Merge remote-tracking branch 'upstream/master' into sty/pepping

* upstream/master:
  [HOTFIX] Incorrect call to warnings.warn
  updating the auto test
  FIX: updates hash to accept newline in realign_json.json
  FIX: Reset change to make hash assertion happy
  Reset change to make hash assertion happy
  STY: adds newline to end of file
  STY: delets heading newline in textfiles
  STY: correct for newline at end of file
  STY: correct for tailing spaces and newline at end of file
  STY: correct for tailing spaces and newline at end of file
  [FIX] Fix surf_reg input trait
  Update dti.py

Author: satra

.dockerignore

@@ -34,4 +34,4 @@ Vagrantfile
 .mailmap
 
 # Previous coverage results
-.coverage
+.coverage

CONTRIBUTING.md

@@ -16,8 +16,8 @@
 * The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
 * Run `make check-before-commit` before submitting the PR.
   This will require you to either install or be in developer mode with: `python setup.py install/develop`.
-* In general, do not catch exceptions without good reason. 
-  * catching non-fatal exceptions. 
+* In general, do not catch exceptions without good reason.
+  * catching non-fatal exceptions.
     Log the exception as a warning.
   * adding more information about what may have caused the error.
     Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.

codecov.yml

@@ -25,4 +25,4 @@ coverage:
   ignore:          # files and folders that will be removed during processing
     - "nipype/external/*"
     - "tools/*"
-    - "doc/*"
+    - "doc/*"

doc/_static/nipype.css

@@ -57,4 +57,4 @@ div.doc2.container ul{
 
 div.doc2 .reference.internal{
     font-size: 14px;
-}
+}

doc/devel/gitwash/git_links.inc

@@ -2,7 +2,7 @@
    and name substitutions.  It may be included in many files,
    therefore it should only contain link targets and name
    substitutions.  Try grepping for "^\.\. _" to find plausible
-   candidates for this list.  
+   candidates for this list.
 
 .. NOTE: reST targets are
    __not_case_sensitive__, so only one target definition is needed for
@@ -42,7 +42,7 @@
 .. _git config: http://www.kernel.org/pub/software/scm/git/docs/git-config.html
 .. _why the -a flag?: http://www.gitready.com/beginner/2009/01/18/the-staging-area.html
 .. _git staging area: http://www.gitready.com/beginner/2009/01/18/the-staging-area.html
-.. _tangled working copy problem: http://tomayko.com/writings/the-thing-about-git 
+.. _tangled working copy problem: http://tomayko.com/writings/the-thing-about-git
 .. _git management: http://kerneltrap.org/Linux/Git_Management
 .. _linux git workflow: http://www.mail-archive.com/[email protected]/msg39091.html
 .. _git parable: http://tom.preston-werner.com/2009/05/19/the-git-parable.html

doc/searchresults.rst

@@ -170,4 +170,4 @@ Search results
       .gsc-resultsHeader {
          clear: none;
       }
-    </style>
+    </style>

doc/users/aws.rst

@@ -99,4 +99,4 @@ s3://mybucket/path/to/output/dir/sub001/motion/realigned_file1.nii.gz
 
 Using S3DataGrabber
 ======================
-Coming soon...
+Coming soon...

doc/users/caching_tutorial.rst

@@ -1,4 +1,3 @@
-
 .. _caching:
 
 ===========================

doc/users/config_file.rst

@@ -170,7 +170,7 @@ Resource Monitor
     Indicates where the summary file collecting all profiling information from the
     resource monitor should be stored after execution of a workflow.
     The ``summary_file`` does not apply to interfaces run independently.
-    (unset by default, in which case the summary file will be written out to 
+    (unset by default, in which case the summary file will be written out to
     ``<base_dir>/resource_monitor.json`` of the top-level workflow).
 
 *summary_append*

doc/users/install.rst

@@ -117,4 +117,4 @@ Developers should start `here <../devel/testing_nipype.html>`_.
 
