DM-50896: Fix click duplicate option warnings

.pre-commit-config.yaml

@@ -1,19 +1,19 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-toml
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.6
+    rev: v0.13.3
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
   - repo: https://github.com/numpy/numpydoc
-    rev: "v1.8.0"
+    rev: "v1.9.0"
     hooks:
       - id: numpydoc-validation

pyproject.toml

@@ -109,7 +109,6 @@ known_first_party = ["lsst"]
 write_to = "python/lsst/ctrl/mpexec/version.py"
 
 [tool.pytest.ini_options]
-open_files_ignore = ["*.ttf", "gen3.sqlite3"]
 
 [tool.pydocstyle]
 convention = "numpy"

python/lsst/ctrl/mpexec/cli/butler_factory.py

@@ -583,7 +583,7 @@ def make_write_butler(
                     # collection from its chain collection first.
                     with butler.transaction():
                         butler.collections.redefine_chain(self.output.name, chain_definition)
-                        butler.removeRuns([replaced], unstore=True)
+                        butler.removeRuns([replaced])
                 elif prune_replaced is not None:
                     raise NotImplementedError(f"Unsupported --prune-replaced option '{prune_replaced}'.")
             if not self.output.exists:

python/lsst/ctrl/mpexec/cli/cmd/commands.py

@@ -141,7 +141,7 @@ def coverage_context(kwargs: dict[str, Any]) -> Iterator[None]:
 @click.command(cls=PipetaskCommand, epilog=epilog)
 @click.pass_context
 @ctrlMpExecOpts.show_option()
-@ctrlMpExecOpts.pipeline_build_options()
+@ctrlMpExecOpts.pipeline_build_options(skip_butler_config=True)
 @ctrlMpExecOpts.qgraph_options()
 @ctrlMpExecOpts.butler_options()
 @option_section(sectionText="")

python/lsst/ctrl/mpexec/cli/opt/optionGroups.py

@@ -54,9 +54,15 @@
 class pipeline_build_options(OptionGroup):  # noqa: N801
     """Decorator to add options to the command function for building a
     pipeline.
+
+    Parameters
+    ----------
+    skip_butler_config : `bool`, optional
+        If `True` the butler configuration option will not be included and will
+        be assumed to be added explicitly elsewhere.
     """
 
-    def __init__(self) -> None:
+    def __init__(self, skip_butler_config: bool = False) -> None:
         self.decorators = [
             option_section(sectionText="Pipeline build options:"),
             ctrlMpExecOpts.pipeline_option(),
@@ -76,8 +82,9 @@ def __init__(self) -> None:
             ctrlMpExecOpts.pipeline_dot_option(),
             ctrlMpExecOpts.pipeline_mermaid_option(),
             pipeBaseOpts.instrument_option(help=instrumentOptionHelp, metavar="instrument", multiple=True),
-            ctrlMpExecOpts.butler_config_option(required=False),
         ]
+        if not skip_butler_config:
+            self.decorators.append(ctrlMpExecOpts.butler_config_option(required=False))
 
 
 class coverage_options(OptionGroup):  # noqa: N801
@@ -95,9 +102,23 @@ def __init__(self) -> None:
 class qgraph_options(OptionGroup):  # noqa: N801
     """Decorator to add options to a command function for creating a quantum
     graph.
+
+    Parameters
+    ----------
+    skip_coverage : `bool`, optional
+        If `True` the coverage configuration options will not be included and
+        will be assumed to be added explicitly elsewhere.
+    skip_clobber : `bool`, optional
+        If `True` the clobber configuration option will not be included and
+        will be assumed to be added explicitly elsewhere.
+    skip_summary : `bool`, optional
+        If `True` the summary configuration option will not be included and
+        will be assumed to be added explicitly elsewhere.
     """
 
-    def __init__(self) -> None:
+    def __init__(
+        self, skip_coverage: bool = False, skip_clobber: bool = False, skip_summary: bool = False
+    ) -> None:
         self.decorators = [
             option_section(sectionText="Quantum graph building options:"),
             ctrlMpExecOpts.qgraph_option(),
@@ -106,18 +127,21 @@ def __init__(self) -> None:
             ctrlMpExecOpts.qgraph_datastore_records_option(),
             ctrlMpExecOpts.skip_existing_in_option(),
             ctrlMpExecOpts.skip_existing_option(),
-            ctrlMpExecOpts.clobber_outputs_option(),
             ctrlMpExecOpts.save_qgraph_option(),
             ctrlMpExecOpts.qgraph_dot_option(),
             ctrlMpExecOpts.qgraph_mermaid_option(),
-            ctrlMpExecOpts.summary_option(),
             ctrlMpExecOpts.dataset_query_constraint(),
             ctrlMpExecOpts.data_id_table_option(),
             ctrlMpExecOpts.mock_option(),
             ctrlMpExecOpts.mock_failure_option(),
             ctrlMpExecOpts.unmocked_dataset_types_option(),
-            coverage_options(),
         ]
+        if not skip_clobber:
+            self.decorators.append(ctrlMpExecOpts.clobber_outputs_option())
+        if not skip_summary:
+            self.decorators.append(ctrlMpExecOpts.summary_option())
+        if not skip_coverage:
+            self.decorators.append(coverage_options())
 
 
 class butler_options(OptionGroup):  # noqa: N801
@@ -187,8 +211,8 @@ def __init__(self) -> None:
             click.pass_context,
             ctrlMpExecOpts.debug_option(),
             ctrlMpExecOpts.show_option(),
-            pipeline_build_options(),
-            qgraph_options(),
+            pipeline_build_options(skip_butler_config=True),
+            qgraph_options(skip_coverage=True, skip_clobber=True, skip_summary=True),
             butler_options(),
             execution_options(),
             meta_info_options(),

python/lsst/ctrl/mpexec/cli/utils.py

@@ -227,7 +227,7 @@ def summarize_quantum_graph(qg: BaseQuantumGraph) -> int:
     Parameters
     ----------
     qg : `lsst.pipe.base.quantum_graph.BaseQuantumGraph`
-        Quantum graph object
+        Quantum graph object.
 
     Returns
     -------