Coverage for python/lsst/ctrl/mpexec/cli/opt/options.py: 75%
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« prev ^ index » next coverage.py v7.5.1, created at 2024-05-07 02:50 -0700
1# This file is part of ctrl_mpexec.
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
34from lsst.daf.butler.cli.utils import MWOptionDecorator, MWPath, split_commas, unwrap
35from lsst.utils.doImport import doImportType
37if TYPE_CHECKING:
38 # Avoid regular module-scope import of test-only code that tinkers with the
39 # storage class singleton.
40 from lsst.pipe.base.tests.mocks import ForcedFailure
43butler_config_option = MWOptionDecorator(
44 "-b", "--butler-config", help="Location of the gen3 butler/registry config file."
45)
48data_query_option = MWOptionDecorator(
49 "-d", "--data-query", help="User data selection expression.", metavar="QUERY"
50)
53debug_option = MWOptionDecorator(
54 "--debug", help="Enable debugging output using lsstDebug facility (imports debug.py).", is_flag=True
55)
57coverage_option = MWOptionDecorator("--coverage", help="Enable coverage output.", is_flag=True)
59coverage_report_option = MWOptionDecorator(
60 "--cov-report/--no-cov-report",
61 help="If coverage is enabled, controls whether to produce an HTML coverage report.",
62 default=True,
63)
65coverage_packages_option = MWOptionDecorator(
66 "--cov-packages",
67 help=unwrap(
68 """Python packages to restrict coverage to. If none are provided, runs coverage on all packages."""
69 ),
70 multiple=True,
71 callback=split_commas,
72)
74delete_option = MWOptionDecorator(
75 "--delete", callback=split_commas, help="Delete task with given label from pipeline.", multiple=True
76)
79pdb_option = MWOptionDecorator(
80 "--pdb",
81 help="Post-mortem debugger to launch for exceptions (defaults to pdb if unspecified; requires a tty).",
82 is_flag=False,
83 flag_value="pdb",
84 default=None,
85)
88extend_run_option = MWOptionDecorator(
89 "--extend-run",
90 help=(
91 "Instead of creating a new RUN collection, insert datasets into either the one given by "
92 "--output-run (if provided) or the first child collection of --output (which must be of type RUN). "
93 "This also enables --skip-existing option when building a graph. "
94 "When executing a graph this option skips quanta with all existing outputs."
95 ),
96 is_flag=True,
97)
100graph_fixup_option = MWOptionDecorator(
101 "--graph-fixup",
102 help="Name of the class or factory method which makes an instance used for execution graph fixup.",
103)
106init_only_option = MWOptionDecorator(
107 "--init-only",
108 help="Do not actually run; just register dataset types and/or save init outputs.",
109 is_flag=True,
110)
113input_option = MWOptionDecorator(
114 "-i",
115 "--input",
116 callback=split_commas,
117 default=[],
118 help="Comma-separated names of the input collection(s).",
119 metavar="COLLECTION",
120 multiple=True,
121)
124rebase_option = MWOptionDecorator(
125 "--rebase",
126 help=unwrap("""Reset output collection chain if it is inconsistent with --inputs"""),
127 is_flag=True,
128)
131no_versions_option = MWOptionDecorator(
132 "--no-versions", help="Do not save or check package versions.", is_flag=True
133)
136order_pipeline_option = MWOptionDecorator(
137 "--order-pipeline",
138 help=unwrap(
139 """Order tasks in pipeline based on their data
140 dependencies, ordering is performed as last step before saving or
141 executing pipeline."""
142 ),
143 is_flag=True,
144)
147output_option = MWOptionDecorator(
148 "-o",
149 "--output",
150 help=unwrap(
151 """Name of the output CHAINED collection. This may either be an
152 existing CHAINED collection to use as both input and output
153 (incompatible with --input), or a new CHAINED collection created
154 to include all inputs (requires --input). In both cases, the
155 collection's children will start with an output RUN collection
156 that directly holds all new datasets (see --output-run)."""
157 ),
158 metavar="COLL",
159)
162output_run_option = MWOptionDecorator(
163 "--output-run",
164 help=unwrap(
165 """Name of the new output RUN collection. If not provided
166 then --output must be provided and a new RUN collection will
167 be created by appending a timestamp to the value passed with
168 --output. If this collection already exists then
169 --extend-run must be passed."""
