Coverage for python/lsst/ctrl/mpexec/cli/cmd/commands.py: 58%

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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# (http://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 

22import sys 

23from collections.abc import Iterator 

24from contextlib import contextmanager 

25from functools import partial 

26from tempfile import NamedTemporaryFile 

27from typing import Any 

28 

29import click 

30import coverage 

31import lsst.pipe.base.cli.opt as pipeBaseOpts 

32from lsst.ctrl.mpexec.showInfo import ShowInfo 

33from lsst.daf.butler.cli.opt import ( 

34 config_file_option, 

35 config_option, 

36 confirm_option, 

37 options_file_option, 

38 processes_option, 

39 repo_argument, 

40) 

41from lsst.daf.butler.cli.utils import MWCtxObj, catch_and_exit, option_section, unwrap 

42 

43from .. import opt as ctrlMpExecOpts 

44from .. import script 

45from ..script import confirmable 

46from ..utils import PipetaskCommand, makePipelineActions 

47 

48epilog = unwrap( 

49 """Notes: 

50 

51--task, --delete, --config, --config-file, and --instrument action options can 

52appear multiple times; all values are used, in order left to right. 

53 

54FILE reads command-line options from the specified file. Data may be 

55distributed among multiple lines (e.g. one option per line). Data after # is 

56treated as a comment and ignored. Blank lines and lines starting with # are 

57ignored.) 

58""" 

59) 

60 

61 

62def _collectActions(ctx: click.Context, **kwargs: Any) -> dict[str, Any]: 

63 """Extract pipeline building options, replace them with PipelineActions, 

64 return updated `kwargs`. 

65 

66 Notes 

67 ----- 

68 The pipeline actions (task, delete, config, config_file, and instrument) 

69 must be handled in the order they appear on the command line, but the CLI 

70 specification gives them all different option names. So, instead of using 

71 the individual action options as they appear in kwargs (because 

72 invocation order can't be known), we capture the CLI arguments by 

73 overriding `click.Command.parse_args` and save them in the Context's 

74 `obj` parameter. We use `makePipelineActions` to create a list of 

75 pipeline actions from the CLI arguments and pass that list to the script 

76 function using the `pipeline_actions` kwarg name, and remove the action 

77 options from kwargs. 

78 """ 

79 for pipelineAction in ( 

80 ctrlMpExecOpts.task_option.name(), 

81 ctrlMpExecOpts.delete_option.name(), 

82 config_option.name(), 

83 config_file_option.name(), 

84 pipeBaseOpts.instrument_option.name(), 

85 ): 

86 kwargs.pop(pipelineAction) 

87 

88 actions = makePipelineActions(MWCtxObj.getFrom(ctx).args) 

89 pipeline_actions = [] 

90 for action in actions: 

91 pipeline_actions.append(action) 

92 

93 kwargs["pipeline_actions"] = pipeline_actions 

94 return kwargs 

95 

96 

97def _unhandledShow(show: ShowInfo, cmd: str) -> None: 

98 if show.unhandled: 98 ↛ 99line 98 didn't jump to line 99, because the condition on line 98 was never true

99 print( 

100 f"The following '--show' options were not known to the {cmd} command: " 

101 f"{', '.join(show.unhandled)}", 

102 file=sys.stderr, 

103 ) 

104 

105 

106@click.command(cls=PipetaskCommand, epilog=epilog, short_help="Build pipeline definition.") 

107@click.pass_context 

108@ctrlMpExecOpts.show_option() 

109@ctrlMpExecOpts.pipeline_build_options() 

110@option_section(sectionText="") 

111@options_file_option() 

112@catch_and_exit 

113def build(ctx: click.Context, **kwargs: Any) -> None: 

114 """Build and optionally save pipeline definition. 

