Fix typo #1443
Workflow file for this run
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name: continuous integration | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
release: | |
types: | |
- published | |
- edited | |
jobs: | |
test: | |
runs-on: self-hosted | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
with: | |
# Check out full history for `setuptools_scm` | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: > | |
3.12 | |
check-latest: true | |
- name: Install Python dependencies | |
run: | | |
python -m pip install \ | |
awscli \ | |
pygithub \ | |
setuptools_scm | |
- name: Set up metadata | |
id: metadata | |
shell: python | |
run: | | |
import os | |
from github import Github | |
from setuptools_scm import get_version | |
pushed_at = "${{ github.event.repository.pushed_at }}" | |
ref = "${{ github.ref }}" | |
repository = "${{ github.repository }}" | |
sha = "${{ github.sha }}" | |
url = "${{ github.event.repository.html_url }}" | |
registry = "${{ secrets.REGISTRY }}" | |
token = "${{ secrets.GITHUB_TOKEN }}" | |
repository_data = Github(token).get_repo(repository) | |
repository_owner, repository_name = repository.lower().split("/") | |
reference, type, name = ref.split("/")[:3] | |
if reference != "refs": | |
raise ValueError(f"Unknown reference: {reference}") | |
if type == "heads": | |
tag = {"main": "latest"}.get(name, name) | |
push = True | |
elif type == "tags": | |
tag = name | |
push = True | |
elif type == "pull": | |
tag = f"{type}-{name}" | |
push = False | |
else: | |
raise ValueError(f"Unknown reference type: {type}") | |
path = f"{registry}/{repository_name}" | |
cache_from = f"type=registry,ref={path}:buildcache" | |
output = dict( | |
cache_from=cache_from, | |
cache_to=f"{cache_from},compression=zstd,mode=max" if push else "", | |
labels=[ | |
f'org.opencontainers.image.created="{pushed_at}"', | |
f'org.opencontainers.image.authors="Lea Waller <lea@fmri.science>"', | |
f'org.opencontainers.image.url="{url}"', | |
f'org.opencontainers.image.documentation="{url}"', | |
f'org.opencontainers.image.source="{url}"', | |
f'org.opencontainers.image.version="{get_version()}"', | |
f'org.opencontainers.image.revision="{sha}"', | |
f'org.opencontainers.image.licenses="{repository_data.license.spdx_id}"', | |
f'org.opencontainers.image.title="{repository_name}"', | |
f'org.opencontainers.image.description="{repository_data.description}"', | |
], | |
push=str(push).lower(), | |
build_tag=f"{repository_name}:{tag}", | |
push_tags=[ | |
f"{path}:{tag}", | |
f"docker.io/{repository_owner}/{repository_name}:{tag}", | |
] | |
if push | |
else [], | |
singularity_name=f"{repository_name}-{tag}.sif", | |
) | |
with open(os.environ["GITHUB_OUTPUT"], "at") as file_handle: | |
for key, value in output.items(): | |
if isinstance(value, list): | |
file_handle.write("\n".join([f"{key}<<eof", *value, "eof"]) + "\n") | |
else: | |
file_handle.write(f"{key}={value}\n") | |
- name: Login to DockerHub | |
uses: docker/login-action@v3 | |
if: ${{ steps.metadata.outputs.push == 'true' }} | |
with: | |
username: ${{ secrets.DOCKERHUB_USERNAME }} | |
password: ${{ secrets.DOCKERHUB_TOKEN }} | |
- name: Login to container registry | |
uses: docker/login-action@v3 | |
if: ${{ steps.metadata.outputs.push == 'true' }} | |
with: | |
registry: ${{ secrets.REGISTRY }} | |
username: ${{ secrets.REGISTRY_USERNAME }} | |