170 ),
171 metavar="COLL",
172)
175pipeline_option = MWOptionDecorator(
176 "-p",
177 "--pipeline",
178 help="Location of a pipeline definition file in YAML format.",
179 type=MWPath(file_okay=True, dir_okay=False, readable=True),
180)
183pipeline_dot_option = MWOptionDecorator(
184 "--pipeline-dot",
185 help="Location for storing GraphViz DOT representation of a pipeline.",
186 type=MWPath(writable=True, file_okay=True, dir_okay=False),
187)
190profile_option = MWOptionDecorator(
191 "--profile", help="Dump cProfile statistics to file name.", type=MWPath(file_okay=True, dir_okay=False)
192)
195prune_replaced_option = MWOptionDecorator(
196 "--prune-replaced",
197 help=unwrap(
198 """Delete the datasets in the collection replaced by
199 --replace-run, either just from the datastore
200 ('unstore') or by removing them and the RUN completely
201 ('purge'). Requires --replace-run."""
202 ),
203 type=click.Choice(choices=("unstore", "purge"), case_sensitive=False),
204)
207qgraph_option = MWOptionDecorator(
208 "-g",
209 "--qgraph",
210 help=unwrap(
211 """Location for a serialized quantum graph definition (pickle
212 file). If this option is given then all input data options and
213 pipeline-building options cannot be used. Can be a URI."""
214 ),
215)
218qgraph_id_option = MWOptionDecorator(
219 "--qgraph-id",
220 help=unwrap(
221 """Quantum graph identifier, if specified must match the
222 identifier of the graph loaded from a file. Ignored if graph
223 is not loaded from a file."""
224 ),
225)
228qgraph_datastore_records_option = MWOptionDecorator(
229 "--qgraph-datastore-records",
230 help=unwrap(
231 """Include datastore records into generated quantum graph, these records are used by a
232 quantum-backed butler.
233 """
234 ),
235 is_flag=True,
236)
239# I wanted to use default=None here to match Python API but click silently
240# replaces None with an empty tuple when multiple=True.
241qgraph_node_id_option = MWOptionDecorator(
242 "--qgraph-node-id",
243 callback=split_commas,
244 multiple=True,
245 help=unwrap(
246 """Only load a specified set of nodes when graph is
247 loaded from a file, nodes are identified by UUID
248 values. One or more comma-separated integers are
249 accepted. By default all nodes are loaded. Ignored if
250 graph is not loaded from a file."""
251 ),
252)
254qgraph_header_data_option = MWOptionDecorator(
255 "--show-qgraph-header",
256 is_flag=True,
257 default=False,
258 help="Print the headerData for Quantum Graph to the console",
259)
261qgraph_dot_option = MWOptionDecorator(
262 "--qgraph-dot",
263 help="Location for storing GraphViz DOT representation of a quantum graph.",
264 type=MWPath(writable=True, file_okay=True, dir_okay=False),
265)
268replace_run_option = MWOptionDecorator(
269 "--replace-run",
270 help=unwrap(
271 """Before creating a new RUN collection in an existing
272 CHAINED collection, remove the first child collection
273 (which must be of type RUN). This can be used to repeatedly
274 write to the same (parent) collection during development,
275 but it does not delete the datasets associated with the
276 replaced run unless --prune-replaced is also passed.
277 Requires --output, and incompatible with --extend-run."""
278 ),
279 is_flag=True,
280)
283save_pipeline_option = MWOptionDecorator(
284 "-s",
285 "--save-pipeline",
286 help="Location for storing resulting pipeline definition in YAML format.",
287 type=MWPath(dir_okay=False, file_okay=True, writable=True),
288)
290save_qgraph_option = MWOptionDecorator(
291 "-q",
292 "--save-qgraph",
293 help="URI location for storing a serialized quantum graph definition (pickle file).",
294)
297save_single_quanta_option = MWOptionDecorator(
298 "--save-single-quanta",
299 help=unwrap(
300 """Format string of locations for storing individual
301 quantum graph definition (pickle files). The curly
302 brace {} in the input string will be replaced by a
303 quantum number. Can be a URI."""
