nipy · oesteban · Jan 9, 2018 · Jan 5, 2018 · Jan 5, 2018 · Jan 5, 2018
diff --git a/.dockerignore b/.dockerignore
@@ -34,4 +34,4 @@ Vagrantfile
 .mailmap
 
 # Previous coverage results
-.coverage
+.coverage
diff --git a/CONTRIBUTING.md b/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``.

diff --git a/codecov.yml b/codecov.yml
@@ -25,4 +25,4 @@ coverage:
   ignore:          # files and folders that will be removed during processing
     - "nipype/external/*"
     - "tools/*"
-    - "doc/*"
+    - "doc/*"
diff --git a/doc/_static/nipype.css b/doc/_static/nipype.css
@@ -57,4 +57,4 @@ div.doc2.container ul{
 
 div.doc2 .reference.internal{
     font-size: 14px;
-}
+}
diff --git a/doc/devel/gitwash/git_links.inc b/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/dri-devel@lists.sourceforge.net/msg39091.html
 .. _git parable: http://tom.preston-werner.com/2009/05/19/the-git-parable.html

diff --git a/doc/searchresults.rst b/doc/searchresults.rst
@@ -170,4 +170,4 @@ Search results
       .gsc-resultsHeader {
          clear: none;
       }
-    </style>
+    </style>
diff --git a/doc/users/aws.rst b/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...
diff --git a/doc/users/caching_tutorial.rst b/doc/users/caching_tutorial.rst
@@ -1,4 +1,3 @@
-
 .. _caching:
 
 ===========================

diff --git a/doc/users/config_file.rst b/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*

diff --git a/doc/users/install.rst b/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
diff --git a/doc/users/plugins.rst b/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::
 

diff --git a/doc/users/sphinx_ext.rst b/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:
diff --git a/examples/nipype_tutorial.ipynb b/examples/nipype_tutorial.ipynb
@@ -1747,4 +1747,4 @@
    "metadata": {}
   }
  ]
-}
+}
diff --git a/nipype/external/d3.js b/nipype/external/d3.js
@@ -9252,4 +9252,4 @@
   } else {
     this.d3 = d3;
   }
-}();
+}();
diff --git a/nipype/interfaces/base/tests/test_support.py b/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:

diff --git a/nipype/interfaces/fsl/model_templates/feat_fe_header.tcl b/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

diff --git a/nipype/interfaces/fsl/model_templates/feat_header.tcl b/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

diff --git a/nipype/interfaces/fsl/model_templates/feat_header_l1.tcl b/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

diff --git a/nipype/interfaces/fsl/model_templates/featreg_header.tcl b/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

diff --git a/nipype/pytest.ini b/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
diff --git a/nipype/refs.py b/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`):

diff --git a/nipype/testing/data/README b/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.
diff --git a/nipype/testing/data/bedpostxout/do_not_delete.txt b/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.
diff --git a/nipype/testing/data/fmri_timeseries_nolabels.csv b/nipype/testing/data/fmri_timeseries_nolabels.csv
diff --git a/nipype/testing/data/jsongrabber.txt b/nipype/testing/data/jsongrabber.txt
@@ -1 +1 @@
-{"param2": 4, "param1": "exampleStr"}
+{"param2": 4, "param1": "exampleStr"}
diff --git a/nipype/testing/data/realign_json.json b/nipype/testing/data/realign_json.json
@@ -31,4 +31,4 @@
     "write_mask": null,
     "write_which": null,
     "write_wrap": null
-}
+}
diff --git a/nipype/testing/data/smri_ants_registration_settings.json b/nipype/testing/data/smri_ants_registration_settings.json
@@ -177,4 +177,4 @@
     ],
     "dimension": 3,
     "collapse_output_transforms": false
-}
+}
diff --git a/nipype/testing/data/spminfo b/nipype/testing/data/spminfo
@@ -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;
diff --git a/nipype/testing/data/tbss_dir/do_not_delete.txt b/nipype/testing/data/tbss_dir/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.
diff --git a/nipype/utils/spm_flat_config.m b/nipype/utils/spm_flat_config.m
@@ -36,4 +36,4 @@
 else
   objlist = {objlist{:} astruct};
 end
-end
+end
diff --git a/nipype/workflows/data/ecc.sch b/nipype/workflows/data/ecc.sch
@@ -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

diff --git a/nipype/workflows/data/hmc.sch b/nipype/workflows/data/hmc.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

diff --git a/nipype/workflows/fmri/fsl/tests/test_preprocess.py b/nipype/workflows/fmri/fsl/tests/test_preprocess.py
@@ -22,4 +22,4 @@ def test_create_featreg_preproc():
 
     # test methods
     assert wf.get_node('extractref')
-    assert wf._get_dot()
+    assert wf._get_dot()
-Original file line number
+Diff line change
@@ Expand Up / @@ -57,4 +57,4 @@ div.doc2.container ul{ @@
     div.doc2 .reference.internal{
         font-size: 14px;
-    }
+    }
Original file line number	Diff line number	Diff line change
		@@ -1,4 +1,3 @@

		.. _caching:

		===========================
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		This file has to be here because git ignores empty folders.
		This file has to be here because git ignores empty folders.
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"param2": 4, "param1": "exampleStr"}
		{"param2": 4, "param1": "exampleStr"}