Merge pull request #84 from effigies/mnt/dependency_updates

MNT: Pybids 0.7 compatibility

fitlins/__about__.py

@@ -34,21 +34,20 @@
 
 REQUIRES = [
     'nibabel>=2.0',
-    'nipype>=1.1.2',
+    'nipype>=1.1.6',
     'seaborn>=0.7.1',
     'numpy>=1.11',
     'nilearn>=0.4.0',
     'pandas>=0.19',
     'tables>=3.2.1',
-    'nistats>=0.0.1a',
-    'grabbit>=0.2.3',
+    'nistats>=0.0.1b0',
     'pybids>=0.6.5',
     'jinja2',
 ]
 
 LINKS_REQUIRES = [
-    'git+https://github.com/nistats/nistats.git@'
-    'ce3695e8f34c6f34323766dc96a60a53b69d2729#egg=nistats',
+    'git+https://github.com/bids-standard/pybids.git@'
+    'dd8c9bc6478bb63e09f6c95566a11677ce12ded7#egg=pybids',
 ]
 
 TESTS_REQUIRES = [

fitlins/cli/run.py

@@ -79,9 +79,9 @@ def get_parser():
                              'removed)')
     g_bids.add_argument('-m', '--model', action='store', default='model.json',
                         help='location of BIDS model description (default bids_dir/model.json)')
-    g_bids.add_argument('-p', '--preproc-dir', action='store', default='fmriprep',
-                        help='location of preprocessed data (if relative path, search '
-                             'bids_dir/derivatives, followed by output_dir)')
+    g_bids.add_argument('-d', '--derivatives', action='store', nargs='+',
+                        help='location of derivatives (including preprocessed images).'
+                        'If none specified, indexes all derivatives under bids_dir/derivatives.')
     g_bids.add_argument('--derivative-label', action='store', type=str,
                         help='execution label to append to derivative directory name')
     g_bids.add_argument('--space', action='store',
@@ -139,13 +139,7 @@ def run_fitlins(argv=None):
     if opts.model in (None, 'default') and not op.exists(model):
         model = 'default'
 
-    preproc_dir = default_path(opts.preproc_dir,
-                               op.join(opts.bids_dir, 'derivatives'),
-                               'fmriprep')
-    if not op.exists(preproc_dir):
-        preproc_dir = default_path(opts.preproc_dir, opts.output_dir, 'fmriprep')
-        if not op.exists(preproc_dir):
-            raise RuntimeError("Preprocessed data could not be found")
+    derivatives = True if not opts.derivatives else opts.derivatives
 
     pipeline_name = 'fitlins'
     if opts.derivative_label:
@@ -158,7 +152,7 @@ def run_fitlins(argv=None):
     work_dir = mkdtemp() if opts.work_dir is None else opts.work_dir
 
     fitlins_wf = init_fitlins_wf(
-        opts.bids_dir, preproc_dir, deriv_dir, opts.space, model=model,
+        opts.bids_dir, derivatives, deriv_dir, opts.space, model=model,
         participants=subject_list, base_dir=work_dir,
         include_pattern=opts.include, exclude_pattern=opts.exclude
         )