From 67b9d739373750ab9036e3ee26acabb26badbb4f Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 24 Feb 2017 13:40:56 -0500 Subject: [PATCH 1/4] fix: auto test --- nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py index 3186317333..cf67b12b2b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py @@ -1,9 +1,9 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..preprocess import ApplyXfm +from ..preprocess import ApplyXFM -def test_ApplyXfm_inputs(): +def test_ApplyXFM_inputs(): input_map = dict(angle_rep=dict(argstr='-anglerep %s', ), apply_isoxfm=dict(argstr='-applyisoxfm %f', @@ -145,19 +145,19 @@ def test_ApplyXfm_inputs(): min_ver='5.0.0', ), ) - inputs = ApplyXfm.input_spec() + inputs = ApplyXFM.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value -def test_ApplyXfm_outputs(): +def test_ApplyXFM_outputs(): output_map = dict(out_file=dict(), out_log=dict(), out_matrix_file=dict(), ) - outputs = ApplyXfm.output_spec() + outputs = ApplyXFM.output_spec() for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): From 87b0df6a4dfb7d7645000be3bf0dc701043334ca Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 24 Feb 2017 13:47:35 -0500 Subject: [PATCH 2/4] rev: remove commandline interface --- nipype/pipeline/plugins/slurm.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index e0b23fb335..2f164235d7 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -60,10 +60,11 @@ def __init__(self, **kwargs): def _is_pending(self, taskid): # subprocess.Popen requires taskid to be a string - res = CommandLine('squeue', - args=' '.join(['-j', '%s' % taskid]), - terminal_output='allatonce').run() - return res.runtime.stdout.find(str(taskid)) > -1 + proc = subprocess.Popen(["squeue", '-j', '%s' % taskid], + stdout=subprocess.PIPE, + stderr=subprocess.PIPE) + o, _ = proc.communicate() + return o.find(str(taskid)) > -1 def _submit_batchtask(self, scriptfile, node): """ From 579733fc4bf6e97dc4f917381800c8ca9d12df2a Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 27 Feb 2017 10:43:00 -0500 Subject: [PATCH 3/4] rev: stop slurm invalid jobid error --- nipype/pipeline/plugins/slurm.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index 2f164235d7..5061ae46cf 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -15,6 +15,7 @@ from ...interfaces.base import CommandLine from .base import (SGELikeBatchManagerBase, logger, iflogger, logging) +import subprocess class SLURMPlugin(SGELikeBatchManagerBase): From c92bfb7929db7a1e35377ac4e329f3aef32a782f Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 27 Feb 2017 10:54:00 -0500 Subject: [PATCH 4/4] fix: autotest --- nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py index cf67b12b2b..3186317333 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py @@ -1,9 +1,9 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..preprocess import ApplyXFM +from ..preprocess import ApplyXfm -def test_ApplyXFM_inputs(): +def test_ApplyXfm_inputs(): input_map = dict(angle_rep=dict(argstr='-anglerep %s', ), apply_isoxfm=dict(argstr='-applyisoxfm %f', @@ -145,19 +145,19 @@ def test_ApplyXFM_inputs(): min_ver='5.0.0', ), ) - inputs = ApplyXFM.input_spec() + inputs = ApplyXfm.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value -def test_ApplyXFM_outputs(): +def test_ApplyXfm_outputs(): output_map = dict(out_file=dict(), out_log=dict(), out_matrix_file=dict(), ) - outputs = ApplyXFM.output_spec() + outputs = ApplyXfm.output_spec() for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()):