Draft MEDIC dynamic distortion correction method (second attempt) #21

Workflow file for this run

.github/workflows/build-test-publish.yml at b164fa3

	name: CI

	on:
	push:
	pull_request:
	schedule:
	- cron: 0 0 * * 0
	# Allow job to be triggered manually from GitHub interface
	workflow_dispatch:

	# Force pytest to use color
	env:
	FORCE_COLOR: true

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

	permissions:
	contents: read

	defaults:
	run:
	shell: bash -el {0}

	jobs:
	build-package:
	name: Build & inspect package
	runs-on: ubuntu-latest
	permissions:
	attestations: write
	id-token: write

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- uses: hynek/build-and-inspect-python-package@v2

	test:
	if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' \|\| github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
	runs-on: ubuntu-latest
	env:
	TEST_DATA_HOME: /home/runner/sdcflows-tests
	FSLOUTPUTTYPE: NIFTI_GZ
	FSLMULTIFILEQUIT: TRUE
	AFNI_HOME: /opt/afni
	AFNI_MODELPATH: /opt/afni/models
	AFNI_IMSAVE_WARNINGS: NO
	AFNI_TTATLAS_DATASET: /opt/afni/atlases
	AFNI_PLUGINPATH: /opt/afni/plugins
	strategy:
	max-parallel: 6
	matrix:
	python-version: ["3.9", "3.10", "3.11", "3.12"]
	marks: ["not slow"]
	include:
	- python-version: "3.9"
	marks: "slow and not veryslow"
	- python-version: "3.12"
	marks: "veryslow"

	steps:
	- uses: actions/cache@v4
	with:
	path: /var/lib/apt
	key: apt-cache-v3
	restore-keys: \|
	apt-cache-v3
	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y --no-install-recommends \
	curl bzip2 ca-certificates \
	tcsh gsl-bin netpbm \
	libjpeg62 xvfb xterm \
	libglu1-mesa-dev libglw1-mesa \
	libxm4 build-essential

	- uses: actions/cache@v4
	with:
	path: /opt/afni
	key: afni-v1
	restore-keys: \|
	afni-v1
	- name: Install AFNI
	run: \|
	if [[ ! -d "${AFNI_HOME}" ]]; then
	curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \
	tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
	fi

	- name: Git settings (pacify DataLad)
	run: \|
	git config --global user.name 'NiPreps Bot'
	git config --global user.email '[email protected]'
	- name: Set up Python ${{ matrix.python-version }}
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	auto-activate-base: true
	python-version: ${{ matrix.python-version }}
	channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
	- uses: actions/cache@v4
	id: conda
	env:
	CACHE_NUM: v5
	with:
	path: \|
	~/conda_pkgs_dir
	/home/runner/.cache/pip
	key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
	restore-keys: \|
	python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
	- name: Install DataLad
	run: \|
	conda install git-annex==alldep pip
	pip install datalad datalad-osf
	- name: Install fsl and ANTs
	run: \|
	conda install fsl-fugue fsl-topup ants
	- uses: actions/checkout@v4
	- name: Install dependencies
	timeout-minutes: 5
	run: \|
	pip install .[tests]


	- uses: actions/cache@v4
	with:
	path: ~/.cache/templateflow
	key: tf-cache-v1
	restore-keys: \|
	tf-cache-
	- name: Get TemplateFlow's required objects
	run: \|
	python tools/cache_templateflow.py

	- uses: actions/cache@v4
	with:
	path: ${{ env.TEST_DATA_HOME }}
	key: data-cache-v2
	restore-keys: \|
	data-cache-
	- name: Install test data
	run: \|
	mkdir -p ${{ env.TEST_DATA_HOME }}
	cd ${{ env.TEST_DATA_HOME }}

	# ds001600
	datalad install -r https://github.com/nipreps-data/ds001600.git
	datalad update -r --merge -d ds001600/
	datalad get -r -J 2 -d ds001600/ ds001600/sub-1/

	# HCP/sub-101006
	datalad install -r https://github.com/nipreps-data/HCP101006.git
	datalad update -r --merge -d HCP101006/
	datalad get -r -J 2 -d HCP101006 HCP101006/*

	# ds001771
	datalad install -r https://github.com/nipreps-data/ds001771.git
	datalad update -r --merge -d ds001771/
	datalad get -r -J 2 -d ds001771/ ds001771/sub-36/*
	datalad get -r -J 2 -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*

	# ds000054
	datalad install -r https://github.com/nipreps-data/ds000054.git
	datalad update --merge -d ds000054/
	datalad get -r -d ds000054/ ds000054/sub-100185/*
	datalad get -r -J 2 -d ds000054/ ds000054/derivatives/smriprep-0.6/sub-100185/anat/

	# ds000206
	datalad install -r https://github.com/nipreps-data/ds000206.git
	datalad update -r --merge -d ds000206/
	datalad get -r -J 2 -d ds000206/ ds000206/sub-05/

	# Brain extraction tests
	datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
	datalad update --merge -d brain-extraction-tests/
	datalad get -r -J 2 -d brain-extraction-tests brain-extraction-tests/*

	# HCPH pilot
	datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
	datalad update -r --merge -d hcph-pilot_fieldmaps/
	datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*

	- name: Set FreeSurfer variables
	run: \|
	echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV
	echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV

	- name: Install FreeSurfer's mri_robust_template
	env:
	MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2
	run: \|
	curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
	sudo install mri_robust_template /usr/local/bin
	mkdir -p $( dirname $FS_LICENSE )
	echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" \| base64 -d > $FS_LICENSE

	- name: Run pytest with coverage
	run: \|
	export PATH=${AFNI_HOME}:$PATH
	export FSLDIR=${CONDA_PREFIX}
	pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
	--durations=20 --durations-min=10 -m "$MARKS"
	env:
	MARKS: ${{ matrix.marks }}

	- uses: codecov/codecov-action@v4
	with:
	file: cov.xml
	token: ${{ secrets.CODECOV_TOKEN }}
	if: ${{ always() }}

	publish:
	name: Publish released package to pypi.org
	environment: release-pypi
	if: github.event.action == 'published'
	runs-on: ubuntu-latest
	needs: [build-package, test]
	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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Draft MEDIC dynamic distortion correction method (second attempt) #21

Workflow file

Draft MEDIC dynamic distortion correction method (second attempt) #21

Jobs

Run details

Workflow file for this run