From 8d9488306d9ad5b99d2de0a2ba68a75f67c2bcc8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 20 Mar 2020 15:46:43 +0000
Subject: [PATCH] RF,ENH: run(submit) args can be passed as a dict or as
kwargs. submit accepts env option
---
fsl/utils/fslsub.py | 6 ++++--
fsl/utils/run.py | 4 ++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/fsl/utils/fslsub.py b/fsl/utils/fslsub.py
index 46bc0466d..eb8bf971c 100644
--- a/fsl/utils/fslsub.py
+++ b/fsl/utils/fslsub.py
@@ -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):
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 7211965d7..70915cf2d 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -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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