Merge pull request #459 from mgxd/enh/normalize-t2w #27

Workflow file for this run

.github/workflows/build_test_deploy.yml at 9a6385b

	name: Build-Test-Deploy

	on:
	push:
	branches:
	- main
	- master
	- maint/*
	tags:
	- "*"
	pull_request:
	branches:
	- main
	- master
	- maint/*
	schedule:
	# 8am EST / 9am EDT Mondays
	- cron: "0 13 * * 1"
	workflow_dispatch:

	defaults:
	run:
	shell: bash

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

	permissions:
	contents: read

	env:
	# Force tox and pytest to use color
	FORCE_COLOR: true
	TEMPLATEFLOW_HOME: /tmp/templateflow

	jobs:
	build:
	name: Build & verify package
	runs-on: ubuntu-latest
	permissions:
	attestations: write
	id-token: write
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	persist-credentials: false
	## Stuck on https://github.com/astral-sh/uv/issues/5450
	## or https://github.com/hynek/build-and-inspect-python-package/issues/155
	# - uses: hynek/build-and-inspect-python-package@v2
	# with:
	# upload-name-suffix: -main
	# attest-build-provenance-github: ${{ github.event_name != 'pull_request' }}
	# - uses: hynek/build-and-inspect-python-package@v2
	# with:
	# path: wrapper
	# upload-name-suffix: -wrapper
	# attest-build-provenance-github: ${{ github.event_name != 'pull_request' }}
	## Manually reproducing with pyproject-build
	## Probably slightly slower
	- name: Install the latest version of uv
	uses: astral-sh/setup-uv@v4
	- name: Build smriprep
	run: uvx --from=build pyproject-build --installer uv .
	- name: Upload smriprep as Packages-main
	uses: actions/upload-artifact@v4
	with:
	name: Packages-main
	path: dist/

	- name: Show package contents hierarchically, including metadata.
	shell: bash
	run: \|
	echo -e '\n<details><summary>SDist contents</summary>\n' >> $GITHUB_STEP_SUMMARY
	tar -tvzf dist/*.tar.gz \| sed 's/^/ /' \| tee -a $GITHUB_STEP_SUMMARY
	echo -e '\n</details>\n' >> $GITHUB_STEP_SUMMARY

	echo -e '\n<details><summary>Wheel contents</summary>\n' >> $GITHUB_STEP_SUMMARY
	unzip -l dist/*.whl \| sed 's/^/ /' \| tee -a $GITHUB_STEP_SUMMARY
	echo -e '\n</details>\n' >> $GITHUB_STEP_SUMMARY

	echo ----- Metadata Follows -----
	echo -e '\n<details><summary>Metadata</summary>\n' >> $GITHUB_STEP_SUMMARY
	tar --wildcards -xOf dist/.tar.gz "/PKG-INFO" \| sed 's/^/ /' \| tee -a $GITHUB_STEP_SUMMARY
	echo -e '\n</details>\n' >> $GITHUB_STEP_SUMMARY
	echo ----- End of Metadata -----

	- name: Report on smriprep packages
	run: \|
	echo "name=Packages-main" >>${GITHUB_OUTPUT}
	- name: Build smriprep-docker
	run: uvx --from=build pyproject-build --installer uv ./wrapper
	- name: Upload smriprep as Packages-wrapper
	uses: actions/upload-artifact@v4
	with:
	name: Packages-wrapper
	path: wrapper/dist/

	- name: Show package contents hierarchically, including metadata.
	shell: bash
	run: \|
	echo -e '\n<details><summary>SDist contents</summary>\n' >> $GITHUB_STEP_SUMMARY
	tar -tvzf wrapper/dist/*.tar.gz \| sed 's/^/ /' \| tee -a $GITHUB_STEP_SUMMARY
	echo -e '\n</details>\n' >> $GITHUB_STEP_SUMMARY

	echo -e '\n<details><summary>Wheel contents</summary>\n' >> $GITHUB_STEP_SUMMARY
	unzip -l wrapper/dist/*.whl \| sed 's/^/ /' \| tee -a $GITHUB_STEP_SUMMARY
	echo -e '\n</details>\n' >> $GITHUB_STEP_SUMMARY

