Merge branch 'rf/submit' into 'master'

Rf/submit

See merge request fsl/fslpy!208

CHANGELOG.rst

@@ -23,8 +23,11 @@ Changed
 
 * The :func:`.gifti.relatedFiles` function now supports files with
   BIDS-style naming conventions.
-* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through
-  any additional keyword arguments to ``subprocess.Popen``.
+* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any
+  additional keyword arguments to ``subprocess.Popen`` or, if ``submit=True``,
+  to :func:`fslsub.submit`.
+* The :func:`.fslsub.submit` function now accepts an ``env`` option, allowing
+  environment variables to be specified.
 * The :func:`.run.runfsl` function now raises an error on attempts to
   run a command which is not present in ``$FSLDIR/bin/`` (e.g. ``ls``).
 * The :mod:`.bids` module has been updated to support files with any

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(

tests/test_run.py

@@ -306,29 +306,33 @@ def test_run_submit():
         mkexec(op.expandvars('$FSLDIR/bin/fsltest'), test_script)
 
         jid = run.run('fsltest', submit=True)
-
         assert jid == '12345'
-
         stdout, stderr = fslsub.output(jid)
-
         assert stdout == 'test_script running\n'
         assert stderr == ''
 
+        # or can pass submit opts as a dict
         kwargs = {'name' : 'abcde', 'ram' : '4GB'}
-
         jid = run.run('fsltest', submit=kwargs)
-
         assert jid == '12345'
-
         stdout, stderr = fslsub.output(jid)
-
         experr = '\n'.join(['{}: {}'.format(k, kwargs[k])
                             for k in sorted(kwargs.keys())]) + '\n'
+        assert stdout == 'test_script running\n'
+        assert stderr == experr
 
+        # or can pass submit opts as kwargs
+        kwargs = {'name' : 'abcde', 'ram' : '4GB'}
+        jid = run.run('fsltest', submit=True, **kwargs)
+        assert jid == '12345'
+        stdout, stderr = fslsub.output(jid)
+        experr = '\n'.join(['{}: {}'.format(k, kwargs[k])
+                            for k in sorted(kwargs.keys())]) + '\n'
         assert stdout == 'test_script running\n'
         assert stderr == experr
 
 
+
 def test_run_streams():
     """
     """