Merge branch 'master' into fsl_b0

* master: (53 commits)
  Added a test for SPM bool conversion.
  Call super for all SPM _format_args()
  call super
  Make all Booleans to be formated as 1,0 in SPM
  updated changelog
  fix: added test for deepcopy bug
  fix: added back deepcopy
  fix: thanks to @rkern we now have a passing test with dynamic traits retaining their type through pickling
  fix: test that fails when traitedspec is not pickled properly
  updated changelog
  Added a default to maintain backwards compatibility
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  added mention about the new interface to the changelog
  Added tests stub files
  Make check-before-commit
  Significantly faster smoothing in tessellation_tutorial with MeshFix, CFF output option
  Interface for MeshFix by Marco Attene, Mirko Windhoff, Axel Thielscher
  Fixed deprecated config option.
  ...
Merge branch 'master' into fsl_model

* master: (53 commits)
  Added a test for SPM bool conversion.
  Call super for all SPM _format_args()
  call super
  Make all Booleans to be formated as 1,0 in SPM
  updated changelog
  fix: added test for deepcopy bug
  fix: added back deepcopy
  fix: thanks to @rkern we now have a passing test with dynamic traits retaining their type through pickling
  fix: test that fails when traitedspec is not pickled properly
  updated changelog
  Added a default to maintain backwards compatibility
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  added mention about the new interface to the changelog
  Added tests stub files
  Make check-before-commit
  Significantly faster smoothing in tessellation_tutorial with MeshFix, CFF output option
  Interface for MeshFix by Marco Attene, Mirko Windhoff, Axel Thielscher
  Fixed deprecated config option.
  ...
Merge branch 'master' into spm_interfaces

* master: (53 commits)
  Added a test for SPM bool conversion.
  Call super for all SPM _format_args()
  call super
  Make all Booleans to be formated as 1,0 in SPM
  updated changelog
  fix: added test for deepcopy bug
  fix: added back deepcopy
  fix: thanks to @rkern we now have a passing test with dynamic traits retaining their type through pickling
  fix: test that fails when traitedspec is not pickled properly
  updated changelog
  Added a default to maintain backwards compatibility
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  added mention about the new interface to the changelog
  Added tests stub files
  Make check-before-commit
  Significantly faster smoothing in tessellation_tutorial with MeshFix, CFF output option
  Interface for MeshFix by Marco Attene, Mirko Windhoff, Axel Thielscher
  Fixed deprecated config option.
  ...
merge
Merge branch 'master' into fsl_model

* master: (57 commits)
  Fixed afni test
  Fixed AFNI tests.
  Escape the expr parameter in 3dcalc.
  fixing TSNR integer data bug
  fix: update getmask to dilate while binarizing
  sty: rest formatting
  ENH: Provide access to all relevant BET outputs when "surfaces" option used.
  Skipping dynamic traits tests for now.
  Fixed failing doctest.
  sty: fixed white space and removed traits fix
  Reverted the traits "fix" workaround.
  Removed redundant example, renamed the antsRegistration template.
  Put interpolation argument back in. Renamed the input/outputspec.
  Added changelog information.
  Revert "fix: added test for deepcopy bug"
  reverted traits change2
  reverted traits change
  ENH: Future proof the API for new template building
  Fixed input/outputspec names.
  Refactoring.
  ...
Merge branch 'master' into fsl_b0

* master:
  Fixed afni test
  Fixed AFNI tests.
  Escape the expr parameter in 3dcalc.
  fixing TSNR integer data bug
  ENH: Provide access to all relevant BET outputs when "surfaces" option used.
adding fsl6 options (bbr)
typo
Merge branch 'master' into enh/fsl/flirt6

* master:
  fix: fsl tests
  sty: white space
  fix: automask bug when apply_mask is not specified
  fix: updated test writer with additional metadata
  fix: remove unnecessary print statement
  fix: trim http link for code
  fix: github url generation
  fix: return full hash
merge
Merge branch 'master' into fsl_model

