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 2023-08-25 09:44 +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)
110no_versions_option = MWOptionDecorator(
111 "--no-versions", help="Do not save or check package versions.", is_flag=True
112)
115order_pipeline_option = MWOptionDecorator(
116 "--order-pipeline",
117 help=unwrap(
118 """Order tasks in pipeline based on their data
119 dependencies, ordering is performed as last step before saving or
120 executing pipeline."""
121 ),
122 is_flag=True,
123)
126output_option = MWOptionDecorator(
127 "-o",
128 "--output",
129 help=unwrap(
130 """Name of the output CHAINED collection. This may either be an
131 existing CHAINED collection to use as both input and output
132 (incompatible with --input), or a new CHAINED collection created
133 to include all inputs (requires --input). In both cases, the
134 collection's children will start with an output RUN collection
135 that directly holds all new datasets (see --output-run)."""
136 ),
137 metavar="COLL",
138)
141output_run_option = MWOptionDecorator(
142 "--output-run",
143 help=unwrap(
144 """Name of the new output RUN collection. If not provided
145 then --output must be provided and a new RUN collection will
146 be created by appending a timestamp to the value passed with
147 --output. If this collection already exists then
148 --extend-run must be passed."""
149 ),
150 metavar="COLL",
151)
154pipeline_option = MWOptionDecorator(
155 "-p",
156 "--pipeline",
157 help="Location of a pipeline definition file in YAML format.",
158 type=MWPath(file_okay=True, dir_okay=False, readable=True),
159)
162pipeline_dot_option = MWOptionDecorator(
163 "--pipeline-dot",
164 help="Location for storing GraphViz DOT representation of a pipeline.",
165 type=MWPath(writable=True, file_okay=True, dir_okay=False),
166)
169profile_option = MWOptionDecorator(
170 "--profile", help="Dump cProfile statistics to file name.", type=MWPath(file_okay=True, dir_okay=False)
171)
174prune_replaced_option = MWOptionDecorator(
175 "--prune-replaced",
176 help=unwrap(
177 """Delete the datasets in the collection replaced by
178 --replace-run, either just from the datastore
179 ('unstore') or by removing them and the RUN completely
180 ('purge'). Requires --replace-run."""
181 ),
182 type=click.Choice(choices=("unstore", "purge"), case_sensitive=False),
183)
186qgraph_option = MWOptionDecorator(
187 "-g",
188 "--qgraph",
189 help=unwrap(
190 """Location for a serialized quantum graph definition (pickle
191 file). If this option is given then all input data options and
192 pipeline-building options cannot be used. Can be a URI."""
193 ),
194)
197qgraph_id_option = MWOptionDecorator(
198 "--qgraph-id",
199 help=unwrap(
200 """Quantum graph identifier, if specified must match the
201 identifier of the graph loaded from a file. Ignored if graph
202 is not loaded from a file."""
203 ),
204)
207qgraph_datastore_records_option = MWOptionDecorator(
208 "--qgraph-datastore-records",
209 help=unwrap(
210 """Include datastore records into generated quantum graph, these records are used by a
211 quantum-backed butler.
212 """
213 ),
214 is_flag=True,
215)
218# I wanted to use default=None here to match Python API but click silently
219# replaces None with an empty tuple when multiple=True.
220qgraph_node_id_option = MWOptionDecorator(
221 "--qgraph-node-id",
222 callback=split_commas,
223 multiple=True,
224 help=unwrap(
225 """Only load a specified set of nodes when graph is
226 loaded from a file, nodes are identified by UUID
227 values. One or more comma-separated integers are
228 accepted. By default all nodes are loaded. Ignored if
229 graph is not loaded from a file."""
230 ),
231)
233qgraph_header_data_option = MWOptionDecorator(
234 "--show-qgraph-header",
235 is_flag=True,
236 default=False,
237 help="Print the headerData for Quantum Graph to the console",
238)
240qgraph_dot_option = MWOptionDecorator(
241 "--qgraph-dot",
242 help="Location for storing GraphViz DOT representation of a quantum graph.",
243 type=MWPath(writable=True, file_okay=True, dir_okay=False),
244)
247replace_run_option = MWOptionDecorator(
248 "--replace-run",
249 help=unwrap(
250 """Before creating a new RUN collection in an existing
251 CHAINED collection, remove the first child collection
252 (which must be of type RUN). This can be used to repeatedly
253 write to the same (parent) collection during development,
254 but it does not delete the datasets associated with the
255 replaced run unless --prune-replaced is also passed.