password: ${{ secrets.REGISTRY_PASSWORD }} | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v3 | |
- name: Build container | |
uses: docker/build-push-action@v5 | |
with: | |
cache-from: ${{ steps.metadata.outputs.cache_from }} | |
cache-to: ${{ steps.metadata.outputs.cache_to }} | |
context: "." | |
file: "./Dockerfile" | |
labels: | | |
${{ steps.metadata.outputs.labels }} | |
load: true | |
platforms: linux/amd64 | |
push: false | |
tags: | | |
${{ steps.metadata.outputs.build_tag }} | |
- name: Cache data | |
uses: actions/cache@v4 | |
with: | |
key: resource-cache | |
path: /resource-cache | |
- name: Setup integration test container | |
run: | | |
docker run \ | |
--detach \ | |
--rm \ | |
--name="test" \ | |
--volume="/resource-cache:/var/cache/halfpipe" \ | |
--volume="/home/runner:/home/runner" \ | |
--volume="$(pwd):/halfpipe" \ | |
--workdir="/halfpipe" \ | |
--entrypoint="tail" \ | |
${{ steps.metadata.outputs.build_tag }} \ | |
--follow /dev/null | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
- name: Run integration tests | |
shell: docker exec test bash -x -e {0} | |
env: | |
# Enable pytest-github-actions-annotate-failures | |
GITHUB_ACTIONS: true | |
run: | | |
# Install the Freesurfer license | |
cat > ${FREESURFER_HOME}/license.txt <<EOF | |
halfpipe@fmri.science | |
73053 | |
*C8FMo8yrzcZA | |
FSCA7.lDgNIow | |
e1n3o06osRFD3qtBRgsTy9f9bQHGOpY/riIUrHoEx5c= | |
EOF | |
# Run the integration tests | |
py.test \ | |
--cov --cov-report=xml --dist=load \ | |
--numprocesses=2 | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
fail_ci_if_error: true | |
- name: Stop integration test container | |
run: | | |
docker kill test | |
- name: Push container to registry | |
if: ${{ steps.metadata.outputs.push == 'true' }} | |
uses: docker/build-push-action@v5 | |
with: | |
cache-from: ${{ steps.metadata.outputs.cache_from }} | |
context: "." | |
file: "./Dockerfile" | |
labels: | | |
${{ steps.metadata.outputs.labels }} | |
platforms: linux/amd64 | |
push: true | |
tags: | | |
${{ steps.metadata.outputs.push_tags }} | |
- name: Build Singularity 2.x container | |
if: ${{ steps.metadata.outputs.push == 'true' }} | |
env: | |
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }} | |
run: | | |
mkdir --parents singularity-2 | |
docker run \ | |
--privileged \ | |
--rm \ | |
--volume="/var/run/docker.sock:/var/run/docker.sock" \ | |
--volume="$(pwd)/singularity-2:/output" \ | |
quay.io/singularity/docker2singularity:v2.6 \ | |
--name ${{ steps.metadata.outputs.singularity_name }} \ | |
${{ steps.metadata.outputs.build_tag }} | |
image_file=$(find singularity-2 -type f | head --lines=1) | |
aws s3 mv \ | |
--only-show-errors \ | |
--acl public-read \ | |
${image_file} \ | |
s3://singularity/ | |
- name: Build Singularity container | |
if: ${{ steps.metadata.outputs.push == 'true' }} | |
env: | |
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }} | |
run: | | |
mkdir --parents singularity | |
docker run \ | |
--rm \ | |
--volume="/var/run/docker.sock:/var/run/docker.sock" \ | |
--volume="$(pwd)/singularity:/output" \ | |
quay.io/singularity/singularity:v4.0.1 \ | |
build \ | |
--disable-cache \ | |
/output/${{ steps.metadata.outputs.singularity_name }} \ | |
docker-daemon://${{ steps.metadata.outputs.build_tag }} | |
image_file=$(find singularity -type f | head --lines=1) | |
aws s3 mv \ | |
--only-show-errors \ | |
--acl public-read \ | |
${image_file} \ | |
s3://singularity/ |