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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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_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
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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="$(git rev-parse --short HEAD)" \
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- run: *generate_dockerfiles
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- run: *modify_nipype_version
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- run: *get_base_image
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- run: *build_main_image_py36
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- run: *build_main_image_py38
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- run: *_get_codecov
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- run: *_download_test_data
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- run: *prepare_working_directory
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if [ "$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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#!/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
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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}:py38" /usr/bin/run_pytests.sh

‎.github/PULL_REQUEST_TEMPLATE.md

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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 <[email protected]> <[email protected]>
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Alexander Schaefer <[email protected]> <aschaefer@aschaefer-U36SD.(none)>
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Alexandre M. Savio <[email protected]>
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Alexandre M. Savio <[email protected]> <[email protected]>
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Andrea Dell'Orco <[email protected]>
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Andrew Floren <[email protected]>
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Andrey Chetverikov <[email protected]>
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Andrey Chetverikov <[email protected]> <[email protected]>
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Leonie Lampe <[email protected]>
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Lukas Snoek <[email protected]>
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Marcel Falkiewicz <[email protected]> <[email protected]>
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Maria de Fatima Dias <[email protected]> <[email protected]>
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Martin Perez-Guevara <[email protected]>
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Mathias Goncalves <[email protected]> <[email protected]>
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Mathias Goncalves <[email protected]> <[email protected]>
@@ -144,6 +146,7 @@ Michael Waskom <[email protected]> <[email protected]>
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Miguel Molina-Romero <[email protected]>
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Murat Bilgel <[email protected]> <[email protected]>
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Nat Lee <[email protected]>
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Ole Numssen <[email protected]>
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Oliver Contier <[email protected]> <[email protected]>
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Olivia Stanley <[email protected]>
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Oscar Esteban <[email protected]>

‎.zenodo.json

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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
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<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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}
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div.sphinxsidebar {
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}
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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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<meta name="keywords" content="nipype, neuroimaging, pipeline, workflow, parallel, python, neuroscience">
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‎doc/_templates/navbar.html

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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: 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)
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* REF: Clean-up the BaseInterface ``run()`` function using context (https://github.com/nipy/nipype/pull/3347)
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* 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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‎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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Additional comments

‎doc/interfaces.rst

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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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---------

‎docker/generate_dockerfiles.sh

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‎nipype/algorithms/confounds.py

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‎nipype/algorithms/icc.py

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