(chore): Update to Ruff 0.9 and add EM lints (#1825)

.pre-commit-config.yaml

@@ -1,12 +1,10 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.1
     hooks:
       - id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--fix"]
       - id: ruff-format
-        types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:

benchmarks/benchmarks/utils.py

@@ -63,9 +63,8 @@ def gen_indexer(adata, dim, index_kind, ratio):
     index_kinds = {"slice", "intarray", "boolarray", "strarray"}
 
     if index_kind not in index_kinds:
-        raise ValueError(
-            f"Argument 'index_kind' must be one of {index_kinds}. Was {index_kind}."
-        )
+        msg = f"Argument 'index_kind' must be one of {index_kinds}. Was {index_kind}."
+        raise ValueError(msg)
 
     axis = dimnames.index(dim)
     subset = [slice(None), slice(None)]

ci/scripts/min-deps.py

@@ -71,7 +71,9 @@ def extract_min_deps(
 
         # If we are referring to other optional dependency lists, resolve them
         if req.name == project_name:
-            assert req.extras, f"Project included itself as dependency, without specifying extras: {req}"
+            assert req.extras, (
+                f"Project included itself as dependency, without specifying extras: {req}"
+            )
             for extra in req.extras:
                 extra_deps = pyproject["project"]["optional-dependencies"][extra]
                 dependencies += map(Requirement, extra_deps)

pyproject.toml

@@ -172,13 +172,14 @@ docstring-code-format = true
 [tool.ruff.lint]
 select = [
     "E",   # Error detected by Pycodestyle
+    "EM",  # Traceback-friendly error messages
     "F",   # Errors detected by Pyflakes
     "FBT", # Boolean positional arguments
     "W",   # Warning detected by Pycodestyle
     "PLW", # Pylint
     "UP",  # pyupgrade
     "I",   # isort
-    "TCH", # manage type checking blocks
+    "TC",  # manage type checking blocks
     "TID", # Banned imports
     "ICN", # Follow import conventions
     "PTH", # Pathlib instead of os.path

src/anndata/__init__.py

@@ -15,9 +15,8 @@
     try:
         from ._version import __version__
     except ModuleNotFoundError:
-        raise RuntimeError(
-            "anndata is not correctly installed. Please install it, e.g. with pip."
-        )
+        msg = "anndata is not correctly installed. Please install it, e.g. with pip."
+        raise RuntimeError(msg)
 
 # Allowing notes to be added to exceptions. See: https://github.com/scverse/anndata/issues/868
 import sys

src/anndata/_core/aligned_df.py

@@ -82,7 +82,8 @@ def _gen_dataframe_1d(
     attr: Literal["obs", "var"],
     length: int | None = None,
 ):
-    raise ValueError(f"Cannot convert {type(anno)} to {attr} DataFrame")
+    msg = f"Cannot convert {type(anno)} to {attr} DataFrame"
+    raise ValueError(msg)
 
 
 def _mk_df_error(

src/anndata/_core/aligned_mapping.py

@@ -175,9 +175,8 @@ def __setitem__(self, key: str, value: Value) -> None:
 
     def __delitem__(self, key: str) -> None:
         if key not in self:
-            raise KeyError(
-                "'{key!r}' not found in view of {self.attrname}"
-            )  # Make sure it exists before bothering with a copy
+            msg = f"{key!r} not found in view of {self.attrname}"
+            raise KeyError(msg)  # Make sure it exists before bothering with a copy
         warnings.warn(
             f"Removing element `.{self.attrname}['{key}']` of view, "
             "initializing view as actual.",