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Merge branch 'master' into enh/bids-uris
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‎.circleci/artifact_path

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/0/tmp/gh-pages/docs/_build/no_version_html/html/index.html
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/0/tmp/gh-pages/docs/_build/no_version_html/html/index.html

‎.circleci/config.yml

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- checkout:
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path: /tmp/src/sdcflows
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- run:
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- run:
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name: Configure git (pacify datalad)
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command: |
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git config --global user.name "First Last"
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datalad update --merge -d brain-extraction-tests/
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datalad get -r -J 2 -d brain-extraction-tests
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- run:
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name: Install HCPh fieldmaps
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command: |
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datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
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datalad update -r --merge -d hcph-pilot_fieldmaps/
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datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
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- save_cache:
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key: data-v6-{{ .Branch }}-{{ .Revision }}
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paths:
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flags: unittests
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build_docs:
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docker:
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- image: python:3.8.5
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<<: *python_defaults
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working_directory: /tmp/gh-pages
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environment:
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- FSLOUTPUTTYPE: NIFTI
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- run:
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name: Install Graphviz
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command: |
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apt-get update -y
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apt-get install -y --no-install-recommends graphviz
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sudo apt-get update -y
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sudo apt-get install -y --no-install-recommends graphviz
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- run:
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name: Install deps
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command: |
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python -m venv /tmp/venv
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source /tmp/venv/bin/activate
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python -m pip install -U pip setuptools_scm
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python -m pip install -U pip setuptools setuptools_scm
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pip install --no-cache-dir -r docs/requirements.txt
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- run:
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name: Build only this commit

‎.github/dependabot.yml

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# Set update schedule for GitHub Actions
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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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# Check for updates to GitHub Actions every week
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interval: "weekly"

‎.github/workflows/docs-build-pr.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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‎.github/workflows/docs-build-update.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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ssh-key: "${{ secrets.NIPREPS_DEPLOY }}"
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fetch-depth: 0

