🔀 Merge develop into dev-define-engines-abc

pre-commit/missing_imports.py

@@ -14,6 +14,7 @@
 import sys
 import tokenize
 from pathlib import Path
+from typing import NoReturn
 
 from requirements_consistency import parse_requirements
 
@@ -135,7 +136,7 @@ def stems(node: ast.Import | ast.ImportFrom) -> list[tuple[str, str]]:
     )
 
 
-def main():
+def main() -> NoReturn:
     """Main entry point."""
     parser = argparse.ArgumentParser(
         description="Static analysis of requirements files and import statements.",
@@ -219,13 +220,13 @@ def find_bad_imports(
     return result
 
 
-def find_comments(path, line_num: int):
+def find_comments(path: str | Path, line_num: int) -> list:
     """Find comments on the given line.
 
     Args:
-        path:
+        path (str | Path):
             Path to the file.
-        line_num:
+        line_num (int):
             Line number to find comments on.
 
     Returns:

pre-commit/requirements_consistency.py

@@ -4,6 +4,7 @@
 import importlib
 import sys
 from pathlib import Path
+from typing import NoReturn
 
 import yaml
 from pkg_resources import Requirement
@@ -100,7 +101,7 @@ def parse_conda(file_path: Path) -> dict[str, Requirement]:
     return packages
 
 
-def parse_setup_py(file_path) -> dict[str, Requirement]:
+def parse_setup_py(file_path: Path) -> dict[str, Requirement]:
     """Parse a setup.py file.
 
     Args:
@@ -233,7 +234,7 @@ def in_common_consistent(all_requirements: dict[Path, dict[str, Requirement]]) -
     return consistent
 
 
-def main():
+def main() -> NoReturn:
     """Main entry point for the hook."""
     root = Path(__file__).parent.parent
     test_files_exist(root)

tests/engines/_test_multi_task_segmentor.py

@@ -32,13 +32,13 @@
 # ----------------------------------------------------
 
 
-def _crash_func(_) -> None:
+def _crash_func(_: object) -> None:
     """Helper to induce crash."""
     msg = "Propagation Crash."
     raise ValueError(msg)
 
 
-def semantic_postproc_func(raw_output):
+def semantic_postproc_func(raw_output: np.ndarray) -> np.ndarray:
     """Function to post process semantic segmentations.
 
     Post processes semantic segmentation to form one map output.

tests/engines/_test_nucleus_instance_segmentor.py

@@ -36,13 +36,13 @@
 # ----------------------------------------------------
 
 
-def _crash_func(_x) -> None:
+def _crash_func(_x: object) -> None:
     """Helper to induce crash."""
     msg = "Propagation Crash."
     raise ValueError(msg)
 
 
-def helper_tile_info():
+def helper_tile_info() -> list:
     """Helper function for tile information."""
     predictor = NucleusInstanceSegmentor(model="A")
     # ! assuming the tiles organized as follows (coming out from

tests/engines/_test_patch_predictor.py

@@ -1,4 +1,5 @@
 """Test for Patch Predictor."""
+from __future__ import annotations
 
 import copy
 import shutil
@@ -32,7 +33,10 @@
 # -------------------------------------------------------------------------------------
 
 
-def test_patch_dataset_path_imgs(sample_patch1, sample_patch2) -> None:
+def test_patch_dataset_path_imgs(
+    sample_patch1: str | Path,
+    sample_patch2: str | Path,
+) -> None:
     """Test for patch dataset with a list of file paths as input."""
     size = (224, 224, 3)
 
@@ -212,32 +216,35 @@ def test_patch_dataset_crash(tmp_path: Path) -> None:
         predefined_preproc_func("secret-dataset")
 
 
-def test_wsi_patch_dataset(sample_wsi_dict, tmp_path: Path) -> None:  # noqa: PLR0915
+def test_wsi_patch_dataset(  # noqa: PLR0915
+    sample_wsi_dict: dict,
+    tmp_path: Path,
+) -> None:
     """A test for creation and bare output."""
     # convert to pathlib Path to prevent wsireader complaint
     mini_wsi_svs = Path(sample_wsi_dict["wsi2_4k_4k_svs"])
     mini_wsi_jpg = Path(sample_wsi_dict["wsi2_4k_4k_jpg"])
     mini_wsi_msk = Path(sample_wsi_dict["wsi2_4k_4k_msk"])
 
