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Merge remote-tracking branch 'upstream/master' into fix/ants_mask_file
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‎.circleci/config.yml

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

‎.circleci/test_pytest.sh

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@@ -1,3 +1,3 @@
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#!/bin/bash
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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
3+
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

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

‎.github/workflows/tests.yml

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

‎.mailmap

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@@ -10,6 +10,7 @@ Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@melisse.cbs.mpg.de>
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Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@aschaefer-U36SD.(none)>
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Alexandre M. Savio <alexsavio@gmail.com>
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Alexandre M. Savio <alexsavio@gmail.com> <alexsavio@users.noreply.github.com>
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Andrea Dell'Orco <orco@paranoici.org>
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Andrew Floren <andrewfloren@gmail.com>
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Andrey Chetverikov <stop.psy@gmail.com>
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Andrey Chetverikov <stop.psy@gmail.com> <achetverikov@users.noreply.github.com>
@@ -120,6 +121,7 @@ Kshitij Chawla <kc.insight.pi@gmail.com>
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Leonie Lampe <leonie.lampe@gmail.com>
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Lukas Snoek <lukassnoek@gmail.com>
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Marcel Falkiewicz <mfalkiewicz@gmail.com> <m.falkiewicz@nencki.gov.pl>
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Maria de Fatima Dias <mfatimamachado13@gmail.com> <fmachado@dei.uc.pt>
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Martin Perez-Guevara <mperezguevara@gmail.com>
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Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@mit.edu>
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Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@stanford.edu>
@@ -144,6 +146,7 @@ Michael Waskom <michael.l.waskom@gmail.com> <mwaskom@stanford.edu>
144146
Miguel Molina-Romero <miguel.molina.romero@gmail.com>
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Murat Bilgel <bilgelm@gmail.com> <murat.bilgel@nih.gov>
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Nat Lee <vip3268@gmail.com>
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Ole Numssen <numssen@cbs.mpg.de>
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Oliver Contier <o.contier@gmail.com> <oliver.contier@ovgu.de>
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Olivia Stanley <oliviawstanley@gmail.com>
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Oscar Esteban <code@oscaresteban.es>

‎.zenodo.json

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

‎README.rst

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Python 2.7 reaches its end-of-life in January 2020, which means it will
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*no longer be maintained* by Python developers. `Many projects
85-
<https://python3statement.org/`__ are removing support in advance of this
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<https://python3statement.org/>`__ are removing support in advance of this
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deadline, which will make it increasingly untenable to try to support
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Python 2, even if we wanted to.
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‎doc/_static/nipype.css

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min-width: 70em;
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}
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div.sphinxsidebar {
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position: relative;
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}
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div.sphinxsidebar h4, div.sphinxsidebar h3 {
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background-color: #2F83C8;
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}

‎doc/_templates/layout.html

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{% set title = 'Neuroimaging in Python - Pipelines and Interfaces' %}
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{% set short_title = 'Nipype' %}
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{% block sidebar1 %}{{ sidebar() }}{% endblock %}
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{% block sidebar2 %}{% endblock %}
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{% block extrahead %}
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{{ super() }}
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<meta name="keywords" content="nipype, neuroimaging, pipeline, workflow, parallel, python, neuroscience">
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{% block relbar1 %}{% endblock %}
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{% block relbar2 %}{% endblock %}
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{% block sidebar1 %}{{ sidebar() }}{% endblock %}
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{% block sidebar2 %}{% endblock %}
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{% block footer %}
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‎doc/_templates/navbar.html

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<link rel="stylesheet" href="https://www.google.com/cse/style/look/default.css" type="text/css" />
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<style type="text/css">
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a.navbar {
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}

