Coverage for python/lsst/ctrl/mpexec/cli/opt/options.py: 83%
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2#
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5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This software is dual licensed under the GNU General Public License and also
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11# to use; please see the files gpl-3.0.txt and/or bsd_license.txt,
12# respectively. If you choose the GPL option then the following text applies
13# (but note that there is still no warranty even if you opt for BSD instead):
14#
15# This program is free software: you can redistribute it and/or modify
16# it under the terms of the GNU General Public License as published by
17# the Free Software Foundation, either version 3 of the License, or
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19#
20# This program is distributed in the hope that it will be useful,
21# but WITHOUT ANY WARRANTY; without even the implied warranty of
22# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23# GNU General Public License for more details.
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25# You should have received a copy of the GNU General Public License
26# along with this program. If not, see <http://www.gnu.org/licenses/>.
28from __future__ import annotations
30from collections.abc import Iterable, Mapping
31from typing import TYPE_CHECKING
33import click
35from lsst.daf.butler.cli.utils import MWOptionDecorator, MWPath, split_commas, unwrap
36from lsst.utils.doImport import doImportType
38if TYPE_CHECKING:
39 # Avoid regular module-scope import of test-only code that tinkers with the
40 # storage class singleton.
41 from lsst.pipe.base.tests.mocks import ForcedFailure
44butler_config_option = MWOptionDecorator(
45 "-b", "--butler-config", help="Location of the gen3 butler/registry config file."
46)
49data_query_option = MWOptionDecorator(
50 "-d", "--data-query", help="User data selection expression.", metavar="QUERY"
51)
54data_id_table_option = MWOptionDecorator(
55 "--data-id-table",
56 multiple=True,
57 default=(),
58 help=(
59 "URI to table of data IDs to join as a constraint; may be any format accepted by astropy.table. "
60 "May be passed multiple times."
61 ),
62 metavar="URI",
63)
66debug_option = MWOptionDecorator(
67 "--debug", help="Enable debugging output using lsstDebug facility (imports debug.py).", is_flag=True
68)
70coverage_option = MWOptionDecorator(
71 "--coverage", help="Enable coverage output (requires coverage package).", is_flag=True
72)
74coverage_report_option = MWOptionDecorator(
75 "--cov-report/--no-cov-report",
76 help="If coverage is enabled, controls whether to produce an HTML coverage report.",
77 default=True,
78)
80coverage_packages_option = MWOptionDecorator(
81 "--cov-packages",
82 help=unwrap(
83 """Python packages to restrict coverage to. If none are provided, runs coverage on all packages."""
84 ),
85 multiple=True,
86 callback=split_commas,
87)
89delete_option = MWOptionDecorator(
90 "--delete", callback=split_commas, help="Delete task with given label from pipeline.", multiple=True
91)
94pdb_option = MWOptionDecorator(
95 "--pdb",
96 help="Post-mortem debugger to launch for exceptions (defaults to pdb if unspecified; requires a tty).",
97 is_flag=False,
98 flag_value="pdb",
99 default=None,
100)
103extend_run_option = MWOptionDecorator(
104 "--extend-run",
105 help=(
106 "Instead of creating a new RUN collection, insert datasets into either the one given by "
107 "--output-run (if provided) or the first child collection of --output (which must be of type RUN). "
108 "This also enables --skip-existing option when building a graph. "
109 "When executing a graph this option skips quanta with all existing outputs."
