Use space definitions from niworkflows (#378)

* Pin Niworkflows version.

* Use Niworkflows' spaces.

* Fix init file.

* Run isort.

aslprep/cli/parser.py

@@ -12,10 +12,10 @@ def _build_parser():
     from functools import partial
     from pathlib import Path
 
+    from niworkflows.utils.spaces import OutputReferencesAction, Reference
     from packaging.version import Version
 
     from aslprep.cli.version import check_latest, is_flagged
-    from aslprep.utils.spaces import OutputReferencesAction, Reference
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""
@@ -624,7 +624,7 @@ def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
 
-    from aslprep.utils.spaces import Reference, SpatialReferences
+    from niworkflows.utils.spaces import Reference, SpatialReferences
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)

aslprep/config.py

@@ -239,7 +239,7 @@ def load(cls, settings, init=True, ignore=None):
     @classmethod
     def get(cls):
         """Return defined settings."""
-        from aslprep.utils.spaces import Reference, SpatialReferences
+        from niworkflows.utils.spaces import Reference, SpatialReferences
 
         out = {}
         for k, v in cls.__dict__.items():
@@ -548,7 +548,7 @@ class workflow(_Config):
     """Skip brain extraction of the T1w image (default is ``force``, meaning that
     *ASLPrep* will run brain extraction of the T1w)."""
     spaces = None
-    """Keeps the :py:class:`~aslprep.utils.spaces.SpatialReferences`
+    """Keeps the :py:class:`~niworkflows.utils.spaces.SpatialReferences`
     instance keeping standard and nonstandard spaces."""
     use_bbr = None
     """Run boundary-based registration for ASL-to-T1w registration."""
@@ -745,7 +745,7 @@ def to_filename(filename):
 
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
-    from aslprep.utils.spaces import Reference, SpatialReferences
+    from niworkflows.utils.spaces import Reference, SpatialReferences
 
     spaces = execution.output_spaces or SpatialReferences()
     if not isinstance(spaces, SpatialReferences):

aslprep/utils/__init__.py

@@ -1,15 +1,5 @@
 """Utility functions for aslprep."""
-from aslprep.utils import (
-    asl,
-    atlas,
-    bids,
-    cbf,
-    confounds,
-    misc,
-    plotting,
-    sentry,
-    spaces,
-)
+from aslprep.utils import asl, atlas, bids, cbf, confounds, misc, plotting, sentry
 
 __all__ = [
     "asl",
@@ -20,5 +10,4 @@
     "misc",
     "plotting",
     "sentry",
-    "spaces",
 ]