256 Requires --output, and incompatible with --extend-run."""
257 ),
258 is_flag=True,
259)
262save_pipeline_option = MWOptionDecorator(
263 "-s",
264 "--save-pipeline",
265 help="Location for storing resulting pipeline definition in YAML format.",
266 type=MWPath(dir_okay=False, file_okay=True, writable=True),
267)
269save_qgraph_option = MWOptionDecorator(
270 "-q",
271 "--save-qgraph",
272 help="URI location for storing a serialized quantum graph definition (pickle file).",
273)
276save_single_quanta_option = MWOptionDecorator(
277 "--save-single-quanta",
278 help=unwrap(
279 """Format string of locations for storing individual
280 quantum graph definition (pickle files). The curly
281 brace {} in the input string will be replaced by a
282 quantum number. Can be a URI."""
283 ),
284)
287show_option = MWOptionDecorator(
288 "--show",
289 callback=split_commas,
290 help=unwrap(
291 """Dump various info to standard output. Possible items are:
292 ``config``, ``config=[Task::]<PATTERN>`` or
293 ``config=[Task::]<PATTERN>:NOIGNORECASE`` to dump configuration
294 fields possibly matching given pattern and/or task label;
295 ``history=<FIELD>`` to dump configuration history for a field,
296 field name is specified as ``[Task::]<PATTERN>``; ``dump-config``,
297 ``dump-config=Task`` to dump complete configuration for a task
298 given its label or all tasks; ``pipeline`` to show pipeline
299 composition; ``graph`` to show information about quanta;
300 ``workflow`` to show information about quanta and their
301 dependency; ``tasks`` to show task composition; ``uri`` to show
302 predicted dataset URIs of quanta."""
303 ),
304 metavar="ITEM|ITEM=VALUE",
305 multiple=True,
306)
309skip_existing_in_option = MWOptionDecorator(
310 "--skip-existing-in",
311 callback=split_commas,
312 default=None,
313 metavar="COLLECTION",
314 multiple=True,
315 help=unwrap(
316 """If all Quantum outputs already exist in the specified list of
317 collections then that Quantum will be excluded from the QuantumGraph.
318 """
319 ),
320)
323skip_existing_option = MWOptionDecorator(
324 "--skip-existing",
325 is_flag=True,
326 help=unwrap(
327 """This option is equivalent to --skip-existing-in with the name of
328 the output RUN collection. If both --skip-existing-in and
329 --skip-existing are given then output RUN collection is appended to
330 the list of collections."""
331 ),
332)
335clobber_outputs_option = MWOptionDecorator(
336 "--clobber-outputs",
337 help=(
338 "Remove outputs of failed quanta from the output run when they would block the execution of new "
339 "quanta with the same data ID (or assume that this will be done, if just building a QuantumGraph). "
340 "Does nothing if --extend-run is not passed."
341 ),
342 is_flag=True,
343)
346skip_init_writes_option = MWOptionDecorator(
347 "--skip-init-writes",
348 help=unwrap(
349 """Do not write collection-wide 'init output' datasets
350 (e.g.schemas)."""
351 ),
352 is_flag=True,
353)
356enable_implicit_threading_option = MWOptionDecorator(
357 "--enable-implicit-threading",
358 help=unwrap(
359 """Do not disable implicit threading use by third-party libraries (e.g. OpenBLAS).
360 Implicit threading is always disabled during execution with multiprocessing."""
361 ),
362 is_flag=True,
363)
365cores_per_quantum_option = MWOptionDecorator(
366 "-n",
367 "--cores-per-quantum",
368 default=1,
369 help=unwrap(
370 """Number of cores available to each quantum when executing.
371 If '-j' is used each subprocess will be allowed to use this number of cores."""
372 ),
373 type=click.IntRange(min=1),
374)
376memory_per_quantum_option = MWOptionDecorator(
377 "--memory-per-quantum",
378 default="",
379 help=unwrap(
380 """Memory allocated for each quantum to use when executing.
381 This memory allocation is not enforced by the execution system and is purely advisory.
382 If '-j' used each subprocess will be allowed to use this amount of memory.
383 Units are allowed and the default units for a plain integer are MB.
384 For example: '3GB', '3000MB' and '3000' would all result in the same
385 memory limit. Default is for no limit."""
386 ),
387 type=str,
388)
390task_option = MWOptionDecorator(
391 "-t",
392 "--task",
393 callback=split_commas,
394 help=unwrap(
395 """Task name to add to pipeline, must be a fully qualified task
396 name. Task name can be followed by colon and label name, if label
397 is not given then task base name (class name) is used as
398 label."""
