refactor: fix four accumulated code quality issues

- run/run.py: replace 4 duplicate profiler if-blocks with data-driven table;
  adding a new profiler now requires one entry in _PROFILERS

- lint_source.py: remove check_pylint_directives — MFC uses ruff, no pylint
  directives exist anywhere in the codebase, check was provably dead code

- bench.py: delete self-deprecating TODO comment

- run/input.py: log Cantera candidate failures instead of swallowing silently;
  previously a Cantera yaml parse error looked identical to file-not-found

Author: sbryngelson

toolchain/mfc/bench.py

@@ -166,8 +166,6 @@ def bench(targets=None):
         cons.unindent()
 
 
-# TODO: This function is too long and not nicely written at all. Someone should
-#       refactor it...
 def diff():
     lhs, rhs = file_load_yaml(ARG("lhs")), file_load_yaml(ARG("rhs"))
     lhs_path = os.path.relpath(ARG("lhs"))

toolchain/mfc/lint_source.py

@@ -312,33 +312,6 @@ def check_junk_comments(repo_root: Path) -> list[str]:
     return errors
 
 
-def check_pylint_directives(repo_root: Path) -> list[str]:
-    """Flag ``# pylint:`` directives in Python files.
-
-    MFC uses ruff for linting; leftover pylint directives are dead code.
-    """
-    errors: list[str] = []
-    pylint_re = re.compile(r"#\s*pylint\s*:", re.IGNORECASE)
-    self_path = Path(__file__).resolve()
-
-    for subdir in ["examples", "benchmarks", "toolchain"]:
-        d = repo_root / subdir
-        if not d.exists():
-            continue
-        for py in sorted(d.rglob("*.py")):
-            if py.resolve() == self_path:
-                continue
-            lines = py.read_text(encoding="utf-8").splitlines()
-            rel = py.relative_to(repo_root)
-
-            for i, line in enumerate(lines):
-                match = pylint_re.search(line)
-                if match:
-                    errors.append(f"  {rel}:{i + 1} pylint directive. Fix: remove (use ruff noqa comments if needed)")
-
-    return errors
-
-
 def main():
     repo_root = Path(__file__).resolve().parents[2]
 
@@ -351,7 +324,6 @@ def main():
     all_errors.extend(check_fypp_list_duplicates(repo_root))
     all_errors.extend(check_duplicate_lines(repo_root))
     all_errors.extend(check_hardcoded_byte_size(repo_root))
-    all_errors.extend(check_pylint_directives(repo_root))
 
     if all_errors:
         print("Source lint failed:")

toolchain/mfc/params/definitions.py

@@ -39,7 +39,6 @@ def _fc(name: str, default: int) -> int:
 NA = 4  # acoustic sources: enumerated individually
 
 
-
 # Parameters that can be hard-coded for GPU case optimization
 CASE_OPT_PARAMS = {
     "mapped_weno",
@@ -496,6 +495,7 @@ def _r(name, ptype, tags=None, desc=None, hint=None, math=None, str_len=None):
         hint = _lookup_hint(name)
     if desc is None:
         from .descriptions import get_description
+
         desc = get_description(name)
     constraint = CONSTRAINTS.get(name)
     if constraint and "value_labels" in constraint:
@@ -1028,78 +1028,259 @@ def _init_registry():
 
 NAMELIST_VARS: dict[str, set[str]] = {}
 
+
 def _nv(targets: set, *names: str) -> None:
     for n in names:
         NAMELIST_VARS[n] = set(targets)
 
+
 _ALL, _PRE_SIM, _SIM_POST = {"pre", "sim", "post"}, {"pre", "sim"}, {"sim", "post"}
 _PRE_POST = {"pre", "post"}
 _SIM = {"sim"}
 _PRE = {"pre"}
 _POST = {"post"}
 