-    def reuse_init(img_path=mini_wsi_svs, **kwargs):
+    def reuse_init(img_path: Path = mini_wsi_svs, **kwargs: dict) -> WSIPatchDataset:
         """Testing function."""
         return WSIPatchDataset(img_path=img_path, **kwargs)
 
-    def reuse_init_wsi(**kwargs):
+    def reuse_init_wsi(**kwargs: dict) -> WSIPatchDataset:
         """Testing function."""
         return reuse_init(mode="wsi", **kwargs)
 
     # test for ABC validate
     # intentionally created to check error
     # skipcq
     class Proto(PatchDatasetABC):
-        def __init__(self) -> None:
+        def __init__(self: Proto) -> None:
             super().__init__()
             self.inputs = "CRASH"
             self._check_input_integrity("wsi")
 
         # skipcq
-        def __getitem__(self, idx):
+        def __getitem__(self: Proto, idx: int) -> object:
             """Get an item from the dataset."""
 
     with pytest.raises(
@@ -416,7 +423,7 @@ def test_patch_dataset_abc() -> None:
     # skipcq
     class Proto(PatchDatasetABC):
         # skipcq
-        def __init__(self) -> None:
+        def __init__(self: Proto) -> None:
             super().__init__()
 
     # crash due to undefined __getitem__
@@ -426,11 +433,11 @@ def __init__(self) -> None:
     # skipcq
     class Proto(PatchDatasetABC):
         # skipcq
-        def __init__(self) -> None:
+        def __init__(self: Proto) -> None:
             super().__init__()
 
         # skipcq
-        def __getitem__(self, idx):
+        def __getitem__(self: Proto, idx: int) -> None:
             """Get an item from the dataset."""
 
     ds = Proto()  # skipcq
@@ -598,7 +605,11 @@ def test_io_config_delegation(remote_sample: Callable, tmp_path: Path) -> None:
     shutil.rmtree(tmp_path / "dump", ignore_errors=True)
 
 
-def test_patch_predictor_api(sample_patch1, sample_patch2, tmp_path: Path) -> None:
+def test_patch_predictor_api(
+    sample_patch1: Path,
+    sample_patch2: Path,
+    tmp_path: Path,
+) -> None:
     """Helper function to get the model output using API 1."""
     save_dir_path = tmp_path
 
@@ -694,7 +705,11 @@ def test_patch_predictor_api(sample_patch1, sample_patch2, tmp_path: Path) -> No
     assert len(output["predictions"]) == len(output["probabilities"])
 
 
-def test_wsi_predictor_api(sample_wsi_dict, tmp_path: Path, chdir: Callable) -> None:
+def test_wsi_predictor_api(
+    sample_wsi_dict: dict,
+    tmp_path: Path,
+    chdir: Callable,
+) -> None:
     """Test normal run of wsi predictor."""
     save_dir_path = tmp_path
 
@@ -814,7 +829,7 @@ def test_wsi_predictor_api(sample_wsi_dict, tmp_path: Path, chdir: Callable) ->
         shutil.rmtree("output", ignore_errors=True)
 
 
-def test_wsi_predictor_merge_predictions(sample_wsi_dict) -> None:
+def test_wsi_predictor_merge_predictions(sample_wsi_dict: dict) -> None:
     """Test normal run of wsi predictor with merge predictions option."""
     # convert to pathlib Path to prevent reader complaint
     mini_wsi_svs = Path(sample_wsi_dict["wsi2_4k_4k_svs"])
@@ -915,11 +930,12 @@ def test_wsi_predictor_merge_predictions(sample_wsi_dict) -> None:
 
 
 def _test_predictor_output(
-    inputs,
-    pretrained_model,
-    probabilities_check=None,
-    predictions_check=None,
-    on_gpu=ON_GPU,
+    inputs: list,
+    pretrained_model: str,
+    probabilities_check: list | None = None,
+    predictions_check: list | None = None,
+    *,
+    on_gpu: bool = ON_GPU,
 ) -> None:
     """Test the predictions of multiple models included in tiatoolbox."""
     predictor = PatchPredictor(
@@ -954,7 +970,10 @@ def _test_predictor_output(
         )
 
