fix ruff issues

Author: sophiamaedler

src/scportrait/pipeline/_utils/helper.py

@@ -3,7 +3,7 @@
 T = TypeVar("T")
 
 
-def flatten(nested_list: list[list[T]]) -> list[T]:
+def flatten(nested_list: list[list[T]]) -> list[T | tuple[T]]:
     """Flatten a list of lists into a single list.
 
     Args:

src/scportrait/pipeline/selection.py

@@ -148,7 +148,7 @@ def _get_coords_multi(self, width: int, arg: tuple[list[int], np.ndarray]) -> li
 
     def _get_coords(
         self, cell_ids: list, centers: list[tuple[int, int]], width: int = 60, batch_size: int = 100, threads: int = 10
-    ) -> dict:
+    ) -> dict[int, np.ndarray]:
         # create batches
         n_batches = int(np.ceil(len(cell_ids) / batch_size))
         slices = [(i * batch_size, i * batch_size + batch_size) for i in range(n_batches - 1)]
@@ -174,8 +174,8 @@ def _get_coords(
                 pool.close()
                 pool.join()
 
-        results = flatten(results)
-        return dict(results)
+        results = flatten(results)  # type: ignore
+        return dict(results)  # type: ignore
 
     def _get_cell_ids(self, cell_sets: list[dict]) -> list[int]:
         cell_ids = []

src/scportrait/tools/stitch/_stitch.py

@@ -23,7 +23,6 @@
 from scportrait.tools.stitch._utils.ashlar_plotting import plot_edge_quality, plot_edge_scatter
 from scportrait.tools.stitch._utils.filewriters import write_ome_zarr, write_spatialdata, write_tif, write_xml
 
-
 class Stitcher:
     """
     Class for stitching of image tiles to assemble a mosaic.
@@ -107,10 +106,6 @@ def __init__(
         """
         self._lazy_imports()
 
-        # workaround for lazy imports of module
-        if self.reader_type == "FilePatternReaderRescale":
-            self.reader_type = self.FilePatternReaderRescale
-
         if orientation is None:
             orientation = {"flip_x": False, "flip_y": True}
 
@@ -139,6 +134,10 @@ def __init__(
         self.orientation = orientation
         self.reader_type = reader_type
 
+        # workaround for lazy imports of module
+        if self.reader_type == "FilePatternReaderRescale":
+            self.reader_type = self.FilePatternReaderRescale
+
         # workflow setup
         self.plot_QC = plot_QC
         self.overwrite = overwrite