Add RUF lints (#3582)

Author: flying-sheep

benchmarks/benchmarks/preprocessing_counts.py

@@ -81,7 +81,7 @@ class FastSuite:
         ["pbmc3k", "pbmc68k_reduced", "bmmc", "lung93k"],
         ["counts", "counts-off-axis"],
     )
-    param_names = ["dataset", "layer"]
+    param_names = ("dataset", "layer")
 
     def time_calculate_qc_metrics(self, *_):
         sc.pp.calculate_qc_metrics(

benchmarks/benchmarks/preprocessing_log.py

@@ -84,7 +84,7 @@ class FastSuite:
         ["pbmc3k", "pbmc68k_reduced", "bmmc", "lung93k"],
         [None, "off-axis"],
     )
-    param_names = ["dataset", "layer"]
+    param_names = ("dataset", "layer")
 
     def time_mean_var(self, *_):
         _get_mean_var(adata.X)

pyproject.toml

@@ -243,7 +243,7 @@ select = [
     "PT",     # Pytest style
     "PTH",    # Pathlib instead of os.path
     "PYI",    # Typing
-    "RUF100", # Unused noqa
+    "RUF",    # Miscellaneous Ruff-only lints
     "SIM",    # Simplify control flow
     "TC",     # Manage type checking blocks
     "UP",     # Update legacy syntax
@@ -252,27 +252,18 @@ select = [
 ]
 external = [ "PLR0917" ] # preview lint that we use
 ignore = [
-    # dict() syntax is preferrable when creating dicts for kwargs
-    "C408",
-    # E266 too many leading '#' for block comment -> Scanpy allows them for comments into sections
-    "E262",
-    # module level import not at top of file -> required to circumvent circular imports for Scanpys API
-    "E402",
-    # line too long -> we accept long comment lines; black gets rid of long code lines
-    "E501",
-    # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
-    "E741",
-    # We ban blank lines before docstrings instead of the opposite
-    "D203",
-    # We want multiline summaries to start on the first line, not the second
-    "D213",
-    # TODO: replace our current param docs reuse with this and remove it here:
-    "D417",
-    # Numbers like “2” aren’t that “magic”.
-    "PLR2004",
-    # `Literal["..."] | str` is useful for autocompletion
-    "PYI051",
+    "C408",    # dict() syntax is preferrable when creating dicts for kwargs
+    "E262",    # E266 too many leading '#' for block comment -> Scanpy allows them for comments into sections
+    "E402",    # module level import not at top of file -> required to circumvent circular imports for Scanpys API
+    "E501",    # line too long -> we accept long comment lines; black gets rid of long code lines
+    "E741",    # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
+    "D203",    # We ban blank lines before docstrings instead of the opposite
+    "D213",    # We want multiline summaries to start on the first line, not the second
+    "D417",    # TODO: replace our current param docs reuse with this and remove it here:
+    "PLR2004", # Numbers like “2” aren’t that “magic”.
+    "PYI051",  # `Literal["..."] | str` is useful for autocompletion
 ]
+allowed-confusables = [ "×", "’", "–", "α" ]
 [tool.ruff.lint.per-file-ignores]
 # Do not assign a lambda expression, use a def
 "src/scanpy/tools/_rank_genes_groups.py" = [ "E731" ]

src/scanpy/__init__.py

@@ -60,9 +60,23 @@
 del sys, annotate_doc_types
 
 __all__ = [
-    "__version__",
     "AnnData",
+    "Neighbors",
+    "Verbosity",
+    "__version__",
     "concat",
+    "datasets",
+    "experimental",
+    "external",
+    "get",
+    "logging",
+    "metrics",
+    "pl",
+    "pp",
+    "queries",
+    "read",
+    "read_10x_h5",
+    "read_10x_mtx",
     "read_csv",
     "read_excel",
     "read_h5ad",
@@ -71,23 +85,9 @@
     "read_mtx",
     "read_text",
     "read_umi_tools",
-    "read",
-    "read_10x_h5",
-    "read_10x_mtx",
     "read_visium",
-    "write",
-    "datasets",
-    "experimental",
-    "external",
-    "get",
-    "logging",
-    "metrics",
-    "queries",
-    "pl",
-    "pp",
-    "tl",
-    "Verbosity",
-    "settings",
-    "Neighbors",
     "set_figure_params",
+    "settings",
+    "tl",
+    "write",
 ]

src/scanpy/_compat.py

@@ -49,13 +49,13 @@
 __all__ = [
     "DaskArray",
     "ZappyArray",
+    "_numba_threading_layer",
+    "deprecated",
     "fullname",
+    "njit",
+    "old_positionals",
     "pkg_metadata",
     "pkg_version",
-    "old_positionals",
-    "deprecated",
-    "njit",
-    "_numba_threading_layer",
 ]
 
 

src/scanpy/datasets/__init__.py

@@ -19,6 +19,7 @@
 __all__ = [
     "blobs",
     "burczynski06",
+    "ebi_expression_atlas",
     "krumsiek11",
     "moignard15",
     "paul15",
@@ -27,5 +28,4 @@
     "pbmc68k_reduced",
     "toggleswitch",
     "visium_sge",
-    "ebi_expression_atlas",
 ]

src/scanpy/external/exporting.py

@@ -22,7 +22,7 @@
 
     from anndata import AnnData
 
-__all__ = ["spring_project", "cellbrowser"]
+__all__ = ["cellbrowser", "spring_project"]
 
 
 @old_positionals(

src/scanpy/external/pl.py

@@ -7,8 +7,8 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from anndata import AnnData  # noqa: TCH002
-from matplotlib.axes import Axes  # noqa: TCH002
+from anndata import AnnData  # noqa: TC002
+from matplotlib.axes import Axes  # noqa: TC002
 from sklearn.utils import deprecated
 
 from .._compat import old_positionals
@@ -30,10 +30,10 @@
 
 
 __all__ = [
-    "phate",
-    "trimap",
     "harmony_timeseries",
+    "phate",
     "sam",
+    "trimap",
     "wishbone_marker_trajectory",
 ]
 

src/scanpy/external/pp/_harmony_integrate.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from collections.abc import Sequence  # noqa: TCH003
+from collections.abc import Sequence  # noqa: TC003
 from typing import TYPE_CHECKING
 
 import numpy as np

src/scanpy/external/tl/__init__.py

@@ -12,14 +12,14 @@
 from ._wishbone import wishbone
 
 __all__ = [
+    "cyclone",
     "harmony_timeseries",
     "palantir",
     "palantir_results",
     "phate",
     "phenograph",
-    "cyclone",
-    "sandbag",
     "sam",
+    "sandbag",
     "trimap",
     "wishbone",
 ]