Corrected Optimizer imports

src/check_neb_results.py

@@ -2,7 +2,6 @@
 from ase.io import read
 from calcs import calc
 import numpy as np
-from ase import Atoms
 from multiprocessing import Pool
 
 
@@ -43,11 +42,14 @@ def process_file(i):
                 energies = [i.get_potential_energy() for i in ase_traj]
                 ts_index = np.argmax(energies)
 
-                mlcalculator = calc()
+                ml_calculator = calc()
                 ts_atoms = read('TS.xyz')
-                mlcalculator.calculate(ts_atoms)
-                energy_ts = mlcalculator.results['energy']
-                rmsd, new_geom = align_geom(ase_traj[ts_index].get_positions(), ts_atoms.get_positions())
+                ml_calculator.calculate(ts_atoms)
+                energy_ts = ml_calculator.results['energy']
+                rmsd, new_geom = align_geom(
+                    ase_traj[ts_index].get_positions(),
+                    ts_atoms.get_positions()
+                )
 
                 fwd_barrier_neb = energies[ts_index] - energies[0]
                 rev_barrier_neb = energies[ts_index] - energies[-1]

src/neb_wrapper.py

@@ -3,7 +3,7 @@
 from ase.io import write
 from setup_images import setup_images
 from ase.neb import NEB
-from ase.optimize import Optimizer
+from ase.optimize.optimize import Optimizer
 
 
 def run_neb_method(

tests/test_setup_images.py

@@ -9,7 +9,11 @@ def test_setup_images(setup_test_environment):
     logdir, xyz_r_p = setup_test_environment
 
     # Call the setup_images function
-    images = setup_images(logdir=str(logdir), xyz_r_p=str(xyz_r_p), n_intermediate=2)
+    images = setup_images(
+        logdir=str(logdir),
+        xyz_r_p=str(xyz_r_p),
+        n_intermediate=2
+    )
 
     # Check that images were returned
     assert len(images) > 0, "No images were generated"