RF: Use scipy.interpolate.BSpline to construct spline basis #789

Workflow file for this run

.github/workflows/unittests.yml at 6061011

	name: Deps & CI

	on:
	push:
	pull_request:
	schedule:
	- cron: 0 0 * * 0

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

	permissions:
	contents: read

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

	jobs:
	build-linux:
	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
	ANTSPATH: /opt/ants
	DEPS: ${{ matrix.deps }}.txt
	strategy:
	max-parallel: 5
	matrix:
	python-version: ["3.8", "3.9", "3.10"]
	deps: ["requirements"]
	include:
	- python-version: "3.8"
	deps: "min-requirements"

	steps:
	- uses: actions/cache@v3
	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@v3
	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

	- uses: actions/cache@v3
	with:
	path: /opt/ants
	key: ants-v1
	restore-keys: \|
	ants-v1
	- name: Install ANTS
	run: \|
	if [[ ! -d "${ANTSPATH}" ]]; then
	sudo mkdir -p $ANTSPATH
	curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \| sudo tar -xzC $ANTSPATH --strip-components 1
	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@v2
	with:
	auto-update-conda: true
	auto-activate-base: true
	python-version: ${{ matrix.python-version }}
	channels: anaconda,https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
	- uses: actions/cache@v3
	id: conda
	env:
	CACHE_NUM: v4
	with:
	path: \|
	~/conda_pkgs_dir
	/home/runner/.cache/pip
	key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
	restore-keys: \|
	python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
	- name: Install DataLad
	run: \|
	conda install git-annex datalad pip
	pip install datalad-osf
	- name: Install fsl
	run: \|
	conda install fsl-fugue fsl-topup
	- uses: actions/checkout@v3
	- name: Install dependencies
	timeout-minutes: 5
	run: \|
	pip install -r $DEPS
	pip install .[tests]


	- uses: actions/cache@v3
	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@v3
	with:
	path: ${{ env.TEST_DATA_HOME }}
	key: data-cache-v1
	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 -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 -d HCP101006

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

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

	- 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 $HOME/.cache/freesurfer/
	echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" \| base64 -d > $HOME/.cache/freesurfer/license.txt

	- name: Run pytest with coverage
	run: \|
	export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
	export PATH=$ANTSPATH:${AFNI_HOME}:/usr/lib/fsl/5.0:$PATH
	pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows

	- uses: codecov/codecov-action@v3
	with:
	file: cov.xml
	if: ${{ always() }}

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RF: Use scipy.interpolate.BSpline to construct spline basis #789

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RF: Use scipy.interpolate.BSpline to construct spline basis #789

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