Coverage for python/lsst/ctrl/mpexec/cli/opt/options.py: 80%
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« prev ^ index » next coverage.py v7.2.7, created at 2023-07-05 09:15 +0000
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 program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22from __future__ import annotations
24from collections.abc import Iterable, Mapping
26import click
27from lsst.daf.butler.cli.utils import MWOptionDecorator, MWPath, split_commas, unwrap
28from lsst.utils.doImport import doImportType
30butler_config_option = MWOptionDecorator(
31 "-b", "--butler-config", help="Location of the gen3 butler/registry config file."
32)
35data_query_option = MWOptionDecorator(
36 "-d", "--data-query", help="User data selection expression.", metavar="QUERY"
37)
40debug_option = MWOptionDecorator(
41 "--debug", help="Enable debugging output using lsstDebug facility (imports debug.py).", is_flag=True
42)
44coverage_option = MWOptionDecorator("--coverage", help="Enable coverage output.", is_flag=True)
46coverage_report_option = MWOptionDecorator(
47 "--cov-report/--no-cov-report",
48 help="If coverage is enabled, controls whether to produce an HTML coverage report.",
49 default=True,
50)
52coverage_packages_option = MWOptionDecorator(
53 "--cov-packages",
54 help=unwrap(
55 """Python packages to restrict coverage to. If none are provided, runs coverage on all packages."""
56 ),
57 multiple=True,
58 callback=split_commas,
59)
61delete_option = MWOptionDecorator(
62 "--delete", callback=split_commas, help="Delete task with given label from pipeline.", multiple=True
63)
66pdb_option = MWOptionDecorator(
67 "--pdb",
68 help="Post-mortem debugger to launch for exceptions (defaults to pdb if unspecified; requires a tty).",
69 is_flag=False,
70 flag_value="pdb",
71 default=None,
72)
75extend_run_option = MWOptionDecorator(
76 "--extend-run",
77 help=(
78 "Instead of creating a new RUN collection, insert datasets into either the one given by "
79 "--output-run (if provided) or the first child collection of --output (which must be of type RUN). "
80 "This also enables --skip-existing option when building a graph. "
81 "When executing a graph this option skips quanta with all existing outputs."
82 ),
83 is_flag=True,
84)
87graph_fixup_option = MWOptionDecorator(
88 "--graph-fixup",
89 help=unwrap(
90 """Name of the class or factory method which makes an
91 instance used for execution graph fixup."""
92 ),
93)
96init_only_option = MWOptionDecorator(
97 "--init-only",
98 help=unwrap(
99 """Do not actually run; just register dataset types and/or
100 save init outputs. """
101 ),
102 is_flag=True,
103)
106input_option = MWOptionDecorator(
107 "-i",
108 "--input",
109 callback=split_commas,
110 default=list(),
111 help=unwrap("""Comma-separated names of the input collection(s)."""),
112 metavar="COLLECTION",
113 multiple=True,
114)
116no_versions_option = MWOptionDecorator(
117 "--no-versions", help="Do not save or check package versions.", is_flag=True
118)
121order_pipeline_option = MWOptionDecorator(
122 "--order-pipeline",
123 help=unwrap(
124 """Order tasks in pipeline based on their data
125 dependencies, ordering is performed as last step before saving or
126 executing pipeline."""
127 ),
128 is_flag=True,
129)
132output_option = MWOptionDecorator(
133 "-o",
134 "--output",
135 help=unwrap(
136 """Name of the output CHAINED collection. This may either be an
137 existing CHAINED collection to use as both input and output
138 (incompatible with --input), or a new CHAINED collection created
139 to include all inputs (requires --input). In both cases, the
140 collection's children will start with an output RUN collection
141 that directly holds all new datasets (see --output-run)."""
