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Commit 12f7023

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man-shuman-shu
authored
Merge branch 'master' into fix/merge_rois_zero_d_array
2 parents 2c8017d + fe20d45 commit 12f7023
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58 files changed

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-120
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‎.git-blame-ignore-revs

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# Fri Feb 21 14:06:53 2025 -0500 - markiewicz@stanford.edu - sty: black [ignore-rev]
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8ed2b2306aeb7d89de4958b5293223ffe27a4f34
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# Tue Apr 13 10:16:17 2021 -0400 - markiewicz@stanford.edu - STY: black
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b1690d5beb391e08c1e5463f1e3c641cf1e9f58e
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# Thu Oct 31 10:01:38 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev]
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bd0d5856d183ba3918eda31f80db3b1d4387c55c
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# Thu Mar 21 13:34:09 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev]

‎nipype/caching/tests/test_memory.py

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""" Test the nipype interface caching mechanism
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"""
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"""Test the nipype interface caching mechanism"""
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from .. import Memory
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from ...pipeline.engine.tests.test_engine import EngineTestInterface

‎nipype/external/cloghandler.py

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

‎nipype/info.py

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""" This file contains defines parameters for nipy that we use to fill
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"""This file contains defines parameters for nipy that we use to fill
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settings in setup.py, the nipy top-level docstring, and for building the
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docs. In setup.py in particular, we exec this file, so it cannot import nipy
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"""
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"acres",
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"etelemetry>=0.3.1",
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"looseversion!=1.2",
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"gputil>=1.4.0",
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"puremagic",
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]
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‎nipype/interfaces/ants/registration.py

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"""The ants module provides basic functions for interfacing with ants
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functions.
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functions.
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"""
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import os

‎nipype/interfaces/ants/resampling.py

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"""ANTS Apply Transforms interface
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"""
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"""ANTS Apply Transforms interface"""
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import os
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‎nipype/interfaces/ants/visualization.py

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"""The ants visualisation module provides basic functions based on ITK.
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"""
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"""The ants visualisation module provides basic functions based on ITK."""
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import os
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‎nipype/interfaces/bru2nii.py

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"""The bru2nii module provides basic functions for dicom conversion
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"""
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"""The bru2nii module provides basic functions for dicom conversion"""
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import os
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from .base import (

‎nipype/interfaces/camino/__init__.py

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

‎nipype/interfaces/cmtk/base.py

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

‎nipype/interfaces/diffusion_toolkit/dti.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various commands provided by diffusion toolkit
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"""
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"""Provides interfaces to various commands provided by diffusion toolkit"""
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import os
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import re
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‎nipype/interfaces/diffusion_toolkit/odf.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various commands provided by diffusion toolkit
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"""
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"""Provides interfaces to various commands provided by diffusion toolkit"""
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import os
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import re
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‎nipype/interfaces/diffusion_toolkit/postproc.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various commands provided by diffusion toolkit
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"""
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"""Provides interfaces to various commands provided by diffusion toolkit"""
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import os
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from ..base import (

‎nipype/interfaces/dipy/base.py

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""" Base interfaces for dipy """
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"""Base interfaces for dipy"""
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import os.path as op
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import inspect

‎nipype/interfaces/freesurfer/longitudinal.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various longitudinal commands provided by freesurfer
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"""
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"""Provides interfaces to various longitudinal commands provided by freesurfer"""
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import os
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‎nipype/interfaces/freesurfer/model.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""The freesurfer module provides basic functions for interfacing with
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freesurfer tools.
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freesurfer tools.
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"""
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import os

‎nipype/interfaces/freesurfer/petsurfer.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various commands for running PET analyses provided by FreeSurfer
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"""
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"""Provides interfaces to various commands for running PET analyses provided by FreeSurfer"""
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import os
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‎nipype/interfaces/freesurfer/preprocess.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various commands provided by FreeSurfer
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"""
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"""Provides interfaces to various commands provided by FreeSurfer"""
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import os
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import os.path as op
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from glob import glob

‎nipype/interfaces/freesurfer/registration.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Provides interfaces to various longitudinal commands provided by freesurfer
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"""
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"""Provides interfaces to various longitudinal commands provided by freesurfer"""
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import os
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import os.path

