Coverage for python/lsst/ctrl/mpexec/cli/opt/options.py: 80%
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« prev ^ index » next coverage.py v7.3.0, created at 2023-09-01 09:30 +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="Name of the class or factory method which makes an instance used for execution graph fixup.",
90)
93init_only_option = MWOptionDecorator(
94 "--init-only",
95 help="Do not actually run; just register dataset types and/or save init outputs.",
96 is_flag=True,
97)
100input_option = MWOptionDecorator(
101 "-i",
102 "--input",
103 callback=split_commas,
104 default=[],
105 help="Comma-separated names of the input collection(s).",
106 metavar="COLLECTION",
107 multiple=True,
108)
111rebase_option = MWOptionDecorator(
112 "--rebase",
113 help=unwrap("""Reset output collection chain if it is inconsistent with --inputs"""),
114 is_flag=True,
115)
118no_versions_option = MWOptionDecorator(
119 "--no-versions", help="Do not save or check package versions.", is_flag=True
120)
123order_pipeline_option = MWOptionDecorator(
124 "--order-pipeline",
125 help=unwrap(
126 """Order tasks in pipeline based on their data
127 dependencies, ordering is performed as last step before saving or
128 executing pipeline."""
129 ),
130 is_flag=True,
131)
134output_option = MWOptionDecorator(
135 "-o",
136 "--output",
137 help=unwrap(
138 """Name of the output CHAINED collection. This may either be an
139 existing CHAINED collection to use as both input and output
140 (incompatible with --input), or a new CHAINED collection created
141 to include all inputs (requires --input). In both cases, the
142 collection's children will start with an output RUN collection
143 that directly holds all new datasets (see --output-run)."""
144 ),
145 metavar="COLL",
146)
149output_run_option = MWOptionDecorator(
150 "--output-run",
151 help=unwrap(
152 """Name of the new output RUN collection. If not provided
153 then --output must be provided and a new RUN collection will
154 be created by appending a timestamp to the value passed with
155 --output. If this collection already exists then
156 --extend-run must be passed."""
157 ),
158 metavar="COLL",
159)
162pipeline_option = MWOptionDecorator(
163 "-p",
164 "--pipeline",
165 help="Location of a pipeline definition file in YAML format.",
166 type=MWPath(file_okay=True, dir_okay=False, readable=True),
167)
170pipeline_dot_option = MWOptionDecorator(
171 "--pipeline-dot",
172 help="Location for storing GraphViz DOT representation of a pipeline.",
173 type=MWPath(writable=True, file_okay=True, dir_okay=False),
174)
177profile_option = MWOptionDecorator(
178 "--profile", help="Dump cProfile statistics to file name.", type=MWPath(file_okay=True, dir_okay=False)
179)
182prune_replaced_option = MWOptionDecorator(
183 "--prune-replaced",
184 help=unwrap(
185 """Delete the datasets in the collection replaced by
186 --replace-run, either just from the datastore
187 ('unstore') or by removing them and the RUN completely
188 ('purge'). Requires --replace-run."""
189 ),
190 type=click.Choice(choices=("unstore", "purge"), case_sensitive=False),
191)
194qgraph_option = MWOptionDecorator(
195 "-g",
196 "--qgraph",
197 help=unwrap(
198 """Location for a serialized quantum graph definition (pickle
199 file). If this option is given then all input data options and
200 pipeline-building options cannot be used. Can be a URI."""
201 ),
202)
205qgraph_id_option = MWOptionDecorator(
206 "--qgraph-id",
207 help=unwrap(
208 """Quantum graph identifier, if specified must match the
209 identifier of the graph loaded from a file. Ignored if graph
210 is not loaded from a file."""
211 ),
212)
215qgraph_datastore_records_option = MWOptionDecorator(
216 "--qgraph-datastore-records",
217 help=unwrap(
218 """Include datastore records into generated quantum graph, these records are used by a
219 quantum-backed butler.
220 """
221 ),
222 is_flag=True,
223)
226# I wanted to use default=None here to match Python API but click silently
227# replaces None with an empty tuple when multiple=True.
228qgraph_node_id_option = MWOptionDecorator(
229 "--qgraph-node-id",
230 callback=split_commas,
231 multiple=True,
232 help=unwrap(
233 """Only load a specified set of nodes when graph is
234 loaded from a file, nodes are identified by UUID
235 values. One or more comma-separated integers are
236 accepted. By default all nodes are loaded. Ignored if
237 graph is not loaded from a file."""