 Developers can also use this docker container: `docker pull nipype/nipype:master`
 
-.. include:: ../links_names.txt
+.. include:: ../links_names.txt

doc/users/plugins.rst

@@ -82,9 +82,9 @@ Optional arguments::
   exceed the total amount of resources available (memory and threads), when
   ``False`` (default), only a warning will be issued.
 
-  maxtasksperchild : number of nodes to run on each process before refreshing 
+  maxtasksperchild : number of nodes to run on each process before refreshing
   the worker (default: 10).
-  
+
 
 To distribute processing on a multicore machine, simply call::
 

doc/users/sphinx_ext.rst

@@ -1,4 +1,3 @@
-
 .. _sphinx_ext:
 
 Sphinx extensions
@@ -11,4 +10,4 @@ and simplify the generation process.
 
 .. automodule:: nipype.sphinxext.plot_workflow
     :undoc-members:
-    :noindex:
+    :noindex:

examples/nipype_tutorial.ipynb

@@ -1747,4 +1747,4 @@
    "metadata": {}
   }
  ]
-}
+}

nipype/external/d3.js

@@ -9252,4 +9252,4 @@
   } else {
     this.d3 = d3;
   }
-}();
+}();

nipype/interfaces/base/tests/test_support.py

@@ -57,7 +57,7 @@ def test_bunch_hash():
                   otherthing='blue',
                   yat=True)
     newbdict, bhash = b._get_bunch_hash()
-    assert bhash == 'ddcc7b4ec5675df8cf317a48bd1857fa'
+    assert bhash == 'd1f46750044c3de102efc847720fc35f'
     # Make sure the hash stored in the json file for `infile` is correct.
     jshash = md5()
     with open(json_pth, 'r') as fp:

nipype/interfaces/diffusion_toolkit/dti.py

@@ -131,7 +131,7 @@ class DTITrackerInputSpec(CommandLineInputSpec):
     angle_threshold_weight = traits.Float(desc="set angle threshold weighting factor. weighting will be be applied \
         on top of the angle_threshold", argstr="-atw %f")
     random_seed = traits.Int(desc="use random location in a voxel instead of the center of the voxel \
-          to seed. can also define number of seed per voxel. default is 1", argstr="-rseed")
+          to seed. can also define number of seed per voxel. default is 1", argstr="-rseed %d")
     invert_x = traits.Bool(desc="invert x component of the vector", argstr="-ix")
     invert_y = traits.Bool(desc="invert y component of the vector", argstr="-iy")
     invert_z = traits.Bool(desc="invert z component of the vector", argstr="-iz")

nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py

@@ -48,7 +48,7 @@ def test_DTITracker_inputs():
     ),
     primary_vector=dict(argstr='-%s',
     ),
-    random_seed=dict(argstr='-rseed',
+    random_seed=dict(argstr='-rseed %d',
     ),
     step_length=dict(argstr='-l %f',
     ),

nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py

@@ -93,7 +93,7 @@ def test_SampleToSurface_inputs():
     ),
     subject_id=dict(),
     subjects_dir=dict(),
-    surf_reg=dict(argstr='--surfreg',
+    surf_reg=dict(argstr='--surfreg %s',
     requires=['target_subject'],
     ),
     surface=dict(argstr='--surf %s',

nipype/interfaces/freesurfer/utils.py

@@ -142,8 +142,9 @@ class SampleToSurfaceInputSpec(FSTraitedSpec):
     subject_id = traits.String(desc="subject id")
     target_subject = traits.String(argstr="--trgsubject %s",
                                    desc="sample to surface of different subject than source")
-    surf_reg = traits.Bool(argstr="--surfreg", requires=["target_subject"],
-                           desc="use surface registration to target subject")
+    surf_reg = traits.Either(traits.Bool, traits.Str(),
+                             argstr="--surfreg %s", requires=["target_subject"],
+                             desc="use surface registration to target subject")
     ico_order = traits.Int(argstr="--icoorder %d", requires=["target_subject"],
                            desc="icosahedron order when target_subject is 'ico'")
 
