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

env option

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):

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(