Coverage for python / lsst / ctrl / mpexec / cli / opt / options.py: 75%
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2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
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
10# under a 3-clause BSD license. Recipients may choose which of these licenses
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
18# (at your option) any later version.
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.
24#
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)
361clobber_outputs_option = MWOptionDecorator(
362 "--clobber-outputs",
363 help=(
364 "Remove outputs of failed quanta from the output run when they would block the execution of new "
365 "quanta with the same data ID (or assume that this will be done, if just building a QuantumGraph). "
366 "Does nothing if --extend-run is not passed."
367 ),
368 is_flag=True,
369)
372no_existing_outputs_option = MWOptionDecorator(
373 "--no-existing-outputs",
374 help=(
375 "Assume that no predicted outputs already exist in the output run collection. "
376 "This will eliminate existence checks that otherwise run before each quantum is executed."
377 ),
378 is_flag=True,
379)
382skip_init_writes_option = MWOptionDecorator(
383 "--skip-init-writes",
384 help=unwrap(
385 """Do not write collection-wide 'init output' datasets
386 (e.g.schemas)."""
387 ),
388 is_flag=True,
389)
392enable_implicit_threading_option = MWOptionDecorator(
393 "--enable-implicit-threading",
394 help=unwrap(
395 """Do not disable implicit threading use by third-party libraries (e.g. OpenBLAS).
396 Implicit threading is always disabled during execution with multiprocessing."""
397 ),
398 is_flag=True,
399)
401cores_per_quantum_option = MWOptionDecorator(
402 "-n",
403 "--cores-per-quantum",
404 default=1,
405 help=unwrap(
406 """Number of cores available to each quantum when executing.
407 If '-j' is used each subprocess will be allowed to use this number of cores."""
408 ),
409 type=click.IntRange(min=1),
410)
412memory_per_quantum_option = MWOptionDecorator(
413 "--memory-per-quantum",
414 default="",
415 help=unwrap(
416 """Memory allocated for each quantum to use when executing.
417 This memory allocation is not enforced by the execution system and is purely advisory.
418 If '-j' used each subprocess will be allowed to use this amount of memory.
419 Units are allowed and the default units for a plain integer are MB.
420 For example: '3GB', '3000MB' and '3000' would all result in the same
421 memory limit. Default is for no limit."""
422 ),
423 type=str,
424)
426task_option = MWOptionDecorator(
427 "-t",
428 "--task",
429 callback=split_commas,
430 help=unwrap(
431 """Task name to add to pipeline, must be a fully qualified task
432 name. Task name can be followed by colon and label name, if label
433 is not given then task base name (class name) is used as
434 label."""
435 ),
436 metavar="TASK[:LABEL]",
437 multiple=True,
438)
440select_tasks_option = MWOptionDecorator(
441 "--select-tasks",
442 metavar="EXPR",
443 default="",
444 help=(
445 "A string expression that filters the tasks to run from the pipeline. "
446 "See https://pipelines.lsst.io/v/weekly/modules/lsst.pipe.base/working-with-pipeline-graphs.html"
447 "#pipeline-graph-subset-expressions for details."
448 ),
449)
452timeout_option = MWOptionDecorator(
453 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)."
454)
457start_method_option = MWOptionDecorator(
458 "--start-method",
459 default=None,
460 type=click.Choice(choices=["spawn", "fork", "forkserver"]),
461 help=(
462 "Multiprocessing start method, default is platform-specific. "
463 "Fork method is no longer supported, spawn is used instead if fork is selected."