142 ),
143 metavar="COLL",
144)
147output_run_option = MWOptionDecorator(
148 "--output-run",
149 help=unwrap(
150 """Name of the new output RUN collection. If not provided
151 then --output must be provided and a new RUN collection will
152 be created by appending a timestamp to the value passed with
153 --output. If this collection already exists then
154 --extend-run must be passed."""
155 ),
156 metavar="COLL",
157)
160pipeline_option = MWOptionDecorator(
161 "-p",
162 "--pipeline",
163 help="Location of a pipeline definition file in YAML format.",
164 type=MWPath(file_okay=True, dir_okay=False, readable=True),
165)
168pipeline_dot_option = MWOptionDecorator(
169 "--pipeline-dot",
170 help=unwrap(
171 """"Location for storing GraphViz DOT representation of a
172 pipeline."""
173 ),
174 type=MWPath(writable=True, file_okay=True, dir_okay=False),
175)
178profile_option = MWOptionDecorator(
179 "--profile", help="Dump cProfile statistics to file name.", type=MWPath(file_okay=True, dir_okay=False)
180)
183prune_replaced_option = MWOptionDecorator(
184 "--prune-replaced",
185 help=unwrap(
186 """Delete the datasets in the collection replaced by
187 --replace-run, either just from the datastore
188 ('unstore') or by removing them and the RUN completely
189 ('purge'). Requires --replace-run."""
190 ),
191 type=click.Choice(choices=("unstore", "purge"), case_sensitive=False),
192)
195qgraph_option = MWOptionDecorator(
196 "-g",
197 "--qgraph",
198 help=unwrap(
199 """Location for a serialized quantum graph definition (pickle
200 file). If this option is given then all input data options and
201 pipeline-building options cannot be used. Can be a URI."""
202 ),
203)
206qgraph_id_option = MWOptionDecorator(
207 "--qgraph-id",
208 help=unwrap(
209 """Quantum graph identifier, if specified must match the
210 identifier of the graph loaded from a file. Ignored if graph
211 is not loaded from a file."""
212 ),
213)
216qgraph_datastore_records_option = MWOptionDecorator(
217 "--qgraph-datastore-records",
218 help=unwrap(
219 """Include datastore records into generated quantum graph, these records are used by a
220 quantum-backed butler.
221 """
222 ),
223 is_flag=True,
224)
227# I wanted to use default=None here to match Python API but click silently
228# replaces None with an empty tuple when multiple=True.
229qgraph_node_id_option = MWOptionDecorator(
230 "--qgraph-node-id",
231 callback=split_commas,
232 multiple=True,
233 help=unwrap(
234 """Only load a specified set of nodes when graph is
235 loaded from a file, nodes are identified by UUID
236 values. One or more comma-separated integers are
237 accepted. By default all nodes are loaded. Ignored if
238 graph is not loaded from a file."""
239 ),
240)
242qgraph_header_data_option = MWOptionDecorator(
243 "--show-qgraph-header",
244 is_flag=True,
245 default=False,
246 help=unwrap(
247 """Print the headerData for Quantum Graph to the
248 console"""
249 ),
250)
252qgraph_dot_option = MWOptionDecorator(
253 "--qgraph-dot",
254 help=unwrap(
255 """Location for storing GraphViz DOT representation of a
256 quantum graph."""
257 ),
258 type=MWPath(writable=True, file_okay=True, dir_okay=False),
259)
262replace_run_option = MWOptionDecorator(
263 "--replace-run",
264 help=unwrap(
265 """Before creating a new RUN collection in an existing
266 CHAINED collection, remove the first child collection
267 (which must be of type RUN). This can be used to repeatedly
268 write to the same (parent) collection during development,
269 but it does not delete the datasets associated with the
270 replaced run unless --prune-replaced is also passed.
