Merge branch 'develop' into dev-define-engines-abc

Author: shaneahmed

.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==0.5.7 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.6.1 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: v0.5.7
+    rev: v0.6.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements_dev.txt

@@ -11,7 +11,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.5.7  # This will be updated by pre-commit bot to latest version
+ruff==0.6.1  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/test_annotation_stores.py

@@ -194,7 +194,7 @@ def sample_triangle() -> Polygon:
     return Polygon([(0, 0), (1, 1), (2, 0)])
 
 
-@pytest.fixture()
+@pytest.fixture
 def fill_store(
     cell_grid: list[Polygon],
     points_grid: list[Point],

tests/test_docs.py

@@ -17,7 +17,7 @@
     from collections.abc import Generator
 
 
-@pytest.fixture()
+@pytest.fixture
 def source_files(root_path: Path) -> Generator:
     """Recursively yield source files from the project."""
     ignore = {"__pycache__"}

tests/test_json_config_bokeh.py

@@ -40,7 +40,7 @@ def annotation_path(data_path: dict[str, Path]) -> dict[str, Path]:
     return data_path
 
 
-@pytest.fixture()
+@pytest.fixture
 def bk_session(data_path: dict[str, Path]) -> ClientSession:
     """Create a bokeh session."""
     run_tileserver()

tests/test_server_bokeh.py

@@ -46,7 +46,7 @@ def annotation_path(data_path: dict[str, Path]) -> dict[str, Path]:
     return data_path
 
 
-@pytest.fixture()
+@pytest.fixture
 def bk_session(data_path: dict[str, Path]) -> ClientSession:
     """Create a bokeh session."""
     run_tileserver()

tests/test_tileserver.py

@@ -87,7 +87,7 @@ def _fill_store(
     return _fill_store
 
 
-@pytest.fixture()
+@pytest.fixture
 def app(remote_sample: Callable, tmp_path: Path) -> TileServer:
     """Create a testing TileServer WSGI app."""
     # Make a low-res .jpg of the right shape to be used as
@@ -122,7 +122,7 @@ def app(remote_sample: Callable, tmp_path: Path) -> TileServer:
     return app
 
 
-@pytest.fixture()
+@pytest.fixture
 def app_alt(fill_store: Callable) -> TileServer:
     """Create a testing TileServer WSGI app, with a different setup."""
     sample_slide = WSIReader.open(np.zeros((1000, 1000, 3), dtype=np.uint8))
@@ -147,7 +147,7 @@ def app_alt(fill_store: Callable) -> TileServer:
     return app
 
 
-@pytest.fixture()
+@pytest.fixture
 def empty_app() -> TileServer:
     """Create a testing TileServer WSGI app with no layers."""
     app = TileServer(

tiatoolbox/annotation/storage.py

@@ -939,7 +939,7 @@ def _eval_where(
             return True
         if isinstance(predicate, str):
             return bool(
-                eval(  # skipcq: PYL-W0123,  # noqa: PGH001, S307
+                eval(  # skipcq: PYL-W0123,  # noqa: S307
                     predicate,
                     PY_GLOBALS,
                     {"props": properties},
@@ -1513,7 +1513,7 @@ def select_values(
 
             if isinstance(select, str):
                 py_locals = {"props": annotation.properties}
-                return eval(  # skipcq: PYL-W0123,  # noqa: PGH001, S307
+                return eval(  # skipcq: PYL-W0123,  # noqa: S307
                     select,
                     PY_GLOBALS,
                     py_locals,
@@ -2831,7 +2831,7 @@ def _initialize_query_string_parameters(
             query_parameters["where"] = where
         # Predicate is a string
         if isinstance(where, str):
-            sql_predicate = eval(  # skipcq: PYL-W0123,  # noqa: PGH001, S307
+            sql_predicate = eval(  # skipcq: PYL-W0123,  # noqa: S307
                 where,
                 SQL_GLOBALS,
                 {},
@@ -3441,7 +3441,7 @@ def pquery(
             return_columns.append("[key]")
         if is_str_query and not is_star_query:
             select = cast(str, select)
-            select_names = eval(  # skipcq: PYL-W0123,  # noqa: PGH001, S307
+            select_names = eval(  # skipcq: PYL-W0123,  # noqa: S307
                 select,
                 SQL_GLOBALS,
                 {},
@@ -3869,7 +3869,7 @@ def create_index(
         if not isinstance(where, str):
             msg = f"Invalid type for `where` ({type(where)})."
             raise TypeError(msg)
-        sql_predicate = eval(  # skipcq: PYL-W0123,  # noqa: PGH001, S307
+        sql_predicate = eval(  # skipcq: PYL-W0123,  # noqa: S307
             where,
             SQL_GLOBALS,
         )