Merge branch 'master' into spm/reslicetoref

* master:
  Put units into descr.
  FIX: strip extraneous whitespace in trait desc
  Added note about PBS optional argument for maximum jobname length.
  BF: moment parameter was ignored.
  Fixed variable name in PBS plugin.  Now works.
  Changes to PBS pipeline plugin.  Added a maximum length to the jobname, using a default value of 15 corresponding to the Torque maximum.  Modified the config file to do a local hash check by default.
  fix: avoid stopping of nipype-workflow caused by temporarily suspended LSF-jobs, And changed logfile of lsf-jobs from <lsf_jobid>.out to <scriptname>.log
  Added FSL output type NIFTI to dmri mrtrix example

Author: bpinsard

doc/users/config_file.rst

@@ -95,7 +95,7 @@ Execution
     Perform the hash check on the job submission machine. This option minimizes
     the number of jobs submitted to a cluster engine or a multiprocessing pool
     to only those that need to be rerun. (possible values: ``true`` and
-    ``false``; default value: ``false``)
+    ``false``; default value: ``true``)
 
 *job_finished_timeout*
     When batch jobs are submitted through, SGE/PBS/Condor they could be killed

doc/users/plugins.rst

@@ -114,6 +114,7 @@ Optional arguments::
 
   template: custom template file to use
   qsub_args: any other command line args to be passed to qsub.
+  max_jobname_len: (PBS only) maximum length of the job name.  Default 15.
 
 For example, the following snippet executes the workflow on myqueue with
 a custom template::

examples/dmri_mrtrix_dti.py

@@ -27,6 +27,8 @@
 import nipype.algorithms.misc as misc
 import os, os.path as op                     # system functions
 
+fsl.FSLCommand.set_default_output_type('NIFTI')
+
 """
 This needs to point to the fdt folder you can find after extracting
 

nipype/algorithms/misc.py

@@ -1036,7 +1036,6 @@ def calc_moments(timeseries_file, moment):
     """
     timeseries = np.genfromtxt(timeseries_file)
 
-    moment = 3
     m2 = stats.moment(timeseries, 2, axis=0)
     m3 = stats.moment(timeseries, moment, axis=0)
     zero = (m2 == 0)

nipype/interfaces/base.py

@@ -13,6 +13,7 @@
 import datetime
 import errno
 import os
+import re
 from socket import gethostname
 from string import Template
 import select
@@ -703,27 +704,37 @@ def _get_trait_desc(self, inputs, name, spec):
         requires = spec.requires
 
         manhelpstr = ['\t%s' % name]
+
         try:
             setattr(inputs, name, None)
         except TraitError as excp:
             def_val = ''
             if getattr(spec, 'usedefault'):
-                def_val = ', nipype default value: %s' % str(getattr(spec, 'default_value')()[1])
+                def_arg = getattr(spec, 'default_value')()[1]
+                def_val = ', nipype default value: %s' % def_arg
             line = "(%s%s)" % (excp.info, def_val)
-            manhelpstr = wrap(line, 90, initial_indent=manhelpstr[0]+': ',
+            manhelpstr = wrap(line, 70,
+                              initial_indent=manhelpstr[0]+': ',
                               subsequent_indent='\t\t ')
+
         if desc:
             for line in desc.split('\n'):
-                manhelpstr += wrap(line, 90, initial_indent='\t\t',
+                line = re.sub("\s+", " ", line)
+                manhelpstr += wrap(line, 70,
+                                   initial_indent='\t\t',
                                    subsequent_indent='\t\t')
+
         if xor:
             line = '%s' % ', '.join(xor)
-            manhelpstr += wrap(line, 90, initial_indent='\t\tmutually_exclusive: ',
+            manhelpstr += wrap(line, 70,
+                               initial_indent='\t\tmutually_exclusive: ',
                                subsequent_indent='\t\t ')
-        if requires: # and name not in xor_done:
+
+        if requires:
             others = [field for field in requires if field != name]
             line = '%s' % ', '.join(others)
-            manhelpstr += wrap(line, 90, initial_indent='\t\trequires: ',
+            manhelpstr += wrap(line, 70,
+                               initial_indent='\t\trequires: ',
                                subsequent_indent='\t\t ')
         return manhelpstr
 