110 ),
111 is_flag=True,
112)
115graph_fixup_option = MWOptionDecorator(
116 "--graph-fixup",
117 help="Name of the class or factory method which makes an instance used for execution graph fixup.",
118)
121init_only_option = MWOptionDecorator(
122 "--init-only",
123 help="Do not actually run; just register dataset types and/or save init outputs.",
124 is_flag=True,
125)
128input_option = MWOptionDecorator(
129 "-i",
130 "--input",
131 callback=split_commas,
132 default=[],
133 help="Comma-separated names of the input collection(s).",
134 metavar="COLLECTION",
135 multiple=True,
136)
139rebase_option = MWOptionDecorator(
140 "--rebase",
141 help=unwrap("""Reset output collection chain if it is inconsistent with --inputs"""),
142 is_flag=True,
143)
146no_versions_option = MWOptionDecorator(
147 "--no-versions", help="Do not save or check package versions.", is_flag=True
148)
151output_option = MWOptionDecorator(
152 "-o",
153 "--output",
154 help=unwrap(
155 """Name of the output CHAINED collection. This may either be an
156 existing CHAINED collection to use as both input and output
157 (incompatible with --input), or a new CHAINED collection created
158 to include all inputs (requires --input). In both cases, the
159 collection's children will start with an output RUN collection
160 that directly holds all new datasets (see --output-run)."""
161 ),
162 metavar="COLL",
163)
166output_run_option = MWOptionDecorator(
167 "--output-run",
168 help=unwrap(
169 """Name of the new output RUN collection. If not provided
170 then --output must be provided and a new RUN collection will
171 be created by appending a timestamp to the value passed with
172 --output. If this collection already exists then
173 --extend-run must be passed."""
174 ),
175 metavar="COLL",
176)
179pipeline_option = MWOptionDecorator(
180 "-p",
181 "--pipeline",
182 help="Location of a pipeline definition file in YAML format.",
183 type=MWPath(file_okay=True, dir_okay=False, readable=True),
184)
187pipeline_dot_option = MWOptionDecorator(
188 "--pipeline-dot",
189 help="Location for storing GraphViz DOT representation of a pipeline.",
190 type=MWPath(writable=True, file_okay=True, dir_okay=False),
191)
194pipeline_mermaid_option = MWOptionDecorator(
195 "--pipeline-mermaid",
196 help="Location for storing Mermaid representation of a pipeline.",
197 type=MWPath(writable=True, file_okay=True, dir_okay=False),
198)
201profile_option = MWOptionDecorator(
202 "--profile", help="Dump cProfile statistics to file name.", type=MWPath(file_okay=True, dir_okay=False)
203)
206prune_replaced_option = MWOptionDecorator(
207 "--prune-replaced",
208 help=unwrap(
209 """Delete the datasets in the collection replaced by
210 --replace-run, either just from the datastore
211 ('unstore') or by removing them and the RUN completely
212 ('purge'). Requires --replace-run."""
213 ),
214 type=click.Choice(choices=("unstore", "purge"), case_sensitive=False),
215)
218qgraph_option = MWOptionDecorator(
219 "-g",
220 "--qgraph",
221 help=unwrap(
222 """Location for a serialized quantum graph definition (pickle
223 file). If this option is given then all input data options and
224 pipeline-building options cannot be used. Can be a URI."""
225 ),
226)
229qgraph_id_option = MWOptionDecorator(
230 "--qgraph-id",
231 help=unwrap(
232 """Quantum graph identifier, if specified must match the
233 identifier of the graph loaded from a file. Ignored if graph
234 is not loaded from a file."""
235 ),
236)
239qgraph_datastore_records_option = MWOptionDecorator(
240 "--qgraph-datastore-records",
241 help=unwrap(
242 """Include datastore records into generated quantum graph, these records are used by a
243 quantum-backed butler.
244 """
245 ),
246 is_flag=True,
247)
250# I wanted to use default=None here to match Python API but click silently
251# replaces None with an empty tuple when multiple=True.
252qgraph_node_id_option = MWOptionDecorator(
253 "--qgraph-node-id",
254 callback=split_commas,
255 multiple=True,
256 help=unwrap(
257 """Only load a specified set of nodes when graph is
258 loaded from a file, nodes are identified by UUID
259 values. One or more comma-separated integers are
260 accepted. By default all nodes are loaded. Ignored if
261 graph is not loaded from a file."""
