woom run

woom run#

Submit the current workflow.

usage: woom run [-h] [--dry-run] [--force] [--skip TASK [TASK ...]]
                [--log-level {debug,info,warning,error,critical}]
                [--log-no-color]

Named Arguments#

--dry-run, --test

run in fake mode for testing purpose

Default: False

--force, --update

do not run if it has already been run

Default: False

--skip

task names to skip: not submitted but kept in the task treeso their artifacts remain accessible

Default: []

--log-level

Possible choices: debug, info, warning, error, critical

logging level

Default: 'info'

--log-no-color

suppress colors in console

Default: False

Example#

$ woom run --log-no-color
woom.cli    : INFO     No extension to load
woom.cli    : INFO     Loaded workflow config
woom.cli    : INFO     App name: academic_all_stages
woom.cli    : INFO     Initialized the host manager
woom.cli    : INFO     Loaded hosts config file: hosts.cfg
woom.cli    : INFO     Infered host: local
woom.cli    : INFO     Initialized the task manager
woom.cli    : INFO     Loaded the task config file: tasks.cfg
woom.cli    : INFO     Initialized the workflow
woom.cli    : INFO     Successfully setup the workflow!
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog
woom.job    : INFO     Started job manager: BackgroundJobManager()
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask0
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask0/job.sh
woom.workflow: INFO     Submitted task: prolog/prolog0/ptask0 with job id 736
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask1
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask1/job.sh
woom.workflow: INFO     Submitted task: prolog/prolog0/ptask1 with job id 738
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/gtask0
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/gtask0/job.sh
woom.workflow: INFO     Submitted task: prolog/prolog0/gtask0 with job id 740
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/gtask1
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/gtask1/job.sh
woom.workflow: INFO     Submitted task: prolog/prolog0/gtask1 with job id 742 depending on [740]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask2/job.sh
woom.workflow: INFO     Submitted task: prolog/prolog1/ptask2 with job id 744 depending on [736, 738, 742]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/prolog/ptask3/job.sh
woom.workflow: INFO     Submitted task: prolog/prolog1/ptask3 with job id 746 depending on [736, 738, 742]
woom.workflow: INFO     Successfully submitted stage: prolog
woom.workflow: INFO     Cycling on independant dates from 2023-08-01 00:00:00+00:00 to 2023-08-03 00:00:00+00:00 in 3 time(s)
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask0
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask0/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/ctask0 with job id 748 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask1
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask1/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/ctask1 with job id 751 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/gtask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/gtask2/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/gtask2 with job id 753 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/gtask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/gtask3/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/gtask3 with job id 755 depending on [753]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask2/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles1/ctask2 with job id 757 depending on [748, 751, 755]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-01T00:00:00+00:00/ctask3/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles1/ctask3 with job id 759 depending on [748, 751, 755]
woom.workflow: INFO     Successfully submitted cycle: 2023-08-01T00:00:00+00:00
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask0
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask0/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/ctask0 with job id 761 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask1
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask1/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/ctask1 with job id 764 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/gtask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/gtask2/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/gtask2 with job id 766 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/gtask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/gtask3/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/gtask3 with job id 768 depending on [766]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask2/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles1/ctask2 with job id 770 depending on [761, 764, 768]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-02T00:00:00+00:00/ctask3/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles1/ctask3 with job id 772 depending on [761, 764, 768]
woom.workflow: INFO     Successfully submitted cycle: 2023-08-02T00:00:00+00:00
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask0
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask0/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/ctask0 with job id 774 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask1
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask1/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/ctask1 with job id 777 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/gtask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/gtask2/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/gtask2 with job id 779 depending on [744, 746]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/gtask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/gtask3/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles0/gtask3 with job id 781 depending on [779]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask2/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles1/ctask2 with job id 786 depending on [774, 777, 781]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/2023-08-03T00:00:00+00:00/ctask3/job.sh
woom.workflow: INFO     Submitted task: cycles/cycles1/ctask3 with job id 788 depending on [774, 777, 781]
woom.workflow: INFO     Successfully submitted cycle: 2023-08-03T00:00:00+00:00
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask0
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask0/job.sh
woom.workflow: INFO     Submitted task: epilog/epilog0/etask0 with job id 790 depending on [757, 759, 770, 772, 786, 788]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask1
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask1/job.sh
woom.workflow: INFO     Submitted task: epilog/epilog0/etask1 with job id 792 depending on [757, 759, 770, 772, 786, 788]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask2
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask2/job.sh
woom.workflow: INFO     Submitted task: epilog/epilog1/etask2 with job id 794 depending on [790, 792]
woom.workflow: INFO     Created directory: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask3
woom.workflow: INFO     Created batch script: /home/docs/checkouts/readthedocs.org/user_builds/woom/checkouts/latest/examples/academic/all_stages/jobs/academic_all_stages/epilog/etask3/job.sh
woom.workflow: INFO     Submitted task: epilog/epilog1/etask3 with job id 796 depending on [790, 792]
woom.workflow: INFO     Successfully submitted stage: epilog
woom.cli    : INFO     Successfully ran the workflow!