test nipype configuration

test_config.py

import os

from nipype import logging, config
config.set('logging', 'workflow_level', 'DEBUG')
logging.update_logging(config)

from nipype.pipeline.engine import Node, Workflow
from nipype.interfaces.utility import Function

def createtwofiles():
    import os
    file1 = os.path.abspath('file1')
    with open(file1, 'wt') as fp:
        fp.writelines('file1')
    file2 = os.path.abspath('file2')
    with open(file2, 'wt') as fp:
        fp.writelines('file2')
    return file1, file2

def copyfilehere(infile):
    from shutil import copyfile
    import os
    outfile = os.path.abspath('outfile')
    copyfile(infile, outfile)
    return outfile

node1 = Node(Function(input_names=[],
                      output_names=['out1', 'out2'], 
                      function=createtwofiles),
             name='create')
node2 = Node(Function(input_names=['infile'], 
                      output_names=['out'], 
                      function=copyfilehere),
             name='copy')
wf = Workflow(name='testconfig')
wf.base_dir = os.getcwd()
wf.connect(node1, 'out2', node2, 'infile')
wf.config['execution'] = {'local_hash_check': 'True',
                          'remove_unnecessary_outputs': 'False'}
wf.run('MultiProc')

test_config_output.txt

120411-21:37:28,738 workflow DEBUG:
	 networkx 1.4 dev or higher detected
120411-21:37:28,743 workflow DEBUG:
	 (testconfig.create, testconfig.copy): No edge data
120411-21:37:28,744 workflow DEBUG:
	 (testconfig.create, testconfig.copy): new edge data: {'connect': [('out2', 'infile')]}
120411-21:37:28,946 workflow DEBUG:
	 Creating flat graph for workflow: testconfig
120411-21:37:28,949 workflow DEBUG:
	 expanding workflow: testconfig
120411-21:37:28,950 workflow DEBUG:
	 processing node: testconfig.create
120411-21:37:28,950 workflow DEBUG:
	 processing node: testconfig.copy
120411-21:37:28,950 workflow DEBUG:
	 finished expanding workflow: testconfig
120411-21:37:28,951 workflow INFO:
	 ['check', 'execution', 'logging']
120411-21:37:28,953 workflow DEBUG:
	 PE: expanding iterables
120411-21:37:28,953 workflow DEBUG:
	 PE: expanding iterables ... done
120411-21:37:28,955 workflow INFO:
	 Running in parallel.
120411-21:37:28,957 workflow INFO:
	 Submitting 1 jobs
120411-21:37:28,957 workflow INFO:
	 Executing: create ID: 0 H:e008c1e0699ef574fec0c0f11710f6f0
120411-21:37:28,957 workflow DEBUG:
	 checking hash locally
120411-21:37:28,958 workflow DEBUG:
	 Hash exists False
120411-21:37:28,958 workflow DEBUG:
	 Finished checking hash True
120411-21:37:28,964 workflow DEBUG:
	 Setting node inputs
120411-21:37:28,964 workflow INFO:
	 Executing node create in dir: /tmp/testconfig/create
120411-21:37:28,964 workflow DEBUG:
	 Node hash: e008c1e0699ef574fec0c0f11710f6f0
120411-21:37:28,965 workflow DEBUG:
	 /tmp/testconfig/create/_0xe008c1e0699ef574fec0c0f11710f6f0_unfinished.json found and can_resume is True or Node is a MapNode - resuming execution
120411-21:37:28,965 workflow DEBUG:
	 Creating /tmp/testconfig/create
120411-21:37:28,965 workflow DEBUG:
	 writing pre-exec report to /tmp/testconfig/create/_report/report.rst
120411-21:37:28,967 workflow DEBUG:
	 Executing node
120411-21:37:28,967 workflow DEBUG:
	 copying files to wd [execute=True, linksonly=False]
120411-21:37:28,970 workflow DEBUG:
	 Needed files: /tmp/testconfig/create/file1;/tmp/testconfig/create/file2;/tmp/testconfig/create/_0xe008c1e0699ef574fec0c0f11710f6f0_unfinished.json;/tmp/testconfig/create/_inputs.pklz;/tmp/testconfig/create/_node.pklz
120411-21:37:28,970 workflow DEBUG:
	 Needed dirs: /tmp/testconfig/create/_report
120411-21:37:28,970 workflow DEBUG:
	 Removing files: 
120411-21:37:28,972 workflow DEBUG:
	 saved results in /tmp/testconfig/create/result_create.pklz
120411-21:37:28,972 workflow DEBUG:
	 writing post-exec report to /tmp/testconfig/create/_report/report.rst
120411-21:37:28,973 workflow DEBUG:
	 Finished running create in dir: /tmp/testconfig/create