238 ),
239)
241qgraph_header_data_option = MWOptionDecorator(
242 "--show-qgraph-header",
243 is_flag=True,
244 default=False,
245 help="Print the headerData for Quantum Graph to the console",
246)
248qgraph_dot_option = MWOptionDecorator(
249 "--qgraph-dot",
250 help="Location for storing GraphViz DOT representation of a quantum graph.",
251 type=MWPath(writable=True, file_okay=True, dir_okay=False),
252)
255replace_run_option = MWOptionDecorator(
256 "--replace-run",
257 help=unwrap(
258 """Before creating a new RUN collection in an existing
259 CHAINED collection, remove the first child collection
260 (which must be of type RUN). This can be used to repeatedly
261 write to the same (parent) collection during development,
262 but it does not delete the datasets associated with the
263 replaced run unless --prune-replaced is also passed.
264 Requires --output, and incompatible with --extend-run."""
265 ),
266 is_flag=True,
267)
270save_pipeline_option = MWOptionDecorator(
271 "-s",
272 "--save-pipeline",
273 help="Location for storing resulting pipeline definition in YAML format.",
274 type=MWPath(dir_okay=False, file_okay=True, writable=True),
275)
277save_qgraph_option = MWOptionDecorator(
278 "-q",
279 "--save-qgraph",
280 help="URI location for storing a serialized quantum graph definition (pickle file).",
281)
284save_single_quanta_option = MWOptionDecorator(
285 "--save-single-quanta",
286 help=unwrap(
287 """Format string of locations for storing individual
288 quantum graph definition (pickle files). The curly
289 brace {} in the input string will be replaced by a
290 quantum number. Can be a URI."""
291 ),
292)
295show_option = MWOptionDecorator(
296 "--show",
297 callback=split_commas,
298 help=unwrap(
299 """Dump various info to standard output. Possible items are:
300 ``config``, ``config=[Task::]<PATTERN>`` or
301 ``config=[Task::]<PATTERN>:NOIGNORECASE`` to dump configuration
302 fields possibly matching given pattern and/or task label;
303 ``history=<FIELD>`` to dump configuration history for a field,
304 field name is specified as ``[Task::]<PATTERN>``; ``dump-config``,
305 ``dump-config=Task`` to dump complete configuration for a task
306 given its label or all tasks; ``pipeline`` to show pipeline
307 composition; ``graph`` to show information about quanta;
308 ``workflow`` to show information about quanta and their
309 dependency; ``tasks`` to show task composition; ``uri`` to show
310 predicted dataset URIs of quanta."""
311 ),
312 metavar="ITEM|ITEM=VALUE",
313 multiple=True,
314)
317skip_existing_in_option = MWOptionDecorator(
318 "--skip-existing-in",
319 callback=split_commas,
320 default=None,
321 metavar="COLLECTION",
322 multiple=True,
323 help=unwrap(
324 """If all Quantum outputs already exist in the specified list of
325 collections then that Quantum will be excluded from the QuantumGraph.
326 """
327 ),
328)
331skip_existing_option = MWOptionDecorator(
332 "--skip-existing",
333 is_flag=True,
334 help=unwrap(
335 """This option is equivalent to --skip-existing-in with the name of
336 the output RUN collection. If both --skip-existing-in and
337 --skip-existing are given then output RUN collection is appended to
338 the list of collections."""
339 ),
340)
343clobber_outputs_option = MWOptionDecorator(
344 "--clobber-outputs",
345 help=(
346 "Remove outputs of failed quanta from the output run when they would block the execution of new "
347 "quanta with the same data ID (or assume that this will be done, if just building a QuantumGraph). "
348 "Does nothing if --extend-run is not passed."
349 ),
350 is_flag=True,
351)
354skip_init_writes_option = MWOptionDecorator(
355 "--skip-init-writes",
356 help=unwrap(
357 """Do not write collection-wide 'init output' datasets
358 (e.g.schemas)."""
359 ),
360 is_flag=True,
361)
364enable_implicit_threading_option = MWOptionDecorator(
365 "--enable-implicit-threading",
366 help=unwrap(
367 """Do not disable implicit threading use by third-party libraries (e.g. OpenBLAS).
368 Implicit threading is always disabled during execution with multiprocessing."""
369 ),
370 is_flag=True,
371)
373cores_per_quantum_option = MWOptionDecorator(
374 "-n",
375 "--cores-per-quantum",
376 default=1,
377 help=unwrap(
378 """Number of cores available to each quantum when executing.
379 If '-j' is used each subprocess will be allowed to use this number of cores."""
380 ),
381 type=click.IntRange(min=1),
382)
384memory_per_quantum_option = MWOptionDecorator(
385 "--memory-per-quantum",
386 default="",
387 help=unwrap(
388 """Memory allocated for each quantum to use when executing.
389 This memory allocation is not enforced by the execution system and is purely advisory.
390 If '-j' used each subprocess will be allowed to use this amount of memory.
391 Units are allowed and the default units for a plain integer are MB.
392 For example: '3GB', '3000MB' and '3000' would all result in the same
393 memory limit. Default is for no limit."""
