From 9455dff8cd9d94093a4fbf498d41ed16dd88d38d Mon Sep 17 00:00:00 2001 From: Jennings Zhang Date: Fri, 27 Sep 2024 11:59:20 -0400 Subject: [PATCH] Update GHA and bump to version 2.5.0.2 --- .github/workflows/ci.yml | 133 ++++++++++++++------------------------- Dockerfile | 4 -- n4wrapper.py | 2 +- 3 files changed, 48 insertions(+), 91 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1c6e772..9de491d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,10 +1,5 @@ # Continuous integration testing for ChRIS Plugin. # https://github.com/FNNDSC/python-chrisapp-template/wiki/Continuous-Integration -# -# - on push and PR: run pytest -# - on push to main: build and push container images as ":latest" -# - on push to semver tag: build and push container image with tag and -# upload plugin description to https://chrisstore.co name: build @@ -13,116 +8,82 @@ on: branches: [ main ] tags: - "v?[0-9]+.[0-9]+.[0-9]+*" - pull_request: - branches: [ main ] jobs: build: name: Build - if: github.event_name == 'push' || github.event_name == 'release' - runs-on: ubuntu-22.04 - + runs-on: ubuntu-24.04 steps: - - name: Decide image tags - id: info - shell: python - run: | - import os - import itertools - - def join_tag(t): - registry, repo, tag = t - return f'{registry}/{repo}:{tag}'.lower() - - registries = ['docker.io', 'ghcr.io'] - repos = ['${{ github.repository }}'] - if '${{ github.ref_type }}' == 'branch': - tags = ['latest'] - elif '${{ github.ref_type }}' == 'tag': - tag = '${{ github.ref_name }}' - version = tag[1:] if tag.startswith('v') else tag - tags = ['latest', version] - else: - tags = [] - - if '${{ github.ref_type }}' == 'tag': - local_tag = join_tag(('ghcr.io', '${{ github.repository }}', version)) - else: - local_tag = join_tag(('localhost', '${{ github.repository }}', 'latest')) - - product = itertools.product(registries, repos, tags) - tags_csv = ','.join(map(join_tag, product)) - outputs = { - 'tags_csv' : tags_csv, - 'push' : 'true' if tags_csv else 'false', - 'local_tag': local_tag - } - with open(os.environ['GITHUB_OUTPUT'], 'a') as out: - for k, v in outputs.items(): - out.write(f'{k}={v}\n') - - - uses: actions/checkout@v3 + - name: Docker meta + id: meta + uses: docker/metadata-action@v5 + with: + images: | + docker.io/${{ github.repository }} + ghcr.io/${{ github.repository }} + tags: | + type=pep440,pattern={{version}} + type=raw,value=latest,enable={{is_default_branch}} # QEMU is used for non-x86_64 builds - uses: docker/setup-qemu-action@v3 # buildx adds additional features to docker build - uses: docker/setup-buildx-action@v3 with: driver-opts: network=host - - # Here, we want to do the docker build twice: - # The first build pushes to our local registry for testing. - # The second build pushes to Docker Hub and ghcr.io - - name: Build (local only) - uses: docker/build-push-action@v3 - id: docker_build - with: - context: . - file: ./Dockerfile - tags: ${{ steps.info.outputs.local_tag }} - load: true - cache-from: type=gha - name: Login to DockerHub - if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io') + if: github.event_name == 'push' && contains(steps.meta.outputs.tags, 'docker.io') uses: docker/login-action@v3 with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASSWORD }} - name: Login to GitHub Container Registry - if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'ghcr.io') + if: github.event_name == 'push' && contains(steps.meta.outputs.tags, 'ghcr.io') uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} password: ${{ secrets.GITHUB_TOKEN }} - name: Build and push - uses: docker/build-push-action@v3 - if: (github.event_name == 'push' || github.event_name == 'release') + uses: docker/build-push-action@v6 + if: github.event_name == 'push' with: - context: . - file: ./Dockerfile - tags: ${{ steps.info.outputs.tags_csv }} + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} # linux/ppc64le not working, see https://github.com/ANTsX/ANTs/issues/1644 platforms: linux/amd64,linux/arm64 - push: ${{ steps.info.outputs.push }} + push: true + cache-from: type=gha cache-to: type=gha,mode=max - + - name: Create README.md + run: | + echo '${{ github.server_url }}/${{ github.repository }}' > README.md + - name: Update DockerHub description + uses: peter-evans/dockerhub-description@v4 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_PASSWORD }} + short-description: ChRIS plugin wrapper for N4BiasFieldCorrection + - name: Get preferred tag + id: preferred + if: startsWith(github.ref, 'refs/tags/v') + run: | + set -o pipefail + echo '${{ toJSON(fromJSON(steps.meta.outputs.json).tags) }}' \ + | jq -r 'map(select(startswith("ghcr.io") and (endswith("latest") | not))).[0]' \ + | xargs printf "tag=%s\n" \ + | tee --append "$GITHUB_OUTPUT" + outputs: + image: ${{ steps.preferred.outputs.tag }} + publish: + needs: build + if: needs.build.outputs.image + runs-on: ubuntu-24.04 + steps: - name: Upload ChRIS Plugin - id: upload - if: github.ref_type == 'tag' - uses: FNNDSC/upload-chris-plugin@v1 + uses: FNNDSC/upload-chris-plugin@main with: - dock_image: ${{ steps.info.outputs.local_tag }} + dock_image: ${{ needs.build.outputs.image }} username: ${{ secrets.CHRISPROJECT_USERNAME }} password: ${{ secrets.CHRISPROJECT_PASSWORD }} chris_url: https://cube.chrisproject.org/api/v1/ - compute_names: host,galena - - - name: Update DockerHub description - if: steps.upload.outcome == 'success' - uses: peter-evans/dockerhub-description@v3 - continue-on-error: true # it is not crucial that this works - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_PASSWORD }} - short-description: ${{ steps.upload.outputs.title }} - readme-filepath: ./README.md + compute_names: NERC diff --git a/Dockerfile b/Dockerfile index 7fa158e..b03dcb4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,5 @@ FROM docker.io/python:3.12.1-slim-bookworm -LABEL org.opencontainers.image.authors="FNNDSC " \ - org.opencontainers.image.title="N4 Bias Field Correction" \ - org.opencontainers.image.description="A ChRIS plugin wrapper for N4BiasFieldCorrection" - # install N4BiasFieldCorrection COPY --from=docker.io/fnndsc/n4biasfieldcorrection:2.5.0 /usr/local/bin/N4BiasFieldCorrection /usr/local/bin/N4BiasFieldCorrection diff --git a/n4wrapper.py b/n4wrapper.py index b432d6c..0bf4e3f 100644 --- a/n4wrapper.py +++ b/n4wrapper.py @@ -11,7 +11,7 @@ from chris_plugin import chris_plugin, PathMapper from loguru import logger -__version__ = '2.5.0.1' +__version__ = '2.5.0.2' DISPLAY_TITLE = r""" _ _ ___ ______ _ ______ _ _ _ _____ _ _