-_nv(_ALL,
-    "m", "n", "p", "cyl_coord", "bc_x", "bc_y", "bc_z", "num_bc_patches", "case_dir",
-    "t_step_start", "cfl_adap_dt", "cfl_const_dt", "n_start",
-    "model_eqns", "mpp_lim", "relax", "relax_model",
-    "fluid_pp", "bub_pp", "rhoref", "pref",
-    "bubbles_euler", "bubbles_lagrange", "R0ref", "polytropic", "thermal",
-    "Ca", "Web", "Re_inv", "polydisperse", "poly_sigma", "qbmm", "sigma", "adv_n",
-    "hypoelasticity", "hyperelasticity", "surface_tension", "relativity",
-    "ib", "num_ibs", "cont_damage", "hyper_cleaning", "Bx0",
-    "precision", "parallel_io", "file_per_process", "fft_wrt", "down_sample",
+_nv(
+    _ALL,
+    "m",
+    "n",
+    "p",
+    "cyl_coord",
+    "bc_x",
+    "bc_y",
+    "bc_z",
+    "num_bc_patches",
+    "case_dir",
+    "t_step_start",
+    "cfl_adap_dt",
+    "cfl_const_dt",
+    "n_start",
+    "model_eqns",
+    "mpp_lim",
+    "relax",
+    "relax_model",
+    "fluid_pp",
+    "bub_pp",
+    "rhoref",
+    "pref",
+    "bubbles_euler",
+    "bubbles_lagrange",
+    "R0ref",
+    "polytropic",
+    "thermal",
+    "Ca",
+    "Web",
+    "Re_inv",
+    "polydisperse",
+    "poly_sigma",
+    "qbmm",
+    "sigma",
+    "adv_n",
+    "hypoelasticity",
+    "hyperelasticity",
+    "surface_tension",
+    "relativity",
+    "ib",
+    "num_ibs",
+    "cont_damage",
+    "hyper_cleaning",
+    "Bx0",
+    "precision",
+    "parallel_io",
+    "file_per_process",
+    "fft_wrt",
+    "down_sample",
 )
-_nv(_SIM_POST,
-    "t_step_stop", "t_step_save", "t_stop", "t_save", "cfl_target",
-    "avg_state", "prim_vars_wrt", "alt_soundspeed", "mixture_err", "fd_order", "ib_state_wrt",
+_nv(
+    _SIM_POST,
+    "t_step_stop",
+    "t_step_save",
+    "t_stop",
+    "t_save",
+    "cfl_target",
+    "avg_state",
+    "prim_vars_wrt",
+    "alt_soundspeed",
+    "mixture_err",
+    "fd_order",
+    "ib_state_wrt",
 )
-_nv(_PRE_SIM,
-    "x_domain", "y_domain", "z_domain",
-    "x_a", "y_a", "z_a", "x_b", "y_b", "z_b",
-    "palpha_eps", "ptgalpha_eps", "t_step_old", "patch_ib", "pi_fac",
+_nv(
+    _PRE_SIM,
+    "x_domain",
+    "y_domain",
+    "z_domain",
+    "x_a",
+    "y_a",
+    "z_a",
+    "x_b",
+    "y_b",
+    "z_b",
+    "palpha_eps",
+    "ptgalpha_eps",
+    "t_step_old",
+    "patch_ib",
+    "pi_fac",
 )
 _nv(_PRE_POST, "num_fluids", "weno_order", "recon_type", "muscl_order", "mhd", "nb", "sigR", "igr", "igr_order")
-_nv(_SIM,
-    "dt", "t_step_print", "time_stepper", "adap_dt", "adap_dt_tol", "adap_dt_max_iters",
-    "weno_eps", "teno_CT", "wenoz_q", "mp_weno", "weno_avg", "weno_Re_flux", "null_weights",
-    "muscl_eps", "int_comp", "ic_eps", "ic_beta",
-    "riemann_solver", "wave_speeds", "low_Mach",
-    "hyper_cleaning_speed", "hyper_cleaning_tau",
-    "run_time_info", "bubble_model", "lag_params",
-    "probe_wrt", "num_probes", "probe", "integral_wrt", "num_integrals", "integral",
-    "acoustic_source", "num_source", "acoustic", "chem_params",
-    "bf_x", "bf_y", "bf_z", "k_x", "k_y", "k_z", "w_x", "w_y", "w_z",
-    "p_x", "p_y", "p_z", "g_x", "g_y", "g_z",
-    "collision_model", "coefficient_of_restitution", "collision_time", "ib_coefficient_of_friction",
-    "tau_star", "cont_damage_s", "alpha_bar",
-    "rdma_mpi", "alf_factor",
-    "num_igr_iters", "num_igr_warm_start_iters", "igr_iter_solver", "igr_pres_lim",
-    "nv_uvm_out_of_core", "nv_uvm_igr_temps_on_gpu", "nv_uvm_pref_gpu",
+_nv(
+    _SIM,
+    "dt",
+    "t_step_print",
+    "time_stepper",
+    "adap_dt",
+    "adap_dt_tol",
+    "adap_dt_max_iters",
+    "weno_eps",
+    "teno_CT",
+    "wenoz_q",
+    "mp_weno",
+    "weno_avg",
+    "weno_Re_flux",
+    "null_weights",
+    "muscl_eps",
+    "int_comp",
+    "ic_eps",
+    "ic_beta",
+    "riemann_solver",
+    "wave_speeds",
+    "low_Mach",
+    "hyper_cleaning_speed",
+    "hyper_cleaning_tau",
+    "run_time_info",
+    "bubble_model",