‎doc/changelog/1.X.X-changelog.rst

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1.7.0 (October 20, 2021)
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========================
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(`Full changelog <https://github.com/nipy/nipype/milestone/1.7.0?closed=1>`__)
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* FIX: Make ants.LaplacianThickness output_image a string, not file (https://github.com/nipy/nipype/pull/3393)
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* FIX: coord for mrconvert (https://github.com/nipy/nipype/pull/3369)
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* FIX: ``antsRegistration`` allows the ``restrict_deformation`` to be float (https://github.com/nipy/nipype/pull/3387)
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* FIX: Also allow `errno.EBUSY` during `emptydirs` on NFS (https://github.com/nipy/nipype/pull/3357)
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* FIX: Removed exists=True from MathsOutput (https://github.com/nipy/nipype/pull/3385)
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* FIX: Extension not extensions, after pybids v0.9 (https://github.com/nipy/nipype/pull/3380)
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* ENH: Add CAT12 SANLM denoising filter (https://github.com/nipy/nipype/pull/3374)
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* ENH: Add expected steps for FreeSurfer 7 recon-all (https://github.com/nipy/nipype/pull/3389)
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* ENH: Stop printing false positive differences when logging cached nodes (https://github.com/nipy/nipype/pull/3376)
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* ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform) (https://github.com/nipy/nipype/pull/3365)
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* ENH: ``verbose`` input should not be hashed in ``ants.Registration`` (https://github.com/nipy/nipype/pull/3377)
17+
* REF: Clean-up the BaseInterface ``run()`` function using context (https://github.com/nipy/nipype/pull/3347)
18+
* DOC: Fix typo in README (https://github.com/nipy/nipype/pull/3386)
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* STY: Make private member name consistent with the rest of them (https://github.com/nipy/nipype/pull/3346)
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* MNT: Simplify interface execution and better error handling of ``Node`` (https://github.com/nipy/nipype/pull/3349)
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* MNT: Add user name and email to Docker to appease git/annex/datalad (https://github.com/nipy/nipype/pull/3378)
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* CI: Update CircleCI machine image (https://github.com/nipy/nipype/pull/3391)
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1.6.1 (June 16, 2021)
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=====================
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‎doc/conf.py

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# General information about the project.
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project = u"nipype"
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copyright = u"2009-20, Neuroimaging in Python team"
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copyright = u"2009-21, Neuroimaging in Python team"
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the

‎doc/devel/testing_nipype.rst

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Nipype is tested inside Docker containers and users can use nipype images to test local versions.
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First, install the `Docker Engine <https://docs.docker.com/engine/installation/>`_.
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Nipype has one base docker image called nipype/nipype:base, that contains several useful tools
93-
(FreeSurfer, AFNI, FSL, ANTs, etc.), and additional test images
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for specific Python versions: py27 for Python 2.7 and py36 for Python 3.6.
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(FreeSurfer, AFNI, FSL, ANTs, etc.), and an additional test image for Python 3.8:
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Users can pull the nipype image for Python 3.6 as follows::
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Users can pull the nipype image for Python 3.8 as follows::
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98-
docker pull nipype/nipype:py36
97+
docker pull nipype/nipype:py38
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In order to test a local version of nipype you can run test within container as follows::
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102-
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101+
docker run -it -v $PWD:/src/nipype --rm nipype/nipype:py38 py.test -v --doctest-modules /src/nipype/nipype
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Additional comments

‎doc/interfaces.rst

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:Release: |version|
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:Date: |today|
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Previous versions: `1.6.0 <http://nipype.readthedocs.io/en/1.6.0/>`_ `1.5.1 <http://nipype.readthedocs.io/en/1.5.1/>`_
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Previous versions: `1.7.0 <http://nipype.readthedocs.io/en/1.7.0/>`_ `1.6.1 <http://nipype.readthedocs.io/en/1.6.1/>`_
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Workflows
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---------

‎docker/generate_dockerfiles.sh

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--user neuro \
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--run 'git config --global user.name nipybot
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--workdir /home/neuro \
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‎nipype/algorithms/confounds.py

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else:
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1438-
variance_explained = (s ** 2) / np.sum(s ** 2)
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variance_explained = (s**2) / np.sum(s**2)
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num_components = int(components_criterion)

‎nipype/algorithms/icc.py

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SSE = (residuals**2).sum()
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residuals.shape = Y.shape
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