ENH: added preliminary support for entire graph submission with initial support for Soma Workflow and PBS
FIX: added blocking and cleaned up test
Merge remote-tracking branch 'upstream/master' into enh/graphsubmission

* upstream/master: (24 commits)
  password and username are mandatory through dependence
  Added config option
  Removed doc warning
  Added MySQL interface.
  fixed docs
  Added similarity calculation interface
  pep8
  Extension is now based on the input file name
  Added missing config
  RF: hash check now ensures that job doesn't get executed if local hash check is set and hash exists
  changelog fix
  imports and pep8 cleanup
  Improved error message.
  Added support for a list of 3d files for TSNR calculation.
  fix: added check for inputs within run
  FIX: local hash check uses proper inputs
  fixed trailing parenthesis
  FIX: Afni outputspec fixes
  fixing implicit_masking option formating
  Forced absolute paths for BEM outputs
  ...
fix: removed matplotlib as a dependency
FIX: added argstr to interp_method
fix: remove matplotlib dependency from test_nitime
fix: remove matplotlib dependency from nitime
fix: removed soma dependency so that tests can pass when not somaflow is not installed.
Merge branch 'master' into enh/graphsubmission

* master:
  Removed unnecessary 'in_file' argument
fix: script generation now uses OrderedDict
fix: updated pbsgraph so that it works at mit
ENH: Whole-graph submission to Condor DAGMan

This is an initial implementation. it should work and should be
reasonable feature-complete. If this gets merged into master it should
replace the qsub-based Condor plugin, as this implementation requires no
additional software (qsub wrapper) it should be more efficient and
versatile.

The code needs to be considered experimental, as it has only been tested
with trivial workflows.

If the old Condor plugin gets removed a documentation update needs to
happen.
Merge remote-tracking branch 'gh-satra/enh/graphsubmission' into enh/graphsubmission
Merge pull request #8 from hanke/enh/graphsubmission

This is an initial implementation of a Condor DAGMan plugin
RF: removed unnecessary agg call - done automatically for all nodes
Merge remote-tracking branch 'upstream/master' into enh/graphsubmission

* upstream/master: (21 commits)
  added changelog message
  removed unused variables
  removed unused imports
  pep8 and reindent
  removed an evil trailing comma from WIMT
  AFNITraitedSpec for Calc
  this is the nth time that I change this...
  test/fixs
  fixing what I messed up
  fixing abspath
  multiple files for tcat and merge
  default suffix more appropriated
  fixing tests accordingly
  use of default_output_type was broken, homogeneizing the inputs/outputs of interfaces, InputMultiPath for Merge and TCat
  adding outfile suffix option to all the interfaces, fixing TCat for it to accept multiple in_files
  Renamed NBS interface
  Threshold to a float
  Typo fix
  Replaced CFF option with multiple network output
  Added optional node position network
  ...
Merge branch 'master' into enh/graphsubmission

* master: (21 commits)
  added changelog message
  removed unused variables
  removed unused imports
  pep8 and reindent
  removed an evil trailing comma from WIMT
  AFNITraitedSpec for Calc
  this is the nth time that I change this...
  test/fixs
  fixing what I messed up
  fixing abspath
  multiple files for tcat and merge
  default suffix more appropriated
  fixing tests accordingly
  use of default_output_type was broken, homogeneizing the inputs/outputs of interfaces, InputMultiPath for Merge and TCat
  adding outfile suffix option to all the interfaces, fixing TCat for it to accept multiple in_files
  Renamed NBS interface
  Threshold to a float
  Typo fix
  Replaced CFF option with multiple network output
  Added optional node position network
  ...
Merge branch 'master' into enh/graphsubmission

* master:
  doc: updated debug config message.
  ants code cleanup (PEP8, unused variables)
  removed in_file from DTLUTGen docstring
  fix: added test to check that inputs are not modified when setting display variable via config
  fix: added tests, actually added display variable to config
  fix: interface environment always overwrites config environ DISPLAY
  doc: change closes #368
  fix: environment inputs not changed by config display variable
  Fixes to fsl interface out_file fields
Merge remote-tracking branch 'upstream/master' into enh/graphsubmission

* upstream/master:
  fixed cleanup bug
  more tests: subdirs, files not listed in outputs, removed_unnecessary_outputs/keep_inputs interaction
  grammar
  Explained the files removal feature better.
  A test case for output removal
  doc: updated debug config message.
  ants code cleanup (PEP8, unused variables)
  removed in_file from DTLUTGen docstring
  fix: added test to check that inputs are not modified when setting display variable via config
  fix: added tests, actually added display variable to config
  fix: interface environment always overwrites config environ DISPLAY
  doc: change closes #368
  fix: environment inputs not changed by config display variable
  Fixes to fsl interface out_file fields
Merge remote-tracking branch 'upstream/master' into enh/graphsubmission

* upstream/master:
  fixed cleanup bug
  more tests: subdirs, files not listed in outputs, removed_unnecessary_outputs/keep_inputs interaction
  grammar
  Explained the files removal feature better.
  A test case for output removal