Coverage for python/lsst/ctrl/mpexec/cli/opt/options.py: 79%

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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/>. 

21 

22from __future__ import annotations 

23 

24from collections.abc import Iterable, Mapping 

25 

26import click 

27from lsst.daf.butler.cli.utils import MWOptionDecorator, MWPath, split_commas, unwrap 

28from lsst.utils.doImport import doImportType 

29 

30butler_config_option = MWOptionDecorator( 

31 "-b", "--butler-config", help="Location of the gen3 butler/registry config file." 

32) 

33 

34 

35data_query_option = MWOptionDecorator( 

36 "-d", "--data-query", help="User data selection expression.", metavar="QUERY" 

37) 

38 

39 

40debug_option = MWOptionDecorator( 

41 "--debug", help="Enable debugging output using lsstDebug facility (imports debug.py).", is_flag=True 

42) 

43 

44coverage_option = MWOptionDecorator("--coverage", help="Enable coverage output.", is_flag=True) 

45 

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) 

51 

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) 

60 

61delete_option = MWOptionDecorator( 

62 "--delete", callback=split_commas, help="Delete task with given label from pipeline.", multiple=True 

63) 

64 

65 

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) 

73 

74 

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) 

85 

86 

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) 

94 

95 

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) 

104 

105 

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) 

115 

116no_versions_option = MWOptionDecorator( 

117 "--no-versions", help="Do not save or check package versions.", is_flag=True 

118) 

119 

120 

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) 

130 

131 

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) 

145 

146 

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) 

158 

159 

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) 

166 

167 

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) 

176 

177 

178profile_option = MWOptionDecorator( 

179 "--profile", help="Dump cProfile statistics to file name.", type=MWPath(file_okay=True, dir_okay=False) 

180) 

181 

182 

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) 

193 

194 

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) 

204 

205 

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) 

214 

215 

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) 

225 

226 

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) 

241 

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) 

251 

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) 

260 

261 

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) 

275 

276 

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) 

286 

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) 

295 

296 

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) 

306 

307 

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) 

328 

329 

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) 

342 

343 

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) 

354 

355 

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) 

365 

366 

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) 

375 

376 

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) 

385 

386 

387task_option = MWOptionDecorator( 

388 "-t", 

389 "--task", 

390 callback=split_commas, 

391 help=unwrap( 

392 """Task name to add to pipeline, must be a fully qualified task 

393 name. Task name can be followed by colon and label name, if label 

394 is not given then task base name (class name) is used as 

395 label.""" 

396 ), 

397 metavar="TASK[:LABEL]", 

398 multiple=True, 

399) 

400 

401 

402timeout_option = MWOptionDecorator( 

403 "--timeout", type=click.IntRange(min=0), help="Timeout for multiprocessing; maximum wall time (sec)." 

404) 

405 

406 

407start_method_option = MWOptionDecorator( 

408 "--start-method", 

409 default=None, 

410 type=click.Choice(choices=["spawn", "fork", "forkserver"]), 

411 help="Multiprocessing start method, default is platform-specific.", 

412) 

413 

414 

415fail_fast_option = MWOptionDecorator( 

416 "--fail-fast", 

417 help=unwrap( 

418 """Stop processing at first error, default is to process 

419 as many tasks as possible.""" 

420 ), 

421 is_flag=True, 

422) 

423 

424save_execution_butler_option = MWOptionDecorator( 

425 "--save-execution-butler", 

426 help=unwrap( 

427 """Export location for an 

428 execution-specific butler after making 

429 QuantumGraph""" 

430 ), 

431) 

432 

433mock_option = MWOptionDecorator( 

434 "--mock", 

435 help=unwrap("""Mock pipeline execution."""), 

436 is_flag=True, 

437) 

438 

439unmocked_dataset_types_option = MWOptionDecorator( 

440 "--unmocked-dataset-types", 

441 callback=split_commas, 

442 default=None, 

443 metavar="COLLECTION", 

444 multiple=True, 

445 help=unwrap("""Names of input dataset types that should not be mocked."""), 

446) 

447 

448 

449def parse_mock_failure( 

450 ctx: click.Context, param: click.Option, value: Iterable[str] | None 

451) -> Mapping[str, tuple[str, type[Exception] | None]]: 

452 """Parse the --mock-failure option values into the mapping accepted by 

453 `lsst.pipe.base.tests.mocks.mock_task_defs`. 

