Merge branch 'master' into enh/cuda_support

Author: effigies

.git-blame-ignore-revs

@@ -1,3 +1,7 @@
+# Fri Feb 21 14:06:53 2025 -0500 - [email protected] - sty: black [ignore-rev]
+8ed2b2306aeb7d89de4958b5293223ffe27a4f34
+# Tue Apr 13 10:16:17 2021 -0400 - [email protected] - STY: black
+b1690d5beb391e08c1e5463f1e3c641cf1e9f58e
 # Thu Oct 31 10:01:38 2024 -0400 - [email protected] - STY: black [ignore-rev]
 bd0d5856d183ba3918eda31f80db3b1d4387c55c
 # Thu Mar 21 13:34:09 2024 -0400 - [email protected] - STY: black [ignore-rev]

nipype/caching/tests/test_memory.py

@@ -1,5 +1,4 @@
-""" Test the nipype interface caching mechanism
-"""
+"""Test the nipype interface caching mechanism"""
 
 from .. import Memory
 from ...pipeline.engine.tests.test_engine import EngineTestInterface

nipype/external/cloghandler.py

@@ -9,7 +9,7 @@
 #   WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
 #   License for the specific language governing permissions and limitations
 #   under the License.
-""" cloghandler.py:  A smart replacement for the standard RotatingFileHandler
+"""cloghandler.py:  A smart replacement for the standard RotatingFileHandler
 
 ConcurrentRotatingFileHandler:  This class is a log handler which is a drop-in
 replacement for the python standard log handler 'RotateFileHandler', the primary

nipype/info.py

@@ -1,4 +1,4 @@
-""" This file contains defines parameters for nipy that we use to fill
+"""This file contains defines parameters for nipy that we use to fill
 settings in setup.py, the nipy top-level docstring, and for building the
 docs.  In setup.py in particular, we exec this file, so it cannot import nipy
 """

nipype/interfaces/ants/registration.py

@@ -1,5 +1,5 @@
 """The ants module provides basic functions for interfacing with ants
-   functions.
+functions.
 """
 
 import os

nipype/interfaces/ants/resampling.py

@@ -1,5 +1,4 @@
-"""ANTS Apply Transforms interface
-"""
+"""ANTS Apply Transforms interface"""
 
 import os
 

nipype/interfaces/ants/visualization.py

@@ -1,5 +1,4 @@
-"""The ants visualisation module provides basic functions based on ITK.
-"""
+"""The ants visualisation module provides basic functions based on ITK."""
 
 import os
 

nipype/interfaces/bru2nii.py

@@ -1,5 +1,4 @@
-"""The bru2nii module provides basic functions for dicom conversion
-"""
+"""The bru2nii module provides basic functions for dicom conversion"""
 
 import os
 from .base import (

nipype/interfaces/camino/__init__.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Camino top level namespace
-"""
+"""Camino top level namespace"""
 
 from .connectivity import Conmat
 from .convert import (

nipype/interfaces/cmtk/base.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" Base interface for cmtk """
+"""Base interface for cmtk"""
 
 from ..base import LibraryBaseInterface
 from ...utils.misc import package_check

nipype/interfaces/diffusion_toolkit/dti.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various commands provided by diffusion toolkit
-"""
+"""Provides interfaces to various commands provided by diffusion toolkit"""
 import os
 import re
 

nipype/interfaces/diffusion_toolkit/odf.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various commands provided by diffusion toolkit
-"""
+"""Provides interfaces to various commands provided by diffusion toolkit"""
 import os
 import re
 

nipype/interfaces/diffusion_toolkit/postproc.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various commands provided by diffusion toolkit
-"""
+"""Provides interfaces to various commands provided by diffusion toolkit"""
 
 import os
 from ..base import (

nipype/interfaces/dipy/base.py

@@ -1,4 +1,4 @@
-""" Base interfaces for dipy """
+"""Base interfaces for dipy"""
 
 import os.path as op
 import inspect

nipype/interfaces/freesurfer/longitudinal.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various longitudinal commands provided by freesurfer
-"""
+"""Provides interfaces to various longitudinal commands provided by freesurfer"""
 
 import os
 

nipype/interfaces/freesurfer/model.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """The freesurfer module provides basic functions for interfacing with
-   freesurfer tools.
+freesurfer tools.
 """
 
 import os

nipype/interfaces/freesurfer/petsurfer.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various commands for running PET analyses provided by FreeSurfer
-"""
+"""Provides interfaces to various commands for running PET analyses provided by FreeSurfer"""
 
 import os
 

nipype/interfaces/freesurfer/preprocess.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various commands provided by FreeSurfer
-"""
+"""Provides interfaces to various commands provided by FreeSurfer"""
 import os
 import os.path as op
 from glob import glob

nipype/interfaces/freesurfer/registration.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Provides interfaces to various longitudinal commands provided by freesurfer
-"""
+"""Provides interfaces to various longitudinal commands provided by freesurfer"""
 
 import os
 import os.path

nipype/interfaces/freesurfer/utils.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Interfaces to assorted Freesurfer utility programs.
-"""
+"""Interfaces to assorted Freesurfer utility programs."""
 import os
 import re
 import shutil

nipype/interfaces/io.py

@@ -1,14 +1,14 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" Set of interfaces that allow interaction with data. Currently
-    available interfaces are:
+"""Set of interfaces that allow interaction with data. Currently
+available interfaces are:
 
