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updated CI/CD for automatic plugin upload
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@Sandip117
Sandip117 committed Oct 2, 2024
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245 changes: 148 additions & 97 deletions .github/workflows/ci.yml
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# Automatically build multi-architectural tagged container images and push them to DockerHub
# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds
# Continuous integration testing for ChRIS Plugin.
# https://github.com/FNNDSC/python-chrisapp-template/wiki/Continuous-Integration
#
# - targeted platforms: x86_64, PowerPC64, ARM64
# - master is built as fnndsc/pl-lld_inference:latest
# - tagged commits are built as fnndsc/pl-lld_inference:<tag>
# - tagged commits are also uploaded to chrisstore.co
#
# In order to use this workflow, see
# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds#steps-to-enable
# - 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: ci
name: build

on:
push:
# we have to guess what the name of the default branch is
branches: [ master, main, trunk ]
tags: [ '**' ]
branches: [ main ]
tags:
- "v?[0-9]+.[0-9]+.[0-9]+*"
pull_request:
branches: [ master, main, trunk ]
branches: [ main ]

jobs:
test:
if: false
runs-on: ubuntu-20.04
name: Unit tests
if: False
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v2
- name: build
run: docker build -t "${GITHUB_REPOSITORY,,}" .
- name: nose tests
run: docker run "${GITHUB_REPOSITORY,,}" nosetests
- uses: actions/checkout@v4
- uses: docker/setup-buildx-action@v3
- name: Build
uses: docker/build-push-action@v5
with:
build-args: extras_require=dev
context: .
load: true
push: false
tags: "localhost/local/app:dev"
cache-from: type=gha
cache-to: type=gha,mode=max
- name: Run pytest
run: |
docker run -v "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/local/app:dev \
pytest -o cache_dir=/tmp/pytest
publish:
build:
name: Build
if: github.event_name == 'push' || github.event_name == 'release'
# needs: [ test ] # uncomment to require passing tests
runs-on: ubuntu-22.04

# we want to both push the build to DockerHub, but also
# keep a local copy so that we can run
#
# docker run fnndsc/pl-app app --json > App.json
#
# buildx currently does not support multiple output locations,
# neither can multi-architectural builds be loaded into docker.
# Here we use a local registry to cache the build.
services:
registry:
image: registry:2
ports:
- 5000:5000

steps:
- name: Get git tag
id: git_info
if: startsWith(github.ref, 'refs/tags/')
run: echo "tag=${GITHUB_REF##*/}" >> $GITHUB_OUTPUT
- name: Get project info
id: determine
env:
git_tag: ${{ steps.git_info.outputs.tag }}
- name: Decide image tags
id: info
shell: python
run: |
repo="${GITHUB_REPOSITORY,,}" # to lower case
# if build triggered by tag, use tag name
tag="${git_tag:-latest}"
dock_image=$repo:$tag
echo $dock_image
echo "dock_image=$dock_image" >> $GITHUB_OUTPUT
echo "repo=$repo" >> $GITHUB_OUTPUT
import os
import itertools
- uses: actions/checkout@v3
def join_tag(t):
registry, repo, tag = t
return f'{registry}/{repo}:{tag}'.lower()
registries = ['docker.io', 'ghcr.io']
repos = ['${{ 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@v4
# QEMU is used for non-x86_64 builds
- uses: docker/setup-qemu-action@v2
- uses: docker/setup-qemu-action@v3
# buildx adds additional features to docker build
- uses: docker/setup-buildx-action@v2
- uses: docker/setup-buildx-action@v3
with:
driver-opts: network=host
# cache slightly improves rebuild time
- name: Cache Docker layers
uses: actions/cache@v3

