Commit 0c1673bc authored by Michiel Cottaar's avatar Michiel Cottaar
Browse files

DOC: added much more detailed documentation to SubmitParams

parent 0ba5b9ea
......@@ -62,6 +62,38 @@ log = logging.getLogger(__name__)
class SubmitParams(object):
Represents the fsl_sub parameters
Any command line script can be submitted by the parameters by calling the `SubmitParams` object:
.. codeblock:: python
submit = SubmitParams(minutes=1, logdir='log', wait_for=['108023', '108019'])
submit('echo finished')
This will run "echo finished" with a maximum runtime of 1 minute after the jobs with IDs 108023 and 108019 are finished.
It is the equivalent of
.. codeblock:: bash
fsl_sub -T 1 -l log -j 108023,108019 "echo finished"
For python scripts that submit themselves to the cluster, it might be useful to give the user some control
over at least some of the submission parameters. This can be done using:
.. codeblock:: python
import argparse
parser = argparse.ArgumentParser("my script doing awesome stuff")
SubmitParams.add_to_parser(parser, include=('wait_for', 'logdir'))
args = parser.parse_args()
submitter = SubmitParams.from_args(args).update(minutes=10)
from fsl import wrappers, output_file, fslsub=submitter)
This submits a BET job using the -j and -l flags set by the user and a maximum time of 10 minutes.
minutes: Optional[float] = None
queue: Optional[str] = None
......@@ -91,6 +123,9 @@ class SubmitParams(object):
def __post_init__(self):
If not set explicitly by the user don't alter the environment in which the script will be submitted
if self.env is None:
self.env = {}
......@@ -205,6 +240,9 @@ class SubmitParams(object):
def from_args(cls, args):
Create a SubmitParams from the command line arguments
as_dict = {value: getattr(args, '_sub_' + value, None) for value in cls.cmd_line_flags.values()}
if args._sub_wait_for is not None:
as_dict['wait_for'] = args._sub_wait_for.split(',')
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