassBalanceWithRealSimulation:
     def test_iv_simulation_conserves_mass(self):
         """Real 35-state ODE IV simulation must pass mass balance (±0.5%)."""