* master: (21 commits)
  fix: fsl tests
  sty: white space
  fix: automask bug when apply_mask is not specified
  fix: updated test writer with additional metadata
  fix: remove unnecessary print statement
  fix: trim http link for code
  fix: github url generation
  fix: return full hash
  Removed unnecessary usedefault.
  fixed typo in a file name
  fix: github authentication
  Going back to distinguishing affine transformations by names. Improved docs.
  fixed typo in randomize parameters
  Removed unnecessary copyfiles and added output_image option.
  BF: Pass plugin_args to child nodes of MapNode
  ENH: Don't require ordereddict for python < 2.7
  BF: Fix for plugins when using python2.7
  Fixed parenthesis.
  Fix fslreorient2std output collection
  Allow FNIRT to take standard names as reference.
  ...
Introduce the non-daemon process pool as an alternative to the original multiprocessing pool. This adds support for hierarchical multiprocessing (child classes can use multiprocessing again).

The code is based on the following StackOverflow answer:
http://stackoverflow.com/a/8963618/1183453
Add the non_daemon option to execute the MultiProcPlugin nodes as non-daemon processes.
Merge branch 'master' into fsl_b0

* master: (188 commits)
  fixed paths
  Back to dev
  0.7 release
  Code cleanup.
  doc: updated inputs help to indicate FSL and AFNI inaccuracy when using bounds_by_brainmask
  Fix #493
  Fixes #459
  fixed doctests
  changelog
  fix: ants workflows setup
  BF: Fixed several issues with GroupAndStack interface
  DOC: Various clean up an improvements to docstrings.
  DOC: Added example to LookupMeta docstring
  ENH: Allow meta_keys input to LookupMeta be a mapping.
  minor fixes
  deprecated version should be a string, added AFNITraitedSpec for backward compatibility
  docs
  PEP8
  name_source can be a list, make "infolder" a deprecated name
  Removed unnecessary outputsspecs
  ...
Merge branch 'master' into fsl_model

* master: (188 commits)
  fixed paths
  Back to dev
  0.7 release
  Code cleanup.
  doc: updated inputs help to indicate FSL and AFNI inaccuracy when using bounds_by_brainmask
  Fix #493
  Fixes #459
  fixed doctests
  changelog
  fix: ants workflows setup
  BF: Fixed several issues with GroupAndStack interface
  DOC: Various clean up an improvements to docstrings.
  DOC: Added example to LookupMeta docstring
  ENH: Allow meta_keys input to LookupMeta be a mapping.
  minor fixes
  deprecated version should be a string, added AFNITraitedSpec for backward compatibility
  docs
  PEP8
  name_source can be a list, make "infolder" a deprecated name
  Removed unnecessary outputsspecs
  ...
Merge branch 'master' into enh/fsl/flirt6

* master: (188 commits)
  fixed paths
  Back to dev
  0.7 release
  Code cleanup.
  doc: updated inputs help to indicate FSL and AFNI inaccuracy when using bounds_by_brainmask
  Fix #493
  Fixes #459
  fixed doctests
  changelog
  fix: ants workflows setup
  BF: Fixed several issues with GroupAndStack interface
  DOC: Various clean up an improvements to docstrings.
  DOC: Added example to LookupMeta docstring
  ENH: Allow meta_keys input to LookupMeta be a mapping.
  minor fixes
  deprecated version should be a string, added AFNITraitedSpec for backward compatibility
  docs
  PEP8
  name_source can be a list, make "infolder" a deprecated name
  Removed unnecessary outputsspecs
  ...
typo
Merge branch 'master' into spm_interfaces

* master: (266 commits)
  fixed paths
  Back to dev
  0.7 release
  Code cleanup.
  doc: updated inputs help to indicate FSL and AFNI inaccuracy when using bounds_by_brainmask
  Fix #493
  Fixes #459
  fixed doctests
  changelog
  fix: ants workflows setup
  BF: Fixed several issues with GroupAndStack interface
  DOC: Various clean up an improvements to docstrings.
  DOC: Added example to LookupMeta docstring
  ENH: Allow meta_keys input to LookupMeta be a mapping.
  minor fixes
  deprecated version should be a string, added AFNITraitedSpec for backward compatibility
  docs
  PEP8
  name_source can be a list, make "infolder" a deprecated name
  Removed unnecessary outputsspecs
  ...
fixing wrong output directory in afni base gen_filename
adding doctest to sigloss