REF: set partial_fill to False again

Still using `partial_fill` when creating FileTreeQuery

fsl/utils/filetree/filetree.py

@@ -354,7 +354,7 @@ class FileTree(object):
         self.variables = {}
 
     @classmethod
-    def read(cls, tree_name: str, directory='.', partial_fill=True, **variables) -> "FileTree":
+    def read(cls, tree_name: str, directory='.', partial_fill=False, **variables) -> "FileTree":
         """
         Reads a FileTree from a specific file
 

fsl/utils/filetree/query.py

@@ -89,6 +89,8 @@ class FileTreeQuery(object):
 
         :arg tree: The :class:`.FileTree` object
         """
+        # Hard-code into the templates any pre-defined variables
+        tree = tree.partial_fill()
 
         # Find all files present in the directory
         # (as Match objects), and find all variables,

tests/test_filetree/test_read.py

@@ -13,14 +13,21 @@ def same_path(p1, p2):
 
 def test_simple_tree():
     tree = filetree.FileTree.read('eddy')
-    assert 'basename' not in tree.variables
+    assert 'basename' in tree.variables
 
     same_path(tree.get('basename'), './eddy_output')
     same_path(tree.get('image'), './eddy_output.nii.gz')
+    same_path(tree.update(basename='eddy').get('image'), './eddy.nii.gz')
 
     tree = filetree.FileTree.read('eddy.tree', basename='out')
+    assert 'basename' in tree.variables
+    same_path(tree.get('basename'), './out')
+    same_path(tree.update(basename='eddy').get('image'), './eddy.nii.gz')
+
+    tree = filetree.FileTree.read('eddy.tree', basename='out', partial_fill=True)
     assert 'basename' not in tree.variables
     same_path(tree.get('basename'), './out')
+    same_path(tree.update(basename='eddy').get('image'), './out.nii.gz')
 
     with pytest.raises(ValueError):
         filetree.FileTree.read('non_existing')