Merge pull request #468 from lsst/tickets/DM-48788

DM-48788: Switch to ruff format

.pre-commit-config.yaml

@@ -6,25 +6,13 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-toml
-  - repo: https://github.com/psf/black
-    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)
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.3
+    rev: v0.9.4
     hooks:
       - id: ruff
+        args: [--fix]
+      - id: ruff-format
   - repo: https://github.com/numpy/numpydoc
     rev: "v1.8.0"
     hooks:

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV1.py

@@ -1,8 +1,9 @@
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV2.py

@@ -1,10 +1,11 @@
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV3.py

@@ -1,11 +1,12 @@
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV4.py

@@ -1,11 +1,12 @@
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV5.py

@@ -1,12 +1,13 @@
 import math
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV6.py

@@ -1,12 +1,13 @@
 import math
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV7.py

@@ -1,12 +1,13 @@
 import math
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV8.py

@@ -3,12 +3,13 @@
 import operator
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/aperturePipelineTaskV9.py

@@ -3,12 +3,13 @@
 import operator
 from collections.abc import Mapping
 
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes
 

doc/_static/pipe_base/PipelineTask_Examples/apertureTask.py

@@ -1,8 +1,9 @@
+import numpy as np
+
 import lsst.afw.image as afwImage
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import numpy as np
 from lsst.geom import Point2I
 from lsst.pipe.base import connectionTypes  # noqa: F401
 

pyproject.toml

@@ -106,6 +106,7 @@ target-version = ["py311"]
 [tool.isort]
 profile = "black"
 line_length = 110
+known_first_party = ["lsst"]
 
 [tool.lsst_versions]
 write_to = "python/lsst/pipe/base/version.py"
@@ -167,8 +168,14 @@ select = [
     "N",  # pep8-naming
     "W",  # pycodestyle
     "D",  # pydocstyle
+    "I",  # isort
+    "RUF022",  # sort __all__
+    "UP",  # pyupgrade
 ]
 
+[tool.ruff.lint.isort]
+known-first-party = ["lsst"]
+
 [tool.ruff.lint.pycodestyle]
 max-doc-length = 79
 

python/lsst/pipe/base/_datasetQueryConstraints.py

@@ -66,9 +66,9 @@ class DatasetQueryConstraintVariant(Iterable, Protocol):
     `fromExpression` class method given a valid string.
     """
 
-    ALL: "type[_ALL]"
-    OFF: "type[_OFF]"
-    LIST: "type[_LIST]"
+    ALL: type[_ALL]
+    OFF: type[_OFF]
+    LIST: type[_LIST]
 
     @classmethod
     def __subclasshook__(cls, subclass):
@@ -77,7 +77,7 @@ def __subclasshook__(cls, subclass):
         return False
 
     @classmethod
-    def fromExpression(cls, expression: str) -> "DatasetQueryConstraintVariant":
+    def fromExpression(cls, expression: str) -> DatasetQueryConstraintVariant:
         """Select and return the correct Variant that corresponds to the input
         expression.
 

python/lsst/pipe/base/_dataset_handle.py

@@ -32,6 +32,7 @@
 from typing import Any, cast
 
 from frozendict import frozendict
+
 from lsst.daf.butler import (
     DataCoordinate,
     DataId,

python/lsst/pipe/base/_instrument.py

@@ -402,7 +402,7 @@ def formatCollectionTimestamp(timestamp: str | datetime.datetime) -> str:
         if not isinstance(timestamp, datetime.datetime):
             raise TypeError(f"Unexpected date/time object: {timestamp!r}.")
         if timestamp.tzinfo is not None:
-            timestamp = timestamp.astimezone(datetime.timezone.utc)
+            timestamp = timestamp.astimezone(datetime.UTC)
         return f"{timestamp:%Y%m%dT%H%M%S}Z"
 
     @staticmethod
@@ -415,7 +415,7 @@ def makeCollectionTimestamp() -> str:
         formatted : `str`
             Standardized string form of the current time.
         """
-        return Instrument.formatCollectionTimestamp(datetime.datetime.now(tz=datetime.timezone.utc))
+        return Instrument.formatCollectionTimestamp(datetime.datetime.now(tz=datetime.UTC))
 
     def makeDefaultRawIngestRunName(self) -> str:
         """Make the default instrument-specific run collection string for raw

python/lsst/pipe/base/_quantumContext.py

@@ -40,6 +40,7 @@
 from typing import Any
 
 import astropy.units as u
+
 from lsst.daf.butler import (
     DataCoordinate,
     DatasetProvenance,

python/lsst/pipe/base/_status.py

@@ -37,14 +37,14 @@
 from ._task_metadata import GetSetDictMetadata, NestedMetadataDict
 
 __all__ = (
-    "QuantumSuccessCaveats",
-    "UnprocessableDataError",
+    "AlgorithmError",
     "AnnotatedPartialOutputsError",
+    "InvalidQuantumError",
     "NoWorkFound",
-    "UpstreamFailureNoWorkFound",
+    "QuantumSuccessCaveats",
     "RepeatableQuantumError",
-    "AlgorithmError",
-    "InvalidQuantumError",
+    "UnprocessableDataError",
+    "UpstreamFailureNoWorkFound",
 )
 
