DM-48788: Enable ruff format

.pre-commit-config.yaml

@@ -7,25 +7,14 @@ repos:
           - "--unsafe"
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
-    hooks:
-      - id: black
-        # It is recommended to specify the latest version of Python
-        # supported by your project here, or alternatively use
-        # pre-commit's default_language_version, see
-        # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.11
-  - repo: https://github.com/pycqa/isort
-    rev: 6.0.0
-    hooks:
-      - id: isort
-        name: isort (python)
+      - id: check-toml
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.3
+    rev: v0.9.5
     hooks:
       - id: ruff
+        args: [--fix]
+      - id: ruff-format
   - repo: https://github.com/numpy/numpydoc
     rev: "v1.8.0"
     hooks:

pyproject.toml

@@ -131,6 +131,7 @@ target-version = ["py311"]
 [tool.isort]
 profile = "black"
 line_length = 110
+known_first_party = ["lsst"]
 
 [tool.lsst_versions]
 write_to = "python/lsst/daf/butler/version.py"
@@ -194,23 +195,33 @@ select = [
     "W",  # pycodestyle
     "D",  # pydocstyle
     "UP",  # pyupgrade
+    "I",  # isort
+    "RUF022",  # sort __all__
 ]
 # Commented out to suppress "unused noqa" in jenkins which has older ruff not
 # generating E721.
-#extend-select = [
-#    "RUF100", # Warn about unused noqa
-#]
+extend-select = [
+    "RUF100", # Warn about unused noqa
+]
 
 [tool.ruff.lint.per-file-ignores]
 # parserYacc docstrings can not be fixed. Docstrings are used to define grammar.
 "python/lsst/daf/butler/registry/queries/expressions/parser/parserYacc.py" = ["D401", "D403"]
 
+[tool.ruff.lint.isort]
+known-first-party = ["lsst"]
+
 [tool.ruff.lint.pycodestyle]
 max-doc-length = 79
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
+[tool.ruff.format]
+docstring-code-format = true
+# Formatter does not know about indenting.
+docstring-code-line-length = 69
+
 [tool.numpydoc_validation]
 checks = [
     "all",  # All except the rules listed below.

python/lsst/daf/butler/_butler.py

@@ -272,8 +272,10 @@ def from_config(
                 "/path/to/repo",
                 run="u/alice/DM-50000/a",
                 collections=[
-                    "u/alice/DM-50000/a", "u/bob/DM-49998", "HSC/defaults"
-                ]
+                    "u/alice/DM-50000/a",
+                    "u/bob/DM-49998",
+                    "HSC/defaults",
+                ],
             )
 
         This butler will `put` new datasets to the run ``u/alice/DM-50000/a``.
@@ -1422,8 +1424,9 @@ def export(
             with butler.export("exports.yaml") as export:
                 # Export all flats, but none of the dimension element rows
                 # (i.e. data ID information) associated with them.
-                export.saveDatasets(butler.registry.queryDatasets("flat"),
-                                    elements=())
+                export.saveDatasets(
+                    butler.registry.queryDatasets("flat"), elements=()
+                )
                 # Export all datasets that start with "deepCoadd_" and all of
                 # their associated data ID information.
                 export.saveDatasets(butler.registry.queryDatasets("deepCoadd_*"))

python/lsst/daf/butler/_butler_config.py

@@ -26,6 +26,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 """Configuration classes specific to the Butler."""
+
 from __future__ import annotations
 
 __all__ = ("ButlerConfig",)

python/lsst/daf/butler/_butler_repo_index.py

@@ -33,9 +33,10 @@
 from typing import Any, ClassVar
 
 import yaml
-from lsst.resources import ResourcePath
 from pydantic import TypeAdapter, ValidationError
 
+from lsst.resources import ResourcePath
+
 from ._config import Config
 from ._utilities.thread_safe_cache import ThreadSafeCache
 

python/lsst/daf/butler/_column_type_info.py

@@ -36,6 +36,7 @@
 
 import astropy.time
 import sqlalchemy
+
 from lsst.daf.relation import ColumnTag, sql
 
 from . import ddl

python/lsst/daf/butler/_config.py

@@ -44,9 +44,10 @@
 from typing import IO, TYPE_CHECKING, Any, ClassVar, cast
 
 import yaml
+from yaml.representer import Representer
+
 from lsst.resources import ResourcePath, ResourcePathExpression
 from lsst.utils import doImportType
-from yaml.representer import Representer
 
 yaml.add_representer(defaultdict, Representer.represent_dict)
 

python/lsst/daf/butler/_config_support.py

@@ -29,7 +29,7 @@
 
 from __future__ import annotations
 
-__all__ = ("LookupKey", "processLookupConfigs", "processLookupConfigList")
+__all__ = ("LookupKey", "processLookupConfigList", "processLookupConfigs")
 
 import logging
 import re

python/lsst/daf/butler/_dataset_ref.py

@@ -56,9 +56,10 @@
 )
 
 import pydantic
-from lsst.utils.classes import immutable
 from pydantic import StrictStr
 
+from lsst.utils.classes import immutable
+
 from ._config_support import LookupKey
 from ._dataset_type import DatasetType, SerializedDatasetType
 from ._named import NamedKeyDict

python/lsst/daf/butler/_deferredDatasetHandle.py

@@ -26,6 +26,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 """Module containing classes used with deferring dataset loading."""
+
 from __future__ import annotations
 
