ci: fix all CI failures from M3 refactor

.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

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",

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"]

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

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")
 

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}")

src/omega_pbpk/api/server.py

@@ -2,6 +2,7 @@
 
 This module is kept for backward compatibility.
 """
+
 import warnings
 
 warnings.warn(

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)

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:

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

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"
 
 

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"

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
 

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),

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,

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