262 ),
263)
265qgraph_dot_option = MWOptionDecorator(
266 "--qgraph-dot",
267 help="Location for storing GraphViz DOT representation of a quantum graph.",
268 type=MWPath(writable=True, file_okay=True, dir_okay=False),
269)
271qgraph_mermaid_option = MWOptionDecorator(
272 "--qgraph-mermaid",
273 help="Location for storing Mermaid representation of a quantum graph.",
274 type=MWPath(writable=True, file_okay=True, dir_okay=False),
275)
278replace_run_option = MWOptionDecorator(
279 "--replace-run",
280 help=unwrap(
281 """Before creating a new RUN collection in an existing
282 CHAINED collection, remove the first child collection
283 (which must be of type RUN). This can be used to repeatedly
284 write to the same (parent) collection during development,
285 but it does not delete the datasets associated with the
286 replaced run unless --prune-replaced is also passed.
287 Requires --output, and incompatible with --extend-run."""
288 ),
289 is_flag=True,
290)
293save_pipeline_option = MWOptionDecorator(
294 "-s",
295 "--save-pipeline",
296 help="Location for storing resulting pipeline definition in YAML format.",
297 type=MWPath(dir_okay=False, file_okay=True, writable=True),
298)
300save_qgraph_option = MWOptionDecorator(
301 "-q",
302 "--save-qgraph",
303 help="URI location for storing a serialized quantum graph definition (pickle file).",
304)
307show_option = MWOptionDecorator(
308 "--show",
309 callback=split_commas,
310 help=unwrap(
311 """Dump various info to standard output. Possible items are:
312 ``config``, ``config=[Task::]<PATTERN>`` or
313 ``config=[Task::]<PATTERN>:NOIGNORECASE`` to dump configuration
314 fields possibly matching given pattern and/or task label;
315 ``history=<FIELD>`` to dump configuration history for a field,
316 field name is specified as ``[Task::]<PATTERN>``; ``dump-config``,
317 ``dump-config=Task`` to dump complete configuration for a task
318 given its label or all tasks; ``pipeline`` to show pipeline
319 composition; ``graph`` to show information about quanta;
320 ``workflow`` to show information about quanta and their
321 dependency; ``tasks`` to show task composition; ``subsets`` to
322 show subset labels and associated tasks; ``uri`` to show
323 predicted dataset URIs of quanta; ``pipeline-graph`` for a
324 text-based visualization of the pipeline (tasks and dataset types);
325 ``task-graph`` for a text-based visualization of just the tasks;
326 ``inputs`` for a list of overall-input dataset types.
327 With -b, pipeline-graph and task-graph include additional information.
328 """
329 ),
330 metavar="ITEM|ITEM=VALUE",
331 multiple=True,
332)
335skip_existing_in_option = MWOptionDecorator(
336 "--skip-existing-in",
337 callback=split_commas,
338 default=None,
339 metavar="COLLECTION",
340 multiple=True,
341 help=unwrap(
342 """If all Quantum outputs already exist in the specified list of
343 collections then that Quantum will be excluded from the QuantumGraph.
344 """
345 ),
346)
349skip_existing_option = MWOptionDecorator(
350 "--skip-existing",
351 is_flag=True,
352 help=unwrap(
353 """This option is equivalent to --skip-existing-in with the name of
354 the output RUN collection. If both --skip-existing-in and
355 --skip-existing are given then output RUN collection is appended to
356 the list of collections."""
357 ),
358)
361retained_dataset_types_option = MWOptionDecorator(
362 "--retained-dataset-types",
363 default=None,
364 metavar="PATH",
365 type=MWPath(file_okay=True, dir_okay=False, readable=True),
366 help=unwrap(
367 """Path to a YAML file listing dataset type names or glob-style wildcard
368 patterns that should exist in --skip-existing-in when the producing
369 task ran successfully. When a quantum should run, the builder propagates the
370 must-run signal backward through non-retained input datasets, forcing
371 the upstream quanta that need to regenerate those intermediates to also
372 run. Has no effect without ``skip_existing_in``.