‎nipype/interfaces/freesurfer/utils.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Interfaces to assorted Freesurfer utility programs.
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"""
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"""Interfaces to assorted Freesurfer utility programs."""
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import os
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import re
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import shutil

‎nipype/interfaces/io.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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""" Set of interfaces that allow interaction with data. Currently
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available interfaces are:
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"""Set of interfaces that allow interaction with data. Currently
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available interfaces are:
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DataSource: Generic nifti to named Nifti interface
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DataSink: Generic named output from interfaces to data store
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XNATSource: preliminary interface to XNAT
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DataSource: Generic nifti to named Nifti interface
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DataSink: Generic named output from interfaces to data store
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XNATSource: preliminary interface to XNAT
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To come :
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XNATSink
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To come :
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XNATSink
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"""
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‎nipype/interfaces/mixins/reporting.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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""" class mixin and utilities for enabling reports for nipype interfaces """
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"""class mixin and utilities for enabling reports for nipype interfaces"""
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import os
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from abc import abstractmethod

‎nipype/interfaces/nipy/base.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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""" Base interface for nipy """
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"""Base interface for nipy"""
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from ..base import LibraryBaseInterface
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from ...utils.misc import package_check

‎nipype/interfaces/nitime/base.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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""" Base interface for nitime """
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"""Base interface for nitime"""
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from ..base import LibraryBaseInterface
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‎nipype/interfaces/spm/preprocess.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""SPM wrappers for preprocessing data
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"""
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"""SPM wrappers for preprocessing data"""
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from copy import deepcopy
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‎nipype/interfaces/utility/base.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""
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# changing to temporary directories
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>>> tmp = getfixture('tmpdir')
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>>> old = tmp.chdir()
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# changing to temporary directories
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>>> tmp = getfixture('tmpdir')
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>>> old = tmp.chdir()
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"""
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‎nipype/interfaces/utility/csv.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""CSV Handling utilities
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"""
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"""CSV Handling utilities"""
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import csv
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from ..io import add_traits

‎nipype/pipeline/engine/nodes.py

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# If the node is cached, check on pklz files and finish
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if not force_run and (updated or (not updated and updatehash)):
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if cached and not force_run and (updated or updatehash):
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inputs_file = op.join(outdir, "_inputs.pklz")
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def is_gpu_node(self):
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return bool(getattr(self.inputs, 'use_cuda', False)) or bool(
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getattr(self.inputs, 'use_gpu', False)
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)
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class JoinNode(Node):
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"""Wraps interface objects that join inputs into a list.

‎nipype/pipeline/engine/tests/test_engine.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Tests for the engine module
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"""Tests for the engine module"""
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from copy import deepcopy
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from glob import glob
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import os

‎nipype/pipeline/engine/tests/test_join.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Tests for join expansion
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"""Tests for join expansion"""
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‎nipype/pipeline/engine/tests/test_utils.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Tests for the engine utils module
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"""
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"""Tests for the engine utils module"""
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import os
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from copy import deepcopy
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import pytest

‎nipype/pipeline/engine/tests/test_workflows.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Tests for the engine workflows module
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"""
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"""Tests for the engine workflows module"""
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from glob import glob
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import os
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from shutil import rmtree

‎nipype/pipeline/plugins/condor.py

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"""Parallel workflow execution via Condor
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"""
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"""Parallel workflow execution via Condor"""
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import os
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from time import sleep

‎nipype/pipeline/plugins/dagman.py

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"""Parallel workflow execution via Condor DAGMan
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"""
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"""Parallel workflow execution via Condor DAGMan"""
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import os
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import sys

‎nipype/pipeline/plugins/debug.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Debug plugin
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"""Debug plugin"""
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import networkx as nx
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from .base import PluginBase, logger

‎nipype/pipeline/plugins/ipython.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Parallel workflow execution via IPython controller
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"""
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"""Parallel workflow execution via IPython controller"""
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import sys

‎nipype/pipeline/plugins/linear.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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"""Local serial workflow execution
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"""
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"""Local serial workflow execution"""
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import os
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from .base import PluginBase, logger, report_crash, report_nodes_not_run, str2bool

‎nipype/pipeline/plugins/lsf.py

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"""Parallel workflow execution via LSF
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"""
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"""Parallel workflow execution via LSF"""
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import os
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import re

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