Merge pull request #2760 from nipy/rel/1.1.4

REL: 1.1.4

Author: effigies

.zenodo.json

@@ -74,20 +74,20 @@
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Waskom, Michael"
     },
-    {
-      "affiliation": "Developer",
-      "name": "Clark, Daniel",
-      "orcid": "0000-0002-8121-8954"
-    },
     {
       "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
       "name": "Wong, Jason"
     },
+    {
+      "name": "Modat, Marc"
+    },
     {
       "name": "Loney, Fred"
     },
     {
-      "name": "Modat, Marc"
+      "affiliation": "Developer",
+      "name": "Clark, Daniel",
+      "orcid": "0000-0002-8121-8954"
     },
     {
       "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
@@ -141,16 +141,6 @@
     {
       "name": "Berleant, Shoshana"
     },
-    {
-      "affiliation": "MIT",
-      "name": "Kaczmarzyk, Jakub",
-      "orcid": "0000-0002-5544-7577"
-    },
-    {
-      "affiliation": "INRIA",
-      "name": "Varoquaux, Gael",
-      "orcid": "0000-0003-1076-5122"
-    },
     {
       "affiliation": "UC San Diego",
       "name": "Cipollini, Ben",
@@ -176,9 +166,24 @@
       "name": "DuPre, Elizabeth",
       "orcid": "0000-0003-1358-196X"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Kaczmarzyk, Jakub",
+      "orcid": "0000-0002-5544-7577"
+    },
     {
       "name": "Moloney, Brendan"
     },
+    {
+      "affiliation": "INRIA",
+      "name": "Varoquaux, Gael",
+      "orcid": "0000-0003-1076-5122"
+    },
+    {
+      "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
+      "name": "Horea, Christian",
+      "orcid": "0000-0001-7037-2449"
+    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann , Demian",
@@ -189,11 +194,6 @@
       "name": "Hanke, Michael",
       "orcid": "0000-0001-6398-6370"
     },
-    {
-      "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
-      "name": "Horea, Christian",
-      "orcid": "0000-0001-7037-2449"
-    },
     {
       "affiliation": "Vrije Universiteit, Amsterdam",
       "name": "Gilles de Hollander",
@@ -268,11 +268,6 @@
     {
       "name": "Cumba, Chad"
     },
-    {
-      "affiliation": "Harvard University - Psychology",
-      "name": "Kastman, Erik",
-      "orcid": "0000-0001-7221-9042"
-    },
     {
       "affiliation": "SRI International",
       "name": "Nichols, B. Nolan",
@@ -283,6 +278,11 @@
       "name": "Eshaghi, Arman",
       "orcid": "0000-0002-6652-3512"
     },
+    {
+      "affiliation": "Harvard University - Psychology",
+      "name": "Kastman, Erik",
+      "orcid": "0000-0001-7221-9042"
+    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -297,8 +297,9 @@
       "orcid": "0000-0001-6392-6634"
     },
     {
-      "affiliation": "Child Mind Institute",
-      "name": "Giavasis, Steven"
+      "affiliation": "University of Zurich",
+      "name": "Liem, Franz",
+      "orcid": "0000-0003-0646-4810"
     },
     {
       "affiliation": "UniversityHospital Heidelberg, Germany",
@@ -308,7 +309,8 @@
       "name": "Erickson, Drew"
     },
     {
-      "name": "K\u00fcttner, Ren\u00e9"
+      "affiliation": "Child Mind Institute",
+      "name": "Giavasis, Steven"
     },
     {
       "name": "Haselgrove, Christian"
@@ -320,9 +322,7 @@
       "name": "Ghayoor, Ali"
     },
     {
-      "affiliation": "University of Zurich",
-      "name": "Liem, Franz",
-      "orcid": "0000-0003-0646-4810"
+      "name": "K\u00fcttner, Ren\u00e9"
     },
     {
       "name": "Millman, Jarrod"
@@ -385,10 +385,6 @@
       "name": "Chetverikov, Andrey",
       "orcid": "0000-0003-2767-6310"
     },
-    {
-      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
-      "name": "Weninger, Leon"
-    },
     {
       "name": "Salvatore, John"
     },
@@ -403,9 +399,6 @@
       "name": "Craddock, R. Cameron",
       "orcid": "0000-0002-4950-1303"
     },
-    {
-      "name": "Inati, Souheil"
-    },
     {
       "name": "Hinds, Oliver"
     },
@@ -414,6 +407,13 @@
       "name": "Cooper, Gavin",
       "orcid": "0000-0002-7186-5293"
     },
+    {
+      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
+      "name": "Weninger, Leon"
+    },
+    {
+      "name": "Inati, Souheil"
+    },
     {
       "affiliation": "Boston University",
       "name": "Perkins, L. Nathan"
@@ -443,9 +443,6 @@
       "name": "Floren, Andrew",
       "orcid": "0000-0003-3618-2056"
     },
-    {
-      "name": "Rothmei, Simon"
-    },
     {
       "name": "Urchs, Sebastian"
     },
@@ -465,6 +462,11 @@
       "name": "Geisler, Daniel",
       "orcid": "0000-0003-2076-5329"
     },
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "De La Vega, Alejandro",
+      "orcid": "0000-0001-9062-3778"
+    },
     {
       "affiliation": "University of illinois urbana champaign",
       "name": "Sharp, Paul"
@@ -493,6 +495,9 @@
     {
       "name": "Saase, Victor"
     },
+    {
+      "name": "Rothmei, Simon"
+    },
     {
       "affiliation": "University of Helsinki",
       "name": "Andberg, Sami Kristian",
@@ -518,11 +523,6 @@
     {
       "name": "Tarbert, Claire"
     },
-    {
-      "affiliation": "University of Texas at Austin",
-      "name": "De La Vega, Alejandro",
-      "orcid": "0000-0001-9062-3778"
-    },
     {
       "affiliation": "Vrije Universiteit Amsterdam",
       "name": "Ort, Eduard"

