Merge pull request #397 from lsst/tickets/DM-40150

DM-40150: Remove some post v26 deprecations

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: trailing-whitespace
       - id: check-toml
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.1
     hooks:
       - id: black
         # It is recommended to specify the latest version of Python
@@ -16,13 +16,13 @@ repos:
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3.11
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.1
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.7
+    rev: v0.1.11
     hooks:
       - id: ruff
   - repo: https://github.com/numpy/numpydoc

doc/changes/DM-40150.removal.rst

@@ -0,0 +1,5 @@
+* Removed ``topLevelOnly`` parameter from ``TaskMetadata.names()``.
+* Removed the ``saveMetadata`` configuration from ``PipelineTask``.
+* Removed ``lsst.pipe.base.cmdLineTask.profile`` (use ``lsst.utils.timer.profile`` instead).
+* Removed ``ButlerQuantumContext`` class. Use ``QuantumContext`` instead.
+* Removed ``recontitutedDimensions`` parameter from ``QuantumNode.from_simple()``

mypy.ini

@@ -72,8 +72,6 @@ disallow_untyped_defs = False
 # worth adding new annotations to them.
 [mypy-lsst.pipe.base.argumentParser.*]
 disallow_untyped_defs = False
-[mypy-lsst.pipe.base.cmdLineTask.*]
-disallow_untyped_defs = False
 [mypy-lsst.pipe.base.shims.*]
 disallow_untyped_defs = False
 

python/lsst/pipe/base/_quantumContext.py

@@ -31,15 +31,14 @@
 
 from __future__ import annotations
 
-__all__ = ("ButlerQuantumContext", "ExecutionResources", "QuantumContext")
+__all__ = ("ExecutionResources", "QuantumContext")
 
 import numbers
 from collections.abc import Callable, Sequence
 from dataclasses import dataclass
 from typing import Any
 
 import astropy.units as u
-from deprecated.sphinx import deprecated
 from lsst.daf.butler import DatasetRef, DimensionUniverse, LimitedButler, Quantum
 from lsst.utils.introspection import get_full_type_name
 from lsst.utils.logging import PeriodicLogger, getLogger
@@ -421,16 +420,3 @@ def dimensions(self) -> DimensionUniverse:
         repository (`~lsst.daf.butler.DimensionUniverse`).
         """
         return self.__butler.dimensions
-
-
-# TODO: remove on DM-40063.
-@deprecated(
-    reason="ButlerQuantumContext has been renamed to QuantumContext and been given extra functionality. "
-    "Please use the new name. Will be removed after v26.",
-    version="v26",
-    category=FutureWarning,
-)
-class ButlerQuantumContext(QuantumContext):
-    """Deprecated version of `QuantumContext`."""
-
-    pass

python/lsst/pipe/base/_task_metadata.py

@@ -30,11 +30,9 @@
 import itertools
 import numbers
 import sys
-import warnings
 from collections.abc import Collection, Iterator, Mapping, Sequence
 from typing import Any, Protocol
 
-from lsst.utils.introspection import find_outside_stacklevel
 from pydantic import BaseModel, Field, StrictBool, StrictFloat, StrictInt, StrictStr
 
 # The types allowed in a Task metadata field are restricted
@@ -260,35 +258,15 @@ def getArray(self, key: str) -> list[Any]:
             # Report the correct key.
             raise KeyError(f"'{key}' not found") from None
 
-    def names(self, topLevelOnly: bool | None = None) -> set[str]:
+    def names(self) -> set[str]:
         """Return the hierarchical keys from the metadata.
 
-        Parameters
-        ----------
-        topLevelOnly : `bool` or `None`, optional
-            This parameter is deprecated and will be removed in the future.
-            If given it can only be `False`.  All names in the hierarchy are
-            always returned.
-
         Returns
         -------
         names : `collections.abc.Set`
             A set of all keys, including those from the hierarchy and the
             top-level hierarchy.
         """
-        if topLevelOnly:
-            raise RuntimeError(
-                "The topLevelOnly parameter is no longer supported and can not have a True value."
-            )
-
-        if topLevelOnly is False:
-            warnings.warn(
-                "The topLevelOnly parameter is deprecated and is always assumed to be False."
-                " It will be removed completely after v26.",
-                category=FutureWarning,
-                stacklevel=find_outside_stacklevel("lsst.pipe.base"),
-            )
-
         names = set()
         for k, v in self.items():
             names.add(k)  # Always include the current level

python/lsst/pipe/base/config.py

@@ -217,12 +217,6 @@ class to allow configuration of the connections class. This dynamically
     based on a PipelineTaskConnections class.
     """
 
-    saveMetadata = pexConfig.Field[bool](
-        default=True,
-        optional=False,
-        doc="Flag to enable/disable metadata saving for a task, enabled by default.",
-        deprecated="This field is deprecated and will be removed after v26.",
-    )
     saveLogOutput = pexConfig.Field[bool](
         default=True,
         optional=False,

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

@@ -1028,7 +1028,7 @@ def _buildSaveObjectImpl(self, returnHeader: bool = False) -> bytearray | tuple[
             # a large impact on on disk size, so it is worth doing
             simpleNode = node.to_simple(accumulator=dimAccumulator)
 
-            dump = lzma.compress(simpleNode.json().encode(), preset=2)
+            dump = lzma.compress(simpleNode.model_dump_json().encode(), preset=2)
             jsonData.append(dump)
             nodeMap.append(
                 (

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

@@ -29,20 +29,17 @@
 __all__ = ("QuantumNode", "NodeId", "BuildId")
 
 import uuid
-import warnings
 from dataclasses import dataclass
 from typing import Any, NewType
 
 import pydantic
 from lsst.daf.butler import (
     DatasetRef,
-    DimensionRecord,
     DimensionRecordsAccumulator,
     DimensionUniverse,
     Quantum,
     SerializedQuantum,
 )
-from lsst.utils.introspection import find_outside_stacklevel
 
 from ..pipeline import TaskDef
 
@@ -143,14 +140,7 @@ def from_simple(
         simple: SerializedQuantumNode,
         taskDefMap: dict[str, TaskDef],
         universe: DimensionUniverse,
-        recontitutedDimensions: dict[int, tuple[str, DimensionRecord]] | None = None,
     ) -> QuantumNode:
-        if recontitutedDimensions is not None:
-            warnings.warn(
-                "The recontitutedDimensions argument is now ignored and may be removed after v26",
-                category=FutureWarning,
-                stacklevel=find_outside_stacklevel("lsst.pipe.base"),
-            )
         return QuantumNode(
             quantum=Quantum.from_simple(simple.quantum, universe),
             taskDef=taskDefMap[simple.taskLabel],

python/lsst/pipe/base/pipeline_graph/_pipeline_graph.py

@@ -1073,7 +1073,7 @@ def _read_stream(
 
         with gzip.open(stream, "rb") as uncompressed_stream:
             data = json.load(uncompressed_stream)
-            serialized_graph = SerializedPipelineGraph.parse_obj(data)
+            serialized_graph = SerializedPipelineGraph.model_validate(data)
             return serialized_graph.deserialize(import_mode)
 
     @classmethod
@@ -1142,7 +1142,7 @@ def _write_stream(self, stream: BinaryIO) -> None:
 
         with gzip.open(stream, mode="wb") as compressed_stream:
             compressed_stream.write(
-                SerializedPipelineGraph.serialize(self).json(exclude_defaults=True).encode("utf-8")
+                SerializedPipelineGraph.serialize(self).model_dump_json(exclude_defaults=True).encode("utf-8")
             )
 
     def _write_uri(self, uri: ResourcePathExpression) -> None:

python/lsst/pipe/base/pipeline_graph/_tasks.py

@@ -158,8 +158,6 @@ def configure(
             acc.CONFIG_INIT_OUTPUT_TEMPLATE.format(label=label),
             acc.CONFIG_INIT_OUTPUT_STORAGE_CLASS,
         )
-        if not config.saveMetadata:
-            raise ValueError(f"Metadata for task {label} cannot be disabled.")
         connection_map[acc.METADATA_OUTPUT_CONNECTION_NAME] = Output(
             acc.METADATA_OUTPUT_TEMPLATE.format(label=label),
             acc.METADATA_OUTPUT_STORAGE_CLASS,

tests/test_task.py

@@ -318,8 +318,8 @@ def testTimeMethod(self):
         # TaskMetadata can serialize to JSON but not YAML
         # and PropertySet can serialize to YAML and not JSON.
         if hasattr(addMultTask.metadata, "json"):
-            j = addMultTask.metadata.json()
-            new_meta = pipeBase.TaskMetadata.parse_obj(json.loads(j))
+            j = addMultTask.metadata.model_dump_json()
+            new_meta = pipeBase.TaskMetadata.model_validate(json.loads(j))
         else:
             y = yaml.dump(addMultTask.metadata)
             new_meta = yaml.safe_load(y)

tests/test_taskmetadata.py

@@ -196,8 +196,8 @@ def testDict(self):
         d2 = meta.to_dict()
         self.assertEqual(d2, d)
 
-        j = meta.json()
-        meta2 = TaskMetadata.parse_obj(json.loads(j))
+        j = meta.model_dump_json()
+        meta2 = TaskMetadata.model_validate(json.loads(j))
         self.assertEqual(meta2, meta)
 
         # Round trip.
@@ -241,14 +241,6 @@ def testNumpy(self):
         with self.assertRaises(ValueError):
             meta["numpy"] = numpy.zeros(5)
 
-    def test_deprecated(self):
-        meta = TaskMetadata()
-        with self.assertRaises(RuntimeError):
-            meta.names(topLevelOnly=True)
-
-        with self.assertWarns(FutureWarning):
-            meta.names(topLevelOnly=False)
-
 
 if __name__ == "__main__":
     unittest.main()