271 Requires --output, and incompatible with --extend-run."""
272 ),
273 is_flag=True,
274)
277save_pipeline_option = MWOptionDecorator(
278 "-s",
279 "--save-pipeline",
280 help=unwrap(
281 """Location for storing resulting pipeline definition in
282 YAML format."""
283 ),
284 type=MWPath(dir_okay=False, file_okay=True, writable=True),
285)
287save_qgraph_option = MWOptionDecorator(
288 "-q",
289 "--save-qgraph",
290 help=unwrap(
291 """URI location for storing a serialized quantum graph
292 definition (pickle file)."""
293 ),
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, field
317 name is specified as [Task::]<PATTERN>; `dump-config`,
318 `dump-config=Task` to dump complete configuration for a task given
319 its label or all tasks; `pipeline` to show pipeline composition;
320 `graph` to show information about quanta; `workflow` to show
321 information about quanta and their dependency; `tasks` to show
322 task composition; `uri` to show predicted dataset URIs of
323 quanta"""
324 ),
325 metavar="ITEM|ITEM=VALUE",
326 multiple=True,
327)
330skip_existing_in_option = MWOptionDecorator(
331 "--skip-existing-in",
332 callback=split_commas,
333 default=None,
334 metavar="COLLECTION",
335 multiple=True,
336 help=unwrap(
337 """If all Quantum outputs already exist in the specified list of
338 collections then that Quantum will be excluded from the QuantumGraph.
339 """
340 ),
341)
344skip_existing_option = MWOptionDecorator(
345 "--skip-existing",
346 is_flag=True,
347 help=unwrap(
348 """This option is equivalent to --skip-existing-in with the name of
349 the output RUN collection. If both --skip-existing-in and
350 --skip-existing are given then output RUN collection is appended to
351 the list of collections."""
352 ),
353)
356clobber_outputs_option = MWOptionDecorator(
357 "--clobber-outputs",
358 help=(
359 "Remove outputs of failed quanta from the output run when they would block the execution of new "
360 "quanta with the same data ID (or assume that this will be done, if just building a QuantumGraph). "
361 "Does nothing if --extend-run is not passed."
362 ),
363 is_flag=True,
364)
367skip_init_writes_option = MWOptionDecorator(
368 "--skip-init-writes",
369 help=unwrap(
370 """Do not write collection-wide 'init output' datasets
371 (e.g.schemas)."""
372 ),
373 is_flag=True,
374)
377enable_implicit_threading_option = MWOptionDecorator(
378 "--enable-implicit-threading",
379 help=unwrap(
380 """Do not disable implicit threading use by third-party libraries (e.g. OpenBLAS).
381 Implicit threading is always disabled during execution with multiprocessing."""
382 ),
383 is_flag=True,
384)
386cores_per_quantum_option = MWOptionDecorator(
387 "-n",
388 "--cores-per-quantum",
389 default=1,
390 help=unwrap(
391 """Number of cores available to each quantum when executing.
392 If '-j' is used each subprocess will be allowed to use this number of cores."""
393 ),
394 type=click.IntRange(min=1),
395)
397memory_per_quantum_option = MWOptionDecorator(
398 "--memory-per-quantum",
399 default="",
400 help=unwrap(
401 """Memory allocated for each quantum to use when executing.
402 This memory allocation is not enforced by the execution system and is purely advisory.
403 If '-j' used each subprocess will be allowed to use this amount of memory.
404 Units are allowed and the default units for a plain integer are MB.
405 For example: '3GB', '3000MB' and '3000' would all result in the same
406 memory limit. Default is for no limit."""
407 ),
408 type=str,
409)
411task_option = MWOptionDecorator(
412 "-t",
413 "--task",
414 callback=split_commas,
415 help=unwrap(
416 """Task name to add to pipeline, must be a fully qualified task
417 name. Task name can be followed by colon and label name, if label
418 is not given then task base name (class name) is used as
419 label."""
420 ),
421 metavar="TASK[:LABEL]",
422 multiple=True,
423)
426timeout_option = MWOptionDecorator(
427 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)."