464 ),
465)
468fail_fast_option = MWOptionDecorator(
469 "--fail-fast",
470 help="Stop processing at first error, default is to process as many tasks as possible.",
471 is_flag=True,
472)
474raise_on_partial_outputs_option = MWOptionDecorator(
475 "--raise-on-partial-outputs/--no-raise-on-partial-outputs",
476 help="Consider partial outputs from a task an error instead of a qualified success.",
477 is_flag=True,
478 default=True,
479)
481mock_option = MWOptionDecorator(
482 "--mock",
483 help="Mock pipeline execution.",
484 is_flag=True,
485)
487unmocked_dataset_types_option = MWOptionDecorator(
488 "--unmocked-dataset-types",
489 callback=split_commas,
490 default=None,
491 metavar="COLLECTION",
492 multiple=True,
493 help="Names of input dataset types that should not be mocked.",
494)
497def parse_mock_failure(
498 ctx: click.Context, param: click.Option, value: Iterable[str] | None
499) -> Mapping[str, ForcedFailure]:
500 """Parse the --mock-failure option values into the mapping accepted by
501 `~lsst.pipe.base.tests.mocks.mock_task_defs`.
503 Parameters
504 ----------
505 ctx : `click.Context`
506 Context provided by Click.
507 param : `click.Option`
508 Click option.
509 value : `~collections.abc.Iterable` [`str`] or `None`
510 Value from option.
511 """
512 # Avoid regular module-scope import of test-only code that tinkers with the
513 # storage class singleton.
514 from lsst.pipe.base.tests.mocks import ForcedFailure
516 result: dict[str, ForcedFailure] = {}
517 if value is None:
518 return result
519 for entry in value:
520 try:
521 task_label, error_type_name, where, *rest = entry.split(":")
522 if rest:
523 (memory_required,) = rest
524 else:
525 memory_required = None
526 except ValueError:
527 raise click.UsageError(
528 f"Invalid value for --mock-failure option: {entry!r}; "
529 "expected a string of the form 'task:error:where[:mem]'."
530 ) from None
531 error_type = doImportType(error_type_name) if error_type_name else None
532 result[task_label] = ForcedFailure(where, error_type, memory_required)
533 return result
536mock_failure_option = MWOptionDecorator(
537 "--mock-failure",
538 callback=parse_mock_failure,
539 metavar="LABEL:EXCEPTION:WHERE",
540 default=None,
541 multiple=True,
542 help=unwrap(
543 """Specifications for tasks that should be configured to fail
544 when mocking execution. This is a colon-separated 3-tuple or 4-tuple,
545 where the first entry the task label, the second the fully-qualified
546 exception type (empty for ValueError, and the third a string (which
547 typically needs to be quoted to be passed as one argument value by the
548 shell) of the form passed to --where, indicating which data IDs should
549 fail. The final optional term is the memory "required" by the task
550 (with units recognized by astropy), which will cause the error to only
551 occur if the "available" memory (according to
552 ExecutionResources.max_mem) is less than this value. Note that actual
553 memory usage is irrelevant here; this is all mock behavior."""
554 ),
555)
557dataset_query_constraint = MWOptionDecorator(
558 "--dataset-query-constraint",
559 help=unwrap(
560 """When constructing a quantum graph constrain by
561 pre-existence of specified dataset types. Valid
562 values are `all` for all inputs dataset types in
563 pipeline, ``off`` to not consider dataset type
564 existence as a constraint, single or comma
565 separated list of dataset type names."""
566 ),
567 default="all",
568)
570summary_option = MWOptionDecorator(
571 "--summary",
572 help=(
573 "Location for storing job summary (JSON file). Note that the"
574 " structure of this file may not be stable."
575 ),
576 type=MWPath(dir_okay=False, file_okay=True, writable=True),
577)
580recursive_option = MWOptionDecorator(
581 "--recursive",
582 is_flag=True,
583)
585config_search_path_option = MWOptionDecorator(
586 "--config-search-path",
587 callback=split_commas,
588 default=[],
589 help="Additional search paths for butler configuration.",
590 metavar="PATH",
591 multiple=True,
592)
594update_graph_id_option = MWOptionDecorator(
595 "--update-graph-id",
596 help=unwrap("Update graph ID with new unique value."),
597 is_flag=True,
598)
600metadata_run_key_option = MWOptionDecorator(
601 "--metadata-run-key",
602 help=(
603 "Quantum graph metadata key for the name of the output run. "
604 "Empty string disables update of the metadata. "
605 "Default value: output_run."
606 ),
607 default="output_run",
608)