ENH: Add volspace and volcohort entities to IO config file #1958

Workflow file for this run

.github/workflows/pythonpackage.yml at 5ee5f1d

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: Python package

	on:
	push:
	branches: [ '**' ]
	tags: [ '*' ]
	pull_request:
	branches: [ master, 'maint/*' ]
	schedule:
	- cron: '0 0 * * *'

	concurrency:
	group: python-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	job_metadata:
	if: github.repository == 'nipreps/niworkflows'
	runs-on: ubuntu-latest
	outputs:
	commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
	version: ${{ steps.show_version.outputs.version }}
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Print head git commit message
	id: get_commit_message
	run: \|
	if [[ -z "$COMMIT_MSG" ]]; then
	COMMIT_MSG=$(git show -s --format=%s $REF)
	fi
	echo commit_message=$COMMIT_MSG \| tee -a $GITHUB_OUTPUT
	env:
	COMMIT_MSG: ${{ github.event.head_commit.message }}
	REF: ${{ github.event.pull_request.head.sha }}
	- name: Detect version
	id: show_version
	run: \|
	if [[ "$GITHUB_REF" == refs/tags/* ]]; then
	VERSION=${GITHUB_REF##*/}
	else
	pipx run hatch version # Once to avoid output of initial setup
	VERSION=$( pipx run hatch version )
	fi
	echo version=$VERSION \| tee -a $GITHUB_OUTPUT

	build:
	if: github.repository == 'nipreps/niworkflows'
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Set up Python 3
	uses: actions/setup-python@v5
	with:
	python-version: 3
	- name: Display Python version
	run: python -c "import sys; print(sys.version)"
	- name: Build niworkflows
	run: pipx run build
	- name: Check distributions
	run: pipx run twine check dist/*
	- uses: actions/upload-artifact@v3
	with:
	name: dist
	path: dist/

	get_data:
	if: github.repository == 'nipreps/niworkflows'
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- name: Create test data directory
	run: mkdir -p $HOME/.cache/stanford-crn
	- name: Load test data cache
	uses: actions/cache@v4
	id: stanford-crn
	with:
	path: ~/.cache/stanford-crn/
	key: data-v0-${{ github.ref_name }}-${{ github.sha }}
	restore-keys: \|
	data-v0-${{ github.ref_name }}-
	data-v0-
	- name: Setup conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-activate-base: true
	activate-environment: ""
	- name: Verify environment
	run: \|
	conda info
	which python
	- name: Install datalad
	run: \|
	python -m pip install datalad-installer
	datalad-installer --sudo ok git-annex
	python -m pip install datalad datalad-osf
	datalad wtf
	- name: Pacify git
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "Niworkflows Action"
	- name: Fetch test data
	run: \|
	DS=$HOME/.cache/stanford-crn
	datalad install -r -s https://github.com/nipreps-data/niworkflows-data.git $DS
	cd $DS
	git -C BIDS-examples-1-enh-ds054 checkout enh/ds054
	datalad update -r --merge -d .
	datalad get -J 2 -r ds000003 ds000030/sub-10228/func

	test:
	needs: [build, get_data, job_metadata]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
	install: [repo]
	include:
	- python-version: "3.11"
	install: sdist
	- python-version: "3.11"
	install: wheel
	- python-version: "3.11"
	install: editable

	env:
	INSTALL_TYPE: ${{ matrix.install }}

	steps:
	- uses: actions/checkout@v4
	if: matrix.install == 'repo' \|\| matrix.install == 'editable'
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Load test data cache
	uses: actions/cache@v4
	id: stanford-crn
	with:
	path: ~/.cache/stanford-crn/
	key: data-v0-${{ github.ref_name }}-${{ github.sha }}
	- name: Load TemplateFlow cache
	uses: actions/cache@v4
	id: templateflow
	with:
	path: ~/.cache/templateflow
	key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
	restore-keys: \|
	templateflow-v0-${{ github.ref_name }}-
	templateflow-v0-
	- name: Fetch packages
	if: matrix.install == 'sdist' \|\| matrix.install == 'wheel'
	uses: actions/download-artifact@v3
	with:
	name: dist
	path: dist/
	- name: Select archive
	run: \|
	if [ "$INSTALL_TYPE" = "sdist" ]; then
	ARCHIVE=$( ls dist/*.tar.gz )
	elif [ "$INSTALL_TYPE" = "wheel" ]; then
	ARCHIVE=$( ls dist/*.whl )
	elif [ "$INSTALL_TYPE" = "repo" ]; then
	ARCHIVE="."
	elif [ "$INSTALL_TYPE" = "editable" ]; then
	ARCHIVE="-e ."
	fi
	echo "ARCHIVE=$ARCHIVE" \| tee -a $GITHUB_ENV
	- name: Install package
	run: python -m pip install $ARCHIVE
	- name: Check version
	run: \|
	INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
	echo "INSTALLED: \"${INSTALLED_VERSION}\""
	test "${INSTALLED_VERSION}" = "${VERSION}"
	env:
	VERSION: ${{ needs.job_metadata.outputs.version }}
	- name: Install test dependencies
	run: python -m pip install "niworkflows[tests]"
	- name: Run tests
	run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
	- uses: codecov/codecov-action@v4
	name: Submit to CodeCov
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

	test-pre:
	needs: [get_data, job_metadata]
	if: ${{ !contains(needs.job_metadata.outputs.commit_message, '[skip pre]') }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
	install: [repo]
	pip-flags: ['--pre']

	env:
	INSTALL_TYPE: ${{ matrix.install }}
	PIP_FLAGS: ${{ matrix.pip-flags }}

	steps:
	- name: Debug commit message
	run: echo "${{ needs.job_metadata.outputs.commit_message }}"
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Load test data cache
	uses: actions/cache@v4
	id: stanford-crn
	with:
	path: ~/.cache/stanford-crn/
	key: data-v0-${{ github.ref_name }}-${{ github.sha }}
	- name: Load TemplateFlow cache
	uses: actions/cache@v4
	id: templateflow
	with:
	path: ~/.cache/templateflow
	key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
	restore-keys: \|
	templateflow-v0-${{ github.ref_name }}-
	templateflow-v0-
	- name: Install package
	run: python -m pip install $PIP_FLAGS .
	- name: Check version
	run: \|
	INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
	echo "INSTALLED: \"${INSTALLED_VERSION}\""
	test "${INSTALLED_VERSION}" = "${VERSION}"
	env:
	VERSION: ${{ needs.job_metadata.outputs.version }}
	- name: Install test dependencies
	run: python -m pip install $PIP_FLAGS "niworkflows[tests]"
	- name: Run tests
	run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
	- uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	name: Submit to CodeCov

	flake8:
	if: github.event_name != 'schedule'
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3
	uses: actions/setup-python@v5
	with:
	python-version: 3
	- run: pipx run flake8 niworkflows/

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ENH: Add volspace and volcohort entities to IO config file #1958

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ENH: Add volspace and volcohort entities to IO config file #1958

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Workflow file for this run