@@ -241,6 +242,10 @@ def _format_arg(self, name, spec, value):
 
             if value in implicit_filetypes:
                 return ""
+        if name == 'surf_reg':
+            if value is True:
+                return spec.argstr % 'sphere.reg'
+
         return super(SampleToSurface, self)._format_arg(name, spec, value)
 
     def _get_outfilename(self, opt="out_file"):

nipype/interfaces/fsl/model_templates/feat_fe_header.tcl

@@ -259,7 +259,7 @@ set fmri(regstandard_dof) 12
 set fmri(regstandard_nonlinear_yn) 0
 
 # Control nonlinear warp field resolution
-set fmri(regstandard_nonlinear_warpres) 10 
+set fmri(regstandard_nonlinear_warpres) 10
 
 # High pass filter cutoff
 set fmri(paradigm_hp) 100

nipype/interfaces/fsl/model_templates/feat_header.tcl

@@ -17,7 +17,7 @@ set fmri(level) 1
 # 2 :             Stats
 # 6 :             Stats + Post-stats
 # 4 :                     Post-stats
-set fmri(analysis) $analysis_stages 
+set fmri(analysis) $analysis_stages
 
 # Use relative filenames
 set fmri(relative_yn) 0
@@ -57,7 +57,7 @@ set fmri(inputtype) 1
 # Carry out pre-stats processing?
 set fmri(filtering_yn) 0
 
-# Brain/background threshold, 
+# Brain/background threshold,
 set fmri(brain_thresh) 10
 
 # Critical z for design efficiency calculation
@@ -157,7 +157,7 @@ set fmri(evs_real) $num_evs
 set fmri(evs_vox) 0
 
 # Number of contrasts
-set fmri(ncon_orig) $num_contrasts 
+set fmri(ncon_orig) $num_contrasts
 set fmri(ncon_real) $num_contrasts
 
 # Number of F-tests
@@ -259,7 +259,7 @@ set fmri(regstandard_dof) 12
 set fmri(regstandard_nonlinear_yn) 0
 
 # Control nonlinear warp field resolution
-set fmri(regstandard_nonlinear_warpres) 10 
+set fmri(regstandard_nonlinear_warpres) 10
 
 # High pass filter cutoff
 set fmri(paradigm_hp) 100

nipype/interfaces/fsl/model_templates/feat_header_l1.tcl

@@ -57,7 +57,7 @@ set fmri(inputtype) 2
 # Carry out pre-stats processing?
 set fmri(filtering_yn) 0
 
-# Brain/background threshold, 
+# Brain/background threshold,
 set fmri(brain_thresh) 10
 
 # Critical z for design efficiency calculation
@@ -259,7 +259,7 @@ set fmri(regstandard_dof) 0
 set fmri(regstandard_nonlinear_yn) 0
 
 # Control nonlinear warp field resolution
-set fmri(regstandard_nonlinear_warpres) 10 
+set fmri(regstandard_nonlinear_warpres) 10
 
 # High pass filter cutoff
 set fmri(paradigm_hp) $high_pass_filter_cutoff

nipype/interfaces/fsl/model_templates/featreg_header.tcl

@@ -259,7 +259,7 @@ set fmri(regstandard_dof) $regdof
 set fmri(regstandard_nonlinear_yn) 0
 
 # Control nonlinear warp field resolution
-set fmri(regstandard_nonlinear_warpres) 10 
+set fmri(regstandard_nonlinear_warpres) 10
 