+    "lag_params",
+    "probe_wrt",
+    "num_probes",
+    "probe",
+    "integral_wrt",
+    "num_integrals",
+    "integral",
+    "acoustic_source",
+    "num_source",
+    "acoustic",
+    "chem_params",
+    "bf_x",
+    "bf_y",
+    "bf_z",
+    "k_x",
+    "k_y",
+    "k_z",
+    "w_x",
+    "w_y",
+    "w_z",
+    "p_x",
+    "p_y",
+    "p_z",
+    "g_x",
+    "g_y",
+    "g_z",
+    "collision_model",
+    "coefficient_of_restitution",
+    "collision_time",
+    "ib_coefficient_of_friction",
+    "tau_star",
+    "cont_damage_s",
+    "alpha_bar",
+    "rdma_mpi",
+    "alf_factor",
+    "num_igr_iters",
+    "num_igr_warm_start_iters",
+    "igr_iter_solver",
+    "igr_pres_lim",
+    "nv_uvm_out_of_core",
+    "nv_uvm_igr_temps_on_gpu",
+    "nv_uvm_pref_gpu",
 )
-_nv(_PRE,
-    "stretch_x", "stretch_y", "stretch_z", "a_x", "a_y", "a_z", "loops_x", "loops_y", "loops_z",
-    "n_start_old", "num_patches", "patch_icpp", "patch_bc",
-    "sigV", "dist_type", "rhoRV", "viscous",
-    "old_grid", "old_ic",
-    "perturb_flow", "perturb_flow_fluid", "perturb_flow_mag",
-    "perturb_sph", "perturb_sph_fluid", "fluid_rho",
-    "mixlayer_vel_profile", "mixlayer_vel_coef", "mixlayer_perturb",
-    "mixlayer_perturb_nk", "mixlayer_perturb_k0",
-    "pre_stress", "elliptic_smoothing", "elliptic_smoothing_iters",
-    "simplex_perturb", "simplex_params",
+_nv(
+    _PRE,
+    "stretch_x",
+    "stretch_y",
+    "stretch_z",
+    "a_x",
+    "a_y",
+    "a_z",
+    "loops_x",
+    "loops_y",
+    "loops_z",
+    "n_start_old",
+    "num_patches",
+    "patch_icpp",
+    "patch_bc",
+    "sigV",
+    "dist_type",
+    "rhoRV",
+    "viscous",
+    "old_grid",
+    "old_ic",
+    "perturb_flow",
+    "perturb_flow_fluid",
+    "perturb_flow_mag",
+    "perturb_sph",
+    "perturb_sph_fluid",
+    "fluid_rho",
+    "mixlayer_vel_profile",
+    "mixlayer_vel_coef",
+    "mixlayer_perturb",
+    "mixlayer_perturb_nk",
+    "mixlayer_perturb_k0",
+    "pre_stress",
+    "elliptic_smoothing",
+    "elliptic_smoothing_iters",
+    "simplex_perturb",
+    "simplex_params",
 )
-_nv(_POST,
-    "x_output", "y_output", "z_output",
-    "format", "output_partial_domain", "sim_data", "G", "flux_lim", "cons_vars_wrt",
-    "rho_wrt", "E_wrt", "pres_wrt", "c_wrt",
-    "gamma_wrt", "heat_ratio_wrt", "pi_inf_wrt", "pres_inf_wrt",
-    "omega_wrt", "qm_wrt", "liutex_wrt", "schlieren_wrt", "schlieren_alpha",
-    "alpha_rho_wrt", "mom_wrt", "vel_wrt", "flux_wrt", "alpha_wrt", "cf_wrt",
-    "chem_wrt_T", "chem_wrt_Y", "alpha_rho_e_wrt",
-    "lag_header", "lag_txt_wrt", "lag_db_wrt", "lag_id_wrt",
-    "lag_pos_wrt", "lag_pos_prev_wrt", "lag_vel_wrt", "lag_rad_wrt", "lag_rvel_wrt",
-    "lag_r0_wrt", "lag_rmax_wrt", "lag_rmin_wrt", "lag_dphidt_wrt",
-    "lag_pres_wrt", "lag_mv_wrt", "lag_mg_wrt", "lag_betaT_wrt", "lag_betaC_wrt",
+_nv(
+    _POST,
+    "x_output",
+    "y_output",
+    "z_output",
+    "format",
+    "output_partial_domain",
+    "sim_data",
+    "G",
+    "flux_lim",
+    "cons_vars_wrt",
+    "rho_wrt",
+    "E_wrt",
+    "pres_wrt",
+    "c_wrt",
+    "gamma_wrt",
+    "heat_ratio_wrt",
+    "pi_inf_wrt",
+    "pres_inf_wrt",
+    "omega_wrt",
+    "qm_wrt",
+    "liutex_wrt",
+    "schlieren_wrt",
+    "schlieren_alpha",
+    "alpha_rho_wrt",
+    "mom_wrt",
+    "vel_wrt",
+    "flux_wrt",
+    "alpha_wrt",
+    "cf_wrt",
+    "chem_wrt_T",
+    "chem_wrt_Y",
+    "alpha_rho_e_wrt",
+    "lag_header",
+    "lag_txt_wrt",
+    "lag_db_wrt",
+    "lag_id_wrt",
+    "lag_pos_wrt",
+    "lag_pos_prev_wrt",
+    "lag_vel_wrt",
+    "lag_rad_wrt",
+    "lag_rvel_wrt",
+    "lag_r0_wrt",
+    "lag_rmax_wrt",
+    "lag_rmin_wrt",
+    "lag_dphidt_wrt",
+    "lag_pres_wrt",
+    "lag_mv_wrt",
+    "lag_mg_wrt",
+    "lag_betaT_wrt",
+    "lag_betaC_wrt",
 )
 
 # Case-optimization params appear in the sim namelist under #:if not MFC_CASE_OPTIMIZATION.