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Merge pull request #396 from juaml/ci/update-images
[CI]: Upgrade Docker images and workflows
2 parents 2ec35f9 + 9074d01 commit b8459c8

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+114
-94
lines changed

‎.github/workflows/ci-docs.yml‎

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- '.github/workflows/**'
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jobs:
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run-tests:
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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strategy:
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fail-fast: false
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matrix:

‎.github/workflows/ci.yml‎

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jobs:
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run-tests:
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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# Use custom docs CI image
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container: ghcr.io/juaml/junifer-ci:main
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strategy:
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run: |
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echo "Using FSL : $(flirt -version)"
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- name: Install system dependencies
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# actions/checkout fails to identify Git as it's not in the CI image
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run: |
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# actions/checkout fails to identify Git as it's not in the CI image
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apt-get -qq update && \
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apt-get -qq install -y \
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sudo apt-get update
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sudo apt-get install -y \
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git \
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git-annex \
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make \
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jq
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# Copy xfms directory
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mkdir -p $HOME/junifer/data/xfms && \
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- name: Copy xfms directory
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mkdir -p $HOME/junifer/data/xfms
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cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
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- name: Checkout repository
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uses: actions/checkout@v4
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git config --global user.email "[email protected]"
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git config --global user.name "GitHub Runner"
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- name: Test with tox
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# https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
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run: |
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# https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
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git config --system --add safe.directory $(pwd)
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tox
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- name: Upload coverage to Codecov

‎.github/workflows/docker-ci-publish.yml‎

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jobs:
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build:
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runs-on: ubuntu-latest
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runs-on: ubuntu-24.04
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permissions:
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contents: read
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packages: write

‎.github/workflows/docker-docs-publish.yml‎

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jobs:
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build:
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runs-on: ubuntu-latest
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runs-on: ubuntu-24.04
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permissions:
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contents: read
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packages: write

‎.github/workflows/docs-preview.yml‎

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@@ -17,7 +17,7 @@ concurrency: preview-${{ github.ref }}
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jobs:
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build-docs:
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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# Use custom docs CI image
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container: ghcr.io/juaml/junifer-docs:main
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steps:

‎.github/workflows/docs.yml‎

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jobs:
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build-docs:
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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# Use custom docs CI image
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container: ghcr.io/juaml/junifer-docs:main
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steps:
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- name: Check ANTs
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run: |
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echo "Using ANTs : $(antsRegistration --version)"
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- name: Install system dependencies
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# actions/checkout fails to identify Git as it's not in the CI image
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run: |
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# actions/checkout fails to identify Git as it's not in the CI image
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apt-get -qq update && \
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apt-get -qq install -y \
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sudo apt-get update
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sudo apt-get install -y \
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git \
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git-annex \
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make \
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jq
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# Copy xfms directory
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mkdir -p $HOME/junifer/data/xfms && \
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- name: Copy xfms directory
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mkdir -p $HOME/junifer/data/xfms
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cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
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- name: Checkout source
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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# require all of history to see all tagged versions' docs
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path: docs/_build
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- name: Build docs
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# Use the args we normally pass to sphinx-build, but run sphinx-multiversion
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# https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
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run: |
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# https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
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git config --system --add safe.directory $(pwd)
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make -C docs/ html
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touch docs/_build/.nojekyll

‎.github/workflows/publish.yml‎

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name: Build and publish
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on:
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push:
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branches:
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- main
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tags:
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- 'v*'
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jobs:
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build-and-publish:
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name: Build and publish
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runs-on: ubuntu-latest
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permissions:
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# Needed for PyPI publishing
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id-token: write
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# Needed for GitHub releases
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contents: write
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steps:
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- name: Checkout source
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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submodules: true
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Install build
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run:
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python -m pip install --upgrade pip
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python -m pip install build
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- name: Build package
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run:
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python -m build
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- name: Publish package to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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- name: Make release on GitHub
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uses: softprops/action-gh-release@v2
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if: startsWith(github.ref, 'refs/tags/')
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with:
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files: |
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dist/*.tar.gz
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dist/*.whl
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generate_release_notes: true
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make_latest: true

‎.github/workflows/pypi.yml‎

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‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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rev: v5.0.0
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hooks:
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- id: check-ast
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- id: check-docstring-first
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- id: trailing-whitespace
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args: [--markdown-linebreak-ext=md]
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- repo: https://github.com/abravalheri/validate-pyproject
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rev: v0.16
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rev: v0.23
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hooks:
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- id: validate-pyproject
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 24.4.2
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rev: 24.10.0
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hooks:
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- id: black
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exclude: ^(docs/|examples/|tools/)
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args: [--check]
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.4.2
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rev: v0.9.3
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hooks:
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- id: ruff
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types_or: [python, jupyter]
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exclude: ^(__init__.py)
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args: [--output-format, grouped, --show-fixes]
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.6
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rev: v2.4.0
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hooks:
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- id: codespell
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exclude: ^(.github/|docs/)
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- id: rst-directive-colons
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- id: rst-inline-touching-normal
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- repo: https://github.com/adamchainz/blacken-docs
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rev: "1.16.0"
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rev: "1.19.1"
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hooks:
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- id: blacken-docs
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additional_dependencies:

‎Dockerfile-ci‎

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file \
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dc \
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libquadmath0 \
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libgomp1
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libgomp1 \
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&& rm -rf /var/lib/apt/lists/*
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# Add xfms
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COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms

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