‎.github/workflows/pythonpackage.yml

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contents: read
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jobs:
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job_metadata:
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if: github.repository == 'nipreps/sdcflows'
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runs-on: ubuntu-latest
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outputs:
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commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
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version: ${{ steps.show_version.outputs.version }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Print head git commit message
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id: get_commit_message
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run: |
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if [[ -z "$COMMIT_MSG" ]]; then
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COMMIT_MSG=$(git show -s --format=%s $REF)
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fi
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echo commit_message=$COMMIT_MSG | tee -a $GITHUB_OUTPUT
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env:
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COMMIT_MSG: ${{ github.event.head_commit.message }}
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REF: ${{ github.event.pull_request.head.sha }}
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- name: Detect version
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id: show_version
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run: |
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if [[ "$GITHUB_REF" == refs/tags/* ]]; then
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VERSION=${GITHUB_REF##*/}
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else
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pip install setuptools_scm
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VERSION=$( python -m setuptools_scm )
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fi
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echo version=$VERSION | tee -a $GITHUB_OUTPUT
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build:
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if: github.repository == 'nipreps/sdcflows'
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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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with:
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fetch-depth: 0
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- name: Set up Python 3
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uses: actions/setup-python@v4
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with:
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python-version: 3
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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: Build niworkflows
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run: pipx run build
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- name: Check distributions
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run: pipx run twine check dist/*
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- uses: actions/upload-artifact@v3
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with:
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name: dist
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path: dist/
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test:
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if: "!startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]')"
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needs: [build, job_metadata]
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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pip: ["pip==21.2", "pip~=22.0"]
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python-version: ["3.8", "3.12"]
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install: [repo, sdist, wheel, editable]
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env:
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INSTALL_TYPE: ${{ matrix.install }}
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steps:
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- uses: actions/checkout@v3
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- name: Fetch all tags (for setuptools_scm to work)
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run: |
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/usr/bin/git -c protocol.version=2 fetch --tags --prune --unshallow origin
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- uses: actions/checkout@v4
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if: matrix.install == 'repo' || matrix.install == 'editable'
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/cache@v3
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- name: Fetch packages
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if: matrix.install == 'sdist' || matrix.install == 'wheel'
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uses: actions/download-artifact@v3
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with:
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path: $HOME/.cache/pip
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key: pip-cache-v1
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restore-keys: |
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pip-cache-
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- name: Build in confined environment and interpolate version
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name: dist
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path: dist/
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- name: Select archive
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run: |
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python -m venv /tmp/buildenv
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source /tmp/buildenv/bin/activate
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python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
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setuptools_scm_git_archive pip twine docutils
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python -m build -s -w
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python -m twine check dist/sdcflows-*
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mv dist /tmp/package
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rm -rf sdcflows.egg-info/
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# Interpolate version
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if [[ "$GITHUB_REF" == refs/tags/* ]]; then
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TAG=${GITHUB_REF##*/}
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if [ "$INSTALL_TYPE" = "sdist" ]; then
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ARCHIVE=$( ls dist/*.tar.gz )
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elif [ "$INSTALL_TYPE" = "wheel" ]; then
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ARCHIVE=$( ls dist/*.whl )
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elif [ "$INSTALL_TYPE" = "repo" ]; then
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ARCHIVE="."
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elif [ "$INSTALL_TYPE" = "editable" ]; then
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ARCHIVE="-e ."
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fi
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THISVERSION=$( python -m setuptools_scm )
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THISVERSION=${TAG:-$THISVERSION}
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echo "Expected VERSION: \"${THISVERSION}\""
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echo "THISVERSION=${THISVERSION}" >> $GITHUB_ENV
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- name: Install in confined environment [pip]
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run: |
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python -m venv /tmp/pip
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source /tmp/pip/bin/activate
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python -m pip install -U "setuptools >= 45" "setuptools_scm >= 6.2" "${{ matrix.pip }}"
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python -m pip install .
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INSTALLED_VERSION=$(python -c 'import sdcflows as sdc; print(sdc.__version__, end="")')
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echo "VERSION: \"${THISVERSION}\""
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [sdist]
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run: |
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python -m venv /tmp/install_sdist
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source /tmp/install_sdist/bin/activate
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python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
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python -m pip install /tmp/package/sdcflows*.tar.gz
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INSTALLED_VERSION=$(python -c 'import sdcflows as sdc; print(sdc.__version__, end="")')
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echo "VERSION: \"${THISVERSION}\""
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [wheel]
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echo "ARCHIVE=$ARCHIVE" | tee -a $GITHUB_ENV
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- name: Install package
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run: python -m pip install $ARCHIVE
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- name: Check version
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run: |
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python -m venv /tmp/install_wheel
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source /tmp/install_wheel/bin/activate
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python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
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python -m pip install /tmp/package/sdcflows*.whl
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INSTALLED_VERSION=$(python -c 'import sdcflows as sdc; print(sdc.__version__, end="")')
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INSTALLED_VERSION=$(python -c 'import sdcflows; print(sdcflows.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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test "${INSTALLED_VERSION}" = "${VERSION}"
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env:
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VERSION: ${{ needs.job_metadata.outputs.version }}
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flake8:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python 3
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uses: actions/setup-python@v4
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with:
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python-version: 3
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- run: pip install flake8
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- run: flake8 sdcflows/
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- run: pipx run flake8 sdcflows/

‎.github/workflows/unittests.yml

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strategy:
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max-parallel: 5
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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deps: ["requirements"]
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include:
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- python-version: "3.8"
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git config --global user.name 'NiPreps Bot'
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git config --global user.email '[email protected]'
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- name: Set up Python ${{ matrix.python-version }}
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uses: conda-incubator/setup-miniconda@v2
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uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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auto-activate-base: true
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python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
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- name: Install DataLad
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conda install git-annex datalad pip
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pip install datalad-osf
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conda install git-annex=*=alldep* pip
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pip install datalad datalad-osf
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- name: Install fsl
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conda install fsl-fugue fsl-topup
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Install dependencies
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timeout-minutes: 5
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run: |

‎.maint/MAINTAINERS.md

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@@ -12,4 +12,3 @@ If you are participating because of your affiliation with another organization (
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| Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland |
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| Goncalves | Mathias | @mgxd | 0000-0002-7252-7771 | Department of Psychology, Stanford University, CA, USA |
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| Markiewicz | Christopher J. | @effigies | 0000-0002-6533-164X | Department of Psychology, Stanford University, CA, USA |
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‎.maint/PIs.md

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| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA |
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| Satterthwaite | Theodore D. | | 0000-0001-7072-9399 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
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| Gorgolewski | Krzysztof J. | @chrisgorgo | 0000-0003-3321-7583 | Google LLC |
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‎.pre-commit-config.yaml

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exclude: ".*/data/.*"
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: check-added-large-files
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- id: check-docstring-first
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- id: check-merge-conflict
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- id: check-json
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- id: check-toml
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- id: check-yaml
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- id: debug-statements
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- id: end-of-file-fixer
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- id: fix-byte-order-marker
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- id: trailing-whitespace
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# Enable when no significant PRs are in progress
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# - repo: https://github.com/psf/black
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# rev: 23.1.0
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# hooks:
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# - id: black
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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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