Merge branch 'bug_fslsub' into 'master'

BUG: use _prepareArgs to unpack input arguments

See merge request fsl/fslpy!167

fsl/utils/fslsub.py

@@ -55,7 +55,7 @@ import importlib
 log = logging.getLogger(__name__)
 
 
-def submit(command,
+def submit(*command,
            minutes=None,
            queue=None,
            architecture=None,
@@ -70,9 +70,12 @@ def submit(command,
            flags=False,
            multi_threaded=None,
            verbose=False):
-    """Submits a given command to the cluster
+    """
+    Submits a given command to the cluster
+
+    You can pass the command and arguments as a single string, or as a regular or unpacked sequence.
 
-    :arg command:        single string with the job command
+    :arg command:        string or regular/unpacked sequence of strings with the job command
     :arg minutes:        Estimated job length in minutes, used to auto-set
                          queue name
     :arg queue:          Explicitly sets the queue name
@@ -101,7 +104,7 @@ def submit(command,
     :return:             string of submitted job id
     """
 
-    from fsl.utils.run import runfsl
+    from fsl.utils.run import runfsl, prepareArgs
 
     base_cmd = ['fsl_sub']
 
@@ -132,7 +135,7 @@ def submit(command,
         base_cmd.append('-s')
         base_cmd.extend(multi_threaded)
 
-    base_cmd.append(command)
+    base_cmd.extend(prepareArgs(command))
 
     return runfsl(*base_cmd).strip()
 

fsl/utils/run.py

@@ -72,7 +72,7 @@ def dryrun(*args):
         DRY_RUN = oldval
 
 
-def _prepareArgs(args):
+def prepareArgs(args):
     """Used by the :func:`run` function. Ensures that the given arguments is a
     list of strings.
     """
@@ -179,7 +179,7 @@ def run(*args, **kwargs):
     logStdout      = log   .get('stdout',   None)
     logStderr      = log   .get('stderr',   None)
     logCmd         = log   .get('cmd',      None)
-    args           = _prepareArgs(args)
+    args           = prepareArgs(args)
 
     if not bool(submit):
         submit = None
@@ -345,7 +345,7 @@ def runfsl(*args, **kwargs):
     if not prefixes:
         raise FSLNotPresent('$FSLDIR is not set - FSL cannot be found!')
 
-    args = _prepareArgs(args)
+    args = prepareArgs(args)
     for prefix in prefixes:
         cmdpath = op.join(prefix, args[0])
         if op.isfile(cmdpath):