399 ),
400 metavar="TASK[:LABEL]",
401 multiple=True,
402)
405timeout_option = MWOptionDecorator(
406 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)."
407)
410start_method_option = MWOptionDecorator(
411 "--start-method",
412 default=None,
413 type=click.Choice(choices=["spawn", "fork", "forkserver"]),
414 help="Multiprocessing start method, default is platform-specific.",
415)
418fail_fast_option = MWOptionDecorator(
419 "--fail-fast",
420 help="Stop processing at first error, default is to process as many tasks as possible.",
421 is_flag=True,
422)
424save_execution_butler_option = MWOptionDecorator(
425 "--save-execution-butler",
426 help="Export location for an execution-specific butler after making QuantumGraph",
427)
429mock_option = MWOptionDecorator(
430 "--mock",
431 help="Mock pipeline execution.",
432 is_flag=True,
433)
435unmocked_dataset_types_option = MWOptionDecorator(
436 "--unmocked-dataset-types",
437 callback=split_commas,
438 default=None,
439 metavar="COLLECTION",
440 multiple=True,
441 help="Names of input dataset types that should not be mocked.",
442)
445def parse_mock_failure(
446 ctx: click.Context, param: click.Option, value: Iterable[str] | None
447) -> Mapping[str, tuple[str, type[Exception] | None]]:
448 """Parse the --mock-failure option values into the mapping accepted by
449 `lsst.pipe.base.tests.mocks.mock_task_defs`.
450 """
451 result: dict[str, tuple[str, type[Exception] | None]] = {}
452 if value is None:
453 return result
454 for entry in value:
455 try:
456 task_label, error_type_name, where = entry.split(":", 2)
457 except ValueError:
458 raise click.UsageError(
459 f"Invalid value for --mock-failure option: {entry!r}; "
460 "expected a string of the form 'task:error:where'."
461 ) from None
462 error_type = doImportType(error_type_name) if error_type_name else None
463 result[task_label] = (where, error_type)
464 return result
467mock_failure_option = MWOptionDecorator(
468 "--mock-failure",
469 callback=parse_mock_failure,
470 metavar="LABEL:EXCEPTION:WHERE",
471 default=None,
472 multiple=True,
473 help=unwrap(
474 """Specifications for tasks that should be configured to fail
475 when mocking execution. This is a colon-separated 3-tuple, where the
476 first entry the task label, the second the fully-qualified exception
477 type (empty for ValueError, and the third a string (which typically
478 needs to be quoted to be passed as one argument value by the shell) of
479 the form passed to --where, indicating which data IDs should fail."""
480 ),
481)
484clobber_execution_butler_option = MWOptionDecorator(
485 "--clobber-execution-butler",
486 help=unwrap(
487 """When creating execution butler overwrite
488 any existing products"""
489 ),
490 is_flag=True,
491)
493target_datastore_root_option = MWOptionDecorator(
494 "--target-datastore-root",
495 help=unwrap(
496 """Root directory for datastore of execution butler.
497 Default is to use the original datastore.
498 """
499 ),
500)
502dataset_query_constraint = MWOptionDecorator(
503 "--dataset-query-constraint",
504 help=unwrap(
505 """When constructing a quantum graph constrain by
506 pre-existence of specified dataset types. Valid
507 values are `all` for all inputs dataset types in
508 pipeline, ``off`` to not consider dataset type
509 existence as a constraint, single or comma
510 separated list of dataset type names."""
511 ),
512 default="all",
513)
515summary_option = MWOptionDecorator(
516 "--summary",
517 help=(
518 "Location for storing job summary (JSON file). Note that the"
519 " structure of this file may not be stable."
520 ),
521 type=MWPath(dir_okay=False, file_okay=True, writable=True),
522)
525recursive_option = MWOptionDecorator(
526 "--recursive",
527 is_flag=True,
528)
530config_search_path_option = MWOptionDecorator(
531 "--config-search-path",
532 callback=split_commas,
533 default=[],
534 help="Additional search paths for butler configuration.",
535 metavar="PATH",
536 multiple=True,
537)
539update_graph_id_option = MWOptionDecorator(
540 "--update-graph-id",
541 help=unwrap("Update graph ID with new unique value."),
542 is_flag=True,
543)
545metadata_run_key_option = MWOptionDecorator(
546 "--metadata-run-key",
547 help=(
548 "Quantum graph metadata key for the name of the output run. "
549 "Empty string disables update of the metadata. "
550 "Default value: output_run."
551 ),
552 default="output_run",
553)