fix: pacify mypy

Author: oesteban

src/nifreeze/cli/run.py

@@ -42,12 +42,17 @@ def main(argv=None) -> None:
     # Open the data with the given file path
     dataset: BaseDataset = BaseDataset.from_filename(args.input_file)
 
-    estimator: Estimator = Estimator()
+    prev_model: Estimator | None = None
+    for model in args.models:
+        estimator: Estimator = Estimator(
+            args.model,
+            prev=prev_model,
+        )
+        prev_model = estimator
 
     _ = estimator.run(
         dataset,
         align_kwargs=args.align_config,
-        models=args.models,
         omp_nthreads=args.nthreads,
         njobs=args.njobs,
         seed=args.seed,

src/nifreeze/estimator.py

@@ -137,7 +137,7 @@ def run(self, dataset: BaseDataset, **kwargs):
 
                     # fit the model
                     test_set = dataset[i]
-                    predicted = self._model.fit_predict(
+                    predicted = self._model.fit_predict(  # type: ignore[union-attr]
                         i,
                         n_jobs=n_jobs,
                     )

src/nifreeze/registration/ants.py

@@ -130,7 +130,6 @@ def _prepare_registration_data(
 
     """
     clip = clip or "none"
-
     predicted_path = Path(dirname) / f"predicted_{vol_idx:05d}.nii.gz"
     sample_path = Path(dirname) / f"sample_{vol_idx:05d}.nii.gz"
     _to_nifti(
@@ -151,7 +150,7 @@ def _prepare_registration_data(
         ImageGrid = namedtuple("ImageGrid", ("shape", "affine"))
         reference = ImageGrid(shape=sample.shape[:3], affine=affine)
         initial_xform = Affine(matrix=init_affine, reference=reference)
-        init_path = dirname / f"init_{vol_idx:05d}.mat"
+        init_path = Path(dirname) / f"init_{vol_idx:05d}.mat"
         initial_xform.to_filename(init_path, fmt="itk")
 
     return predicted_path, sample_path, init_path