	echo ----- Metadata Follows -----
	echo -e '\n<details><summary>Metadata</summary>\n' >> $GITHUB_STEP_SUMMARY
	tar --wildcards -xOf wrapper/dist/.tar.gz "/PKG-INFO" \| sed 's/^/ /' \| tee -a $GITHUB_STEP_SUMMARY
	echo -e '\n</details>\n' >> $GITHUB_STEP_SUMMARY
	echo ----- End of Metadata -----

	test:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ["ubuntu-latest"]
	python-version: ["3.10", "3.11", "3.12", "3.13"]
	dependencies: [latest] # , pre]
	architecture: ["x64"]
	include:
	# Test minimum dependencies on oldest supported Python
	- os: ubuntu-latest
	python-version: "3.10"
	dependencies: min
	exclude:
	# Do not test pre-releases for versions out of SPEC0
	- os: ubuntu-latest
	python-version: "3.10"
	dependencies: pre

	env:
	DEPENDS: ${{ matrix.dependencies }}

	steps:
	- uses: actions/checkout@v4
	with:
	persist-credentials: false
	- name: Install the latest version of uv
	uses: astral-sh/setup-uv@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	architecture: ${{ matrix.architecture }}
	- name: Display Python version
	run: python -c "import sys; print(sys.version)"

	- name: Restore cached templateflow
	id: tf-cache-restore
	uses: actions/cache@v4
	with:
	path: /tmp/templateflow
	key: templateflow-v0
	# Use the following to fall back to and build on v0 when bumping to v1
	# If the cache need to be cleared, remove this when bumping key version
	# restore-keys: \|
	# templateflow-v0
	- name: Initialize templateflow
	if: steps.tf-cache-restore.outputs.cache-hit != 'true'
	run: \|
	uvx templateflow update --no-overwrite

	- name: Install tox
	run: \|
	uv tool install tox --with=tox-uv --with=tox-gh-actions
	- name: Show tox config
	run: tox c
	- name: Run tox
	run: tox -v --exit-and-dump-after 1200
	- uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	if: ${{ always() }}

	test-packages:
	runs-on: ${{ matrix.os }}
	needs: [build]
	strategy:
	matrix:
	os: ["ubuntu-latest"]
	python-version: ["3.12"]

	env:
	DEPENDS: ${{ matrix.dependencies }}

	steps:
	- name: Download packages built by build-and-inspect-python-package
	uses: actions/download-artifact@v4
	with:
	pattern: Packages-*
	path: dist
	- run: ls -lR

	- name: Install the latest version of uv
	uses: astral-sh/setup-uv@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Restore cached templateflow
	id: tf-cache-restore
	uses: actions/cache@v4
	with:
	path: /tmp/templateflow
	key: templateflow-v0
	# Use the following to fall back to and build on v0 when bumping to v1
	# If the cache need to be cleared, remove this when bumping key version
	# restore-keys: \|
	# templateflow-v0
	- name: Check wrapper version
	run: \|
	echo n \| uvx --from=$( ls dist//smriprep_docker.whl ) smriprep-docker --version

	- name: Unpack sdist
	run: \|
	tar --strip-components=1 -xzf dist//smriprep-.tar.gz

	- name: Install tox
	run: \|
	uv tool install tox --with=tox-uv --with=tox-gh-actions
	- name: Show tox config
	run: tox c
	- name: Run tox
	run: tox -v --exit-and-dump-after 1200
	- uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	if: ${{ always() }}

	publish:
	name: Publish released package to pypi.org
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
	runs-on: ubuntu-latest
	environment: PyPI
	needs: [test, test-packages]
	permissions:
	attestations: write
	id-token: write

	steps:
	- name: Download packages built by build-and-inspect-python-package
	uses: actions/download-artifact@v4
	with:
	name: Packages
	path: dist

	- name: Upload package to PyPI
	uses: pypa/gh-action-pypi-publish@release/v1

	checks:
	runs-on: "ubuntu-latest"
	continue-on-error: true
	strategy:
	matrix:
	check: ["style", "spellcheck"]

	steps:
	- uses: actions/checkout@v4
	with:
	persist-credentials: false
	- name: Install the latest version of uv
	uses: astral-sh/setup-uv@v4
	- name: Install tox
	run: uv tool install tox --with=tox-uv
	- name: Show tox config
	run: tox c -e ${{ matrix.check }}
	- name: Run check
	run: tox -e ${{ matrix.check }}

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Merge pull request #459 from mgxd/enh/normalize-t2w #27

Workflow file

Merge pull request #459 from mgxd/enh/normalize-t2w #27

Jobs

Run details

Workflow file for this run