FIX: More

mne_bids_pipeline/_run.py

@@ -379,15 +379,18 @@ def _prep_out_files(
     exec_params: SimpleNamespace,
     out_files: dict[str, BIDSPath],
     check_relative: Optional[pathlib.Path] = None,
+    bids_only: bool = True,
 ):
     if check_relative is None:
         check_relative = exec_params.deriv_root
     for key, fname in out_files.items():
         # Sanity check that we only ever write to the derivatives directory
-        assert isinstance(fname, BIDSPath), type(fname)  # only write BIDSPath
-        if fname.suffix not in ("raw", "epochs"):
-            # raw and epochs can split on write, and .save should check for us
-            assert fname.split is None, fname.split
+        if bids_only:
+            assert isinstance(fname, BIDSPath), (type(fname), fname)
+        if isinstance(fname, BIDSPath):
+            if fname.suffix not in ("raw", "epochs"):
+                # raw and epochs can split on write, and .save should check for us
+                assert fname.split is None, fname.split
         fname = pathlib.Path(fname)
         if not fname.is_relative_to(check_relative):
             raise RuntimeError(

mne_bids_pipeline/steps/freesurfer/_02_coreg_surfaces.py

@@ -73,7 +73,10 @@ def make_coreg_surfaces(
     )
     out_files = get_output_fnames_coreg_surfaces(cfg=cfg, subject=subject)
     return _prep_out_files(
-        exec_params=exec_params, out_files=out_files, check_relative=cfg.fs_subjects_dir
+        exec_params=exec_params,
+        out_files=out_files,
+        check_relative=cfg.fs_subjects_dir,
+        bids_only=False,
     )
 
 

mne_bids_pipeline/steps/preprocessing/_07_make_epochs.py

@@ -214,7 +214,10 @@ def run_epochs(
     logger.info(**gen_log_kwargs(message=msg))
     out_files = dict()
     out_files["epochs"] = bids_path_in.copy().update(
-        suffix="epo", processing=None, check=False
+        suffix="epo",
+        processing=None,
+        check=False,
+        split=None,
     )
     epochs.save(
         out_files["epochs"],

mne_bids_pipeline/steps/source/_01_make_bem_surfaces.py

@@ -113,7 +113,10 @@ def make_bem_surfaces(
         session=session,
     )
     return _prep_out_files(
-        exec_params=exec_params, out_files=out_files, check_relative=cfg.fs_subjects_dir
+        exec_params=exec_params,
+        out_files=out_files,
+        check_relative=cfg.fs_subjects_dir,
+        bids_only=False,
     )
 
 

mne_bids_pipeline/steps/source/_03_setup_source_space.py

@@ -56,7 +56,10 @@ def run_setup_source_space(
     out_files = get_output_fnames_setup_source_space(cfg=cfg, subject=subject)
     mne.write_source_spaces(out_files["src"], src, overwrite=True)
     return _prep_out_files(
-        exec_params=exec_params, out_files=out_files, check_relative=cfg.fs_subjects_dir
+        exec_params=exec_params,
+        out_files=out_files,
+        check_relative=cfg.fs_subjects_dir,
+        bids_only=False,
     )