bilby_pipe fails if options are given before arguments
bilby_pipe
is having a hard time understanding how to parse positional arguments relative to options, and it seems to require that all options are placed after any positional arguments (config file paths), which is directly against what is suggested from the --help
message (which places ini
at the end:
bilby_pipe version
$ bilby_pipe --version
bilby_pipe=0.3.5: (CLEAN) 243200e 2019-12-05 20:03:53 -0800 bilby=0.6.1:
Failure with options before arguments
$ bilby_pipe --prior-file GW150914.prior GW150914.ini
usage: bilby_pipe [-h] [-v] [--version]
[--calibration-model {CubicSpline,None}]
[--spline-calibration-envelope-dict SPLINE_CALIBRATION_ENVELOPE_DICT]
[--spline-calibration-nodes SPLINE_CALIBRATION_NODES]
[--spline-calibration-amplitude-uncertainty-dict SPLINE_CALIBRATION_AMPLITUDE_UNCERTAINTY_DICT]
[--spline-calibration-phase-uncertainty-dict SPLINE_CALIBRATION_PHASE_UNCERTAINTY_DICT]
[--ignore-gwpy-data-quality-check IGNORE_GWPY_DATA_QUALITY_CHECK]
[--gps-file GPS_FILE] [--timeslide-file TIMESLIDE_FILE]
[--trigger-time TRIGGER_TIME] [--gaussian-noise]
[--n-simulation N_SIMULATION] [--data-dict DATA_DICT]
[--data-format DATA_FORMAT] [--channel-dict CHANNEL_DICT]
[--coherence-test] [--detectors DETECTORS]
[--duration DURATION] [--generation-seed GENERATION_SEED]
[--psd-dict PSD_DICT]
[--psd-fractional-overlap PSD_FRACTIONAL_OVERLAP]
[--post-trigger-duration POST_TRIGGER_DURATION]
[--sampling-frequency SAMPLING_FREQUENCY]
[--psd-length PSD_LENGTH]
[--psd-maximum-duration PSD_MAXIMUM_DURATION]
[--psd-method PSD_METHOD] [--psd-start-time PSD_START_TIME]
[--maximum-frequency MAXIMUM_FREQUENCY]
[--minimum-frequency MINIMUM_FREQUENCY]
[--zero-noise ZERO_NOISE] [--tukey-roll-off TUKEY_ROLL_OFF]
[--injection] [--injection-file INJECTION_FILE]
[--injection-waveform-approximant INJECTION_WAVEFORM_APPROXIMANT]
--accounting ACCOUNTING [--label LABEL] [--local]
[--local-generation] [--local-plot] [--outdir OUTDIR]
[--periodic-restart-time PERIODIC_RESTART_TIME]
[--request-memory REQUEST_MEMORY]
[--request-memory-generation REQUEST_MEMORY_GENERATION]
[--request-cpus REQUEST_CPUS]
[--singularity-image SINGULARITY_IMAGE]
[--scheduler SCHEDULER] [--scheduler-args SCHEDULER_ARGS]
[--scheduler-module SCHEDULER_MODULE]
[--scheduler-env SCHEDULER_ENV] [--submit]
[--transfer-files TRANSFER_FILES] [--online-pe] [--osg]
[--distance-marginalization]
[--distance-marginalization-lookup-table DISTANCE_MARGINALIZATION_LOOKUP_TABLE]
[--phase-marginalization] [--time-marginalization]
[--jitter-time JITTER_TIME]
[--likelihood-type LIKELIHOOD_TYPE]
[--roq-folder ROQ_FOLDER]
[--roq-scale-factor ROQ_SCALE_FACTOR] [--create-plots]
[--create-summary] [--email EMAIL]
[--existing-dir EXISTING_DIR] [--webdir WEBDIR]
[--default-prior DEFAULT_PRIOR] [--deltaT DELTAT]
[--prior-file PRIOR_FILE]
[--convert-to-flat-in-component-mass CONVERT_TO_FLAT_IN_COMPONENT_MASS]
[--postprocessing-executable POSTPROCESSING_EXECUTABLE]
[--postprocessing-arguments [POSTPROCESSING_ARGUMENTS [POSTPROCESSING_ARGUMENTS ...]]]
[--sampler SAMPLER] [--sampling-seed SAMPLING_SEED]
[--n-parallel N_PARALLEL] [--sampler-kwargs SAMPLER_KWARGS]
[--reference-frequency REFERENCE_FREQUENCY]
[--waveform-approximant WAVEFORM_APPROXIMANT]
[--frequency-domain-source-model FREQUENCY_DOMAIN_SOURCE_MODEL]
ini
bilby_pipe: error: the following arguments are required: --accounting
Success with arguments before options
$ bilby_pipe GW150914.ini --prior-file GW150914.prior
04:22 bilby_pipe INFO : Running bilby_pipe version: 0.3.5: (CLEAN) 243200e 2019-12-05 20:03:53 -0800
04:22 bilby_pipe INFO : Running bilby: 0.6.1:
04:22 bilby_pipe INFO : Setting segment duration 4.0s
04:22 bilby_pipe INFO : Setting prior-file to GW150914.prior
04:22 bilby_pipe INFO : Setting trigger time 1126259462.4
04:22 bilby_pipe INFO : Setting n_simulation=0
04:22 bilby_pipe INFO : Setting analysis request_memory=4GB
04:22 bilby_pipe INFO : Setting request_memory_generation=8GB
04:22 bilby_pipe INFO : Setting analysis request_cpus = 1
04:22 bilby_pipe INFO : Setting segment trigger-times [1126259462.4]
04:22 bilby_pipe INFO : DAG generation complete, to submit jobs run:
$ condor_submit_dag results_GW150914/submit/dag_GW150914.submit
04:22 bilby_pipe WARNING : File results_GW150914/GW150914_config_complete.ini already exists, not writing to file.