Merge branch 'master' into eddy

Author: niklasfoe

.circleci/config.yml

@@ -1,5 +1,5 @@
 _machine_kwds: &machine_kwds
-  image: circleci/classic:201710-02
+  image: circleci/classic:201808-01
 
 _store_artifacts_kwds: &store_artifacts_kwds
   path: /home/circleci/work/tests
@@ -356,6 +356,16 @@ jobs:
             pip install dist/nipype-*-py2.py3-none-any.whl
             # Futures should not install in Python 3
             test $(pip show futures 2>/dev/null | wc -l) = "0"
+      - run:
+          name: Validate Python 3.7 installation
+          command: |
+            pyenv local 3.7.0
+            pip install --upgrade pip
+            # Pre-install a version of numpy that will not pass
+            pip install numpy==1.15.0
+            pip install dist/nipype-*-py2.py3-none-any.whl
+            # Numpy should be upgraded to >= 1.15.3
+            test "$(pip show numpy | grep Version)" \> "Version: 1.15.2"
       - store_artifacts:
           path: /home/circleci/nipype/dist
 

.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"
@@ -320,7 +322,7 @@
       "name": "Ghayoor, Ali"
     },
     {
-      "name": "Liem, Franz"
+      "name": "K\u00fcttner, Ren\u00e9"
     },
     {
       "name": "Millman, Jarrod"
@@ -378,15 +380,16 @@
     {
       "name": "Hallquist, Michael"
     },
+    {
+      "affiliation": "GIGA Institute",
+      "name": "Grignard, Martin",
+      "orcid": "0000-0001-5549-1861"
+    },
     {
       "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
       "name": "Chetverikov, Andrey",
       "orcid": "0000-0003-2767-6310"
     },
-    {
-      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
-      "name": "Weninger, Leon"
-    },
     {
       "name": "Salvatore, John"
     },
@@ -401,9 +404,6 @@
       "name": "Craddock, R. Cameron",
       "orcid": "0000-0002-4950-1303"
     },
-    {
-      "name": "Inati, Souheil"
-    },
     {
       "name": "Hinds, Oliver"
     },
@@ -412,6 +412,13 @@
       "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"
@@ -441,9 +448,6 @@
       "name": "Floren, Andrew",
       "orcid": "0000-0003-3618-2056"
     },
-    {
-      "name": "Rothmei, Simon"
-    },
     {
       "name": "Urchs, Sebastian"
     },
@@ -452,17 +456,16 @@
       "name": "Durnez, Joke",
       "orcid": "0000-0001-9030-2202"
     },
-    {
-      "name": "Mertz, Fred"
-    },
-    {
-      "name": "Haehn, Daniel"
-    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "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"
@@ -477,6 +480,9 @@
       "name": "Molina-Romero, Miguel",
       "orcid": "0000-0001-8054-0426"
     },
+    {
+      "name": "Haehn, Daniel"
+    },
     {
       "name": "Weinstein, Alejandro"
     },
@@ -491,6 +497,9 @@
     {
       "name": "Saase, Victor"
     },
+    {
+      "name": "Rothmei, Simon"
+    },
     {
       "affiliation": "University of Helsinki",
       "name": "Andberg, Sami Kristian",
@@ -516,11 +525,6 @@
     {
       "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"

README.rst

@@ -11,8 +11,8 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 .. image:: https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/nipy/nipype
 
-.. image:: https://www.codacy.com/project/badge/182f27944c51474490b369d0a23e2f32
-  :target: https://www.codacy.com/app/krzysztof-gorgolewski/nipy_nipype
+.. image:: https://api.codacy.com/project/badge/Grade/452bfc0d4de342c99b177d2c29abda7b
+  :target: https://www.codacy.com/app/nipype/nipype?utm_source=github.com&utm_medium=referral&utm_content=nipy/nipype&utm_campaign=Badge_Grade
 
 .. image:: https://img.shields.io/pypi/v/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
@@ -34,8 +34,9 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
     :target: http://gitter.im/nipy/nipype
     :alt: Chat
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.581704.svg
-   :target: https://doi.org/10.5281/zenodo.581704
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.596855.svg
+   :target: https://doi.org/10.5281/zenodo.596855
+   :alt: Citable DOI
 
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has

doc/_static/nipy-logo-bg-138x120.png

@@ -1,4 +1,4 @@
-<link rel="stylesheet" href="http://www.google.com/cse/style/look/default.css" type="text/css" />
+<link rel="stylesheet" href="https://www.google.com/cse/style/look/default.css" type="text/css" />
 <style type="text/css">
     a.navbar {
     color: {{ theme_linkcolor }};

doc/_static/reggie2.png

@@ -1,3 +1,63 @@
+1.1.6 (November 26, 2018)
+=========================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/27?closed=1)
+
+  * [FIX] MapNodes fail when ``MultiProcPlugin`` passed by instance (https://github.com/nipy/nipype/pull/2786)
+  * [FIX] --fineTune arguments order for MeshFix command (https://github.com/nipy/nipype/pull/2780)
+  * [ENH] Add mp_context plugin arg for MultiProc (https://github.com/nipy/nipype/pull/2778)
+  * [ENH] Create a crashfile even if 'stop_on_first_crash' is set (https://github.com/nipy/nipype/pull/2774)
+  * [ENH] Add ExtractedBrainN4 output to ANTs CorticalThickness interface (https://github.com/nipy/nipype/pull/2784)
+  * [STY] Combine split import (https://github.com/nipy/nipype/pull/2801)
+  * [DOC] use https in css stylesheet url (https://github.com/nipy/nipype/pull/2779)
+  * [MAINT] Outsource ``get_filecopy_info()`` from interfaces (https://github.com/nipy/nipype/pull/2798)
+  * [MAINT] Import only Sequence to avoid DeprecationWarning (https://github.com/nipy/nipype/pull/2793)
+  * [MAINT] One less DeprecationWarning (configparser) (https://github.com/nipy/nipype/pull/2794)
+  * [MAINT] DeprecationWarning: use ``HasTraits.trait_set`` instead (https://github.com/nipy/nipype/pull/2792)
+  * [MAINT] Stop using deprecated ``logger.warn()`` (https://github.com/nipy/nipype/pull/2788)
+  * [MAINT] Move ``interfaces.base.run_command`` to ``nipype.utils.subprocess`` (https://github.com/nipy/nipype/pull/2777)
+  * [MAINT] Force numpy>=1.15.4 when Python>=3.7 (https://github.com/nipy/nipype/pull/2775)
+
+
+1.1.5 (November 08, 2018)
+=========================
+
+Hotfix release.
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/26?closed=1)
+
+  * ENH: Allow timeouts during SLURM job status checks (https://github.com/nipy/nipype/pull/2767)
+  * RF: Subclass non-daemon variants of all multiprocessing contexts (https://github.com/nipy/nipype/pull/2771)
+
+
+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/_templates/navbar.html

@@ -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 = "1.1.5"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.