# 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:
path: /tmp/.buildx-cache
key: ${{ runner.os }}-buildx-${{ github.sha }}
restore-keys: |
${{ runner.os }}-buildx-
context: .
file: ./Dockerfile
tags: ${{ steps.info.outputs.local_tag }}
load: true
cache-from: type=gha
# If you have a directory called examples/incoming/ and examples/outgoing/, then
# run your ChRIS plugin with no parameters, and assert that it creates all the files
# which are expected. File contents are not compared.
- name: Run examples
id: run_examples
run: |
if ! [ -d 'examples/incoming/' ] || ! [ -d 'examples/outgoing/' ]; then
echo "No examples."
exit 0
fi
dock_image=${{ steps.info.outputs.local_tag }}
output_dir=$(mktemp -d)
cmd=$(docker image inspect -f '{{ (index .Config.Cmd 0) }}' $dock_image)
docker run --rm -u "$(id -u):$(id -g)" \
-v "$PWD/examples/incoming:/incoming:ro" \
-v "$output_dir:/outgoing:rw" \
$dock_image $cmd /incoming /outgoing
for expected_file in $(find examples/outgoing -type f); do
fname="${expected_file##*/}"
out_path="$output_dir/$fname"
printf "Checking output %s exists..." "$out_path"
if [ -f "$out_path" ]; then
echo "ok"
else
echo "not found"
exit 1
fi
done
- name: Login to DockerHub
id: dockerhub_login
uses: docker/login-action@v2
if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io')
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_PASSWORD }}

- name: Login to GitHub Container Registry
uses: docker/login-action@v2
if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, '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
id: docker_build
uses: docker/build-push-action@v5
if: (github.event_name == 'push' || github.event_name == 'release')
with:
context: .
file: ./Dockerfile
tags: |
localhost:5000/${{ steps.determine.outputs.dock_image }}
docker.io/${{ steps.determine.outputs.dock_image }}
ghcr.io/${{ steps.determine.outputs.dock_image }}
platforms: linux/amd64
push: true
cache-from: type=local,src=/tmp/.buildx-cache
cache-to: type=local,dest=/tmp/.buildx-cache
tags: ${{ steps.info.outputs.tags_csv }}
# if non-x86_84 architectures are supported, add them here
platforms: linux/amd64 #,linux/arm64,linux/ppc64le
push: ${{ steps.info.outputs.push }}
cache-to: type=gha,mode=max

- name: Get plugin meta
id: pluginmeta
run: |
repo=${{ steps.determine.outputs.repo }}
dock_image=${{ steps.determine.outputs.dock_image }}
docker pull localhost:5000/$dock_image
docker tag localhost:5000/$dock_image $dock_image
script=$(docker inspect --format '{{ (index .Config.Cmd 0) }}' $dock_image)
docker run --rm $dock_image $script --json > /tmp/description.json
repo=${{ steps.determine.outputs.repo }}
dock_image=${{ steps.determine.outputs.dock_image }}
docker pull localhost:5000/$dock_image
docker tag localhost:5000/$dock_image $dock_image
script=$(docker inspect --format '{{ (index .Config.Cmd 0) }}' $dock_image)
json="$(docker run --rm $dock_image $script --json)"
jq <<< "$json" # pretty print in log
echo "::set-output name=json::$json"
echo "::set-output name=title::$(jq -r '.title' <<< "$json")"
jq < /tmp/description.json # pretty print in log
echo "title=$(jq -r '.title' < /tmp/description.json)" >> $GITHUB_OUTPUT
- name: Upload ChRIS Plugin
id: upload
if: github.ref_type == 'tag'
uses: FNNDSC/upload-chris-plugin@v1
with:
description_json: ${{ steps.pluginmeta.outputs.json }}
username: ${{ secrets.CHRISPROJECT_USERNAME }}
password: ${{ secrets.CHRISPROJECT_PASSWORD }}
chris_url: https://cube.chrisproject.org/api/v1/
compute_names: NERC

- 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.pluginmeta.outputs.title }}
readme-filepath: ./README.rst
repository: ${{ steps.determine.outputs.repo }}

- name: Upload to ChRIS Store
if: steps.git_info.outcome != 'skipped'
uses: FNNDSC/chrisstore-action@master
with:
descriptor_file: /tmp/description.json
auth: ${{ secrets.CHRIS_STORE_USER }}
chris_admin_auth: ${{ secrets.CUBE_CHRISPROJECT_ORG_ADMIN_USER }}
chris_admin_url: https://cube.chrisproject.org/chris-admin/api/v1/
compute_resources: galena-avx
short-description: ${{ steps.upload.outputs.title }}
readme-filepath: ./README.md
2 changes: 1 addition & 1 deletion setup.py
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setup(
name = 'lld_inference',
version = '2.2.11',
version = '2.2.12',
description = 'An app to run LLD inference',
author = 'FNNDSC',
author_email = '[email protected]',
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