Merge remote-tracking branch 'upstream/master' into fix/ants_mask_file

Author: effigies

.circleci/config.yml

@@ -1,5 +1,5 @@
 _machine_kwds: &machine_kwds
-  image: circleci/classic:201808-01
+  image: ubuntu-2004:202107-02
 
 _store_artifacts_kwds: &store_artifacts_kwds
   path: /home/circleci/work/tests
@@ -43,15 +43,15 @@ _get_base_image: &get_base_image
       exit 1
     fi
 
-_build_main_image_py36: &build_main_image_py36
-  name: Build main image (py36)
+_build_main_image_py38: &build_main_image_py38
+  name: Build main image (py38)
   no_output_timeout: 60m
   command: |
     tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:latest \
-        --tag nipype/nipype:py36 \
+        --tag nipype/nipype:py38 \
         $(test -z "${CIRCLE_TAG}" || echo --tag nipype/nipype:"${CIRCLE_TAG}") \
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
@@ -146,7 +146,7 @@ jobs:
       - run: *generate_dockerfiles
       - run: *modify_nipype_version
       - run: *get_base_image
-      - run: *build_main_image_py36
+      - run: *build_main_image_py38
       - run: *_get_codecov
       - run: *_download_test_data
       - run: *prepare_working_directory
@@ -165,8 +165,8 @@ jobs:
             if [ "$CIRCLE_BRANCH" = "master" -a -z "$CIRCLE_PULL_REQUEST" ]; then
               docker save nipype/nipype:base \
                           nipype/nipype:latest \
-                          nipype/nipype:py36 | gzip -1 > /tmp/docker/nipype-base-latest-py36.tar.gz \
-              && du -h /tmp/docker/nipype-base-latest-py36.tar.gz
+                          nipype/nipype:py38 | gzip -1 > /tmp/docker/nipype-base-latest-py38.tar.gz \
+              && du -h /tmp/docker/nipype-base-latest-py38.tar.gz
             fi
       - persist_to_workspace:
           root: /tmp
@@ -184,15 +184,15 @@ jobs:
           name: Load saved Docker images.
           no_output_timeout: 60m
           command: |
-            docker load < /tmp/docker/nipype-base-latest-py36.tar.gz
+            docker load < /tmp/docker/nipype-base-latest-py38.tar.gz
       - run:
           name: Push to DockerHub
           no_output_timeout: 120m
           command: |
             echo "$DOCKER_PASS" | docker login -u "$DOCKER_USER" --password-stdin
             docker push nipype/nipype:base
             docker push nipype/nipype:latest
-            docker push nipype/nipype:py36
+            docker push nipype/nipype:py38
             test -z "${CIRCLE_TAG}" || docker push nipype/nipype:"${CIRCLE_TAG}"
       - run:
           name: Move pruned Dockerfile to /tmp/docker/cache directory

.circleci/test_pytest.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py36" /usr/bin/run_pytests.sh
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh

.github/PULL_REQUEST_TEMPLATE.md

@@ -17,7 +17,3 @@ Fixes # .
 
 ## List of changes proposed in this PR (pull-request)
 <!-- We suggest using bullets (indicated by * or -) and filled checkboxes [x] here -->
-
-## Acknowledgment
-
-- [ ] \(Mandatory\) I acknowledge that this contribution will be available under the Apache 2 license.

.github/workflows/tests.yml

@@ -26,8 +26,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-18.04']
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: ['ubuntu-latest']
+        python-version: [3.6, 3.7, 3.8, 3.9, "3.10"]
         check: ['test']
         pip-flags: ['']
         depends: ['REQUIREMENTS']

.mailmap

@@ -10,6 +10,7 @@ Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@melisse.cbs.mpg.de>
 Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@aschaefer-U36SD.(none)>
 Alexandre M. Savio <alexsavio@gmail.com>
 Alexandre M. Savio <alexsavio@gmail.com> <alexsavio@users.noreply.github.com>
+Andrea Dell'Orco <orco@paranoici.org>
 Andrew Floren <andrewfloren@gmail.com>
 Andrey Chetverikov <stop.psy@gmail.com>
 Andrey Chetverikov <stop.psy@gmail.com> <achetverikov@users.noreply.github.com>
@@ -120,6 +121,7 @@ Kshitij Chawla <kc.insight.pi@gmail.com>
 Leonie Lampe <leonie.lampe@gmail.com>
 Lukas Snoek <lukassnoek@gmail.com>
 Marcel Falkiewicz <mfalkiewicz@gmail.com> <m.falkiewicz@nencki.gov.pl>
+Maria de Fatima Dias <mfatimamachado13@gmail.com> <fmachado@dei.uc.pt>
 Martin Perez-Guevara <mperezguevara@gmail.com>
 Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@mit.edu>
 Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@stanford.edu>
@@ -144,6 +146,7 @@ Michael Waskom <michael.l.waskom@gmail.com> <mwaskom@stanford.edu>
 Miguel Molina-Romero <miguel.molina.romero@gmail.com>
 Murat Bilgel <bilgelm@gmail.com> <murat.bilgel@nih.gov>
 Nat Lee <vip3268@gmail.com>
+Ole Numssen <numssen@cbs.mpg.de>
 Oliver Contier <o.contier@gmail.com> <oliver.contier@ovgu.de>
 Olivia Stanley <oliviawstanley@gmail.com>
 Oscar Esteban <code@oscaresteban.es>

