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Merge pull request #14 from tsalo/infrastructure
Work on infrastructure
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‎.github/dependabot.yml

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version: 2
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updates:
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- package-ecosystem: 'github-actions'
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directory: '/'
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schedule:
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interval: 'monthly'
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groups:
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actions-infrastructure:
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patterns:
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- 'actions/*'
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- package-ecosystem: 'pip'
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directory: '/services/datalad'
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schedule:
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interval: 'monthly'
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groups:
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pipenv:
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patterns:
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- '*'

‎.github/pull_request_template.md

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<!--
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Text in these brackets are comments, and won't be visible when you submit your pull request.
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If this is your first contribution, please take the time to read these, in particular the comment
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beginning "Welcome, new contributors!".
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-->
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## Changes proposed in this pull request
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<!--
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Please describe here the main features / changes proposed for review and integration in fMRIPost-AROMA
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If this PR addresses some existing problem, please use GitHub's citing tools
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(eg. ref #, closes # or fixes #).
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If there is not an existing issue open describing the problem, please consider opening a new
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issue first and then link it from here (so the *fMRIPost-AROMA* community has a better understanding
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of ongoing development efforts and possible overlaps between contributions).
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-->
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## Documentation that should be reviewed
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<!--
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Please summarize here the main changes to the documentation that the reviewers should be aware of.
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-->
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<!--
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Welcome, new contributors!
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We ask you to read through the Contributing Guide:
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https://github.com/nipreps/fmripost-aroma/blob/master/CONTRIBUTING.md
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These are guidelines intended to make communication easier by describing a consistent process, but
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don't worry if you don't get it everything exactly "right" on the first try.
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To boil it down, here are some highlights:
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1) Consider starting a conversation in the issues list before submitting a pull request. The discussion might save you a
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lot of time coding.
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2) Please use descriptive prefixes in your pull request title, such as "ENH:" for an enhancement or "FIX:" for a bug fix.
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(See the Contributing guide for the full set.) And consider adding a "WIP" tag for works-in-progress.
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3) Any code you submit will be licensed under the same terms (Apache License 2.0) as the rest of fMRIPost-AROMA.
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4) We invite every contributor to add themselves to the `.zenodo.json` file
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(https://github.com/nipreps/fmripost-aroma/blob/master/.zenodo.json), which will result in your being listed as an author
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at the next release. Please add yourself as the next-to-last entry, just above Russ.
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A pull request is a conversation. We may ask you to make some changes before accepting your PR,
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and likewise, you should feel free to ask us any questions you have.
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-->

‎.github/workflows/contrib.yml

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name: Contribution checks
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on:
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push:
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branches:
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- main
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- maint/*
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pull_request:
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branches:
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- main
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- maint/*
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defaults:
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run:
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shell: bash
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concurrency:
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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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contents: read
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jobs:
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style:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- run: pipx run ruff check .
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- run: pipx run ruff format --diff .
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codespell:
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name: Check for spelling errors
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Codespell
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uses: codespell-project/actions-codespell@v2

‎.github/workflows/pre-release.yml

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name: Pre-release checks
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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defaults:
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run:
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shell: bash
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concurrency:
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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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contents: read
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jobs:
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pre-release:
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# Check pre-releases of dependencies on stable Python
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runs-on: ${{ matrix.os }}
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continue-on-error: true
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strategy:
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matrix:
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os: ['ubuntu-latest']
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python-version: ['3.10', '3.11', '3.12']
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install: ['pip']
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check: ['tests']
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pip-flags: ['PRE_PIP_FLAGS']
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env:
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INSTALL_TYPE: ${{ matrix.install }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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OS_TYPE: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Install dependencies
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run: .maint/ci/install_dependencies.sh
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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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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: .maint/ci/create_venv.sh
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- name: Build archive
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run: |
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source .maint/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install fMRIPost-AROMA
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run: .maint/ci/install.sh
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- name: Install extras
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run: .maint/ci/install_extras.sh
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- name: Run tests
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run: .maint/ci/check.sh
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- uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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token: ${{ secrets.CODECOV_TOKEN }}
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if: ${{ always() }}

‎.github/workflows/stable.yml

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name: Stable tests
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on:
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push:
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branches:
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- main
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- maint/*
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- next
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pull_request:
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branches:
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- main
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- maint/*
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- next
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defaults:
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run:
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shell: bash
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concurrency:
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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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contents: read
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jobs:
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stable:
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# Check each OS, all supported Python, minimum versions and latest releases
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-latest']
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python-version: ['3.10', '3.11', '3.12']
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install: ['pip']
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check: ['tests']
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pip-flags: ['']
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env:
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INSTALL_TYPE: ${{ matrix.install }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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OS_TYPE: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Install dependencies
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run: .maint/ci/install_dependencies.sh
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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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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: .maint/ci/create_venv.sh
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- name: Build archive
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run: |
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source .maint/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install fMRIPost-AROMA
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run: .maint/ci/install.sh
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- name: Install extras
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run: .maint/ci/install_extras.sh
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- name: Run tests
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run: .maint/ci/check.sh
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- uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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token: ${{ secrets.CODECOV_TOKEN }}
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if: ${{ always() }}

‎.gitignore

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.DS_Store
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.*.swp
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.mypy_cache
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.pytest_cache
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.ruff_cache
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.coverage
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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.pytest_cache/
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# C extensions
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*.so
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*.c
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# Distribution / packaging
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.Python
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env/
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# build/ # commented due to some strangeness with Docker/circle setup
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develop-eggs/
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dist/
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build/lib*
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build/temp*
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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*.egg-info/
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.installed.cfg
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*.egg
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pip-wheel-metadata/
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*,cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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# Sphinx documentation
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docs/_build/
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build/
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# PyBuilder
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target/
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#Ipython Notebook
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.ipynb_checkpoints
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# pycharm project settings
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.idea
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# Spyder project settings
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.spyderproject
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.spyproject
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auth/
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secrets.py
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local_settings.py
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*.swp
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_version.py

‎.pre-commit-config.yaml

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rev: 23.1.0
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hooks:
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- id: black
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files: ^fmriprep/|^wrapper/
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files: ^src/fmripost_aroma/
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- repo: https://github.com/pycqa/isort
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rev: 5.12.0
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hooks:
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- id: isort
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files: ^fmriprep/|^wrapper/
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files: ^src/fmripost_aroma/

‎Dockerfile

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--exclude "fsl/tcl" \
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--exclude "fsl/bin/FSLeyes" \
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&& find /opt/fsl-6.0.5.1/bin -type f -not \( \
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-name "applywarp" -or \
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-name "bet" -or \
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-name "bet2" -or \
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-name "convert_xfm" -or \
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-name "fast" -or \
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-name "flirt" -or \
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-name "fsl_regfilt" -or \
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-name "fslhd" -or \
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-name "fslinfo" -or \
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-name "fslmaths" -or \
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-name "fslmerge" -or \
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-name "fslroi" -or \
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-name "fslsplit" -or \
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-name "fslstats" -or \
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-name "imtest" -or \
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-name "mcflirt" -or \
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-name "melodic" -or \
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-name "prelude" -or \
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-name "remove_ext" -or \
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-name "susan" -or \
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-name "topup" -or \
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-name "zeropad" \) -delete \
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-name "susan" -or \) -delete \
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&& find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
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ENV FSLDIR="/opt/fsl-6.0.5.1" \
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PATH="/opt/fsl-6.0.5.1/bin:$PATH" \

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