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Commit 133dc0a

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Merge branch 'enh/cuda_support' of https://github.com/mauriliogenovese/nipype into enh/cuda_support
2 parents 2c2c066 + 7e57ab9 commit 133dc0a

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‎.circleci/config.yml

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workflows:
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version: 2
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build_test_deploy:
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jobs:
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- compare_base_dockerfiles:
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filters:
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branches:
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ignore:
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- /docs?\/.*/
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tags:
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only: /.*/
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- get_test_data:
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filters:
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branches:
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ignore:
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- /docs?\/.*/
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tags:
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only: /.*/
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- test_pytest:
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filters:
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branches:
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ignore:
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- /docs?\/.*/
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tags:
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only: /.*/
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requires:
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- compare_base_dockerfiles
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- get_test_data
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- deploy_dockerhub:
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filters:
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branches:
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only: master
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tags:
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only: /.*/
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requires:
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- test_pytest
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- update_feedstock:
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context: nipybot
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filters:
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branches:
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only: /rel\/\d.*/
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tags:
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only: /.*/
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jobs: []

‎.codespellrc

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# ALS, FWE - neuroimaging specific abbrevs
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# Comision - foreign word used
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# expad - AFNI flag
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ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile,expad
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ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile,expad,burnin

‎.git-blame-ignore-revs

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# Thu Oct 31 10:01:38 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev]
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bd0d5856d183ba3918eda31f80db3b1d4387c55c
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# Thu Mar 21 13:34:09 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev]
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c52fece0cf154c1a93a55b202d088f08924a023e
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# Sun Mar 17 10:58:12 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev]
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e447b92bcb3b9ed9e35394d6edef1d91b7c424e6
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# Sun Mar 17 10:44:57 2024 -0400 - effigies@gmail.com - STY: black
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f1a8909d233ed2a707b6ee8937504eea9ee7f154
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# Tue Feb 27 14:28:18 2024 -0500 - effigies@gmail.com - STY: black 2024.2 [ignore-rev]
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f1cbc1c941f8d02659f8ef245aac0862efb80ccf
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# Mon Sep 11 13:36:40 2023 +0200 - 37933899+servoz@users.noreply.github.com - run black for nipype/interfaces/spm/preprocess.py

‎.github/workflows/contrib.yml

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‎.github/workflows/tests.yml

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name: Stable tests
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# This file tests the claimed support range of nipype including
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#
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# * Operating systems: Linux, OSX
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# * Dependencies: minimum requirements, optional requirements
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# * Installation methods: setup.py, sdist, wheel, archive
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name: Tox
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on:
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push:
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branches:
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- master
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- maint/*
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tags:
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- "*"
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branches: [ master, main, 'maint/*' ]
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tags: [ '*' ]
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pull_request:
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branches:
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- master
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- maint/*
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branches: [ master, main, 'maint/*' ]
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schedule:
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# 8am EST / 9am EDT Mondays
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- cron: "0 13 * * 1"
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shell: bash
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concurrency:
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group: tests-${{ github.ref }}
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions: {}
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permissions:
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contents: read
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env:
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# Force tox and pytest to use color
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FORCE_COLOR: true
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jobs:
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build:
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permissions:
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contents: read # to fetch code (actions/checkout)
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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with:
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python-version: 3
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- run: pip install --upgrade build twine
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- name: Build sdist and wheel
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run: python -m build
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- run: twine check dist/*
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v5
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- run: uv build
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- run: uvx twine check dist/*
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- uses: actions/upload-artifact@v4
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- name: Run tests
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run: pytest --doctest-modules -v --pyargs nipype
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stable:
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test:
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# Check each OS, all supported Python, minimum versions and latest releases
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permissions:
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contents: read # to fetch code (actions/checkout)
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strategy:
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matrix:
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os: ["ubuntu-22.04"]
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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check: ["test"]
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pip-flags: [""]
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depends: ["REQUIREMENTS"]
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deb-depends: [false]
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nipype-extras: ["doc,tests,profiler"]
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os: ["ubuntu-latest"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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dependencies: [none, full, pre]
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include:
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- os: ubuntu-22.04
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python-version: "3.8"
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check: test
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pip-flags: ""
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,profiler,duecredit,ssh
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- os: ubuntu-20.04
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python-version: 3.8
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check: test
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pip-flags: ""
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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- os: ubuntu-latest
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python-version: "3.9"
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dependencies: min
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exclude:
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# Skip some intermediate versions for full tests
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- python-version: "3.10"
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dependencies: full
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- python-version: "3.11"
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dependencies: full
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# Do not test pre-releases for versions out of SPEC0
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- python-version: "3.9"
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dependencies: pre
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- python-version: "3.10"
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dependencies: pre
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DEPENDS: ${{ matrix.depends }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
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NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
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INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
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DEPENDS: ${{ matrix.dependencies }}
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steps:
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- uses: actions/checkout@v4
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v5
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_venv.sh
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- name: Build archive
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- name: Install tox
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
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if: ${{ matrix.os == 'ubuntu-latest' }}
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install Nipype
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v4
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uv tool install tox --with=tox-uv --with=tox-gh-actions
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- name: Show tox config
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run: tox c
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- name: Run tox
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run: tox -v --exit-and-dump-after 1200
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- uses: codecov/codecov-action@v5
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file: coverage.xml
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token: ${{ secrets.CODECOV_TOKEN }}
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if: ${{ always() }}
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- name: Upload pytest test results
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publish:
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runs-on: ubuntu-latest
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environment: "Package deployment"
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needs: [stable, test-package]
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needs: [test, test-package]
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
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- uses: actions/download-artifact@v4
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checks:
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runs-on: 'ubuntu-latest'
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continue-on-error: true
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strategy:
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matrix:
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check: ['specs', 'style']
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steps:
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- uses: actions/checkout@v4
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v5
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- name: Show tox config
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run: uvx tox c
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- name: Show tox config (this call)
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run: uvx tox c -e ${{ matrix.check }}
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- name: Run check
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run: uvx tox -e ${{ matrix.check }}

‎.github/workflows/tutorials.yml

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id: start
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run: echo "::set-output name=start_time::$(date +'%Y-%m-%dT%H:%M:%S%z')"
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run: echo start_time=$(date +'%Y-%m-%dT%H:%M:%S%z') >> $GITHUB_OUTPUT
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- name: Trigger Nipype tutorial Github Action
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set -x
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echo run_id=$RUN_ID >> $GITHUB_OUTPUT
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- name: Check if action completed
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timeout-minutes: 120
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run: |

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