115 

116 This does not require input data to be specified. 

117 """ 

118 kwargs = _collectActions(ctx, **kwargs) 

119 show = ShowInfo(kwargs.pop("show", [])) 

120 script.build(**kwargs, show=show) 

121 _unhandledShow(show, "build") 

122 

123 

124@contextmanager 

125def coverage_context(kwargs: dict[str, Any]) -> Iterator[None]: 

126 packages = kwargs.pop("cov_packages", ()) 

127 report = kwargs.pop("cov_report", True) 

128 if not kwargs.pop("coverage", False): 

129 yield 

130 return 

131 with NamedTemporaryFile("w") as rcfile: 

132 rcfile.write( 

133 """ 

134[run] 

135branch = True 

136concurrency = multiprocessing 

137""" 

138 ) 

139 if packages: 

140 packages_str = ",".join(packages) 

141 rcfile.write(f"source_pkgs = {packages_str}\n") 

142 rcfile.flush() 

143 cov = coverage.Coverage(config_file=rcfile.name) 

144 cov.start() 

145 try: 

146 yield 

147 finally: 

148 cov.stop() 

149 cov.save() 

150 if report: 

151 outdir = "./covhtml" 

152 cov.html_report(directory=outdir) 

153 click.echo(f"Coverage report written to {outdir}.") 

154 

155 

156@click.command(cls=PipetaskCommand, epilog=epilog) 

157@click.pass_context 

158@ctrlMpExecOpts.show_option() 

159@ctrlMpExecOpts.pipeline_build_options() 

160@ctrlMpExecOpts.qgraph_options() 

161@ctrlMpExecOpts.butler_options() 

162@option_section(sectionText="") 

163@options_file_option() 

164@catch_and_exit 

165def qgraph(ctx: click.Context, **kwargs: Any) -> None: 

166 """Build and optionally save quantum graph.""" 

167 kwargs = _collectActions(ctx, **kwargs) 

168 with coverage_context(kwargs): 

169 show = ShowInfo(kwargs.pop("show", [])) 

170 pipeline = script.build(**kwargs, show=show) 

171 if show.handled and not show.unhandled: 

172 print( 

173 "No quantum graph generated. The --show option was given and all options were processed.", 

174 file=sys.stderr, 

175 ) 

176 return 

177 if script.qgraph(pipelineObj=pipeline, **kwargs, show=show) is None: 

178 raise click.ClickException("QuantumGraph was empty; CRITICAL logs above should provide details.") 

179 _unhandledShow(show, "qgraph") 

180 

181 

182@click.command(cls=PipetaskCommand, epilog=epilog) 

183@ctrlMpExecOpts.run_options() 

184@catch_and_exit 

185def run(ctx: click.Context, **kwargs: Any) -> None: 

186 """Build and execute pipeline and quantum graph.""" 

187 kwargs = _collectActions(ctx, **kwargs) 

188 with coverage_context(kwargs): 

189 show = ShowInfo(kwargs.pop("show", [])) 

190 pipeline = script.build(**kwargs, show=show) 

191 if show.handled and not show.unhandled: 

192 print( 

193 "No quantum graph generated or pipeline executed. " 

194 "The --show option was given and all options were processed.", 

195 file=sys.stderr, 

196 ) 

197 return 

198 if (qgraph := script.qgraph(pipelineObj=pipeline, **kwargs, show=show)) is None: 

199 raise click.ClickException("QuantumGraph was empty; CRITICAL logs above should provide details.") 

200 _unhandledShow(show, "run") 

201 if show.handled: 

202 print( 

203 "No pipeline executed. The --show option was given and all options were processed.", 

204 file=sys.stderr, 

205 ) 

206 return 

207 script.run(qgraphObj=qgraph, **kwargs) 

208 

209 

210@click.command(cls=PipetaskCommand) 

211@ctrlMpExecOpts.butler_config_option() 

212@ctrlMpExecOpts.collection_argument() 

213@confirm_option() 

214@ctrlMpExecOpts.recursive_option( 

215 help="""If the parent CHAINED collection has child CHAINED collections, 

216 search the children until nested chains that start with the parent's name 

217 are removed.""" 

218) 

219def purge(confirm: bool, **kwargs: Any) -> None: 

220 """Remove a CHAINED collection and its contained collections. 

