From 166f20966887fefa7d8be6c26cf1ff1a9ebda41a Mon Sep 17 00:00:00 2001 From: akeshavan Date: Mon, 4 Apr 2016 14:14:37 -0700 Subject: [PATCH 1/2] fix: sge plugin - no zombies at ucsf --- nipype/pipeline/plugins/sge.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index 547a3cbbb8..bbe5be9db8 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -60,7 +60,7 @@ def is_initializing(self): return self._job_queue_state == "initializing" def is_zombie(self): - return self._job_queue_state == "zombie" + return self._job_queue_state == "zombie" or self._job_queue_state == "finished" def is_running(self): return self._job_queue_state == "running" From 9fd5187fcd71f20f42f621473df404541b94f3f7 Mon Sep 17 00:00:00 2001 From: akeshavan Date: Mon, 11 Apr 2016 16:14:44 -0700 Subject: [PATCH 2/2] doc: make check-before-commit --- nipype/workflows/smri/freesurfer/recon.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py index c9206812f3..b574314f35 100644 --- a/nipype/workflows/smri/freesurfer/recon.py +++ b/nipype/workflows/smri/freesurfer/recon.py @@ -82,7 +82,7 @@ def link_masks(subjects_dir, subject_id): def create_reconall_workflow(name="ReconAll", plugin_args=None, recoding_file=None): """Creates the ReconAll workflow in nipype. - + Example ------- >>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow @@ -200,7 +200,7 @@ def checkarg(arg, default): 'lookup_table', 'wm_lookup_table', 'awk_file'] - + config_node = pe.Node(niu.Function(params, params, setconfig), @@ -509,7 +509,7 @@ def completemethod(datasinked_files, subject_id): reconall.connect([(datasink, completion, [('out_file', 'datasinked_files')]), (inputspec, completion, [('subject_id', 'subject_id')]), (completion, postds_outputspec, [('subject_id', 'subject_id')])]) - + #### Workflow additions go here if recoding_file: