inputs and tests

Author: jpillai00

src/rbc/cli/longitudinal.py

@@ -46,7 +46,7 @@ def validate_namespace(cls, ns: argparse.Namespace) -> LongitudinalArgs:
 def main(args: LongitudinalArgs) -> int:
     """Main entrypoint of longitudinal workflow."""
     run(
-        input_dirs=args.input_dirs,
+        input_dirs=list(args.input_dirs),
         output_dir=args.output_dir,
         filters=Filters(
             participant_label=args.participant_label,

src/rbc/workflows/functional.py

@@ -393,8 +393,7 @@ class FunctionalLongOutputs(NamedTuple):
         forward_xfm: BOLD-to-longitudinal-template composite warp.
         sbref: Motion reference volume warped to longitudinal template space.
         bold: Preprocessed BOLD warped to longitudinal template space.
-        bold_mask: Brain mask warped to longitudinal template space,
-            or *None* if no mask was provided.
+        bold_mask: Brain mask warped to longitudinal template space.
         regressed_bold: Nuisance-regressed (non-bandpassed) BOLD in longitudinal
             template space. Suitable for ALFF/fALFF.
         cleaned_bold: Nuisance-regressed + bandpass-filtered BOLD in longitudinal

tests/unit/bids/test_exports.py

@@ -202,7 +202,7 @@ def test_file_count_single_regressor(
         outputs = _make_func_outputs(workdir, ["36-parameter"])
         export_functional(func_bids, outputs, regressors=["36-parameter"])
         saved = list(pipe_ctx.output_dir.rglob("*.*"))
-        assert len(saved) == 13
+        assert len(saved) == 14
 
     def test_file_count_two_regressors(
         self, func_bids: Bids, workdir: Path, pipe_ctx: RunContext
@@ -215,7 +215,7 @@ def test_file_count_two_regressors(
         outputs = _make_func_outputs(workdir, regs)
         export_functional(func_bids, outputs, regressors=regs)
         saved = list(pipe_ctx.output_dir.rglob("*.*"))
-        assert len(saved) == 16
+        assert len(saved) == 18
 
 
 # ---------------------------------------------------------------------------

tests/unit/orchestration/test_longitudinal.py

@@ -373,30 +373,6 @@ def test_missing_required_file_raises(
                 regressors=["36-parameter"],
             )
 
-    def test_optional_bold_mask_file_not_found(
-        self, func_df: pl.DataFrame, tpl_df: pl.DataFrame, tmp_path: Path
-    ) -> None:
-        """Optional bold_mask not found is caught; 3 exports emitted."""
-        pipe_ctx = RunContext(sub="01", ses="baseline", output_dir=tmp_path)
-        with (
-            patch(
-                "rbc.orchestration.longitudinal.functional_longitudinal",
-                return_value=_mock_func_outputs(with_bold_mask=False),
-            ),
-            patch(
-                "rbc.bids.query.find_file",
-                side_effect=_none_for(suffix="mask", desc="brain"),
-            ),
-            patch("rbc.bids.builder.shutil.copy2") as mock_copy,
-        ):
-            process_func(
-                pipe_ctx=pipe_ctx,
-                func_df=func_df,
-                tpl_df=tpl_df,
-                regressors=["36-parameter"],
-            )
-            assert mock_copy.call_count == 5
-
 
 class TestLongitudinalDispatch:
     """Tests for run() dispatch logic (not filtering, which is in test_filters)."""