Merge master

Author: adelavega

.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

@@ -74,47 +74,47 @@
       "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": "Loney, Fred"
+      "name": "Modat, Marc"
     },
     {
-      "name": "Modat, Marc"
+      "name": "Loney, Fred"
     },
     {
-      "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
-      "name": "Dewey, Blake E",
-      "orcid": "0000-0003-4554-5058"
+      "affiliation": "Developer",
+      "name": "Clark, Daniel",
+      "orcid": "0000-0002-8121-8954"
     },
     {
       "affiliation": "National Institute of Mental Health",
       "name": "Nielson, Dylan M.",
       "orcid": "0000-0003-4613-6643"
     },
+    {
+      "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
+      "name": "Dewey, Blake E",
+      "orcid": "0000-0003-4554-5058"
+    },
     {
       "name": "Madison, Cindee"
     },
     {
       "affiliation": "Molecular Imaging Research Center, CEA, France",
       "name": "Bougacha, Salma"
     },
+    {
+      "affiliation": "National Institutes of Health",
+      "name": "Clark, Michael G. "
+    },
     {
       "affiliation": "Dartmouth College",
       "name": "Visconti di Oleggio Castello, Matteo",
       "orcid": "0000-0001-7931-5272"
     },
-    {
-      "affiliation": "National Institutes of Health",
-      "name": "Clark, Michael G. "
-    },
     {
       "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA",
       "name": "Dayan, Michael",
@@ -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",
@@ -189,24 +194,19 @@
       "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",
       "orcid": "0000-0003-1988-5091"
     },
+    {
+      "name": "Mordom, David"
+    },
     {
       "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland",
       "name": "Gillman, Ashley",
       "orcid": "0000-0001-9130-1092"
     },
-    {
-      "name": "Mordom, David"
-    },
     {
       "name": "Buchanan, Colin"
     },
@@ -218,11 +218,6 @@
       "name": "Pauli, Wolfgang M.",
       "orcid": "0000-0002-0966-0254"
     },
-    {
-      "affiliation": "Duke University",
-      "name": "Iqbal, Shariq",
-      "orcid": "0000-0003-2766-8425"
-    },
     {
       "affiliation": "Nathan s Kline institute for psychiatric research",
       "name": "Sikka, Sharad"
@@ -235,6 +230,11 @@
     {
       "name": "Forbes, Jessica"
     },
+    {
+      "affiliation": "Duke University",
+      "name": "Iqbal, Shariq",
+      "orcid": "0000-0003-2766-8425"
+    },
     {
       "name": "Schwartz, Yannick"
     },
@@ -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",
@@ -291,14 +286,20 @@
       "name": "Schaefer, Alexander",
       "orcid": "0000-0001-6488-4739"
     },
+    {
+      "affiliation": "Harvard University - Psychology",
+      "name": "Kastman, Erik",
+      "orcid": "0000-0001-7221-9042"
+    },
     {
       "affiliation": "Washington University in St Louis",
       "name": "Acland, Benjamin",
       "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",
@@ -308,10 +309,8 @@
       "name": "Erickson, Drew"
     },
     {
-      "name": "K\u00fcttner, Ren\u00e9"
-    },
-    {
-      "name": "Haselgrove, Christian"
+      "affiliation": "Child Mind Institute",
+      "name": "Giavasis, Steven"
     },
     {
       "name": "Correa, Carlos"
@@ -320,7 +319,7 @@
       "name": "Ghayoor, Ali"
     },
     {
-      "name": "Liem, Franz"
+      "name": "K\u00fcttner, Ren\u00e9"
     },
     {
       "name": "Millman, Jarrod"
@@ -334,6 +333,9 @@
     {
       "name": "Blair, Ross"
     },
+    {
+      "name": "Haselgrove, Christian"
+    },
     {
       "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
       "name": "Glatard, Tristan",
@@ -384,8 +386,9 @@
       "orcid": "0000-0003-2767-6310"
     },
     {
-      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
-      "name": "Weninger, Leon"
+      "affiliation": "GIGA Institute",
+      "name": "Grignard, Martin",
+      "orcid": "0000-0001-5549-1861"
     },
     {
       "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

@@ -215,7 +215,7 @@ this way you can use the initial paper published in 2011 (see below).
 	month            = "08",
 	doi              = "10.3389/fninf.2011.00013",
 	pubmed           = "21897815",
-	url              = "http://dx.doi.org/10.3389/fninf.2011.00013",
+	url              = "https://doi.org/10.3389/fninf.2011.00013",
 	issn             = "1662-5196"}