Commit 8d948830 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

RF,ENH: run(submit) args can be passed as a dict or as kwargs. submit accepts

env option
parent 6d59ac9e
......@@ -68,7 +68,8 @@ def submit(*command,
output=None,
flags=False,
multi_threaded=None,
verbose=False):
verbose=False,
env=None):
"""
Submits a given command to the cluster
......@@ -99,6 +100,7 @@ def submit(*command,
- <threads>: number of threads to run
:arg verbose: If True, use verbose mode
:arg env: Dict containing environment variables
:return: string of submitted job id
"""
......@@ -136,7 +138,7 @@ def submit(*command,
base_cmd.extend(prepareArgs(command))
return runfsl(*base_cmd).strip()
return runfsl(*base_cmd, env=env).strip()
def info(job_id):
......
......@@ -168,7 +168,7 @@ def run(*args, **kwargs):
All other keyword arguments are passed through to the ``subprocess.Popen``
object (via :func:`_realrun`), unless ``submit=True``, in which case they
are ignored.
are passed through to the :func:`.fslsub.submit` function.
:returns: If ``submit`` is provided, the return value of
:func:`.fslsub` is returned. Otherwise returns a single
......@@ -208,7 +208,7 @@ def run(*args, **kwargs):
# submit - delegate to fslsub
if submit is not None:
return fslsub.submit(' '.join(args), **submit)
return fslsub.submit(' '.join(args), **submit, **kwargs)
# Run directly - delegate to _realrun
stdout, stderr, exitcode = _realrun(
......
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