221 

222 COLLECTION is the name of the chained collection to purge. it must not be a 

223 child of any other CHAINED collections 

224 

225 Child collections must be members of exactly one collection. 

226 

227 The collections that will be removed will be printed, there will be an 

228 option to continue or abort (unless using --no-confirm). 

229 """ 

230 confirmable.confirm(partial(script.purge, **kwargs), confirm) 

231 

232 

233@click.command(cls=PipetaskCommand) 

234@ctrlMpExecOpts.butler_config_option() 

235@ctrlMpExecOpts.collection_argument() 

236@confirm_option() 

237def cleanup(confirm: bool, **kwargs: Any) -> None: 

238 """Remove non-members of CHAINED collections. 

239 

240 Removes collections that start with the same name as a CHAINED 

241 collection but are not members of that collection. 

242 """ 

243 confirmable.confirm(partial(script.cleanup, **kwargs), confirm) 

244 

245 

246@click.command(cls=PipetaskCommand) 

247@repo_argument() 

248@ctrlMpExecOpts.qgraph_argument() 

249@ctrlMpExecOpts.config_search_path_option() 

250@ctrlMpExecOpts.qgraph_id_option() 

251@ctrlMpExecOpts.coverage_options() 

252def pre_exec_init_qbb(repo: str, qgraph: str, **kwargs: Any) -> None: 

253 """Execute pre-exec-init on Quantum-Backed Butler. 

254 

255 REPO is the location of the butler/registry config file. 

256 

257 QGRAPH is the path to a serialized Quantum Graph file. 

258 """ 

259 with coverage_context(kwargs): 

260 script.pre_exec_init_qbb(repo, qgraph, **kwargs) 

261 

262 

263@click.command(cls=PipetaskCommand) 

264@repo_argument() 

265@ctrlMpExecOpts.qgraph_argument() 

266@ctrlMpExecOpts.config_search_path_option() 

267@ctrlMpExecOpts.qgraph_id_option() 

268@ctrlMpExecOpts.qgraph_node_id_option() 

269@processes_option() 

270@ctrlMpExecOpts.pdb_option() 

271@ctrlMpExecOpts.profile_option() 

272@ctrlMpExecOpts.coverage_options() 

273@ctrlMpExecOpts.debug_option() 

274@ctrlMpExecOpts.start_method_option() 

275@ctrlMpExecOpts.timeout_option() 

276@ctrlMpExecOpts.fail_fast_option() 

277@ctrlMpExecOpts.summary_option() 

278@ctrlMpExecOpts.enable_implicit_threading_option() 

279def run_qbb(repo: str, qgraph: str, **kwargs: Any) -> None: 

280 """Execute pipeline using Quantum-Backed Butler. 

281 

282 REPO is the location of the butler/registry config file. 

283 

284 QGRAPH is the path to a serialized Quantum Graph file. 

285 """ 

286 with coverage_context(kwargs): 

287 script.run_qbb(repo, qgraph, **kwargs) 

288 

289 

290@click.command(cls=PipetaskCommand) 

291@ctrlMpExecOpts.qgraph_argument() 

292@ctrlMpExecOpts.run_argument() 

293@ctrlMpExecOpts.output_qgraph_argument() 

294@ctrlMpExecOpts.metadata_run_key_option() 

295@ctrlMpExecOpts.update_graph_id_option() 

296def update_graph_run( 

297 qgraph: str, 

298 run: str, 

299 output_qgraph: str, 

300 metadata_run_key: str, 

301 update_graph_id: bool, 

302) -> None: 

303 """Update existing quantum graph with new output run name and re-generate 

304 output dataset IDs. 

305 

306 QGRAPH is the URL to a serialized Quantum Graph file. 

307 

308 RUN is the new RUN collection name for output graph. 

309 

310 OUTPUT_QGRAPH is the URL to store the updated Quantum Graph. 

311 """ 

312 script.update_graph_run(qgraph, run, output_qgraph, metadata_run_key, update_graph_id)