From 0c1673bcd87e0200a62aceb9a7d00d4ce2d01a40 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Sun, 7 Jun 2020 16:08:54 +0100
Subject: [PATCH] DOC: added much more detailed documentation to SubmitParams
---
fsl/utils/fslsub.py | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/fsl/utils/fslsub.py b/fsl/utils/fslsub.py
index e5fe94313..27b455f40 100644
--- a/fsl/utils/fslsub.py
+++ b/fsl/utils/fslsub.py
@@ -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")
+ parser.add_argument("input_file")
+ parser.add_argument("output_file")
+ 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
+ wrappers.bet(input_file, 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):
@classmethod
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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