 

python/lsst/pipe/base/_task_metadata.py

@@ -26,11 +26,11 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 __all__ = [
-    "TaskMetadata",
-    "SetDictMetadata",
     "GetDictMetadata",
     "GetSetDictMetadata",
     "NestedMetadataDict",
+    "SetDictMetadata",
+    "TaskMetadata",
 ]
 
 import itertools

python/lsst/pipe/base/automatic_connection_constants.py

@@ -33,16 +33,16 @@
 
 __all__ = (
     "CONFIG_INIT_OUTPUT_CONNECTION_NAME",
-    "CONFIG_INIT_OUTPUT_TEMPLATE",
     "CONFIG_INIT_OUTPUT_STORAGE_CLASS",
-    "PACKAGES_INIT_OUTPUT_NAME",
-    "PACKAGES_INIT_OUTPUT_STORAGE_CLASS",
+    "CONFIG_INIT_OUTPUT_TEMPLATE",
     "LOG_OUTPUT_CONNECTION_NAME",
-    "LOG_OUTPUT_TEMPLATE",
     "LOG_OUTPUT_STORAGE_CLASS",
+    "LOG_OUTPUT_TEMPLATE",
     "METADATA_OUTPUT_CONNECTION_NAME",
-    "METADATA_OUTPUT_TEMPLATE",
     "METADATA_OUTPUT_STORAGE_CLASS",
+    "METADATA_OUTPUT_TEMPLATE",
+    "PACKAGES_INIT_OUTPUT_NAME",
+    "PACKAGES_INIT_OUTPUT_STORAGE_CLASS",
 )
 
 

python/lsst/pipe/base/caching_limited_butler.py

@@ -30,8 +30,8 @@
 __all__ = ["CachingLimitedButler"]
 
 import logging
-from collections.abc import Set
-from typing import Any, Iterable
+from collections.abc import Iterable, Set
+from typing import Any
 
 from lsst.daf.butler import (
     DatasetId,

python/lsst/pipe/base/cli/cmd/commands.py

@@ -28,6 +28,7 @@
 from typing import Any
 
 import click
+
 from lsst.daf.butler.cli.opt import (
     dataset_type_option,
     options_file_option,

python/lsst/pipe/base/configOverrides.py

@@ -26,6 +26,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 """Module which defines ConfigOverrides class and related methods."""
+
 from __future__ import annotations
 
 __all__ = ["ConfigOverrides"]

python/lsst/pipe/base/connectionTypes.py

@@ -29,7 +29,7 @@
 `PipelineTaskConnections` class.
 """
 
-__all__ = ["InitInput", "InitOutput", "Input", "PrerequisiteInput", "Output", "BaseConnection"]
+__all__ = ["BaseConnection", "InitInput", "InitOutput", "Input", "Output", "PrerequisiteInput"]
 
 import dataclasses
 from collections.abc import Callable, Iterable, Sequence

python/lsst/pipe/base/connections.py

@@ -35,10 +35,10 @@
     "InputQuantizedConnection",
     "OutputQuantizedConnection",
     "PipelineTaskConnections",
+    "QuantizedConnection",
     "ScalarError",
-    "iterConnections",
     "ScalarError",
-    "QuantizedConnection",
+    "iterConnections",
 ]
 
 import dataclasses
@@ -334,7 +334,8 @@ def __call__(cls, *, config: PipelineTaskConfig | None = None) -> PipelineTaskCo
         # by looping over the keys of the defaultTemplates dict specified at
         # class declaration time.
         templateValues = {
-            name: getattr(config.connections, name) for name in cls.defaultTemplates  # type: ignore
+            name: getattr(config.connections, name)
+            for name in cls.defaultTemplates  # type: ignore
         }
 
         # We now assemble a mapping of all connection instances keyed by

python/lsst/pipe/base/execution_reports.py

@@ -21,9 +21,9 @@
 from __future__ import annotations
 
 __all__ = (
+    "DatasetTypeExecutionReport",
     "QuantumGraphExecutionReport",
     "TaskExecutionReport",
-    "DatasetTypeExecutionReport",
     "lookup_quantum_data_id",
 )
 
@@ -36,6 +36,7 @@
 
 import networkx
 import yaml
+
 from lsst.daf.butler import Butler, DataCoordinate, DatasetRef, Quantum
 from lsst.resources import ResourcePathExpression
 

python/lsst/pipe/base/graph/_implDetails.py

@@ -26,7 +26,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 from __future__ import annotations
 
-__all__ = ("_DatasetTracker", "DatasetTypeName")
+__all__ = ("DatasetTypeName", "_DatasetTracker")
 
 from collections import defaultdict
 from typing import NewType

python/lsst/pipe/base/graph/_loadHelpers.py

@@ -258,7 +258,7 @@ def _readBytes(self, start: int, stop: int) -> bytes:
         self._resourceHandle.seek(start)
         return self._resourceHandle.read(stop - start)
 
-    def __enter__(self) -> "LoadHelper":
+    def __enter__(self) -> LoadHelper:
         if isinstance(self.uri, BinaryIO | BytesIO | BufferedRandom):
             self._resourceHandle = self.uri
         else: