lsst-pipe-base 29.2025.4200__tar.gz → 29.2025.4400__tar.gz

{lsst_pipe_base-29.2025.4200/python/lsst_pipe_base.egg-info → lsst_pipe_base-29.2025.4400}/PKG-INFO

@@ -1,18 +1,18 @@
 Metadata-Version: 2.4
 Name: lsst-pipe-base
-Version: 29.2025.4200
+Version: 29.2025.4400
 Summary: Pipeline infrastructure for the Rubin Science Pipelines.
 Author-email: Rubin Observatory Data Management <dm-admin@lists.lsst.org>
-License: BSD 3-Clause License
+License-Expression: BSD-3-Clause OR GPL-3.0-or-later
 Project-URL: Homepage, https://github.com/lsst/pipe_base
 Keywords: lsst
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Requires-Python: >=3.11.0
 Description-Content-Type: text/markdown

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/pyproject.toml

@@ -6,19 +6,20 @@ build-backend = "setuptools.build_meta"
 name = "lsst-pipe-base"
 requires-python = ">=3.11.0"
 description = "Pipeline infrastructure for the Rubin Science Pipelines."
-license = {text = "BSD 3-Clause License"}
+license = "BSD-3-Clause OR GPL-3.0-or-later"
+license-files = ["COPYRIGHT", "LICENSE", "bsd_license.txt", "gpl-v3.0.txt"]
 readme = "README.md"
 authors = [
     {name="Rubin Observatory Data Management", email="dm-admin@lists.lsst.org"},
 ]
 classifiers = [
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Astronomy",
 ]
 keywords=["lsst"]
@@ -54,7 +55,6 @@ where = ["python"]
 
 [tool.setuptools]
 zip-safe = true
-license-files = ["COPYRIGHT", "LICENSE", "bsd_license.txt", "gpl-v3.0.txt"]
 
 [tool.setuptools.package-data]
 "lsst.pipe.base" = ["py.typed", "cli/resources.yaml"]
@@ -124,6 +124,7 @@ exclude_lines = [
     "if __name__ == .__main__.:",
     "if TYPE_CHECKING:",
     'if "sphinx" in sys.modules:',
+    'if "sphinx" in sys.modules and not TYPE_CHECKING:'
 ]
 
 [tool.pydocstyle]

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/_status.py

@@ -166,7 +166,7 @@ class QuantumSuccessCaveats(enum.Flag):
         """
         return {
             "+": "at least one predicted output was missing, but not all were",
-            "*": "all predicated outputs were missing (besides logs and metadata)",
+            "*": "all predicted outputs were missing (besides logs and metadata)",
             "A": "adjustQuantum raised NoWorkFound; a regenerated QG would not include this quantum",
             "D": "algorithm considers data too bad to be processable",
             "U": "one or more input dataset was incomplete due to an upstream failure",

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/cli/cmd/__init__.py

@@ -25,6 +25,6 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-__all__ = ["register_instrument", "transfer_from_graph", "zip_from_graph", "retrieve_artifacts_for_quanta"]
+__all__ = ["register_instrument", "transfer_from_graph", "zip_from_graph", "retrieve_artifacts_for_quanta", "aggregate_graph"]
 
-from .commands import register_instrument, retrieve_artifacts_for_quanta, transfer_from_graph, zip_from_graph
+from .commands import (register_instrument, retrieve_artifacts_for_quanta, transfer_from_graph, zip_from_graph, aggregate_graph)

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/cli/cmd/commands.py

@@ -40,6 +40,7 @@ from lsst.daf.butler.cli.opt import (
 from lsst.daf.butler.cli.utils import ButlerCommand, split_commas, unwrap
 
 from ... import script
+from ...quantum_graph import aggregator
 from ..opt import instrument_argument, update_output_chain_option
 
 
@@ -140,7 +141,7 @@ def zip_from_graph(**kwargs: Any) -> None:
     "--include-outputs/--no-include-outputs",
     is_flag=True,
     default=True,
-    help="Whether to include outut datasets in retrieval.",
+    help="Whether to include output datasets in retrieval.",
 )
 @options_file_option()
 def retrieve_artifacts_for_quanta(**kwargs: Any) -> None:
@@ -153,3 +154,117 @@ def retrieve_artifacts_for_quanta(**kwargs: Any) -> None:
     """
     artifacts = script.retrieve_artifacts_for_quanta(**kwargs)
     print(f"Written {len(artifacts)} artifacts to {kwargs['dest']}.")
+
+
+_AGGREGATOR_DEFAULTS = aggregator.AggregatorConfig()
+
+
+@click.command(short_help="Scan for the outputs of an active or completed quantum graph.", cls=ButlerCommand)
+@click.argument("predicted_graph", required=True)
+@repo_argument(required=True, help="Path to the central butler repository.")
+@click.option(
+    "-o",
+    "--output",
+    "output_path",
+    default=_AGGREGATOR_DEFAULTS.output_path,
+    help=(
+        "Path to the output provenance quantum graph.  THIS OPTION IS FOR "
+        "DEVELOPMENT AND DEBUGGING ONLY.  IT MAY BE REMOVED IN THE FUTURE."
+    ),
+)
+@click.option(
+    "--processes",
+    "-j",
+    "n_processes",
+    default=_AGGREGATOR_DEFAULTS.n_processes,
+    type=click.IntRange(min=1),
+    help="Number of processes to use.",
+)
+@click.option(
+    "--complete/--incomplete",
+    "assume_complete",
+    default=_AGGREGATOR_DEFAULTS.assume_complete,
+    help="Whether execution has completed (and failures cannot be retried).",
+)
+@click.option(
+    "--dry-run",
+    is_flag=True,
+    default=_AGGREGATOR_DEFAULTS.dry_run,
+    help="Do not actually perform any central database ingests.",
+)
+@click.option(
+    "--interactive-status/--no-interactive-status",
+    "interactive_status",
+    default=_AGGREGATOR_DEFAULTS.interactive_status,
+    help="Use progress bars for status reporting instead of periodic logging.",
+)
+@click.option(
+    "--log-status-interval",
+    type=int,
+    default=_AGGREGATOR_DEFAULTS.log_status_interval,
+    help="Interval (in seconds) between periodic logger status updates.",
+)
+@click.option(
+    "--register-dataset-types/--no-register-dataset-types",
+    default=_AGGREGATOR_DEFAULTS.register_dataset_types,
+    help="Register output dataset types.",
+)
+@click.option(
+    "--update-output-chain/--no-update-output-chain",
+    default=_AGGREGATOR_DEFAULTS.update_output_chain,
+    help="Prepend the output RUN collection to the output CHAINED collection.",
+)
+@click.option(
+    "--worker-log-dir",
+    type=str,
+    default=_AGGREGATOR_DEFAULTS.worker_log_dir,
+    help="Path to a directory (POSIX only) for parallel worker logs.",
+)
+@click.option(
+    "--worker-log-level",
+    type=str,
+    default=_AGGREGATOR_DEFAULTS.worker_log_level,
+    help="Log level for worker processes/threads (use DEBUG for per-quantum messages).",
+)
+@click.option(
+    "--zstd-level",
+    type=int,
+    default=_AGGREGATOR_DEFAULTS.zstd_level,
+    help="Compression level for the provenance quantum graph file.",
+)
+@click.option(
+    "--zstd-dict-size",
+    type=int,
+    default=_AGGREGATOR_DEFAULTS.zstd_dict_size,
+    help="Size (in bytes) of the ZStandard compression dictionary.",
+)
+@click.option(
+    "--zstd-dict-n-inputs",
+    type=int,
+    default=_AGGREGATOR_DEFAULTS.zstd_dict_n_inputs,
+    help=("Number of samples of each type to include in ZStandard compression dictionary training."),
+)
+@click.option(
+    "--mock-storage-classes/--no-mock-storage-classes",
+    default=_AGGREGATOR_DEFAULTS.mock_storage_classes,
+    help="Enable support for storage classes created by the lsst.pipe.base.tests.mocks package.",
+)
+def aggregate_graph(predicted_graph: str, repo: str, **kwargs: Any) -> None:
+    """Scan for quantum graph's outputs to gather provenance, ingest datasets
+    into the central butler repository, and delete datasets that are no
+    longer needed.
+    """
+    # It'd be nice to allow to the user to provide a path to an
+    # AggregatorConfig JSON file for options that weren't provided, but Click
+    # 8.1 fundamentally cannot handle flag options that default to None rather
+    # than True or False (i.e. so they fall back to the config value when not
+    # set).  It's not clear whether Click 8.2.x has actually fixed this; Click
+    # 8.2.0 tried but caused new problems.
+
+    config = aggregator.AggregatorConfig(**kwargs)
+    try:
+        aggregator.aggregate_graph(predicted_graph, repo, config)
+    except aggregator.FatalWorkerError as err:
+        # When this exception is raised, we'll have already logged the relevant
+        # traceback from a separate worker.
+        raise click.ClickException(str(err)) from None

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/graph_walker.py

@@ -81,10 +81,12 @@ class GraphWalker(Generic[_T]):
         Parameters
         ----------
         key : unspecified
-            NetworkX key of the node to mark finished.
+            NetworkX key of the node to mark finished.  Does not need to have
+            been returned by the iterator yet.
         """
-        self._active.remove(key)
         self._incomplete.remove(key)
+        self._active.discard(key)
+        self._ready.discard(key)
         successors = list(self._xgraph.successors(key))
         for successor in successors:
             assert successor not in self._active, (
@@ -102,7 +104,8 @@ class GraphWalker(Generic[_T]):
         Parameters
         ----------
         key : unspecified
-            NetworkX key of the node to mark as a failure.
+            NetworkX key of the node to mark as a failure.  Does not need to
+            have been returned by the iterator yet.
 
         Returns
         -------
@@ -110,8 +113,9 @@ class GraphWalker(Generic[_T]):
             NetworkX keys of nodes that were recursive descendants of the
             failed node, and will hence never be yielded by the iterator.
         """
-        self._active.remove(key)
         self._incomplete.remove(key)
+        self._active.discard(key)
+        self._ready.discard(key)
         descendants = list(networkx.dag.descendants(self._xgraph, key))
         self._xgraph.remove_node(key)
         self._xgraph.remove_nodes_from(descendants)

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/pipeline_graph/_pipeline_graph.py

@@ -1697,7 +1697,15 @@ class PipelineGraph:
             PACKAGES_INIT_OUTPUT_NAME, self._universe.empty, PACKAGES_INIT_OUTPUT_STORAGE_CLASS
         )
 
-    def register_dataset_types(self, butler: Butler, include_packages: bool = True) -> None:
+    def register_dataset_types(
+        self,
+        butler: Butler,
+        include_packages: bool = True,
+        *,
+        include_inputs: bool = True,
+        include_configs: bool = True,
+        include_logs: bool = True,
+    ) -> None:
         """Register all dataset types in a data repository.
 
         Parameters
@@ -1709,11 +1717,28 @@ class PipelineGraph:
             software versions (this is not associated with a task and hence is
             not considered part of the pipeline graph in other respects, but it
             does get written with other provenance datasets).
-        """
-        dataset_types = [node.dataset_type for node in self.dataset_types.values()]
+        include_inputs : `bool`, optional
+            Whether to register overall-input dataset types as well as outputs.
+        include_configs : `bool`, optional
+            Whether to register task config dataset types.
+        include_logs : `bool`, optional
+            Whether to register task log dataset types.
+        """
+        dataset_types = {
+            node.name: node.dataset_type
+            for node in self.dataset_types.values()
+            if include_inputs or self.producer_of(node.name) is not None
+        }
         if include_packages:
-            dataset_types.append(self.packages_dataset_type)
-        for dataset_type in dataset_types:
+            dataset_types[self.packages_dataset_type.name] = self.packages_dataset_type
+        if not include_configs:
+            for task_node in self.tasks.values():
+                del dataset_types[task_node.init.config_output.dataset_type_name]
+        if not include_logs:
+            for task_node in self.tasks.values():
+                if task_node.log_output is not None:
+                    del dataset_types[task_node.log_output.dataset_type_name]
+        for dataset_type in dataset_types.values():
             butler.registry.registerDatasetType(dataset_type)
 
     def check_dataset_type_registrations(self, butler: Butler, include_packages: bool = True) -> None:

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/quantum_graph/__init__.py

@@ -30,3 +30,4 @@ from __future__ import annotations
 from ._common import *
 from ._multiblock import *
 from ._predicted import *
+from ._provenance import *

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/quantum_graph/_common.py

@@ -82,6 +82,7 @@ if TYPE_CHECKING:
 TaskLabel: TypeAlias = str
 DatasetTypeName: TypeAlias = str
 ConnectionName: TypeAlias = str
+DatasetIndex: TypeAlias = int
 QuantumIndex: TypeAlias = int
 DatastoreName: TypeAlias = str
 DimensionElementName: TypeAlias = str
@@ -326,7 +327,7 @@ class BaseQuantumGraph(ABC):
     ----------
     header : `HeaderModel`
         Structured metadata for the graph.
-    pipeline_graph : `..pipeline_graph.PipelineGraph`
+    pipeline_graph : `.pipeline_graph.PipelineGraph`
         Graph of tasks and dataset types.  May contain a superset of the tasks
         and dataset types that actually have quanta and datasets in the quantum
         graph.

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/quantum_graph/_multiblock.py

@@ -41,6 +41,7 @@ __all__ = (
 
 import dataclasses
 import logging
+import tempfile
 import uuid
 from collections.abc import Iterator
 from contextlib import contextmanager
@@ -501,13 +502,13 @@ class AddressReader:
         self.pages.clear()
         return self.rows
 
-    def find(self, key: uuid.UUID) -> AddressRow:
-        """Read the row for the given UUID.
+    def find(self, key: uuid.UUID | int) -> AddressRow:
+        """Read the row for the given UUID or integer index.
 
         Parameters
         ----------
-        key : `uuid.UUID`
-            UUID to find.
+        key : `uuid.UUID` or `int`
+            UUID or integer index to find.
 
         Returns
         -------
@@ -517,6 +518,8 @@ class AddressReader:
         match key:
             case uuid.UUID():
                 return self._find_uuid(key)
+            case int():
+                return self._find_index(key)
             case _:
                 raise TypeError(f"Invalid argument: {key}.")
 
@@ -546,6 +549,22 @@ class AddressReader:
         # Ran out of pages to search.
         raise LookupError(f"Address for {target} not found.")
 
+    def _find_index(self, target: int) -> AddressRow:
+        # First shortcut if we've already loaded this row.
+        if (row := self.rows_by_index.get(target)) is not None:
+            return row
+        if target < 0 or target >= self.n_rows:
+            raise LookupError(f"Address for index {target} not found.")
+        # Since all indexes should be present, we can predict the right page
+        # exactly.
+        page_index = target // self.rows_per_page
+        self._read_page(page_index)
+        try:
+            return self.rows_by_index[target]
+        except KeyError:
+            _LOG.debug("Index find failed: %s should have been in page %s.", target, page_index)
+            raise LookupError(f"Address for {target} not found.") from None
+
     def _read_page(self, page_index: int, page_stream: BytesIO | None = None) -> bool:
         page = self.pages[page_index]
         if page.read:
@@ -594,7 +613,9 @@ class MultiblockWriter:
 
     @classmethod
     @contextmanager
-    def open_in_zip(cls, zf: zipfile.ZipFile, name: str, int_size: int) -> Iterator[MultiblockWriter]:
+    def open_in_zip(
+        cls, zf: zipfile.ZipFile, name: str, int_size: int, use_tempfile: bool = False
+    ) -> Iterator[MultiblockWriter]:
         """Open a writer for a file in a zip archive.
 
         Parameters
@@ -605,14 +626,26 @@ class MultiblockWriter:
             Base name for the multi-block file; an extension will be added.
         int_size : `int`
             Number of bytes to use for all integers.
+        use_tempfile : `bool`, optional
+            If `True`, send writes to a temporary file and only add the file to
+            the zip archive when the context manager closes.  This involves
+            more overall I/O, but it permits multiple multi-block files to be
+            open for writing in the same zip archive at once.
 
         Returns
         -------
         writer : `contextlib.AbstractContextManager` [ `MultiblockWriter` ]
             Context manager that returns a writer when entered.
         """
-        with zf.open(f"{name}.mb", mode="w", force_zip64=True) as stream:
-            yield MultiblockWriter(stream, int_size)
+        filename = f"{name}.mb"
+        if use_tempfile:
+            with tempfile.NamedTemporaryFile(suffix=filename) as tmp:
+                yield MultiblockWriter(tmp, int_size)
+                tmp.flush()
+                zf.write(tmp.name, filename)
+        else:
+            with zf.open(f"{name}.mb", mode="w", force_zip64=True) as stream:
+                yield MultiblockWriter(stream, int_size)
 
     def write_bytes(self, id: uuid.UUID, data: bytes) -> Address:
         """Write raw bytes to the multi-block file.
@@ -629,6 +662,7 @@ class MultiblockWriter:
         address : `Address`
             Address of the bytes just written.
         """
+        assert id not in self.addresses, "Duplicate write to multi-block file detected."
         self.stream.write(len(data).to_bytes(self.int_size))
         self.stream.write(data)
         block_size = len(data) + self.int_size

{lsst_pipe_base-29.2025.4200 → lsst_pipe_base-29.2025.4400}/python/lsst/pipe/base/quantum_graph/_predicted.py

@@ -347,8 +347,21 @@ class PredictedQuantumDatasetsModel(pydantic.BaseModel):
     the data repository.
     """
 
-    def iter_dataset_ids(self) -> Iterator[uuid.UUID]:
-        """Return an iterator over the UUIDs of all datasets referenced by this
+    def iter_input_dataset_ids(self) -> Iterator[uuid.UUID]:
+        """Return an iterator over the UUIDs of all datasets consumed by this
+        quantum.
+
+        Returns
+        -------
+        iter : `~collections.abc.Iterator` [ `uuid.UUID` ]
+            Iterator over dataset IDs.
+        """
+        for datasets in self.inputs.values():
+            for dataset in datasets:
+                yield dataset.dataset_id
+
+    def iter_output_dataset_ids(self) -> Iterator[uuid.UUID]:
+        """Return an iterator over the UUIDs of all datasets produced by this
         quantum.
 
         Returns
@@ -356,10 +369,22 @@ class PredictedQuantumDatasetsModel(pydantic.BaseModel):
         iter : `~collections.abc.Iterator` [ `uuid.UUID` ]
             Iterator over dataset IDs.
         """
-        for datasets in itertools.chain(self.inputs.values(), self.outputs.values()):
+        for datasets in self.outputs.values():
             for dataset in datasets:
                 yield dataset.dataset_id
 
+    def iter_dataset_ids(self) -> Iterator[uuid.UUID]:
+        """Return an iterator over the UUIDs of all datasets referenced by this
+        quantum.
+
+        Returns
+        -------
+        iter : `~collections.abc.Iterator` [ `uuid.UUID` ]
+            Iterator over dataset IDs.
+        """
+        yield from self.iter_input_dataset_ids()
+        yield from self.iter_output_dataset_ids()
+
     def deserialize_datastore_records(self) -> dict[DatastoreName, DatastoreRecordData]:
         """Deserialize the mapping of datastore records."""
         return {
@@ -774,7 +799,7 @@ class PredictedQuantumGraph(BaseQuantumGraph):
             Approximate number of bytes to read at once from address files.
             Note that this does not set a page size for *all* reads, but it
             does affect the smallest, most numerous reads.
-        import_mode : `..pipeline_graph.TaskImportMode`, optional
+        import_mode : `.pipeline_graph.TaskImportMode`, optional
             How to handle importing the task classes referenced in the pipeline
             graph.
 
@@ -1498,6 +1523,38 @@ class PredictedQuantumGraphComponents:
     This does include special "init" quanta.
     """
 
+    def make_dataset_ref(self, predicted: PredictedDatasetModel) -> DatasetRef:
+        """Make a `lsst.daf.butler.DatasetRef` from information in the
+        predicted quantum graph.
+
+        Parameters
+        ----------
+        predicted : `PredictedDatasetModel`
+            Model for the dataset in the predicted graph.
+
+        Returns
+        -------
+        ref : `lsst.daf.butler.DatasetRef`
+            A dataset reference.  Data ID will be expanded if and only if
+            the dimension data has been loaded.
+        """
+        try:
+            dataset_type = self.pipeline_graph.dataset_types[predicted.dataset_type_name].dataset_type
+        except KeyError:
+            if predicted.dataset_type_name == acc.PACKAGES_INIT_OUTPUT_NAME:
+                dataset_type = self.pipeline_graph.packages_dataset_type
+            else:
+                raise
+        data_id = DataCoordinate.from_full_values(dataset_type.dimensions, tuple(predicted.data_coordinate))
+        if self.dimension_data is not None:
+            (data_id,) = self.dimension_data.attach(dataset_type.dimensions, [data_id])
+        return DatasetRef(
+            dataset_type,
+            data_id,
+            run=predicted.run,
+            id=predicted.dataset_id,
+        )
+
     def set_quantum_indices(self) -> None:
         """Populate the `quantum_indices` component by sorting the UUIDs in the
         `init_quanta` and `quantum_datasets` components (which must both be
@@ -1813,7 +1870,7 @@ class PredictedQuantumGraphReader(BaseQuantumGraphReader):
             Approximate number of bytes to read at once from address files.
             Note that this does not set a page size for *all* reads, but it
             does affect the smallest, most numerous reads.
-        import_mode : `..pipeline_graph.TaskImportMode`, optional
+        import_mode : `.pipeline_graph.TaskImportMode`, optional
             How to handle importing the task classes referenced in the pipeline
             graph.