nipype/interfaces/fsl/maths.py

@@ -143,9 +143,9 @@ class MaxImage(MathsCommand):
 class IsotropicSmoothInput(MathsInput):
 
     fwhm = traits.Float(mandatory=True, xor=["sigma"], position=4, argstr="-s %.5f",
-                        desc="fwhm of smoothing kernel")
+                        desc="fwhm of smoothing kernel [mm]")
     sigma = traits.Float(mandatory=True, xor=["fwhm"], position=4, argstr="-s %.5f",
-                         desc="sigma of smoothing kernel")
+                         desc="sigma of smoothing kernel [mm]")
 
 
 class IsotropicSmooth(MathsCommand):

nipype/pipeline/plugins/lsf.py

@@ -52,10 +52,10 @@ def _is_pending(self, taskid):
         result = cmd.run(ignore_exception=True)
         iflogger.setLevel(oldlevel)
         # logger.debug(result.runtime.stdout)
-        if 'PEND' in result.runtime.stdout or 'RUN' in result.runtime.stdout:
-            return True
-        else:
+        if 'DONE' in result.runtime.stdout or 'EXIT' in result.runtime.stdout:
             return False
+        else:
+            return True
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine('bsub', environ=os.environ.data,
@@ -71,9 +71,9 @@ def _submit_batchtask(self, scriptfile, node):
             else:
                 bsubargs += (" " + node.plugin_args['bsub_args'])
         if '-o' not in bsubargs:  # -o outfile
-            bsubargs = '%s -o %s' % (bsubargs, path)
+            bsubargs = '%s -o %s' % (bsubargs, scriptfile + ".log")
         if '-e' not in bsubargs:
-            bsubargs = '%s -e %s' % (bsubargs, path)  # -e error file
+            bsubargs = '%s -e %s' % (bsubargs, scriptfile + ".log")  # -e error file
         if node._hierarchy:
             jobname = '.'.join((os.environ.data['LOGNAME'],
                                 node._hierarchy,

nipype/pipeline/plugins/pbs.py

@@ -19,20 +19,27 @@ class PBSPlugin(SGELikeBatchManagerBase):
     - template : template to use for batch job submission
     - qsub_args : arguments to be prepended to the job execution script in the
                   qsub call
+    - max_jobname_len: maximum length of the job name.  Default 15.
 
     """
 
+    # Addtional class variables
+    _max_jobname_len = 15
+    
     def __init__(self, **kwargs):
         template = """
 #PBS -V
         """
         self._retry_timeout = 2
         self._max_tries = 2
+        self._max_jobname_length = 15
         if 'plugin_args' in kwargs and kwargs['plugin_args']:
             if 'retry_timeout' in kwargs['plugin_args']:
                 self._retry_timeout = kwargs['plugin_args']['retry_timeout']
             if  'max_tries' in kwargs['plugin_args']:
                 self._max_tries = kwargs['plugin_args']['max_tries']
+            if  'max_jobname_len' in kwargs['plugin_args']:
+                self._max_jobname_len = kwargs['plugin_args']['max_jobname_len']
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
@@ -71,6 +78,7 @@ def _submit_batchtask(self, scriptfile, node):
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()
         jobname = '.'.join(jobnameitems)
+        jobname = jobname[0:self._max_jobname_len]
         cmd.inputs.args = '%s -N %s %s' % (qsubargs,
                                            jobname,
                                            scriptfile)

nipype/utils/config.py

@@ -36,7 +36,7 @@
 hash_method = timestamp
 job_finished_timeout = 5
 keep_inputs = false
-local_hash_check = false
+local_hash_check = true
 matplotlib_backend = Agg
 plugin = Linear
 remove_node_directories = false