Well -- the regular -- codespell support #386

Workflow file for this run

.github/workflows/workflows.yml at b33385d

	---
	name: "CI build and test jobs"

	on:
	pull_request:
	branches-ignore:
	- /doc\/.*/
	push:
	branches:
	- dev
	- maint/*
	tags:
	- '*'
	schedule:
	# 7am EST / 8am EDT, daily
	- cron: '0 12 * * *'

	env:
	REGISTRY: ghcr.io
	IMAGE_NAME: ${{ github.repository }}
	INSTALL_TYPE: pip

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

	jobs:
	build:
	runs-on: ubuntu-latest
	steps:
	- name: Setup python
	uses: actions/setup-python@v4
	with:
	python-version: 3.9

	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	submodules: recursive

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3

	- name: Add version to environment
	run: \|
	python -c 'import fitlins; print(f"VERSION={fitlins.__version__}")' >> $GITHUB_ENV

	- name: Check version matches tag
	if: startsWith(github.ref, 'refs/tags/')
	run: test "$VERSION" = "${{ github.ref_name }}"

	- name: Build image and export
	timeout-minutes: 30
	uses: docker/build-push-action@v5
	with:
	context: .
	build-args: \|
	BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
	VCS_REF="$(git rev-parse --short HEAD)"
	VERSION=${{ env.VERSION }}
	push: false
	tags: \|
	${{ env.IMAGE_NAME }}:latest
	${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest
	load: true

	- name: Verify executable can be run
	run: \|
	docker images
	docker run --rm $IMAGE_NAME:latest --help

	- name: Check version
	run: \|
	DOCKERVERSION=$(docker run --rm $IMAGE_NAME:latest --version \
	\| tail -n 1 \| sed -e 's/.*fit/fit/' -e 's/[\r\n]//g')
	echo "$VERSION"
	echo "$DOCKERVERSION"
	test "$DOCKERVERSION" = "fitlins v$VERSION"

	- name: Export docker image to a tar file
	run: \|
	docker save ${{ github.repository }} > /tmp/docker.tar
	ls -l /tmp/

	- name: Upload docker.tar as artifact
	uses: actions/upload-artifact@v3
	with:
	name: docker
	path: /tmp/docker.tar

	cache_test_data:
	runs-on: ubuntu-latest
	steps:
	- name: "Make cachedir"
	run: \|
	mkdir -p /tmp/.cache/data && \
	chmod 777 /tmp/.cache/data

	- name: Set git ID
	run: \|
	git config --global user.name 'Fitlins GH-Action User' && \
	git config --global user.email '[email protected]'

	- name: Set up Python 3.9
	uses: actions/setup-python@v4
	with:
	python-version: 3.9

	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y git-annex
	python -m pip install --upgrade pip
	pip install datalad==0.14.7

	- name: Datalad WTF
	run: \|
	datalad wtf

	- name: Install cached data
	uses: actions/cache@v3
	id: cache
	with:
	path: /tmp/.cache/data
	key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}
	restore-keys: \|
	ds003-v5-${{ github.ref_name }}-
	ds003-v5-

	- name: "Install fMRIPrep derivatives of ds000003 and reference data"
	# if: steps.cache.outputs.cache-hit != 'true'
	run: \|
	cd /tmp/.cache/data
	datalad install -r -s https://gin.g-node.org/markiewicz/fitlins-tests
	datalad update --merge -d fitlins-tests
	cd fitlins-tests
	datalad get inputs/ds000003-fmriprep/sub-0{1,2,3}/func/_space-MNI152NLin2009cAsym_desc-.nii.gz \
	inputs/ds000003-fmriprep/sub-0{1,2,3}/func/_desc-confounds_.tsv \
	inputs/ds000003-fmriprep/dataset_description.json \
	inputs/ds000003-fmriprep/sub-//*.json \
	outputs
	datalad status

	- name: "Check installed derivatives data"
	run: \|
	cd /tmp/.cache/data/fitlins-tests/
	git log --oneline --graph
	du -sh .

	run_pytest:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ['ubuntu-latest']
	python-version: ["3.7", "3.8", "3.9", "3.10"]
	pip-flags: ['']
	check: ['test']
	env:
	CHECK_TYPE: ${{ matrix.check }}
	EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
	OS_TYPE: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	fetch-depth: 0
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	auto-update-conda: true
	activate-environment: fitlins-ci
	environment-file: tools/ci/conda_environment.yml
	python-version: ${{ matrix.python-version }}
	show-channel-urls: true
	auto-activate-base: false
	- name: Test conda installation
	run: \|
	conda info
	conda list
	conda env list
	conda config --show-sources
	conda config --show
	- name: Install dependencies
	run: \|
	conda install -y --channel leej3 "afni-minimal"
	conda list \| grep afni
	- name: Display Python version
	run: \|
	which python
	which pip
	python -c "import sys; print(sys.version)"
	- name: Install fitlins
	run: tools/ci/install.sh
	- name: Run tests
	run: tools/ci/check.sh
	- uses: codecov/codecov-action@v3
	with:
	verbose: true
	if: ${{ always() }}

	pre-release:
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: ['ubuntu-latest']
	python-version: ['3.10']
	# Check pre-release pybids and pre-release everything
	pip-flags: ['', 'PRE_PIP_FLAGS']
	check: ['test']
	env:
	CHECK_TYPE: ${{ matrix.check }}
	EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
	OS_TYPE: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	fetch-depth: 0
	- uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: fitlins-ci
	environment-file: tools/ci/conda_environment.yml
	python-version: ${{ matrix.python-version }}
	- name: Test conda installation
	run: \|
	conda info
	conda list
	conda env list
	conda config --show-sources
	conda config --show
	- name: Install dependencies
	run: \|
	conda install -y --channel leej3 "afni-minimal"
	conda list \| grep afni
	- name: Display Python version
	run: \|
	which python
	which pip
	python -c "import sys; print(sys.version)"
	- name: Install fitlins
	run: tools/ci/install.sh
	- name: Install pybids from GitHub
	run: pip install git+https://github.com/bids-standard/pybids.git
	- name: Run tests
	run: tools/ci/check.sh
	- uses: codecov/codecov-action@v3
	with:
	verbose: true
	if: ${{ always() }}

	test_ds003_nistats_smooth:
	needs: [cache_test_data]
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: [3.9]
	test_name: ["nistats_smooth"]
	pip-flags: ['']
	check: ['workflow']
	env:
	CHECK_TYPE: ${{ matrix.check }}
	EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
	OS_TYPE: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	fetch-depth: 0
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install fitlins
	run: tools/ci/install.sh

	- name: Restore cached test data
	uses: actions/cache@v3
	id: cache
	with:
	path: /tmp/.cache/data
	key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}

	- name: Run fitlins tests
	timeout-minutes: 240
	run: \|
	mkdir -p $WORK_DIR $OUTPUT_DIR
	chmod 777 $WORK_DIR $OUTPUT_DIR
	tools/ci/check.sh
	env:
	DATA: /tmp/.cache/data/fitlins-tests
	TEST_NAME: ${{ matrix.test_name }}
	OUTPUT_DIR: /tmp/ds003/derivatives
	WORK_DIR: /tmp/ds003/work
	- name: Combine coverage and submit
	uses: codecov/codecov-action@v3
	with:
	verbose: true

	test_ds003_afni:
	needs: [cache_test_data]
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: [3.9]
	test_name: ["afni_smooth", "afni_blurto"]
	pip-flags: ['']
	check: ['workflow']
	env:
	CHECK_TYPE: ${{ matrix.check }}
	EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
	OS_TYPE: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	fetch-depth: 0
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	auto-update-conda: true
	activate-environment: fitlins-ci
	environment-file: tools/ci/conda_environment.yml
	python-version: ${{ matrix.python-version }}
	show-channel-urls: true
	auto-activate-base: false
	- name: Test conda installation
	run: \|
	conda info
	conda list
	conda env list
	- name: Install dependencies
	run: \|
	conda install -y --channel leej3 "afni-minimal"
	conda list \| grep afni
	- name: Install fitlins
	run: tools/ci/install.sh

	- name: Restore cached test data
	uses: actions/cache@v3
	id: cache
	with:
	path: /tmp/.cache/data
	key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}

	- name: Run fitlins tests
	timeout-minutes: 240
	run: \|
	mkdir -p $WORK_DIR $OUTPUT_DIR
	chmod 777 $WORK_DIR $OUTPUT_DIR
	tools/ci/check.sh
	env:
	DATA: /tmp/.cache/data/fitlins-tests
	TEST_NAME: ${{ matrix.test_name }}
	OUTPUT_DIR: /tmp/ds003/derivatives
	WORK_DIR: /tmp/ds003/work
	- name: Combine coverage and submit
	uses: codecov/codecov-action@v3
	with:
	verbose: true

	test_ds003_nistats_blurto:
	needs: [build, cache_test_data]
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	test_name: ["nistats_blurto"]
	steps:
	- uses: actions/checkout@v4

	- name: Set up docker buildx
	uses: docker/setup-buildx-action@v3

	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: docker
	path: /tmp

	- name: Load docker image
	run: \|
	docker info
	set +o pipefail
	ls -l /tmp/docker.tar
	docker load < /tmp/docker.tar
	docker images

	- name: Restore cached test data
	uses: actions/cache@v3
	id: cache
	with:
	path: /tmp/.cache/data
	key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}

	- name: Run fitlins tests
	timeout-minutes: 240
	run: \|
	mkdir -p $WORK_DIR $OUTPUT_DIR
	chmod 777 $WORK_DIR $OUTPUT_DIR
	docker run --rm \
	-v $DATA:$DATA \
	-v $WORK_DIR:$WORK_DIR \
	-v $OUTPUT_DIR:$OUTPUT_DIR \
	-v $PWD:/work \
	-e CHECK_TYPE -e TEST_NAME \
	-e DATA -e WORK_DIR -e OUTPUT_DIR \
	-u $UID \
	--entrypoint=/neurodocker/startup.sh \
	$IMAGE tools/ci/check.sh
	env:
	IMAGE: ${{ github.repository }}:latest
	CHECK_TYPE: workflow
	DATA: /tmp/.cache/data/fitlins-tests
	TEST_NAME: ${{ matrix.test_name }}
	OUTPUT_DIR: /tmp/ds003/derivatives
	WORK_DIR: /tmp/ds003/work

	- name: Combine coverage and submit
	uses: codecov/codecov-action@v3
	with:
	verbose: true

	deploy_docker:
	needs: [test_ds003_afni, test_ds003_nistats_smooth, test_ds003_nistats_blurto]
	if: github.ref == 'refs/heads/dev' \|\| startsWith(github.ref, 'refs/tags/')
	runs-on: ubuntu-latest
	steps:
	- name: Set up docker buildx
	uses: docker/setup-buildx-action@v3

	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: docker
	path: /tmp

	- name: Load docker image
	run: \|
	docker info
	set +o pipefail
	ls -l /tmp/docker.tar
	docker load < /tmp/docker.tar
	docker images

	- name: Set version/dev tags
	run: \|
	# GHCR
	docker tag $IMAGE_NAME $REGISTRY/$IMAGE_NAME:${{ github.ref_name }}
	# DockerHub
	docker tag $IMAGE_NAME $IMAGE_NAME:${{ github.ref_name }}

	- name: Check images
	run: docker images

	- name: Login to Github Container Registry
	uses: docker/login-action@v3
	with:
	registry: ghcr.io
	username: ${{ github.repository_owner }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Deploy to GHCR
	timeout-minutes: 60
	run: docker push $REGISTRY/$IMAGE_NAME:${{ github.ref_name }}

	- name: Login to DockerHub
	uses: docker/login-action@v3
	with:
	username: ${{ secrets.DOCKERHUB_USERNAME }}
	password: ${{ secrets.DOCKERHUB_TOKEN }}

	- name: Deploy to DockerHub
	timeout-minutes: 60
	run: docker push $IMAGE_NAME:${{ github.ref_name }}

	- name: Deploy ":latest" to DockerHub
	timeout-minutes: 10
	if: startsWith(github.ref, 'refs/tags/')
	run: docker push $IMAGE_NAME:latest

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Well -- the regular -- codespell support #386

Workflow file

Well -- the regular -- codespell support #386

Jobs

Run details

Workflow file for this run