Merge pull request #141 from oesteban/fix/parser-exceptions

FIX: Allow setting nonstandard spaces for parser

smriprep/cli/tests/test_utils.py

@@ -42,3 +42,18 @@ def test_template_parser(monkeypatch):
 
         with pytest.raises(ValueError):
             u._template(['MNI152NLin6Asym:res-2', 'UnkownTemplate:res-2'])
+
+        with pytest.raises(ValueError):
+            u._template(['MNI152NLin6Asym:res-2', 'func'])
+
+        assert u._template(['MNI152NLin6Asym:res-2', 'fsnative']) == \
+            OrderedDict([('MNI152NLin6Asym', {'res': '2'}), ('fsnative', None)])
+
+        u.ParseTemplates.set_nonstandard_spaces('func')
+        assert u._template(['MNI152NLin2009cAsym:res-2', 'func']) == \
+            OrderedDict([('MNI152NLin2009cAsym', {'res': '2'}), ('func', None)])
+
+        u.ParseTemplates.set_nonstandard_spaces(['func', 'fsnative'])
+        assert u._template(['MNI152NLin2009cAsym:res-2', 'func', 'fsnative']) == \
+            OrderedDict([('MNI152NLin2009cAsym', {'res': '2'}),
+                         ('func', None), ('fsnative', None)])

smriprep/cli/utils.py

@@ -2,15 +2,25 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """CLI Utilities."""
 from argparse import Action
-from ..conf import TF_TEMPLATES as _TF_TEMPLATES
+from ..conf import TF_TEMPLATES as _TF_TEMPLATES, LEGACY_SPACES
 
 
 class ParseTemplates(Action):
     """Manipulate a string of templates with modifiers."""
 
+    EXCEPTIONS = tuple()
+
     def __call__(self, parser, namespace, values, option_string=None):
         setattr(namespace, self.dest, _template(values))
 
+    @classmethod
+    def set_nonstandard_spaces(cls, inlist):
+        """Set permissible nonstandard spaces names."""
+        if isinstance(inlist, str):
+            inlist = [inlist]
+
+        cls.EXCEPTIONS = tuple(inlist)
+
 
 def _template(inlist):
     """Return an OrderedDict with templates."""
@@ -34,6 +44,12 @@ def output_space(value):
         mitems = modifier.split('-', 1)
         spec[mitems[0]] = len(mitems) == 1 or mitems[1]
 
+    if template in ParseTemplates.EXCEPTIONS:
+        return template, None
+
+    if template in LEGACY_SPACES:
+        return template, None
+
     if template not in _TF_TEMPLATES:
         raise ValueError("""\
 Template identifier "{}" not found. Please, make sure TemplateFlow is \

smriprep/conf/__init__.py

@@ -2,3 +2,5 @@
 from templateflow.api import templates as _get_templates
 
 TF_TEMPLATES = tuple(_get_templates())
+LEGACY_SPACES = ('fsnative', 'fsaverage4', 'fsaverage5',
+                 'fsaverage6', 'fsaverage')