Merge pull request #81 from grabbles/fix/int

Fix natural sort for non-strings

.gitignore

@@ -1,5 +1,5 @@
 historical/
-# 
+#
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -92,3 +92,5 @@ ENV/
 
 *.DS_Store
 *.orig
+
+.pytest_cache

grabbit/core.py

@@ -273,10 +273,7 @@ def match_file(self, f, update_file=False):
             m = self.regex.search(f.path)
             val = m.group(1) if m is not None else None
 
-        if val is not None and self.dtype is not None:
-            val = self.dtype(val)
-
-        return val
+        return self._astype(val)
 
     def add_file(self, filename, value):
         """ Adds the specified filename to tracking. """
@@ -296,6 +293,11 @@ def count(self, files=False):
         """
         return len(self.files) if files else len(self.unique())
 
+    def _astype(self, val):
+        if val is not None and self.dtype is not None:
+            val = self.dtype(val)
+        return val
+
 
 class Layout(object):
 
@@ -860,7 +862,7 @@ def get_nearest(self, path, return_type='file', strict=True, all_=False,
         for ent in self.entities.values():
             m = ent.regex.search(path)
             if m:
-                entities[ent.name] = m.group(1)
+                entities[ent.name] = ent._astype(m.group(1))
 
         # Remove any entities we want to ignore when strict matching is on
         if strict and ignore_strict_entities is not None:

grabbit/tests/test_core.py

@@ -243,6 +243,7 @@ def test_dynamic_getters(self, data_dir, config):
         layout = Layout([(data_dir, config)], dynamic_getters=True)
         assert hasattr(layout, 'get_subjects')
         assert '01' in getattr(layout, 'get_subjects')()
+        assert 1 in getattr(layout, 'get_runs')()
 
     def test_querying(self, bids_layout):
 
@@ -312,6 +313,12 @@ def test_get_nearest(self, bids_layout):
         assert len(nearest) == 3
         assert nearest[0].subject == '01'
 
+        # Check for file with matching run (fails if types don't match)
+        nearest = bids_layout.get_nearest(
+            result, type='phasediff', extensions='.nii.gz')
+        assert nearest is not None
+        assert os.path.basename(nearest) == 'sub-01_ses-1_run-1_phasediff.nii.gz'
+
     def test_index_regex(self, bids_layout, layout_include):
         targ = join('derivatives', 'excluded.json')
         assert targ not in bids_layout.files

grabbit/utils.py

@@ -13,6 +13,8 @@ def natural_sort(l, field=None):
     def alphanum_key(key):
         if field is not None:
             key = getattr(key, field)
+        if not isinstance(key, str):
+            key = str(key)
         return [convert(c) for c in re.split('([0-9]+)', key)]
     return sorted(l, key=alphanum_key)