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name: LAPIS-SILO | ||
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on: | ||
pull_request: | ||
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concurrency: | ||
group: ci-${{ github.ref }} | ||
cancel-in-progress: true | ||
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env: | ||
DOCKER_DEPENDENCY_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo-dependencies | ||
DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo | ||
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jobs: | ||
dockerImageUnitTests: | ||
name: Build Docker Image and Run Unit Tests | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
args: | ||
['linux/amd64', 'linux/arm64'] | ||
permissions: | ||
packages: write | ||
steps: | ||
- uses: actions/checkout@v4 | ||
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- name: Generate dependency files hash | ||
id: files-hash | ||
run: | | ||
DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }}) | ||
echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV | ||
- name: Docker metadata | ||
id: dockerMetadata | ||
uses: docker/metadata-action@v5 | ||
with: | ||
images: ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }} | ||
tags: | | ||
type=ref,event=branch | ||
type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }} | ||
type=raw,value=${{ env.DIR_HASH }} | ||
type=sha,format=long,prefix=commit- | ||
- name: Login to GitHub Container Registry | ||
uses: docker/login-action@v3 | ||
with: | ||
registry: ghcr.io | ||
username: ${{ github.actor }} | ||
password: ${{ secrets.GITHUB_TOKEN }} | ||
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- name: Check if image exists | ||
run: | | ||
if [[ $(docker manifest inspect ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1) ]]; then | ||
echo "Cache hit, do not require rebuild of this docker image. Retagging old image instead." | ||
echo "CACHE_HIT=true" >> $GITHUB_ENV | ||
else | ||
echo "CACHE_HIT=false" >> $GITHUB_ENV | ||
fi | ||
- name: Determine platform build necessity | ||
if: env.CACHE_HIT == 'false' | ||
id: platform-check | ||
run: | | ||
if [[ "${{ matrix.platform }}" == "linux/amd64" || "${{ github.event_name }}" == "workflow_dispatch" || "${{ github.ref }}" == "refs/heads/main" ]]; then | ||
echo "PLATFORM_BUILD=true" >> $GITHUB_ENV | ||
else | ||
echo "Skipping build for this platform" | ||
echo "PLATFORM_BUILD=false" >> $GITHUB_ENV | ||
fi | ||
shell: bash | ||
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- name: Set up Docker Buildx | ||
if: env.PLATFORM_BUILD == 'true' | ||
uses: docker/setup-buildx-action@v3 | ||
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- name: Build and push image if input files changed | ||
if: env.CACHE_HIT == 'false' && env.PLATFORM_BUILD == 'true' | ||
uses: docker/build-push-action@v6 | ||
with: | ||
context: . | ||
file: Dockerfile_dependencies | ||
push: true | ||
tags: ${{ steps.dockerMetadata.outputs.tags }} | ||
cache-from: type=gha,ref=builder-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile') }} | ||
cache-to: type=gha,mode=min,ref=builder-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile') }} | ||
platforms: ${{ matrix.platform }} | ||
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- name: Retag and push existing image if cache hit | ||
if: env.CACHE_HIT == 'true' && env.PLATFORM_BUILD == 'true' | ||
run: | | ||
TAGS=(${{ steps.dockerMetadata.outputs.tags }}) | ||
for TAG in "${TAGS[@]}"; do | ||
docker buildx imagetools create --tag $TAG ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} | ||
done | ||
- name: Docker metadata | ||
if: env.PLATFORM_BUILD == 'true' | ||
id: dockerMetadata | ||
uses: docker/metadata-action@v5 | ||
with: | ||
images: ${{ env.DOCKER_IMAGE_NAME }} | ||
tags: | | ||
type=ref,event=branch | ||
type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }} | ||
type=sha,format=long,prefix=commit- | ||
- name: Build unit test image | ||
if: env.PLATFORM_BUILD == 'true' | ||
uses: docker/build-push-action@v6 | ||
with: | ||
context: . | ||
