Merge branch 'dev-define-engines-abc' into dev-convert-modelabc-to-torch-nn-model

Author: shaneahmed

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.11.13 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.12.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.13
+    rev: v0.12.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

benchmarks/annotation_store_alloc.py

@@ -141,6 +141,7 @@ def __exit__(self: memray, *args: object) -> None:
 
 import numpy as np
 import psutil
+from shapely import affinity
 from shapely.geometry import Polygon
 from tqdm import tqdm
 
@@ -188,8 +189,6 @@ def cell_polygon(
         round_coords (bool): Round coordinates to integers. Defaults to False.
 
     """
-    from shapely import affinity
-
     rand_state = np.random.default_rng().__getstate__()
     rng = np.random.default_rng(seed)
     if repeat_first:

pre-commit/notebook_urls.py

@@ -14,7 +14,7 @@
 def git_branch_name() -> str:
     """Get the current branch name."""
     return (
-        subprocess.check_output(  # noqa: S603
+        subprocess.check_output(
             ["/usr/bin/git", "rev-parse", "--abbrev-ref", "HEAD"],
         )
         .decode()
@@ -45,7 +45,7 @@ def git_previous_commit_modified_paths() -> set[Path]:
     """Get a set of file paths modified in the previous commit."""
     return {
         Path(p)
-        for p in subprocess.check_output(  # noqa: S603
+        for p in subprocess.check_output(
             ["/usr/bin/git", "diff", "--name-only", "HEAD~"],
         )
         .decode()

pre-commit/requirements_consistency.py

@@ -115,7 +115,7 @@ def parse_setup_py(file_path: Path) -> dict[str, Requirement]:
             pkg_resources.Requirement.
     """
     mock_setup = {}
-    import setuptools
+    import setuptools  # noqa: PLC0415
 
     setuptools.setup = lambda **kw: mock_setup.update(kw)
     spec = importlib.util.spec_from_file_location("setup", str(file_path))

requirements/requirements_dev.txt

@@ -10,7 +10,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.11.13  # This will be updated by pre-commit bot to latest version
+ruff==0.12.2  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/conftest.py

@@ -589,9 +589,9 @@ def chdir() -> Callable:
 
     """
     try:
-        from contextlib import chdir
+        from contextlib import chdir  # noqa: PLC0415
     except ImportError:
-        from contextlib import AbstractContextManager
+        from contextlib import AbstractContextManager  # noqa: PLC0415
 
         class chdir(AbstractContextManager):  # noqa: N801
             """Non thread-safe context manager to change the current working directory.

tests/engines/test_engine_abc.py

@@ -37,6 +37,7 @@ def __init__(
         self: TestEngineABC,
         model: str | torch.nn.Module,
         weights: str | Path | None = None,
+        *,
         verbose: bool | None = None,
     ) -> NoReturn:
         """Test EngineABC init."""

tests/test_init.py

@@ -16,7 +16,7 @@ def test_set_root_dir(tmp_path: Path) -> None:
     """Test for setting new root dir."""
     # skipcq
     importlib.reload(tiatoolbox)
-    from tiatoolbox import rcParam
+    from tiatoolbox import rcParam  # noqa: PLC0415
 
     old_root_dir = rcParam["TIATOOLBOX_HOME"]
     test_dir_path = tmp_path / "tmp_check"
@@ -27,7 +27,7 @@ def test_set_root_dir(tmp_path: Path) -> None:
     # reimport to see if it overwrites
     # silence Deep Source because this is an intentional check
     # skipcq
-    from tiatoolbox import rcParam
+    from tiatoolbox import rcParam  # noqa: PLC0415
 
     rcParam["TIATOOLBOX_HOME"].mkdir(parents=True)
     if not Path.exists(test_dir_path):
@@ -135,9 +135,9 @@ def test_duplicate_filter(caplog: pytest.LogCaptureFixture) -> None:
 
 def test_lazy_import() -> None:
     """Test lazy import for tiatoolbox."""
-    import sys
+    import sys  # noqa: PLC0415
 
-    from tiatoolbox import _lazy_import
+    from tiatoolbox import _lazy_import  # noqa: PLC0415
 
     assert "exceptions" not in sys.modules
 
@@ -151,7 +151,7 @@ def test_lazy_import() -> None:
 
 def test_lazy_import_module_not_found() -> None:
     """'Test lazy import for ModuleNotFoundError."""
-    from tiatoolbox import _lazy_import
+    from tiatoolbox import _lazy_import  # noqa: PLC0415
 
     with pytest.raises(ModuleNotFoundError):
         _lazy_import(

tests/test_utils.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import hashlib
+import json
 import shutil
 from pathlib import Path
 from typing import TYPE_CHECKING, NoReturn
@@ -27,7 +28,10 @@
 from tiatoolbox.annotation.storage import DictionaryStore, SQLiteStore
 from tiatoolbox.enums import GeometryType
 from tiatoolbox.models.architecture import fetch_pretrained_weights
-from tiatoolbox.models.architecture.utils import compile_model
+from tiatoolbox.models.architecture.utils import (
+    compile_model,
+    is_torch_compile_compatible,
+)
 from tiatoolbox.utils import misc
 from tiatoolbox.utils.exceptions import FileNotSupportedError
 from tiatoolbox.utils.transforms import locsize2bounds
@@ -1348,8 +1352,6 @@ def test_select_device() -> None:
 def test_save_as_json(tmp_path: Path) -> None:
     """Test save data to json."""
     # This should be broken up into separate tests!
-    import json
-
     # dict with nested dict, list, and np.array
     key_dict = {
         "a1": {"name": "John", "age": 23, "sex": "male"},
@@ -1872,8 +1874,6 @@ def test_torch_compile_disable() -> None:
 
 def test_torch_compile_compatibility(caplog: pytest.LogCaptureFixture) -> None:
     """Test if torch-compile compatibility is checked correctly."""
-    from tiatoolbox.models.architecture.utils import is_torch_compile_compatible
-
     is_torch_compile_compatible()
     assert "torch.compile" in caplog.text