394 ),
395 type=str,
396)
398task_option = MWOptionDecorator(
399 "-t",
400 "--task",
401 callback=split_commas,
402 help=unwrap(
403 """Task name to add to pipeline, must be a fully qualified task
404 name. Task name can be followed by colon and label name, if label
405 is not given then task base name (class name) is used as
406 label."""
407 ),
408 metavar="TASK[:LABEL]",
409 multiple=True,
410)
413timeout_option = MWOptionDecorator(
414 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)."
415)
418start_method_option = MWOptionDecorator(
419 "--start-method",
420 default=None,
421 type=click.Choice(choices=["spawn", "fork", "forkserver"]),
422 help="Multiprocessing start method, default is platform-specific.",
423)
426fail_fast_option = MWOptionDecorator(
427 "--fail-fast",
428 help="Stop processing at first error, default is to process as many tasks as possible.",
429 is_flag=True,
430)
432save_execution_butler_option = MWOptionDecorator(
433 "--save-execution-butler",
434 help="Export location for an execution-specific butler after making QuantumGraph",
435)
437mock_option = MWOptionDecorator(
438 "--mock",
439 help="Mock pipeline execution.",
440 is_flag=True,
441)
443unmocked_dataset_types_option = MWOptionDecorator(
444 "--unmocked-dataset-types",
445 callback=split_commas,
446 default=None,
447 metavar="COLLECTION",
448 multiple=True,
449 help="Names of input dataset types that should not be mocked.",
450)
453def parse_mock_failure(
454 ctx: click.Context, param: click.Option, value: Iterable[str] | None
455) -> Mapping[str, tuple[str, type[Exception] | None]]:
456 """Parse the --mock-failure option values into the mapping accepted by
457 `lsst.pipe.base.tests.mocks.mock_task_defs`.
458 """
459 result: dict[str, tuple[str, type[Exception] | None]] = {}
460 if value is None:
461 return result
462 for entry in value:
463 try:
464 task_label, error_type_name, where = entry.split(":", 2)
465 except ValueError:
466 raise click.UsageError(
467 f"Invalid value for --mock-failure option: {entry!r}; "
468 "expected a string of the form 'task:error:where'."
469 ) from None
470 error_type = doImportType(error_type_name) if error_type_name else None
471 result[task_label] = (where, error_type)
472 return result
475mock_failure_option = MWOptionDecorator(
476 "--mock-failure",
477 callback=parse_mock_failure,
478 metavar="LABEL:EXCEPTION:WHERE",
479 default=None,
480 multiple=True,
481 help=unwrap(
482 """Specifications for tasks that should be configured to fail
483 when mocking execution. This is a colon-separated 3-tuple, where the
484 first entry the task label, the second the fully-qualified exception
485 type (empty for ValueError, and the third a string (which typically
486 needs to be quoted to be passed as one argument value by the shell) of
487 the form passed to --where, indicating which data IDs should fail."""
488 ),
489)
492clobber_execution_butler_option = MWOptionDecorator(
493 "--clobber-execution-butler",
494 help=unwrap(
495 """When creating execution butler overwrite
496 any existing products"""
497 ),
498 is_flag=True,
499)
501target_datastore_root_option = MWOptionDecorator(
502 "--target-datastore-root",
503 help=unwrap(
504 """Root directory for datastore of execution butler.
505 Default is to use the original datastore.
506 """
507 ),
508)
510dataset_query_constraint = MWOptionDecorator(
511 "--dataset-query-constraint",
512 help=unwrap(
513 """When constructing a quantum graph constrain by
514 pre-existence of specified dataset types. Valid
515 values are `all` for all inputs dataset types in
516 pipeline, ``off`` to not consider dataset type
517 existence as a constraint, single or comma
518 separated list of dataset type names."""
519 ),
520 default="all",
521)
523summary_option = MWOptionDecorator(
524 "--summary",
525 help=(
526 "Location for storing job summary (JSON file). Note that the"
527 " structure of this file may not be stable."
528 ),
529 type=MWPath(dir_okay=False, file_okay=True, writable=True),
530)
533recursive_option = MWOptionDecorator(
534 "--recursive",
535 is_flag=True,
536)
538config_search_path_option = MWOptionDecorator(
539 "--config-search-path",
540 callback=split_commas,
541 default=[],
542 help="Additional search paths for butler configuration.",
543 metavar="PATH",
544 multiple=True,
545)
547update_graph_id_option = MWOptionDecorator(
548 "--update-graph-id",
549 help=unwrap("Update graph ID with new unique value."),
550 is_flag=True,
551)
553metadata_run_key_option = MWOptionDecorator(
554 "--metadata-run-key",
555 help=(
556 "Quantum graph metadata key for the name of the output run. "
557 "Empty string disables update of the metadata. "
558 "Default value: output_run."
559 ),
560 default="output_run",
561)