target: builder | ||
tags: builder | ||
load: true | ||
cache-from: type=gha,ref=${{ github.ref_name }}-image-cache | ||
cache-to: type=gha,mode=min,ref=${{ github.ref_name }}-image-cache | ||
build-args: | | ||
DEPENDENCY_IMAGE=${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:commit-${{ github.sha }} | ||
- name: Run tests | ||
if: env.PLATFORM_BUILD == 'true' | ||
uses: addnab/docker-run-action@v3 | ||
with: | ||
image: builder | ||
run: ./silo_test | ||
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- name: Build and push production image | ||
uses: docker/build-push-action@v6 | ||
with: | ||
context: . | ||
push: true | ||
platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }} | ||
tags: ${{ steps.dockerMetadata.outputs.tags }} | ||
build-args: | | ||
DEPENDENCY_IMAGE=ghcr.io/genspectrum/lapis-silo-dependencies:${{ env.DIR_HASH }} | ||
endToEndTests: | ||
name: Run End To End Tests | ||
needs: dockerImageUnitTests | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
preprocessing-docker-compose: [ | ||
docker-compose-for-tests-preprocessing-from-ndjson.yml | ||
] | ||
steps: | ||
- uses: actions/checkout@v4 | ||
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- name: Use Node.js ${{ matrix.node-version }} | ||
uses: actions/setup-node@v4 | ||
with: | ||
node-version: 18.x | ||
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- uses: actions/cache@v4 | ||
with: | ||
path: ~/.npm | ||
key: "${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}" | ||
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- name: npm install | ||
run: cd endToEndTests && npm ci | ||
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- name: Check Format | ||
run: cd endToEndTests && npm run check-format | ||
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- name: Docker Metadata | ||
id: dockerMetadata | ||
uses: docker/metadata-action@v5 | ||
with: | ||
images: ${{ env.DOCKER_IMAGE_NAME }} | ||
tags: type=ref,event=branch | ||
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- name: Start Docker Container and preprocess data | ||
run: docker compose -f ${{ matrix.preprocessing-docker-compose }} up | ||
env: | ||
SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }} | ||
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- name: Start Docker Container and run api | ||
run: docker compose -f docker-compose-for-tests-api.yml up -d --wait | ||
env: | ||
SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }} | ||
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- name: Run Tests | ||
run: cd endToEndTests && SILO_URL=localhost:8080 npm run test | ||
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linter: | ||
name: Build And Run linter | ||
needs: dockerImageUnitTests | ||
runs-on: ubuntu-latest | ||
env: | ||
PR_NUMBER: ${{ github.event.number }} | ||
container: | ||
image: ghcr.io/genspectrum/lapis-silo-dependencies:commit-${{ github.sha }}" | ||
steps: | ||
- uses: actions/checkout@v4 | ||
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- shell: bash | ||
name: Configure and run clang-tidy on changed files | ||
run: | | ||
mv /src/build . | ||
cmake -DBUILD_WITH_CLANG_TIDY=on -D CMAKE_BUILD_TYPE=Debug -B build/Debug | ||
echo "Successfully configured cmake" | ||
files="" | ||
PAGE=1 | ||
while true; do | ||
page_files=$(curl -s \ | ||
"https://api.github.com/repos/${{ github.repository }}/pulls/${PR_NUMBER}/files?per_page=100&page=$PAGE" \ | ||
| jq -r '.[] | select(.status != "removed") | .filename') | ||
# If there are no more files, break the loop | ||
if [[ -z "$page_files" ]]; then | ||
break | ||
fi | ||
files+="$page_files"$'\n' | ||
PAGE=$((PAGE + 1)) | ||
done | ||
echo "Changed files of this PR:" | ||
echo "$files" | ||
IFS=$'\n' | ||
for file in $files; do | ||
echo "Check ending for file: $file" | ||
if [[ $file == *.cpp ]]; then | ||
echo "Now linting the file: $file" | ||
echo "cmake --build build/Debug --target ${file%.cpp}.o" | ||
cmake --build build/Debug --target ${file%.cpp}.o | ||
fi | ||
done |
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