-    DataSource: Generic nifti to named Nifti interface
-    DataSink: Generic named output from interfaces to data store
-    XNATSource: preliminary interface to XNAT
+DataSource: Generic nifti to named Nifti interface
+DataSink: Generic named output from interfaces to data store
+XNATSource: preliminary interface to XNAT
 
-    To come :
-    XNATSink
+To come :
+XNATSink
 """
 import glob
 import fnmatch

nipype/interfaces/mixins/reporting.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" class mixin and utilities for enabling reports for nipype interfaces """
+"""class mixin and utilities for enabling reports for nipype interfaces"""
 
 import os
 from abc import abstractmethod

nipype/interfaces/nipy/base.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" Base interface for nipy """
+"""Base interface for nipy"""
 
 from ..base import LibraryBaseInterface
 from ...utils.misc import package_check

nipype/interfaces/nitime/base.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" Base interface for nitime """
+"""Base interface for nitime"""
 
 from ..base import LibraryBaseInterface
 

nipype/interfaces/spm/preprocess.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""SPM wrappers for preprocessing data
-"""
+"""SPM wrappers for preprocessing data"""
 import os
 from copy import deepcopy
 

nipype/interfaces/utility/base.py

@@ -1,9 +1,9 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
-    # changing to temporary directories
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir()
+# changing to temporary directories
+>>> tmp = getfixture('tmpdir')
+>>> old = tmp.chdir()
 """
 import os
 import re

nipype/interfaces/utility/csv.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""CSV Handling utilities
-"""
+"""CSV Handling utilities"""
 import csv
 from ..base import traits, TraitedSpec, DynamicTraitedSpec, File, BaseInterface
 from ..io import add_traits

nipype/pipeline/engine/nodes.py

@@ -452,7 +452,7 @@ def run(self, updatehash=False):
         cached, updated = self.is_cached()
 
         # If the node is cached, check on pklz files and finish
-        if not force_run and (updated or (not updated and updatehash)):
+        if cached and not force_run and (updated or updatehash):
             logger.debug("Only updating node hashes or skipping execution")
             inputs_file = op.join(outdir, "_inputs.pklz")
             if not op.exists(inputs_file):

nipype/pipeline/engine/tests/test_engine.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Tests for the engine module
-"""
+"""Tests for the engine module"""
 from copy import deepcopy
 from glob import glob
 import os

nipype/pipeline/engine/tests/test_join.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Tests for join expansion
-"""
+"""Tests for join expansion"""
 import pytest
 
 from .... import config

nipype/pipeline/engine/tests/test_utils.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Tests for the engine utils module
-"""
+"""Tests for the engine utils module"""
 import os
 from copy import deepcopy
 import pytest

nipype/pipeline/engine/tests/test_workflows.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Tests for the engine workflows module
-"""
+"""Tests for the engine workflows module"""
 from glob import glob
 import os
 from shutil import rmtree

nipype/pipeline/plugins/condor.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via Condor
-"""
+"""Parallel workflow execution via Condor"""
 
 import os
 from time import sleep

nipype/pipeline/plugins/dagman.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via Condor DAGMan
-"""
+"""Parallel workflow execution via Condor DAGMan"""
 
 import os
 import sys

nipype/pipeline/plugins/debug.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Debug plugin
-"""
+"""Debug plugin"""
 
 import networkx as nx
 from .base import PluginBase, logger

nipype/pipeline/plugins/ipython.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Parallel workflow execution via IPython controller
-"""
+"""Parallel workflow execution via IPython controller"""
 from pickle import dumps
 
 import sys

nipype/pipeline/plugins/linear.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Local serial workflow execution
-"""
+"""Local serial workflow execution"""
 
 import os
 from .base import PluginBase, logger, report_crash, report_nodes_not_run, str2bool

nipype/pipeline/plugins/lsf.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via LSF
-"""
+"""Parallel workflow execution via LSF"""
 
 import os
 import re

nipype/pipeline/plugins/multiproc.py

@@ -379,8 +379,11 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
             if self._local_hash_check(jobid, graph):
                 continue
 
+            cached, updated = self.procs[jobid].is_cached()
             # updatehash and run_without_submitting are also run locally
-            if updatehash or self.procs[jobid].run_without_submitting:
+            if (cached and updatehash and not updated) or self.procs[
+                jobid
+            ].run_without_submitting:
                 logger.debug("Running node %s on master thread", self.procs[jobid])
                 try:
                     self.procs[jobid].run(updatehash=updatehash)

nipype/pipeline/plugins/oar.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via OAR http://oar.imag.fr
-"""
+"""Parallel workflow execution via OAR http://oar.imag.fr"""
 
 import os
 import stat

nipype/pipeline/plugins/pbs.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via PBS/Torque
-"""
+"""Parallel workflow execution via PBS/Torque"""
 
 import os
 from time import sleep

nipype/pipeline/plugins/pbsgraph.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via PBS/Torque
-"""
+"""Parallel workflow execution via PBS/Torque"""
 
 import os
 import sys

nipype/pipeline/plugins/sge.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via SGE
-"""
+"""Parallel workflow execution via SGE"""
 
 import os
 import pwd

nipype/pipeline/plugins/sgegraph.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via SGE
-"""
+"""Parallel workflow execution via SGE"""
 
 import os
 import sys

nipype/pipeline/plugins/slurmgraph.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via SLURM
-"""
+"""Parallel workflow execution via SLURM"""
 
 import os
 import sys

nipype/pipeline/plugins/somaflow.py

@@ -1,5 +1,4 @@
-"""Parallel workflow execution via PBS/Torque
-"""
+"""Parallel workflow execution via PBS/Torque"""
 
 import os
 import sys