Merge branch 'master' of https://github.com/nipy/nipype

Author: kesshijordan

.circleci/config.yml

@@ -36,9 +36,8 @@ _get_base_image: &get_base_image
       echo "Pulling base image ..."
       docker pull nipype/nipype:base
     elif [ "$GET_BASE" == "BUILD" ]; then
-      e=1 && for i in {1..5}; do
-        docker build -t nipype/nipype:base - < docker/Dockerfile.base  && e=0 && break || sleep 15
-      done && [ "$e" -eq "0" ]
+      tools/retry_cmd.sh -n 5 -s 15 \
+        docker build -t nipype/nipype:base - < docker/Dockerfile.base
     else
       echo "Error: method to get base image not understood"
       exit 1
@@ -48,22 +47,20 @@ _build_main_image_py36: &build_main_image_py36
   name: Build main image (py36)
   no_output_timeout: 60m
   command: |
-    e=1 && for i in {1..5}; do
+    tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:latest \
         --tag nipype/nipype:py36 \
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}" /home/circleci/nipype \
-      && e=0 && break || sleep 15
-    done && [ "$e" -eq "0" ]
 
 _build_main_image_py27: &build_main_image_py27
   name: Build main image (py27)
   no_output_timeout: 60m
   command: |
-    e=1 && for i in {1..5}; do
+    tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:py27 \
@@ -72,8 +69,6 @@ _build_main_image_py27: &build_main_image_py27
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}-py27" /home/circleci/nipype \
-      && e=0 && break || sleep 15
-    done && [ "$e" -eq "0" ]
 
 _download_test_data: &_download_test_data
   name: Download test data

.travis.yml

@@ -12,7 +12,7 @@ python:
 env:
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit" CI_SKIP_TEST=1
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
 
 addons:
@@ -40,7 +40,7 @@ before_install:
   fi;
 
 # handle python operations separately to reduce timeouts
-- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-4.3.31-Linux-x86_64.sh
+- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
     -O /home/travis/.cache/conda.sh
 - bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
 - export PATH=${HOME}/conda/bin:$PATH