 # High pass filter cutoff
 set fmri(paradigm_hp) 100

nipype/pytest.ini

@@ -1,4 +1,4 @@
 [pytest]
 norecursedirs = .git build dist doc nipype/external tools examples src
 addopts = --doctest-modules
-doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE
+doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE

nipype/refs.py

@@ -1,4 +1,3 @@
-
 # Use duecredit (duecredit.org) to provide a citation to relevant work to
 # be cited. This does nothing, unless the user has duecredit installed,
 # And calls this with duecredit (as in `python -m duecredit script.py`):

nipype/testing/data/README

@@ -3,4 +3,4 @@ in the doctests of nipype.  For verion 0.3 of nipype, we're using
 Traits and for input files, the code checks to confirm the assigned
 files actually exist.  It doesn't matter what the files are, or even
 if they contain "real data", only that they exist.  Again, these files
-are only meant to serve as documentation in the doctests.
+are only meant to serve as documentation in the doctests.

nipype/testing/data/bedpostxout/do_not_delete.txt

@@ -1 +1 @@
-This file has to be here because git ignores empty folders.
+This file has to be here because git ignores empty folders.

nipype/testing/data/fmri_timeseries_nolabels.csv

@@ -1 +1 @@
-{"param2": 4, "param1": "exampleStr"}
+{"param2": 4, "param1": "exampleStr"}

nipype/testing/data/jsongrabber.txt

@@ -31,4 +31,4 @@
     "write_mask": null,
     "write_which": null,
     "write_wrap": null
-}
+}

nipype/testing/data/realign_json.json

@@ -177,4 +177,4 @@
     ],
     "dimension": 3,
     "collapse_output_transforms": false
-}
+}

nipype/testing/data/smri_ants_registration_settings.json

@@ -6,9 +6,9 @@ try,
         end;
         spm_path = spm('dir');
         fprintf(1, 'NIPYPE  %s', spm_path);
-        
+
 ,catch ME,
 fprintf(2,'MATLAB code threw an exception:\n');
 fprintf(2,'%s\n',ME.message);
 if length(ME.stack) ~= 0, fprintf(2,'File:%s\nName:%s\nLine:%d\n',ME.stack.file,ME.stack.name,ME.stack.line);, end;
-end;
+end;

nipype/testing/data/spminfo

@@ -1 +1 @@
-This file has to be here because git ignores empty folders.
+This file has to be here because git ignores empty folders.

nipype/testing/data/tbss_dir/do_not_delete.txt

@@ -126,8 +126,8 @@ def cwd(self):
             try:
                 self._cwd = os.getcwd()
             except OSError:
-                warn('Trying to run Nipype from a nonexistent directory "%s".',
-                     os.getenv('PWD', 'unknown'))
+                warn('Trying to run Nipype from a nonexistent directory "{}".'.format(
+                     os.getenv('PWD', 'unknown')), RuntimeWarning)
                 raise
         return self._cwd
 

nipype/utils/config.py

@@ -36,4 +36,4 @@
 else
   objlist = {objlist{:} astruct};
 end
-end
+end

nipype/utils/spm_flat_config.m

@@ -3,7 +3,7 @@ setscale 4
 setoption smoothing 6
 setoption paramsubset 1  0 0 0 0 0 0 1 1 1 1 1 1
 clear U
-clear UA 
+clear UA
 clear UB
 clear US
 clear UP
@@ -53,7 +53,7 @@ clear U
 setrow UG  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1
 optimise 7 UG  0.0   0.0   0.0   0.0   0.0   0.0   0.0  abs 2
 sort U
-copy U UG 
+copy U UG
 # 1mm scale
 setscale 1
 setoption smoothing 2

nipype/workflows/data/ecc.sch

@@ -2,7 +2,7 @@
 setscale 4
 setoption smoothing 6
 clear U
-clear UA 
+clear UA
 clear UB
 clear US
 clear UP
@@ -51,7 +51,7 @@ clear U
 setrow UG  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1
 optimise 7 UG  0.0   0.0   0.0   0.0   0.0   0.0   0.0  abs 2
 sort U
-copy U UG 
+copy U UG
 # 1mm scale
 setscale 1
 setoption smoothing 2