Deprecate tsv fasta #324
Workflow file for this run
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| name: Run Linter | |
| on: | |
| pull_request: | |
| concurrency: | |
| group: linter-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| DOCKER_LINTER_DEPENDENCY_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo-linter-dependencies | |
| jobs: | |
| linterDependencies: | |
| name: Build linter dependencies | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Generate dependency files hash | |
| id: files-hash | |
| run: | | |
| DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/linter.yml', './Dockerfile_linter_dependencies') }}) | |
| echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV | |
| - name: Docker metadata | |
| id: dockerMetadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_LINTER_DEPENDENCY_IMAGE_NAME }} | |
| tags: | | |
| type=ref,event=branch | |
| type=raw,value=latest,enable=${{ 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: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Check if image exists | |
| id: check-image | |
| run: | | |
| EXISTS=$(docker manifest inspect ${{ env.DOCKER_LINTER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1 && echo "true" || echo "false") | |
| echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV | |
| - name: Set up Docker Buildx | |
| if: env.CACHE_HIT == 'false' | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build linter dependencies image | |
| if: env.CACHE_HIT == 'false' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| push: true | |
| tags: ${{ steps.dockerMetadata.outputs.tags }} | |
| file: ./Dockerfile_linter_dependencies | |
| cache-from: type=gha,ref=linter-dependencies-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile_linter') }} | |
| cache-to: type=gha,mode=min,ref=linter-dependencies-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile_linter') }} | |
| - name: Retag and push existing image if cache hit | |
| if: env.CACHE_HIT == 'true' | |
| run: | | |
| TAGS=(${{ steps.dockerMetadata.outputs.tags }}) | |
| for TAG in "${TAGS[@]}"; do | |
| docker buildx imagetools create --tag $TAG ${{ env.DOCKER_LINTER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} | |
| done | |
| linter: | |
| name: Build And Run linter | |
| needs: linterDependencies | |
| runs-on: ubuntu-latest | |
| env: | |
| PR_NUMBER: ${{ github.event.number }} | |
| container: | |
| image: ghcr.io/genspectrum/lapis-silo-linter-dependencies:commit-${{ github.sha }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - 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 |