373 """
374 ),
375)
378clobber_outputs_option = MWOptionDecorator(
379 "--clobber-outputs",
380 help=(
381 "Remove outputs of failed quanta from the output run when they would block the execution of new "
382 "quanta with the same data ID (or assume that this will be done, if just building a QuantumGraph). "
383 "Does nothing if --extend-run is not passed."
384 ),
385 is_flag=True,
386)
389no_existing_outputs_option = MWOptionDecorator(
390 "--no-existing-outputs",
391 help=(
392 "Assume that no predicted outputs already exist in the output run collection. "
393 "This will eliminate existence checks that otherwise run before each quantum is executed."
394 ),
395 is_flag=True,
396)
399skip_init_writes_option = MWOptionDecorator(
400 "--skip-init-writes",
401 help=unwrap(
402 """Do not write collection-wide 'init output' datasets
403 (e.g.schemas)."""
404 ),
405 is_flag=True,
406)
409enable_implicit_threading_option = MWOptionDecorator(
410 "--enable-implicit-threading",
411 help=unwrap(
412 """Do not disable implicit threading use by third-party libraries (e.g. OpenBLAS).
413 Implicit threading is always disabled during execution with multiprocessing."""
414 ),
415 is_flag=True,
416)
418cores_per_quantum_option = MWOptionDecorator(
419 "-n",
420 "--cores-per-quantum",
421 default=1,
422 help=unwrap(
423 """Number of cores available to each quantum when executing.
424 If '-j' is used each subprocess will be allowed to use this number of cores."""
425 ),
426 type=click.IntRange(min=1),
427)
429memory_per_quantum_option = MWOptionDecorator(
430 "--memory-per-quantum",
431 default="",
432 help=unwrap(
433 """Memory allocated for each quantum to use when executing.
434 This memory allocation is not enforced by the execution system and is purely advisory.
435 If '-j' used each subprocess will be allowed to use this amount of memory.
436 Units are allowed and the default units for a plain integer are MB.
437 For example: '3GB', '3000MB' and '3000' would all result in the same
438 memory limit. Default is for no limit."""
439 ),
440 type=str,
441)
443task_option = MWOptionDecorator(
444 "-t",
445 "--task",
446 callback=split_commas,
447 help=unwrap(
448 """Task name to add to pipeline, must be a fully qualified task
449 name. Task name can be followed by colon and label name, if label
450 is not given then task base name (class name) is used as
451 label."""
452 ),
453 metavar="TASK[:LABEL]",
454 multiple=True,
455)
457select_tasks_option = MWOptionDecorator(
458 "--select-tasks",
459 metavar="EXPR",
460 default="",
461 help=(
462 "A string expression that filters the tasks to run from the pipeline. "
463 "See https://pipelines.lsst.io/v/weekly/modules/lsst.pipe.base/working-with-pipeline-graphs.html"
464 "#pipeline-graph-subset-expressions for details."
465 ),
466)
469timeout_option = MWOptionDecorator(
470 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)."
471)
474start_method_option = MWOptionDecorator(
475 "--start-method",
476 default=None,
477 type=click.Choice(choices=["spawn", "fork", "forkserver"]),
478 help=(
479 "Multiprocessing start method, default is platform-specific. "
480 "Fork method is no longer supported, spawn is used instead if fork is selected."
481 ),
482)
485fail_fast_option = MWOptionDecorator(
486 "--fail-fast",
487 help="Stop processing at first error, default is to process as many tasks as possible.",
488 is_flag=True,
489)
491raise_on_partial_outputs_option = MWOptionDecorator(
492 "--raise-on-partial-outputs/--no-raise-on-partial-outputs",
493 help="Consider partial outputs from a task an error instead of a qualified success.",
494 is_flag=True,
495 default=True,
496)
498mock_option = MWOptionDecorator(
499 "--mock",
500 help="Mock pipeline execution.",
501 is_flag=True,
502)
504unmocked_dataset_types_option = MWOptionDecorator(
505 "--unmocked-dataset-types",
506 callback=split_commas,
507 default=None,
508 metavar="COLLECTION",
509 multiple=True,
510 help="Names of input dataset types that should not be mocked.",
511)
514def parse_mock_failure(
515 ctx: click.Context, param: click.Option, value: Iterable[str] | None
516) -> Mapping[str, ForcedFailure]:
517 """Parse the --mock-failure option values into the mapping accepted by
518 `~lsst.pipe.base.tests.mocks.mock_task_defs`.
