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mavis.schedule.pipeline

PROGNAME

PROGNAME = shutil.which('mavis')

SHEBANG

SHEBANG = '#!/bin/bash'

SCHEDULERS_BY_NAME

SCHEDULERS_BY_NAME = {
    sched.NAME: sched for sched in [SlurmScheduler, TorqueScheduler, LocalScheduler, SgeScheduler]

class mavis.schedule.pipeline.Pipeline

mavis.schedule.pipeline.Pipeline.check_status()

Check all jobs for completetion. Report any failures, etc.

def check_status(self, submit=False, resubmit=False, log=DEVNULL):

Args

  • submit (bool): submit any pending jobs
  • resubmit
  • log

mavis.schedule.pipeline.Pipeline.read_build_file()

read the configuration file which stored the build information concerning jobs and dependencies

@classmethod
def read_build_file(cls, filepath):

Args

  • filepath (str): path to the input config file

mavis.schedule.pipeline.Pipeline.write_build_file()

write the build.cfg file for the current pipeline. This is the file used in re-loading the pipeline to check the status and report failures, etc. later.

def write_build_file(self, filename):

Args

  • filename (str): path to the output config file

mavis.schedule.pipeline.stringify_args_to_command()

takes a list of arguments and prepares them for writing to a bash script

def stringify_args_to_command(args):

Args

  • args

mavis.schedule.pipeline.parse_run_time()

parses the run time listed at the end of a file following mavis conventions

def parse_run_time(filename):

Args

  • filename

mavis.schedule.pipeline.run_conversion()

Converts files if not already converted. Returns a list of filenames

def run_conversion(config, libconf, conversion_dir, assume_no_untemplated=True):

Args

  • config
  • libconf
  • conversion_dir
  • assume_no_untemplated

mavis.schedule.pipeline.validate_args()

Pull arguments from the main config and library specific config to pass to validate

def validate_args(config, libconf):

Args

  • config (MavisConfig): the main program config
  • libconf (LibraryConfig): library specific configuration

mavis.schedule.pipeline.annotate_args()

Pull arguments from the main config and library specific config to pass to annotate

def annotate_args(config, libconf):

Args

  • config (MavisConfig): the main program config
  • libconf (LibraryConfig): library specific configuration

mavis.schedule.pipeline.summary_args()

Pull arguments from the main config and library specific config to pass to summary

def summary_args(config):

Args

  • config (MavisConfig): the main program config

mavis.schedule.pipeline.cluster_args()

Pull arguments from the main config and library specific config to pass to cluster

def cluster_args(config, libconf):

Args

  • config (MavisConfig): the main program config
  • libconf (LibraryConfig): library specific configuration