DOC: listen to sphinx warnings

CHANGELOG.rst

@@ -223,8 +223,8 @@ Changed
 
 * The :class:`.Cache` class has a new ``lru`` option, allowing it to be used
   as a least-recently-used cache.
-* The :mod:`.filetree` module has been refactored to make it easier for the
-  :mod:`.query` module to work with file tree hierarchies.
+* The :mod:`fsl.utils.filetree` module has been refactored to make it easier
+  for the :mod:`.query` module to work with file tree hierarchies.
 * The :meth:`.LabelAtlas.get` method has a new ``binary`` flag, allowing
   either a binary mask, or a mask with the original label value, to be
   returned.

fsl/utils/image/__init__.py

@@ -10,8 +10,7 @@ manipulating and working with :class:`.Image` objects.
 The following modules are available:
 
 .. autosummary::
-   :nosignature
 
-   .image.resample
-   .image.roi
+   fsl.utils.image.resample
+   fsl.utils.image.roi
 """

fsl/wrappers/wrapperutils.py

@@ -463,8 +463,9 @@ class _FileOrThing(object):
 
     This is because most functions that are decorated with the
     :func:`fileOrImage` or :func:`fileOrArray` decorators will invoke a call
-    to :func:`.run` or :func:`.runfsl`, where a value of ``submit=True`` will
-    cause the command to be executed asynchronously on a cluster platform.
+    to :func:`.run.run` or :func:`.runfsl`, where a value of ``submit=True``
+    will cause the command to be executed asynchronously on a cluster
+    platform.
 
 
     A :exc:`ValueError` will be raised if the decorated function is called