.zenodo.json

@@ -148,15 +148,15 @@
       "name": "Visconti di Oleggio Castello, Matteo",
       "orcid": "0000-0001-7931-5272"
     },
-    {
-      "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
-      "name": "Wong, Jason"
-    },
     {
       "affiliation": "University of Texas at Austin",
       "name": "De La Vega, Alejandro",
       "orcid": "0000-0001-9062-3778"
     },
+    {
+      "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
+      "name": "Wong, Jason"
+    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -217,6 +217,11 @@
       "name": "de Hollander, Gilles",
       "orcid": "0000-0003-1988-5091"
     },
+    {
+      "affiliation": "Charit\u00e8 Universit\u00e4tsmedizin Berlin, Germany",
+      "name": "Dell'Orco, Andrea",
+      "orcid": "0000-0002-3964-8360"
+    },
     {
       "affiliation": "University College London",
       "name": "Eshaghi, Arman",
@@ -251,21 +256,21 @@
     {
       "name": "Mordom, David"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "affiliation": "CIBIT, UC",
-      "name": "Machado, F\u00e1tima",
+      "name": "Dias, Maria de Fatima",
       "orcid": "0000-0001-8878-1750"
     },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
       "name": "Guillon, Je\u0301re\u0301my",
       "orcid": "0000-0002-2672-7510"
     },
-    {
-      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
-      "name": "Waller, Lea",
-      "orcid": "0000-0002-3239-6957"
-    },
     {
       "affiliation": "Indiana University, IN, USA",
       "name": "Koudoro, Serge"
@@ -313,6 +318,11 @@
       "name": "Geisler, Daniel",
       "orcid": "0000-0003-2076-5329"
     },
+    {
+      "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universit\u00e4t Dresden, Dresden, Germany",
+      "name": "Bernardoni, Fabio",
+      "orcid": "0000-0002-5112-405X"
+    },
     {
       "name": "Salvatore, John"
     },
@@ -429,7 +439,8 @@
     },
     {
       "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
-      "name": "Baratz, Zvi"
+      "name": "Baratz, Zvi",
+      "orcid": "0000-0001-7159-1387"
     },
     {
       "affiliation": "University of Iowa",
@@ -726,6 +737,11 @@
       "affiliation": "Universidad de Guadalajara",
       "name": "Gonz\u00e1lez Orozco, Abel A."
     },
+    {
+      "affiliation": "ARAMIS Lab",
+      "name": "Routier, Alexandre",
+      "orcid": "0000-0003-1603-8049"
+    },
     {
       "name": "Marina, Ana"
     },
@@ -794,9 +810,19 @@
       "name": "Pannetier, Nicolas",
       "orcid": "0000-0002-0744-5155"
     },
+    {
+      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences",
+      "name": "Numssen, Ole",
+      "orcid": "0000-0001-7164-2682"
+    },
     {
       "name": "Khanuja, Ranjeet"
     },
+    {
+      "affiliation": "University of Waterloo",
+      "name": "Mukhometzianov, Rinat",
+      "orcid": "0000-0003-1274-4827"
+    },
     {
       "name": "Urchs, Sebastian"
     },
@@ -835,7 +861,16 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
-    }
+    },
+    {
+      "name": "Hui Qian, Tan"
+    },
+	{
+      "affiliation": "Insitiute and Polyclinc for Diagnostic and Interventional Neuroradiology, University Hospital Carl Gustav Carus, Dresden, Germany",
+      "name": "Kuntke, Paul",
+      "orcid": "0000-0003-1838-2230"
+	}
+
   ],
   "keywords": [
     "neuroimaging",

README.rst

@@ -82,7 +82,7 @@ Python 2 Statement
 
 Python 2.7 reaches its end-of-life in January 2020, which means it will
 *no longer be maintained* by Python developers. `Many projects
-<https://python3statement.org/`__ are removing support in advance of this
+<https://python3statement.org/>`__ are removing support in advance of this
 deadline, which will make it increasingly untenable to try to support
 Python 2, even if we wanted to.
 

doc/_static/nipype.css

@@ -5,6 +5,10 @@ body {
     min-width: 70em;
 }
 
+div.sphinxsidebar {
+    position: relative;
+}
+
 div.sphinxsidebar h4, div.sphinxsidebar h3 {
     background-color: #2F83C8;
 }

doc/_templates/layout.html

@@ -2,6 +2,9 @@
 {% set title = 'Neuroimaging in Python - Pipelines and Interfaces' %}
 {% set short_title = 'Nipype' %}
 
+{% block sidebar1 %}{{ sidebar() }}{% endblock %}
+{% block sidebar2 %}{% endblock %}
+
 {% block extrahead %}
 {{ super() }}
 <meta name="keywords" content="nipype, neuroimaging, pipeline, workflow, parallel, python, neuroscience">
@@ -42,8 +45,6 @@
 
 {% block relbar1 %}{% endblock %}
 {% block relbar2 %}{% endblock %}
-{% block sidebar1 %}{{ sidebar() }}{% endblock %}
-{% block sidebar2 %}{% endblock %}
 
 {% block footer %}
 {{ super() }}

doc/_templates/navbar.html

@@ -1,7 +1,6 @@
 <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 }};
     letter-spacing: .05em;
     font-weight: bold;
         }