 __all__ = ("DeferredDatasetHandle",)

python/lsst/daf/butler/_exceptions.py

@@ -26,20 +26,21 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 """Specialized Butler exceptions."""
+
 __all__ = (
     "ButlerUserError",
     "CalibrationLookupError",
     "CollectionCycleError",
     "CollectionTypeError",
     "DataIdValueError",
     "DatasetNotFoundError",
-    "DimensionNameError",
     "DatasetTypeNotSupportedError",
+    "DimensionNameError",
     "EmptyQueryResultError",
     "InconsistentDataIdError",
     "InvalidQueryError",
-    "MissingDatasetTypeError",
     "MissingCollectionError",
+    "MissingDatasetTypeError",
     "ValidationError",
 )
 
@@ -228,9 +229,9 @@ class UnknownButlerUserError(ButlerUserError):
     UnknownButlerUserError,
 )
 _USER_ERROR_MAPPING = {e.error_type: e for e in _USER_ERROR_TYPES}
-assert len(_USER_ERROR_MAPPING) == len(
-    _USER_ERROR_TYPES
-), "Subclasses of ButlerUserError must have unique 'error_type' property"
+assert len(_USER_ERROR_MAPPING) == len(_USER_ERROR_TYPES), (
+    "Subclasses of ButlerUserError must have unique 'error_type' property"
+)
 
 
 def create_butler_user_error(error_type: str, message: str) -> ButlerUserError:

python/lsst/daf/butler/_formatter.py

@@ -28,13 +28,13 @@
 from __future__ import annotations
 
 __all__ = (
+    "FileIntegrityError",
     "Formatter",
-    "FormatterV2",
-    "FormatterV1inV2",
     "FormatterFactory",
-    "FormatterParameter",
     "FormatterNotImplementedError",
-    "FileIntegrityError",
+    "FormatterParameter",
+    "FormatterV1inV2",
+    "FormatterV2",
 )
 
 import contextlib
@@ -742,7 +742,6 @@ def read_from_possibly_cached_local_file(
                         self.name(),
                     ),
                 ):
-
                     if self.can_read_from_local_file:
                         result = self.read_from_local_file(
                             local_uri.ospath, component=component, expected_size=expected_size

python/lsst/daf/butler/_named.py

@@ -27,13 +27,13 @@
 from __future__ import annotations
 
 __all__ = (
+    "NameLookupMapping",
+    "NameMappingSetView",
     "NamedKeyDict",
     "NamedKeyMapping",
     "NamedValueAbstractSet",
     "NamedValueMutableSet",
     "NamedValueSet",
-    "NameLookupMapping",
-    "NameMappingSetView",
 )
 
 import contextlib

python/lsst/daf/butler/_quantum.py

@@ -27,13 +27,14 @@
 
 from __future__ import annotations
 
-__all__ = ("Quantum", "SerializedQuantum", "DimensionRecordsAccumulator")
+__all__ = ("DimensionRecordsAccumulator", "Quantum", "SerializedQuantum")
 
 import sys
 from collections.abc import Iterable, Mapping, MutableMapping, Sequence
 from typing import Any
 
 import pydantic
+
 from lsst.utils import doImportType
 
 from ._dataset_ref import DatasetRef, SerializedDatasetRef

python/lsst/daf/butler/_quantum_backed.py

@@ -39,6 +39,7 @@
 from typing import TYPE_CHECKING, Any
 
 import pydantic
+
 from lsst.resources import ResourcePath, ResourcePathExpression
 
 from ._butler_config import ButlerConfig

python/lsst/daf/butler/_storage_class.py

@@ -29,7 +29,7 @@
 
 from __future__ import annotations
 
-__all__ = ("StorageClass", "StorageClassFactory", "StorageClassConfig")
+__all__ = ("StorageClass", "StorageClassConfig", "StorageClassFactory")
 
 import builtins
 import itertools

python/lsst/daf/butler/_topology.py

@@ -28,9 +28,9 @@
 from __future__ import annotations
 
 __all__ = (
-    "TopologicalSpace",
     "TopologicalFamily",
     "TopologicalRelationshipEndpoint",
+    "TopologicalSpace",
 )
 
 import enum

python/lsst/daf/butler/arrow_utils.py

@@ -28,15 +28,15 @@
 from __future__ import annotations
 
 __all__ = (
-    "ToArrow",
-    "RegionArrowType",
+    "DateTimeArrowScalar",
+    "DateTimeArrowType",
     "RegionArrowScalar",
-    "TimespanArrowType",
+    "RegionArrowType",
     "TimespanArrowScalar",
-    "DateTimeArrowType",
-    "DateTimeArrowScalar",
-    "UUIDArrowType",
+    "TimespanArrowType",
+    "ToArrow",
     "UUIDArrowScalar",
+    "UUIDArrowType",
 )
 
 import uuid
@@ -45,6 +45,7 @@
 
 import astropy.time
 import pyarrow as pa
+
 from lsst.sphgeom import Region
 
 from ._timespan import Timespan

python/lsst/daf/butler/cli/butler.py

@@ -27,8 +27,8 @@
 from __future__ import annotations
 
 __all__ = (
-    "LoaderCLI",
     "ButlerCLI",
+    "LoaderCLI",
     "cli",
     "main",
 )
@@ -47,6 +47,7 @@
 
 import click
 import yaml
+
 from lsst.resources import ResourcePath
 from lsst.utils import doImport
 from lsst.utils.introspection import get_full_type_name

python/lsst/daf/butler/cli/cliLog.py

@@ -27,8 +27,8 @@
 from __future__ import annotations
 
 __all__ = (
-    "PrecisionLogFormatter",
     "CliLog",
+    "PrecisionLogFormatter",
 )
 
 import datetime

python/lsst/daf/butler/cli/opt/arguments.py

@@ -29,13 +29,13 @@
 __all__ = (
     "collection_argument",
     "collections_argument",
+    "destination_argument",
     "dimensions_argument",
     "directory_argument",
     "element_argument",
     "glob_argument",
     "locations_argument",
     "repo_argument",
-    "destination_argument",
 )