304 ),
305)
308show_option = MWOptionDecorator(
309 "--show",
310 callback=split_commas,
311 help=unwrap(
312 """Dump various info to standard output. Possible items are:
313 ``config``, ``config=[Task::]<PATTERN>`` or
314 ``config=[Task::]<PATTERN>:NOIGNORECASE`` to dump configuration
315 fields possibly matching given pattern and/or task label;
316 ``history=<FIELD>`` to dump configuration history for a field,
317 field name is specified as ``[Task::]<PATTERN>``; ``dump-config``,
318 ``dump-config=Task`` to dump complete configuration for a task
319 given its label or all tasks; ``pipeline`` to show pipeline
320 composition; ``graph`` to show information about quanta;
321 ``workflow`` to show information about quanta and their
322 dependency; ``tasks`` to show task composition; ``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 With -b, pipeline-graph and task-graph include additional information.
327 """
328 ),
329 metavar="ITEM|ITEM=VALUE",
330 multiple=True,
331)
334skip_existing_in_option = MWOptionDecorator(
335 "--skip-existing-in",
336 callback=split_commas,
337 default=None,
338 metavar="COLLECTION",
339 multiple=True,
340 help=unwrap(
341 """If all Quantum outputs already exist in the specified list of
342 collections then that Quantum will be excluded from the QuantumGraph.
343 """
344 ),
345)
348skip_existing_option = MWOptionDecorator(
349 "--skip-existing",
350 is_flag=True,
351 help=unwrap(
352 """This option is equivalent to --skip-existing-in with the name of
353 the output RUN collection. If both --skip-existing-in and
354 --skip-existing are given then output RUN collection is appended to
355 the list of collections."""
356 ),
357)
360clobber_outputs_option = MWOptionDecorator(
361 "--clobber-outputs",
362 help=(
363 "Remove outputs of failed quanta from the output run when they would block the execution of new "
364 "quanta with the same data ID (or assume that this will be done, if just building a QuantumGraph). "
365 "Does nothing if --extend-run is not passed."
366 ),
367 is_flag=True,
368)
371skip_init_writes_option = MWOptionDecorator(
372 "--skip-init-writes",
373 help=unwrap(
374 """Do not write collection-wide 'init output' datasets
375 (e.g.schemas)."""
376 ),
377 is_flag=True,
378)
381enable_implicit_threading_option = MWOptionDecorator(
382 "--enable-implicit-threading",
383 help=unwrap(
384 """Do not disable implicit threading use by third-party libraries (e.g. OpenBLAS).
385 Implicit threading is always disabled during execution with multiprocessing."""
386 ),
387 is_flag=True,
388)
390cores_per_quantum_option = MWOptionDecorator(
391 "-n",
392 "--cores-per-quantum",
393 default=1,
394 help=unwrap(
395 """Number of cores available to each quantum when executing.
396 If '-j' is used each subprocess will be allowed to use this number of cores."""
397 ),
398 type=click.IntRange(min=1),
399)
401memory_per_quantum_option = MWOptionDecorator(
402 "--memory-per-quantum",
403 default="",
404 help=unwrap(
405 """Memory allocated for each quantum to use when executing.
406 This memory allocation is not enforced by the execution system and is purely advisory.
407 If '-j' used each subprocess will be allowed to use this amount of memory.
408 Units are allowed and the default units for a plain integer are MB.
409 For example: '3GB', '3000MB' and '3000' would all result in the same
410 memory limit. Default is for no limit."""
411 ),
412 type=str,
413)
415task_option = MWOptionDecorator(
416 "-t",
417 "--task",
418 callback=split_commas,
419 help=unwrap(
420 """Task name to add to pipeline, must be a fully qualified task
421 name. Task name can be followed by colon and label name, if label
422 is not given then task base name (class name) is used as
423 label."""
424 ),
425 metavar="TASK[:LABEL]",
426 multiple=True,
427)
430timeout_option = MWOptionDecorator(
431 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)."
432)
435start_method_option = MWOptionDecorator(
436 "--start-method",
437 default=None,
438 type=click.Choice(choices=["spawn", "fork", "forkserver"]),
439 help=(
440 "Multiprocessing start method, default is platform-specific. "
441 "Fork method is no longer supported, spawn is used instead if fork is selected."
