remove old -S switch

CHANGES.rst

@@ -1,6 +1,7 @@
 Release 0.1.2
 =============
 
+* [DEP] Deprecated -S/--subject-id tag
 * [ENH] Accept subjects with several T1w images (#114)
 * [ENH] Documentation updates (#130, #131)
 * [TST] Re-enabled CircleCI tests on one subject from ds054 of OpenfMRI
@@ -27,4 +28,4 @@ Release 0.0.1
 * Set up CircleCI with a first smoke test on one subject.
 * BIDS tree scrubbing and subject-session-run selection.
 * Refactored big workflow into consistent pieces.
-* Migrated Craig's original code
+* Migrated Craig's original code

fmriprep/info.py

@@ -6,7 +6,7 @@
 """
 from __future__ import unicode_literals
 
-__version__ = '0.1.2a0'
+__version__ = '0.1.2a1'
 __author__ = 'The CRN developers'
 __copyright__ = 'Copyright 2016, Center for Reproducible Neuroscience, Stanford University'
 __credits__ = ['Craig Moodie', 'Ross Blair', 'Oscar Esteban', 'Chris F. Gorgolewski',

fmriprep/run_workflow.py

@@ -3,7 +3,7 @@
 # @Author: oesteban
 # @Date:   2015-11-19 16:44:27
 # @Last Modified by:   oesteban
-# @Last Modified time: 2016-09-13 13:37:43
+# @Last Modified time: 2016-10-03 09:06:10
 """
 fMRI preprocessing workflow
 =====
@@ -35,8 +35,7 @@ def main():
     parser.add_argument('analysis_level', choices=['participant'])
 
     # optional arguments
-    parser.add_argument('-S', '--subject-id', '--participant_label',
-                         action='store', nargs='+')
+    parser.add_argument('--participant_label', action='store', nargs='+')
     parser.add_argument('-v', '--version', action='version',
                          version='fmriprep v{}'.format(__version__))
 
@@ -138,7 +137,7 @@ def create_workflow(opts):
             plugin_settings['plugin_args'] = {'n_procs': settings['nthreads']}
 
     # Determine subjects to be processed
-    subject_list = opts.subject_id
+    subject_list = opts.participant_label
 
     if subject_list is None or not subject_list:
         subject_list = [op.basename(subdir)[4:] for subdir in glob.glob(