428)
431start_method_option = MWOptionDecorator(
432 "--start-method",
433 default=None,
434 type=click.Choice(choices=["spawn", "fork", "forkserver"]),
435 help="Multiprocessing start method, default is platform-specific.",
436)
439fail_fast_option = MWOptionDecorator(
440 "--fail-fast",
441 help=unwrap(
442 """Stop processing at first error, default is to process
443 as many tasks as possible."""
444 ),
445 is_flag=True,
446)
448save_execution_butler_option = MWOptionDecorator(
449 "--save-execution-butler",
450 help=unwrap(
451 """Export location for an
452 execution-specific butler after making
453 QuantumGraph"""
454 ),
455)
457mock_option = MWOptionDecorator(
458 "--mock",
459 help=unwrap("""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=unwrap("""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, tuple[str, type[Exception] | None]]:
476 """Parse the --mock-failure option values into the mapping accepted by
477 `lsst.pipe.base.tests.mocks.mock_task_defs`.
478 """
479 result: dict[str, tuple[str, type[Exception] | None]] = {}
480 if value is None:
481 return result
482 for entry in value:
483 try:
484 task_label, error_type_name, where = entry.split(":", 2)
485 except ValueError:
486 raise click.UsageError(
487 f"Invalid value for --mock-failure option: {entry!r}; "
488 "expected a string of the form 'task:error:where'."
489 ) from None
490 error_type = doImportType(error_type_name) if error_type_name else None
491 result[task_label] = (where, error_type)
492 return result
495mock_failure_option = MWOptionDecorator(
496 "--mock-failure",
497 callback=parse_mock_failure,
498 metavar="LABEL:EXCEPTION:WHERE",
499 default=None,
500 multiple=True,
501 help=unwrap(
502 """Specifications for tasks that should be configured to fail
503 when mocking execution. This is a colon-separated 3-tuple, where the
504 first entry the task label, the second the fully-qualified exception
505 type (empty for ValueError, and the third a string (which typically
506 needs to be quoted to be passed as one argument value by the shell) of
507 the form passed to --where, indicating which data IDs should fail."""
508 ),
509)
512clobber_execution_butler_option = MWOptionDecorator(
513 "--clobber-execution-butler",
514 help=unwrap(
515 """When creating execution butler overwrite
516 any existing products"""
517 ),
518 is_flag=True,
519)
521target_datastore_root_option = MWOptionDecorator(
522 "--target-datastore-root",
523 help=unwrap(
524 """Root directory for datastore of execution butler.
525 Default is to use the original datastore.
526 """
527 ),
528)
530dataset_query_constraint = MWOptionDecorator(
531 "--dataset-query-constraint",
532 help=unwrap(
533 """When constructing a quantum graph constrain by
534 pre-existence of specified dataset types. Valid
535 values are `all` for all inputs dataset types in
536 pipeline, `off` to not consider dataset type
537 existance as a constraint, single or comma
538 separated list of dataset type names"""
539 ),
540 default="all",
541)
543summary_option = MWOptionDecorator(
544 "--summary",
545 help=(
546 "Location for storing job summary (JSON file). Note that the"
547 " structure of this file may not be stable."
548 ),
549 type=MWPath(dir_okay=False, file_okay=True, writable=True),
550)
553recursive_option = MWOptionDecorator(
554 "--recursive",
555 is_flag=True,
556)
558config_search_path_option = MWOptionDecorator(
559 "--config-search-path",
560 callback=split_commas,
561 default=list(),
562 help="Additional search paths for butler configuration.",
563 metavar="PATH",
564 multiple=True,
565)
567update_graph_id_option = MWOptionDecorator(
568 "--update-graph-id",
569 help=unwrap("Update graph ID with new unique value."),
570 is_flag=True,
571)
573metadata_run_key_option = MWOptionDecorator(
574 "--metadata-run-key",
575 help=(
576 "Quantum graph metadata key for the name of the output run. "
577 "Empty string disables update of the metadata. "
578 "Default value: output_run."
579 ),
580 default="output_run",
581)