doc/changelog/1.X.X-changelog

@@ -1,3 +1,31 @@
+1.1.4 (October 31, 2018)
+========================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/25?closed=1)
+
+  * FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754)
+  * FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757)
+  * FIX: Refine FSL.split output identification (https://github.com/nipy/nipype/pull/2746)
+  * FIX: Reuse _gen_filename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734)
+  * FIX: Remove 'reg_term' default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731)
+  * FIX: Keep profile files when ``remove_unnecessary_outputs = true`` (https://github.com/nipy/nipype/pull/2718)
+  * ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (https://github.com/nipy/nipype/pull/2740)
+  * ENH: Add compression option for bru2nii (https://github.com/nipy/nipype/pull/2762)
+  * ENH: Add slice_encoding_direction input to TShift (https://github.com/nipy/nipype/pull/2753)
+  * ENH: Add 'sse' output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749)
+  * ENH: Update ``ants.LaplacianThickness`` to use ``name_source`` (https://github.com/nipy/nipype/pull/2747)
+  * ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735)
+  * ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725)
+  * TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730)
+  * DOC: Move user docs from nipype to nipype_tutorial (https://github.com/nipy/nipype/pull/2726)
+  * DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758)
+  * MAINT: Use neurodocker 0.4.1 + apt install afni (https://github.com/nipy/nipype/pull/2707)
+  * MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701)
+  * MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723)
+  * MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728)
+  * CI: Lock travis pybids 0.6.5 (https://github.com/nipy/nipype/pull/2720)
+
+
 1.1.3 (September 24, 2018)
 ==========================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.3"
+release = "1.1.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

nipype/info.py

@@ -11,7 +11,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.1.4-dev'
+__version__ = '1.1.4'
 
 
 def get_nipype_gitversion():

nipype/interfaces/afni/tests/test_auto_TShift.py

@@ -30,6 +30,7 @@ def test_TShift_inputs():
         outputtype=dict(),
         rlt=dict(argstr='-rlt', ),
         rltplus=dict(argstr='-rlt+', ),
+        slice_encoding_direction=dict(usedefault=True, ),
         slice_timing=dict(
             argstr='-tpattern @%s',
             xor=['tpattern'],

nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py

@@ -52,8 +52,8 @@ def test_AntsJointFusion_inputs():
             hash_files=False,
         ),
         out_label_post_prob_name_format=dict(
-            requires=['out_label_fusion', 'out_intensity_fusion_name_format'],
-        ),
+            requires=['out_label_fusion',
+                      'out_intensity_fusion_name_format'], ),
         patch_metric=dict(argstr='-m %s', ),
         patch_radius=dict(
             argstr='-p %s',

nipype/interfaces/dipy/tests/test_auto_DTI.py

@@ -20,6 +20,7 @@ def test_DTI_inputs():
 def test_DTI_outputs():
     output_map = dict(
         ad_file=dict(),
+        color_fa_file=dict(),
         fa_file=dict(),
         md_file=dict(),
         out_file=dict(),

nipype/interfaces/fsl/tests/test_auto_DTIFit.py

@@ -65,8 +65,8 @@ def test_DTIFit_outputs():
         V1=dict(),
         V2=dict(),
         V3=dict(),
-        tensor=dict(),
         sse=dict(),
+        tensor=dict(),
     )
     outputs = DTIFit.output_spec()
 

nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py

@@ -0,0 +1,85 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import RealignUnwarp
+
+
+def test_RealignUnwarp_inputs():
+    input_map = dict(
+        est_basis_func=dict(field='uweoptions.basfcn', ),
+        est_first_order_effects=dict(field='uweoptions.fot', ),
+        est_jacobian_deformations=dict(field='uweoptions.jm', ),
+        est_num_of_interations=dict(
+            field='uweoptions.noi',
+            maxlen=1,
+            minlen=1,
+            usedfault=True,
+        ),
+        est_re_est_mov_par=dict(field='uweoptions.rem', ),
+        est_reg_factor=dict(
+            field='uweoptions.lambda',
+            maxlen=1,
+            minlen=1,
+            usedefault=True,
+        ),
+        est_reg_order=dict(field='uweoptions.regorder', ),
+        est_second_order_effects=dict(field='uweoptions.sot', ),
+        est_taylor_expansion_point=dict(
+            field='uweoptions.expround',
+            usedefault=True,
+        ),
+        est_unwarp_fwhm=dict(field='uweoptions.uwfwhm', ),
+        fwhm=dict(field='eoptions.fwhm', ),
+        in_files=dict(
+            copyfile=True,
+            field='data.scans',
+            mandatory=True,
+        ),
+        interp=dict(field='eoptions.einterp', ),
+        matlab_cmd=dict(),
+        mfile=dict(usedefault=True, ),
+        out_prefix=dict(
+            field='uwroptions.prefix',
+            usedefault=True,
+        ),
+        paths=dict(),
+        phase_map=dict(
+            copyfile=False,
+            field='data.pmscan',
+        ),
+        quality=dict(field='eoptions.quality', ),
+        register_to_mean=dict(field='eoptions.rtm', ),
+        reslice_interp=dict(field='uwroptions.rinterp', ),
+        reslice_mask=dict(field='uwroptions.mask', ),
+        reslice_which=dict(
+            field='uwroptions.uwwhich',
+            maxlen=2,
+            minlen=2,
+            usedefault=True,
+        ),
+        reslice_wrap=dict(field='uwroptions.wrap', ),
+        separation=dict(field='eoptions.sep', ),
+        use_mcr=dict(),
+        use_v8struct=dict(
+            min_ver='8',
+            usedefault=True,
+        ),
+        weight_img=dict(field='eoptions.weight', ),
+        wrap=dict(field='eoptions.ewrap', ),
+    )
+    inputs = RealignUnwarp.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_RealignUnwarp_outputs():
+    output_map = dict(
+        mean_image=dict(),
+        modified_in_files=dict(),
+        realigned_unwarped_files=dict(),
+        realignment_parameters=dict(),
+    )
+    outputs = RealignUnwarp.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value