454 """ 

455 result: dict[str, tuple[str, type[Exception] | None]] = {} 

456 if value is None: 

457 return result 

458 for entry in value: 

459 try: 

460 task_label, error_type_name, where = entry.split(":", 2) 

461 except ValueError: 

462 raise click.UsageError( 

463 f"Invalid value for --mock-failure option: {entry!r}; " 

464 "expected a string of the form 'task:error:where'." 

465 ) from None 

466 error_type = doImportType(error_type_name) if error_type_name else None 

467 result[task_label] = (where, error_type) 

468 return result 

469 

470 

471mock_failure_option = MWOptionDecorator( 

472 "--mock-failure", 

473 callback=parse_mock_failure, 

474 metavar="LABEL:EXCEPTION:WHERE", 

475 default=None, 

476 multiple=True, 

477 help=unwrap( 

478 """Specifications for tasks that should be configured to fail 

479 when mocking execution. This is a colon-separated 3-tuple, where the 

480 first entry the task label, the second the fully-qualified exception 

481 type (empty for ValueError, and the third a string (which typically 

482 needs to be quoted to be passed as one argument value by the shell) of 

483 the form passed to --where, indicating which data IDs should fail.""" 

484 ), 

485) 

486 

487 

488clobber_execution_butler_option = MWOptionDecorator( 

489 "--clobber-execution-butler", 

490 help=unwrap( 

491 """When creating execution butler overwrite 

492 any existing products""" 

493 ), 

494 is_flag=True, 

495) 

496 

497target_datastore_root_option = MWOptionDecorator( 

498 "--target-datastore-root", 

499 help=unwrap( 

500 """Root directory for datastore of execution butler. 

501 Default is to use the original datastore. 

502 """ 

503 ), 

504) 

505 

506dataset_query_constraint = MWOptionDecorator( 

507 "--dataset-query-constraint", 

508 help=unwrap( 

509 """When constructing a quantum graph constrain by 

510 pre-existence of specified dataset types. Valid 

511 values are `all` for all inputs dataset types in 

512 pipeline, `off` to not consider dataset type 

513 existance as a constraint, single or comma 

514 separated list of dataset type names""" 

515 ), 

516 default="all", 

517) 

518 

519summary_option = MWOptionDecorator( 

520 "--summary", 

521 help=( 

522 "Location for storing job summary (JSON file). Note that the" 

523 " structure of this file may not be stable." 

524 ), 

525 type=MWPath(dir_okay=False, file_okay=True, writable=True), 

526) 

527 

528 

529recursive_option = MWOptionDecorator( 

530 "--recursive", 

531 is_flag=True, 

532) 

533 

534config_search_path_option = MWOptionDecorator( 

535 "--config-search-path", 

536 callback=split_commas, 

537 default=list(), 

538 help="Additional search paths for butler configuration.", 

539 metavar="PATH", 

540 multiple=True, 

541) 

542 

543update_graph_id_option = MWOptionDecorator( 

544 "--update-graph-id", 

545 help=unwrap("Update graph ID with new unique value."), 

546 is_flag=True, 

547) 

548 

549metadata_run_key_option = MWOptionDecorator( 

550 "--metadata-run-key", 

551 help=( 

552 "Quantum graph metadata key for the name of the output run. " 

553 "Empty string disables update of the metadata. " 

554 "Default value: output_run." 

555 ), 

556 default="output_run", 

557)