520 Parameters
521 ----------
522 ctx : `click.Context`
523 Context provided by Click.
524 param : `click.Option`
525 Click option.
526 value : `~collections.abc.Iterable` [`str`] or `None`
527 Value from option.
528 """
529 # Avoid regular module-scope import of test-only code that tinkers with the
530 # storage class singleton.
531 from lsst.pipe.base.tests.mocks import ForcedFailure
533 result: dict[str, ForcedFailure] = {}
534 if value is None: 534 ↛ 535line 534 didn't jump to line 535 because the condition on line 534 was never true
535 return result
536 for entry in value: 536 ↛ 537line 536 didn't jump to line 537 because the loop on line 536 never started
537 try:
538 task_label, error_type_name, where, *rest = entry.split(":")
539 if rest:
540 (memory_required,) = rest
541 else:
542 memory_required = None
543 except ValueError:
544 raise click.UsageError(
545 f"Invalid value for --mock-failure option: {entry!r}; "
546 "expected a string of the form 'task:error:where[:mem]'."
547 ) from None
548 error_type = doImportType(error_type_name) if error_type_name else None
549 result[task_label] = ForcedFailure(where, error_type, memory_required)
550 return result
553mock_failure_option = MWOptionDecorator(
554 "--mock-failure",
555 callback=parse_mock_failure,
556 metavar="LABEL:EXCEPTION:WHERE",
557 default=None,
558 multiple=True,
559 help=unwrap(
560 """Specifications for tasks that should be configured to fail
561 when mocking execution. This is a colon-separated 3-tuple or 4-tuple,
562 where the first entry the task label, the second the fully-qualified
563 exception type (empty for ValueError, and the third a string (which
564 typically needs to be quoted to be passed as one argument value by the
565 shell) of the form passed to --where, indicating which data IDs should
566 fail. The final optional term is the memory "required" by the task
567 (with units recognized by astropy), which will cause the error to only
568 occur if the "available" memory (according to
569 ExecutionResources.max_mem) is less than this value. Note that actual
570 memory usage is irrelevant here; this is all mock behavior."""
571 ),
572)
574dataset_query_constraint = MWOptionDecorator(
575 "--dataset-query-constraint",
576 help=unwrap(
577 """When constructing a quantum graph constrain by
578 pre-existence of specified dataset types. Valid
579 values are `all` for all inputs dataset types in
580 pipeline, ``off`` to not consider dataset type
581 existence as a constraint, single or comma
582 separated list of dataset type names."""
583 ),
584 default="all",
585)
587summary_option = MWOptionDecorator(
588 "--summary",
589 help=(
590 "Location for storing job summary (JSON file). Note that the"
591 " structure of this file may not be stable."
592 ),
593 type=MWPath(dir_okay=False, file_okay=True, writable=True),
594)
597recursive_option = MWOptionDecorator(
598 "--recursive",
599 is_flag=True,
600)
602config_search_path_option = MWOptionDecorator(
603 "--config-search-path",
604 callback=split_commas,
605 default=[],
606 help="Additional search paths for butler configuration.",
607 metavar="PATH",
608 multiple=True,
609)
611update_graph_id_option = MWOptionDecorator(
612 "--update-graph-id",
613 help=unwrap("Update graph ID with new unique value."),
614 is_flag=True,
615)
617metadata_run_key_option = MWOptionDecorator(
618 "--metadata-run-key",
619 help=(
620 "Quantum graph metadata key for the name of the output run. "
621 "Empty string disables update of the metadata. "
622 "Default value: output_run."
623 ),
624 default="output_run",
625)