[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

Diff for: pre-commit/notebook_urls.py

@@ -197,7 +197,9 @@ def check_notebook(
         for line_num, line in enumerate(cell["source"]):
             new_line = replace_line(line, to_ref, replacements)
             if new_line != line:
-                print(f"{path.name}: Changed (cell {cell_num+1}, line {line_num+1})")
+                print(
+                    f"{path.name}: Changed (cell {cell_num + 1}, line {line_num + 1})"
+                )
                 changed = True
                 cell["source"][line_num] = new_line
     return changed, notebook

Diff for: tests/models/test_multi_task_segmentor.py

@@ -128,9 +128,9 @@ def test_functionality_hovernetplus(remote_sample: Callable, tmp_path: Path) ->
 
     assert len(inst_dict) > 0, "Must have some nuclei."
     assert layer_map is not None, "Must have some layers."
-    assert (
-        layer_map.shape == required_dims
-    ), "Output layer map dimensions must be same as the expected output shape"
+    assert layer_map.shape == required_dims, (
+        "Output layer map dimensions must be same as the expected output shape"
+    )
 
 
 def test_functionality_hovernet(remote_sample: Callable, tmp_path: Path) -> None:

Diff for: tests/test_docs.py

@@ -141,7 +141,7 @@ def raise_source_exception(
         for n, line in enumerate(source.splitlines())
     ]
     if source_offset:
-        source_lines.insert(source_lineno, f"{' '*(source_offset+3)}^ {message}")
+        source_lines.insert(source_lineno, f"{' ' * (source_offset + 3)}^ {message}")
     annotated_source = "\n".join(source_lines)
     exception = type(exception) if exception else SyntaxError
     msg = f"{rel_path}:{file_lineno}: {message}\n{annotated_source}"

Diff for: tests/test_tileserver.py

@@ -461,7 +461,7 @@ def test_change_overlay(  # noqa: PLR0915
         assert response.status_code == 200
         assert response.content_type == "text/html; charset=utf-8"
         # check that the overlay has been correctly added
-        lname = f"layer{len(empty_app.pyramids[session_id])-1}"
+        lname = f"layer{len(empty_app.pyramids[session_id]) - 1}"
         layer = empty_app.pyramids[session_id][lname]
         assert layer.wsi.info.file_path == overlay_path
 
@@ -493,7 +493,7 @@ def test_change_overlay(  # noqa: PLR0915
             data={"overlay_path": safe_str(jpg_path)},
         )
         # check that the overlay has been correctly added
-        lname = f"layer{len(empty_app.pyramids[session_id])-1}"
+        lname = f"layer{len(empty_app.pyramids[session_id]) - 1}"
         layer = empty_app.pyramids[session_id][lname]
         assert np.all(layer.wsi.img == imread(jpg_path))
 
@@ -517,7 +517,7 @@ def test_change_overlay(  # noqa: PLR0915
             data={"overlay_path": safe_str(tiff_path)},
         )
         # check that the overlay has been correctly added
-        lname = f"layer{len(empty_app.pyramids[session_id])-1}"
+        lname = f"layer{len(empty_app.pyramids[session_id]) - 1}"
         layer = empty_app.pyramids[session_id][lname]
         assert layer.wsi.info.file_path == tiff_path
 

Diff for: tiatoolbox/models/architecture/hovernet.py

@@ -338,8 +338,7 @@ def __init__(
 
         if mode not in ["original", "fast"]:
             msg = (
-                f"Invalid mode {mode} for HoVerNet. "
-                f"Only support `original` or `fast`."
+                f"Invalid mode {mode} for HoVerNet. Only support `original` or `fast`."
             )
             raise ValueError(
                 msg,

Diff for: tiatoolbox/utils/misc.py

@@ -220,8 +220,7 @@ def load_stain_matrix(stain_matrix_input: np.ndarray | PathLike) -> np.ndarray:
         _, __, suffixes = split_path_name_ext(stain_matrix_input)
         if suffixes[-1] not in [".csv", ".npy"]:
             msg = (
-                "If supplying a path to a stain matrix, "
-                "use either a npy or a csv file"
+                "If supplying a path to a stain matrix, use either a npy or a csv file"
             )
             raise FileNotSupportedError(
                 msg,

Diff for: tiatoolbox/visualization/bokeh_app/main.py

@@ -1204,7 +1204,7 @@ def segment_on_box() -> None:
     # Make a mask defining the box
     thumb = UI["vstate"].wsi.slide_thumbnail()
     conv_mpp = UI["vstate"].dims[0] / thumb.shape[1]
-    msg = f'box tl: {UI["box_source"].data["x"][0]}, {UI["box_source"].data["y"][0]}'
+    msg = f"box tl: {UI['box_source'].data['x'][0]}, {UI['box_source'].data['y'][0]}"
     logger.info(msg)
     x = round(
         (UI["box_source"].data["x"][0] - 0.5 * UI["box_source"].data["width"][0])

Diff for: tiatoolbox/visualization/tileserver.py

@@ -102,7 +102,7 @@ def __init__(  # noqa: PLR0915
         if isinstance(layers, list):
             layers_dict = {"slide": layers[0]}
             for i, p in enumerate(layers[1:]):
-                layers_dict[f"layer-{i+1}"] = p
+                layers_dict[f"layer-{i + 1}"] = p
             layers = layers_dict
         # Set up the layer dict.
         meta = None