442 ),
443)
446fail_fast_option = MWOptionDecorator(
447 "--fail-fast",
448 help="Stop processing at first error, default is to process as many tasks as possible.",
449 is_flag=True,
450)
452save_execution_butler_option = MWOptionDecorator(
453 "--save-execution-butler",
454 help="Export location for an execution-specific butler after making QuantumGraph",
455)
457mock_option = MWOptionDecorator(
458 "--mock",
459 help="Mock pipeline execution.",
460 is_flag=True,
461)
463unmocked_dataset_types_option = MWOptionDecorator(
464 "--unmocked-dataset-types",
465 callback=split_commas,
466 default=None,
467 metavar="COLLECTION",
468 multiple=True,
469 help="Names of input dataset types that should not be mocked.",
470)
473def parse_mock_failure(
474 ctx: click.Context, param: click.Option, value: Iterable[str] | None
475) -> Mapping[str, ForcedFailure]:
476 """Parse the --mock-failure option values into the mapping accepted by
477 `~lsst.pipe.base.tests.mocks.mock_task_defs`.
479 Parameters
480 ----------
481 ctx : `click.Context`
482 Context provided by Click.
483 param : `click.Option`
484 Click option.
485 value : `~collections.abc.Iterable` [`str`] or `None`
486 Value from option.
487 """
488 # Avoid regular module-scope import of test-only code that tinkers with the
489 # storage class singleton.
490 from lsst.pipe.base.tests.mocks import ForcedFailure
492 result: dict[str, ForcedFailure] = {}
493 if value is None:
494 return result
495 for entry in value:
496 try:
497 task_label, error_type_name, where, *rest = entry.split(":")
498 if rest:
499 (memory_required,) = rest
500 else:
501 memory_required = None
502 except ValueError:
503 raise click.UsageError(
504 f"Invalid value for --mock-failure option: {entry!r}; "
505 "expected a string of the form 'task:error:where[:mem]'."
506 ) from None
507 error_type = doImportType(error_type_name) if error_type_name else None
508 result[task_label] = ForcedFailure(where, error_type, memory_required)
509 return result
512mock_failure_option = MWOptionDecorator(
513 "--mock-failure",
514 callback=parse_mock_failure,
515 metavar="LABEL:EXCEPTION:WHERE",
516 default=None,
517 multiple=True,
518 help=unwrap(
519 """Specifications for tasks that should be configured to fail
520 when mocking execution. This is a colon-separated 3-tuple or 4-tuple,
521 where the first entry the task label, the second the fully-qualified
522 exception type (empty for ValueError, and the third a string (which
523 typically needs to be quoted to be passed as one argument value by the
524 shell) of the form passed to --where, indicating which data IDs should
525 fail. The final optional term is the memory "required" by the task
526 (with units recognized by astropy), which will cause the error to only
527 occur if the "available" memory (according to
528 ExecutionResources.max_mem) is less than this value. Note that actual
529 memory usage is irrelevant here; this is all mock behavior."""
530 ),
531)
534clobber_execution_butler_option = MWOptionDecorator(
535 "--clobber-execution-butler",
536 help=unwrap(
537 """When creating execution butler overwrite
538 any existing products"""
539 ),
540 is_flag=True,
541)
543target_datastore_root_option = MWOptionDecorator(
544 "--target-datastore-root",
545 help=unwrap(
546 """Root directory for datastore of execution butler.
547 Default is to use the original datastore.
548 """
549 ),
550)
552dataset_query_constraint = MWOptionDecorator(
553 "--dataset-query-constraint",
554 help=unwrap(
555 """When constructing a quantum graph constrain by
556 pre-existence of specified dataset types. Valid
557 values are `all` for all inputs dataset types in
558 pipeline, ``off`` to not consider dataset type
559 existence as a constraint, single or comma
560 separated list of dataset type names."""
561 ),
562 default="all",
563)
565summary_option = MWOptionDecorator(
566 "--summary",
567 help=(
568 "Location for storing job summary (JSON file). Note that the"
569 " structure of this file may not be stable."
570 ),
571 type=MWPath(dir_okay=False, file_okay=True, writable=True),
572)
575recursive_option = MWOptionDecorator(
576 "--recursive",
577 is_flag=True,
578)
580config_search_path_option = MWOptionDecorator(
581 "--config-search-path",
582 callback=split_commas,
583 default=[],
584 help="Additional search paths for butler configuration.",
585 metavar="PATH",
586 multiple=True,
587)
589update_graph_id_option = MWOptionDecorator(
590 "--update-graph-id",
591 help=unwrap("Update graph ID with new unique value."),
592 is_flag=True,
593)
595metadata_run_key_option = MWOptionDecorator(
596 "--metadata-run-key",
597 help=(
598 "Quantum graph metadata key for the name of the output run. "
599 "Empty string disables update of the metadata. "
600 "Default value: output_run."
601 ),
602 default="output_run",
603)