 
-def test_patch_predictor_kather100k_output(sample_patch1, sample_patch2) -> None:
+def test_patch_predictor_kather100k_output(
+    sample_patch1: Path,
+    sample_patch2: Path,
+) -> None:
     """Test the output of patch prediction models on Kather100K dataset."""
     inputs = [Path(sample_patch1), Path(sample_patch2)]
     pretrained_info = {
@@ -989,7 +1008,7 @@ def test_patch_predictor_kather100k_output(sample_patch1, sample_patch2) -> None
             break
 
 
-def test_patch_predictor_pcam_output(sample_patch3, sample_patch4) -> None:
+def test_patch_predictor_pcam_output(sample_patch3: Path, sample_patch4: Path) -> None:
     """Test the output of patch prediction models on PCam dataset."""
     inputs = [Path(sample_patch3), Path(sample_patch4)]
     pretrained_info = {
@@ -1029,7 +1048,7 @@ def test_patch_predictor_pcam_output(sample_patch3, sample_patch4) -> None:
 # -------------------------------------------------------------------------------------
 
 
-def test_command_line_models_file_not_found(sample_svs, tmp_path: Path) -> None:
+def test_command_line_models_file_not_found(sample_svs: Path, tmp_path: Path) -> None:
     """Test for models CLI file not found error."""
     runner = CliRunner()
     model_file_not_found_result = runner.invoke(
@@ -1050,7 +1069,7 @@ def test_command_line_models_file_not_found(sample_svs, tmp_path: Path) -> None:
     assert isinstance(model_file_not_found_result.exception, FileNotFoundError)
 
 
-def test_command_line_models_incorrect_mode(sample_svs, tmp_path: Path) -> None:
+def test_command_line_models_incorrect_mode(sample_svs: Path, tmp_path: Path) -> None:
     """Test for models CLI mode not in wsi, tile."""
     runner = CliRunner()
     mode_not_in_wsi_tile_result = runner.invoke(
@@ -1073,7 +1092,7 @@ def test_command_line_models_incorrect_mode(sample_svs, tmp_path: Path) -> None:
     assert isinstance(mode_not_in_wsi_tile_result.exception, SystemExit)
 
 
-def test_cli_model_single_file(sample_svs, tmp_path: Path) -> None:
+def test_cli_model_single_file(sample_svs: Path, tmp_path: Path) -> None:
     """Test for models CLI single file."""
     runner = CliRunner()
     models_wsi_result = runner.invoke(

tests/models/test_dataset.py

@@ -1,4 +1,5 @@
 """Test for predefined dataset within toolbox."""
+from __future__ import annotations
 
 import shutil
 from pathlib import Path
@@ -16,23 +17,23 @@
 class Proto1(DatasetInfoABC):
     """Intentionally created to check error with new attribute a."""
 
-    def __init__(self) -> None:
+    def __init__(self: Proto1) -> None:
         """Proto1 initialization."""
         self.a = "a"
 
 
 class Proto2(DatasetInfoABC):
     """Intentionally created to check error with attribute inputs."""
 
-    def __init__(self) -> None:
+    def __init__(self: Proto2) -> None:
         """Proto2 initialization."""
         self.inputs = "a"
 
 
 class Proto3(DatasetInfoABC):
     """Intentionally created to check error with attribute inputs and labels."""
 
-    def __init__(self) -> None:
+    def __init__(self: Proto3) -> None:
         """Proto3 initialization."""
         self.inputs = "a"
         self.labels = "a"
@@ -41,7 +42,7 @@ def __init__(self) -> None:
 class Proto4(DatasetInfoABC):
     """Intentionally created to check error with attribute inputs and label names."""
 
-    def __init__(self) -> None:
+    def __init__(self: Proto4) -> None:
         """Proto4 initialization."""
         self.inputs = "a"
         self.label_names = "a"