[pre-commit.ci] pre-commit autoupdate (#838)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.2 → v0.5.6](astral-sh/ruff-pre-commit@v0.5.2...v0.5.6) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 📌 Update `ruff` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> * 🐛 Fix PLR1714 Consider merging multiple comparisons. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> * fix mypy error * ignore mypy bug * 🐛 Add logger info to debug error Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> * 📌 Pin pytest version Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> * 📌 Pin pytest version Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> * 🔥 Remove logger Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> --------- Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com>
TissueImageAnalytics · Aug 9, 2024 · aed63b6 · aed63b6
1 parent 964c846
commit aed63b6
Show file tree

Hide file tree

Showing 9 changed files with 12 additions and 14 deletions.
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.5.2 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.5.6 "pytest<8.3.0" pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

diff --git a/.pre-commit-config.yaml b/.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: v0.5.2
+    rev: v0.5.6
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

diff --git a/requirements/requirements_dev.txt b/requirements/requirements_dev.txt
@@ -7,11 +7,11 @@ mypy>=1.6.1
 pip>=22.3
 poetry-bumpversion>=0.3.1
 pre-commit>=2.20.0
-pytest>=7.2.0
+pytest>=7.2.0, <8.3.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.5.2  # This will be updated by pre-commit bot to latest version
+ruff==0.5.6  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1
diff --git a/tiatoolbox/annotation/storage.py b/tiatoolbox/annotation/storage.py
@@ -1841,10 +1841,10 @@ def _dump_cases(
             # It is a file-like object, write to it
             if hasattr(fp, "write"):
                 file_handle = cast(IO, fp)
-                return file_fn(file_handle)
+                return file_fn(file_handle)  # type: ignore[func-returns-value]
             # Turn a path into a file handle, then write to it
             with Path(fp).open("w", encoding="utf-8") as file_handle:
-                return file_fn(file_handle)
+                return file_fn(file_handle)  # type: ignore[func-returns-value]
         # Return as str or bytes if no handle/path is given
         return none_fn()
 
@@ -2826,7 +2826,7 @@ def _initialize_query_string_parameters(
 
         return query_string, query_parameters
 
-    def _query(  # noqa: PLR0913
+    def _query(
         self: SQLiteStore,
         columns: str,
         geometry: Geometry | None = None,

diff --git a/tiatoolbox/models/dataset/classification.py b/tiatoolbox/models/dataset/classification.py
@@ -163,7 +163,7 @@ class WSIPatchDataset(dataset_abc.PatchDatasetABC):
 
     """
 
-    def __init__(  # skipcq: PY-R1000  # noqa: PLR0913, PLR0915
+    def __init__(  # skipcq: PY-R1000  # noqa: PLR0915
         self: WSIPatchDataset,
         img_path: str | Path,
         mode: str = "wsi",

diff --git a/tiatoolbox/models/engine/multi_task_segmentor.py b/tiatoolbox/models/engine/multi_task_segmentor.py
@@ -243,7 +243,7 @@ class MultiTaskSegmentor(NucleusInstanceSegmentor):
 
     """
 
-    def __init__(  # noqa: PLR0913
+    def __init__(
         self: MultiTaskSegmentor,
         batch_size: int = 8,
         num_loader_workers: int = 0,

diff --git a/tiatoolbox/tools/patchextraction.py b/tiatoolbox/tools/patchextraction.py
@@ -623,7 +623,7 @@ class SlidingWindowPatchExtractor(PatchExtractor):
 
     """
 
-    def __init__(  # noqa: PLR0913
+    def __init__(
         self: SlidingWindowPatchExtractor,
         input_img: str | Path | np.ndarray,
         patch_size: int | tuple[int, int],

diff --git a/tiatoolbox/utils/misc.py b/tiatoolbox/utils/misc.py
@@ -1190,9 +1190,7 @@ def add_from_dat(
         anns = []
         for subcat in data:
             if (
-                subcat == "resolution"
-                or subcat == "proc_dimensions"
-                or subcat == "base_dimensions"
+                subcat in {"resolution", "proc_dimensions", "base_dimensions"}
                 or "resolution" in subcat
             ):
                 continue

diff --git a/tiatoolbox/wsicore/wsimeta.py b/tiatoolbox/wsicore/wsimeta.py
@@ -96,7 +96,7 @@ class WSIMeta:
 
     _valid_axes_characters = "YXSTZ"
 
-    def __init__(  # noqa: PLR0913
+    def __init__(
         self: WSIMeta,
         slide_dimensions: tuple[int, int],
         axes: str,