refactor!: one conformer filter, gated writers, and drop reasons that say why

src/Auto3D/ASE/geometry.py

@@ -20,11 +20,10 @@
 from Auto3D.torch_config import TorchConfig, configure_torch
 from Auto3D.utils.atomic_io import atomic_write_path
 from Auto3D.utils.energy import E_TOT_HARTREE_PROP, E_TOT_PROP
+from Auto3D.utils.output_guard import check_output_not_input, check_output_overwrite
 from Auto3D.utils.validation import (
     check_engine_supports_molecules,
     check_gpu_requested,
-    check_output_not_input,
-    check_output_overwrite,
 )
 
 __all__ = ["opt_geometry"]

src/Auto3D/ASE/thermo.py

@@ -42,11 +42,10 @@
 from Auto3D.torch_config import TorchConfig, configure_torch
 from Auto3D.utils.energy import hartree2ev
 from Auto3D.utils.logging_config import get_logger
+from Auto3D.utils.output_guard import check_output_not_input, check_output_overwrite
 from Auto3D.utils.validation import (
     check_engine_supports_molecules,
     check_gpu_requested,
-    check_output_not_input,
-    check_output_overwrite,
 )
 
 __all__ = ["calc_thermo"]
@@ -686,7 +685,11 @@ def vib_hessian(mol: Chem.Mol, ase_calculator, model,
     # mass weighting, and the rotational partition function silently disagree
     # for isotopically labeled input.
     atoms = mol2atoms(mol, positions=positions)
-    atoms.set_calculator(ase_calculator)
+    # atoms.set_calculator() is deprecated since ase 3.22.1 in favor of the
+    # `.calc` attribute (Minor 6); `pyproject.toml` pins no ase upper bound
+    # and globally ignores DeprecationWarning, so removal would otherwise
+    # land as a silent-until-runtime AttributeError with no advance warning.
+    atoms.calc = ase_calculator
     charge = rdmolops.GetFormalCharge(mol)
 
     # get the Hessian
@@ -1194,7 +1197,9 @@ def do_mol_thermo(mol: Chem.Mol,
     # them via the explicit `positions=` argument, not from mol's conformer),
     # so nothing here depends on mol's conformer being in sync yet.
     coord = atoms.get_positions()
-    vib = vib_hessian(mol, atoms.get_calculator(), model, device,
+    # atoms.get_calculator() is deprecated since ase 3.22.1; use `.calc`
+    # (Minor 6, same rationale as the set_calculator() call above).
+    vib = vib_hessian(mol, atoms.calc, model, device,
                       model_name=model_name, positions=coord)
     e = atoms.get_potential_energy()
     geometry = _detect_geometry(atoms)
@@ -1691,7 +1696,9 @@ def calc_thermo(path: str, model_name: str, mol_info_func=None,
         atoms = mol2atoms(mol)
 
         calculator.set_charge(charge)
-        atoms.set_calculator(calculator)
+        # atoms.set_calculator() is deprecated since ase 3.22.1; use `.calc`
+        # (Minor 6, same rationale as vib_hessian's call above).
+        atoms.calc = calculator
 
         if mol_info_func is None:
             idx = mol.GetProp("_Name").strip()

src/Auto3D/SPE.py

@@ -13,11 +13,10 @@
 from Auto3D.models.preflight import resolve_engine_name
 from Auto3D.torch_config import TorchConfig, configure_torch
 from Auto3D.utils.logging_config import get_logger
+from Auto3D.utils.output_guard import check_output_not_input, check_output_overwrite
 from Auto3D.utils.validation import (
     check_engine_supports_molecules,
     check_gpu_requested,
-    check_output_not_input,
-    check_output_overwrite,
 )
 
 logger = get_logger(__name__)

src/Auto3D/batch_opt/optimization_engine.py

@@ -272,7 +272,7 @@ def _step_active_subset(
     not_oscillating = oscillating_count < patience
 
     # Combine the convergence criteria. An `& ~energy_converged` term stood
-    # here until 4.0.0; `energy_converged` required `fmax < opttol` while
+    # here until 3.0.0; `energy_converged` required `fmax < opttol` while
     # `not_converged_post1` is `fmax > opttol`, so the term was the identity
     # of `&` wherever it was consulted and false-dominated elsewhere -- it
     # could never change an outcome, including at the `fmax == opttol`
@@ -373,7 +373,7 @@ def n_steps(
     2. Oscillation detection: drops structures that don't improve for patience steps
 
     There is deliberately no energy-stability criterion. One existed until
-    4.0.0 but could never fire: it required ``fmax < opttol``, which is
+    3.0.0 but could never fire: it required ``fmax < opttol``, which is
     exactly the condition under which the force criterion has already stopped
     the structure, so the term was the identity of ``&`` at every element (see
     ``test_convergence_outcome_never_depends_on_energy_stability``).

src/Auto3D/cli/commands/config.py

@@ -119,7 +119,7 @@ def execute_config_init(
     Both refusals below are configuration problems, so both leave through
     ``handle_error`` at exit **2**. The overwrite refusal in particular had to
     move: the CLI's own ``-o`` overwrite gate
-    (``utils.validation.check_output_overwrite``) raises ``ConfigurationError``
+    (``utils.output_guard.check_output_overwrite``) raises ``ConfigurationError``
     and exits 2, and the CHANGELOG described the two as printing "the same
     message" -- while this one hard-coded ``SystemExit(1)``, so a script
     branching on 2 saw one of them and not the other.

src/Auto3D/cli/commands/properties.py

@@ -18,11 +18,8 @@
 from Auto3D.cli.errors import handle_error
 from Auto3D.exceptions import ConfigurationError, DependencyError
 from Auto3D.models.preflight import resolve_engine_name
-from Auto3D.utils.validation import (
-    check_gpu_requested,
-    check_output_not_input,
-    check_output_overwrite,
-)
+from Auto3D.utils.output_guard import check_output_not_input, check_output_overwrite
+from Auto3D.utils.validation import check_gpu_requested
 
 # Engine names offered for shell completion. Free-form registry names and custom
 # model paths are also accepted -- each command below validates them with

src/Auto3D/config.py

@@ -484,7 +484,7 @@ class OptimizationConfig:
     memory but may be faster."""
 
     # There is deliberately no energy_tol/energy_patience here. Both existed
-    # until 4.0.0 and reached an optimizer criterion that could never fire
+    # until 3.0.0 and reached an optimizer criterion that could never fire
     # (audit M1), so they were knobs that changed nothing. Removed rather than
     # kept as inert configuration.
 

src/Auto3D/constants.py

@@ -71,7 +71,7 @@
 DEFAULT_PATIENCE = 250  # Steps before dropping oscillating conformer
 DEFAULT_BATCHSIZE_ATOMS = 1024  # Atoms per batch for GPU optimization
 DEFAULT_ENERGY_CLUSTER_WINDOW = 0.1  # eV, for RMSD clustering
-# DEFAULT_ENERGY_TOL / DEFAULT_ENERGY_PATIENCE were removed in 4.0.0 along with
+# DEFAULT_ENERGY_TOL / DEFAULT_ENERGY_PATIENCE were removed in 3.0.0 along with
 # the optimizer's energy-stability criterion, which could never fire (audit M1).
 # Tuning the tolerance -- for fp32 noise or anything else -- changed nothing.
 DEFAULT_RANDOM_SEED = 42  # Default random seed for reproducibility