.zenodo.json

@@ -20,16 +20,16 @@
       "name": "Ellis, David Gage",
       "orcid": "0000-0002-3718-6836"
     },
-    {
-      "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
-      "name": "Notter, Michael Philipp",
-      "orcid": "0000-0002-5866-047X"
-    },
     {
       "affiliation": "Stanford University",
       "name": "Markiewicz, Christopher J.",
       "orcid": "0000-0002-6533-164X"
     },
+    {
+      "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
+      "name": "Notter, Michael Philipp",
+      "orcid": "0000-0002-5866-047X"
+    },
     {
       "affiliation": "University of Iowa",
       "name": "Johnson, Hans",
@@ -105,11 +105,6 @@
       "name": "Dayan, Michael",
       "orcid": "0000-0002-2666-0969"
     },
-    {
-      "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
-      "name": "Keshavan, Anisha",
-      "orcid": "0000-0003-3554-043X"
-    },
     {
       "affiliation": "UC Berkeley",
       "name": "Clark, Dav",
@@ -120,6 +115,11 @@
       "name": "Visconti di Oleggio Castello, Matteo",
       "orcid": "0000-0001-7931-5272"
     },
+    {
+      "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
+      "name": "Keshavan, Anisha",
+      "orcid": "0000-0003-3554-043X"
+    },
     {
       "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay",
       "name": "Gramfort, Alexandre",
@@ -156,14 +156,18 @@
       "name": "Rokem, Ariel",
       "orcid": "0000-0003-0679-1985"
     },
+    {
+      "name": "Moloney, Brendan"
+    },
+    {
+      "affiliation": "Molecular Imaging Research Center, CEA, France",
+      "name": "Bougacha, Salma"
+    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann , Demian",
       "orcid": "0000-0001-5194-6056"
     },
-    {
-      "name": "Moloney, Brendan"
-    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
@@ -179,10 +183,6 @@
       "name": "Horea, Christian",
       "orcid": "0000-0001-7037-2449"
     },
-    {
-      "affiliation": "Molecular Imaging Research Center, CEA, France",
-      "name": "Bougacha, Salma"
-    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -193,6 +193,16 @@
       "name": "Gilles de Hollander",
       "orcid": "0000-0003-1988-5091"
     },
+    {
+      "affiliation": "Montreal Neurological Institute and Hospital",
+      "name": "DuPre, Elizabeth",
+      "orcid": "0000-0003-1358-196X"
+    },
+    {
+      "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"
     },
@@ -229,11 +239,6 @@
       "name": "Malone, Ian B.",
       "orcid": "0000-0001-7512-7856"
     },
-    {
-      "affiliation": "Montreal Neurological Institute and Hospital",
-      "name": "DuPre, Elizabeth",
-      "orcid": "0000-0003-1358-196X"
-    },
     {
       "name": "Dubois, Mathieu"
     },
@@ -259,11 +264,6 @@
       "name": "Huntenburg, Julia M.",
       "orcid": "0000-0003-0579-9811"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Eshaghi, Arman",
-      "orcid": "0000-0002-6652-3512"
-    },
     {
       "affiliation": "Harvard University - Psychology",
       "name": "Kastman, Erik",
@@ -274,6 +274,11 @@
       "name": "Nichols, B. Nolan",
       "orcid": "0000-0003-1099-3328"
     },
+    {
+      "affiliation": "University College London",
+      "name": "Eshaghi, Arman",
+      "orcid": "0000-0002-6652-3512"
+    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -290,11 +295,6 @@
     {
       "name": "Kent, James"
     },
-    {
-      "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland",
-      "name": "Gillman, Ashley",
-      "orcid": "0000-0001-9130-1092"
-    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
@@ -356,6 +356,11 @@
       "name": "Kahn, Ari E.",
       "orcid": "0000-0002-2127-0507"
     },
+    {
+      "affiliation": "University College London",
+      "name": "P\u00e9rez-Garc\u00eda, Fernando",
+      "orcid": "0000-0001-9090-3024"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Triplett, William",
@@ -384,9 +389,6 @@
     {
       "name": "Salvatore, John"
     },
-    {
-      "name": "Mertz, Fred"
-    },
     {
       "name": "Park, Anne"
     },
@@ -409,11 +411,6 @@
     {
       "name": "Hinds, Oliver"
     },
-    {
-      "affiliation": "Technical University Munich",
-      "name": "Molina-Romero, Miguel",
-      "orcid": "0000-0001-8054-0426"
-    },
     {
       "affiliation": "University of Newcastle, Australia",
       "name": "Cooper, Gavin",
@@ -467,6 +464,9 @@
       "name": "Durnez, Joke",
       "orcid": "0000-0001-9030-2202"
     },
+    {
+      "name": "Mertz, Fred"
+    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "name": "Geisler, Daniel",
@@ -476,14 +476,15 @@
       "affiliation": "The University of Texas at Austin",
       "name": "Floren, Andrew",
       "orcid": "0000-0003-3618-2056"
-    },
+      },
     {
       "affiliation": "University of illinois urbana champaign",
       "name": "Sharp, Paul"
     },
     {
-      "affiliation": "Vrije Universiteit Amsterdam",
-      "name": "Ort, Eduard"
+      "affiliation": "Technical University Munich",
+      "name": "Molina-Romero, Miguel",
+      "orcid": "0000-0001-8054-0426"
     },
     {
       "name": "Weinstein, Alejandro"
@@ -558,9 +559,8 @@
       "name": "Flandin, Guillaume"
     },
     {
-      "affiliation": "Stereotaxy Core, Brain & Spine Institute",
-      "name": "P\u00e9rez-Garc\u00eda, Fernando",
-      "orcid": "0000-0001-9090-3024"
+      "affiliation": "Vrije Universiteit Amsterdam",
+      "name": "Ort, Eduard"
     },
     {
       "name": "Shachnev, Dmitry"