120411-21:37:30,962 workflow INFO:
	 [Job finished] jobname: create jobid: 0
120411-21:37:31,12 workflow INFO:
	 Submitting 1 jobs
120411-21:37:31,13 workflow INFO:
	 Executing: copy ID: 1 H:933316ea8421862ed50cab9a824c4234
120411-21:37:31,13 workflow DEBUG:
	 checking hash locally
120411-21:37:31,13 workflow DEBUG:
	 Hash exists False
120411-21:37:31,13 workflow DEBUG:
	 Finished checking hash True
120411-21:37:31,15 workflow DEBUG:
	 Setting node inputs
120411-21:37:31,15 workflow DEBUG:
	 input: infile
120411-21:37:31,15 workflow DEBUG:
	 results file: /tmp/testconfig/create/result_create.pklz
120411-21:37:31,18 workflow DEBUG:
	 output: out2
120411-21:37:31,18 workflow DEBUG:
	 setting nodelevel(testconfig.copy) input infile = /tmp/testconfig/create/file2
120411-21:37:31,18 workflow INFO:
	 Executing node copy in dir: /tmp/testconfig/copy
120411-21:37:31,19 workflow DEBUG:
	 Node hash: 5ca2ff61d87cb4a92049fb578c811808
120411-21:37:31,19 workflow DEBUG:
	 /tmp/testconfig/copy/_0x5ca2ff61d87cb4a92049fb578c811808_unfinished.json found and can_resume is True or Node is a MapNode - resuming execution
120411-21:37:31,19 workflow DEBUG:
	 Creating /tmp/testconfig/copy
120411-21:37:31,19 workflow DEBUG:
	 writing pre-exec report to /tmp/testconfig/copy/_report/report.rst
120411-21:37:31,21 workflow DEBUG:
	 Executing node
120411-21:37:31,21 workflow DEBUG:
	 copying files to wd [execute=True, linksonly=False]
120411-21:37:31,22 workflow DEBUG:
	 Needed files: /tmp/testconfig/copy/outfile;/tmp/testconfig/copy/_0x5ca2ff61d87cb4a92049fb578c811808_unfinished.json;/tmp/testconfig/copy/_inputs.pklz;/tmp/testconfig/copy/_node.pklz
120411-21:37:31,22 workflow DEBUG:
	 Needed dirs: /tmp/testconfig/copy/_report
120411-21:37:31,23 workflow DEBUG:
	 Removing files: 
120411-21:37:31,24 workflow DEBUG:
	 saved results in /tmp/testconfig/copy/result_copy.pklz
120411-21:37:31,24 workflow DEBUG:
	 writing post-exec report to /tmp/testconfig/copy/_report/report.rst
120411-21:37:31,25 workflow DEBUG:
	 Finished running copy in dir: /tmp/testconfig/copy

120411-21:37:33,16 workflow INFO:
	 [Job finished] jobname: copy jobid: 1
0.5.3
{'nibabel_version': '1.2.0.dev', 'networkx_version': '1.6', 'numpy_version': '1.6.1', 'sys_platform': 'linux2', 'sys_version': '2.7.2 |CUSTOM| (default, Jul  3 2011, 15:17:51) \n[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)]', 'commit_source': 'installation', 'commit_hash': '2672703', 'pkg_path': '/srv/software/python/EPD/virtualenvs/7.2/nipype0.5/lib/python2.7/site-packages/nipype', 'sys_executable': '/srv/software/python/EPD/virtualenvs/7.2/nipype0.5/bin/python', 'traits_version': '4.1.0', 'scipy_version': '0.10.0'}