STY: Apply ruff/Pyflakes rule F821

F821 Undefined name

I have left some occurrences, to be fixed in a later pull request.

nipype/interfaces/ants/resampling.py

@@ -122,7 +122,7 @@ def _format_arg(self, opt, spec, val):
             if isdefined(self.inputs.invert_affine):
                 diff_inv = set(self.inputs.invert_affine) - set(affine_invert)
                 if diff_inv:
-                    raise Exceptions(
+                    raise Exception(
                         "Review invert_affine, not all indexes from invert_affine were used, "
                         "check the description for the full definition"
                     )
@@ -275,7 +275,7 @@ def _format_arg(self, opt, spec, val):
             if isdefined(self.inputs.invert_affine):
                 diff_inv = set(self.inputs.invert_affine) - set(affine_invert)
                 if diff_inv:
-                    raise Exceptions(
+                    raise Exception(
                         "Review invert_affine, not all indexes from invert_affine were used, "
                         "check the description for the full definition"
                     )

nipype/interfaces/cmtk/parcellation.py

@@ -23,15 +23,15 @@
 
 
 def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
-    import cmp
+    from cmp.configuration import PipelineConfiguration
     from cmp.util import runCmd
 
     iflogger.info("Create the cortical labels necessary for our ROIs")
     iflogger.info("=================================================")
     fs_label_dir = op.join(op.join(subjects_dir, subject_id), "label")
     output_dir = op.abspath(op.curdir)
     paths = []
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     for hemi in ["lh", "rh"]:
         spath = (
@@ -332,13 +332,13 @@ def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
 def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
     """Creates the ROI_%s.nii.gz files using the given parcellation information
     from networks. Iteratively create volume."""
-    import cmp
+    from cmp.configuration import PipelineConfiguration
     from cmp.util import runCmd
 
     iflogger.info("Create the ROIs:")
     output_dir = op.abspath(op.curdir)
     fs_dir = op.join(subjects_dir, subject_id)
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     log = cmp_config.get_logger()
     parval = cmp_config._get_lausanne_parcellation("Lausanne2008")[parcellation_name]
@@ -467,12 +467,12 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
 
 
 def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
-    import cmp
+    from cmp.configuration import PipelineConfiguration
     import scipy.ndimage.morphology as nd
 
     iflogger.info("Create white matter mask")
     fs_dir = op.join(subjects_dir, subject_id)
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     pgpath = cmp_config._get_lausanne_parcellation("Lausanne2008")[parcellation_name][
         "node_information_graphml"
@@ -618,10 +618,11 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
 def crop_and_move_datasets(
     subject_id, subjects_dir, fs_dir, parcellation_name, out_roi_file, dilation
 ):
+    from cmp.configuration import PipelineConfiguration
     from cmp.util import runCmd
 
     fs_dir = op.join(subjects_dir, subject_id)
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     log = cmp_config.get_logger()
     output_dir = op.abspath(op.curdir)

nipype/interfaces/mrtrix3/connectivity.py

@@ -212,7 +212,7 @@ def _parse_inputs(self, skip=None):
 
             path = which(self._cmd)
             if path is None:
-                path = os.getenv(MRTRIX3_HOME, "/opt/mrtrix3")
+                path = os.getenv("MRTRIX3_HOME", "/opt/mrtrix3")
             else:
                 path = op.dirname(op.dirname(path))
 
@@ -304,7 +304,7 @@ def _parse_inputs(self, skip=None):
 
             path = which(self._cmd)
             if path is None:
-                path = os.getenv(MRTRIX3_HOME, "/opt/mrtrix3")
+                path = os.getenv("MRTRIX3_HOME", "/opt/mrtrix3")
             else:
                 path = op.dirname(op.dirname(path))
 

nipype/interfaces/vtkbase.py

@@ -63,7 +63,7 @@ def vtk_old():
     """Checks if VTK uses the old-style pipeline (VTK<6.0)"""
     global _vtk_version
     if _vtk_version is None:
-        raise RuntimeException("VTK is not correctly installed.")
+        raise RuntimeError("VTK is not correctly installed.")
     return _vtk_version[0] < 6
 
 

nipype/pipeline/plugins/tests/test_oar.py

@@ -1,3 +1,4 @@
+import os
 from shutil import which
 
 import nipype.interfaces.base as nib

nipype/utils/filemanip.py

@@ -47,7 +47,7 @@ def split_filename(fname):
     fname : str
         filename from fname, without extension
     ext : str
-        file extension from fname
+        file extension from fname706
 
     Examples
     --------
@@ -702,8 +702,8 @@ def savepkl(filename, record, versioning=False):
         except FileNotFoundError as e:
             fmlogger.debug(str(e))
             sleep(2)
-    else:
-        raise e
+        else:
+            raise
 
 
 rst_levels = ["=", "-", "~", "+"]