fix: add codespell config and fix typos with it (#3277) #3003
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| name: ena-submission-image | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| inputs: | |
| build_arm: | |
| type: boolean | |
| description: "Build for ARM as well" | |
| default: false | |
| required: false | |
| workflow_call: | |
| inputs: | |
| build_arm: | |
| type: boolean | |
| description: "Build for ARM as well" | |
| default: false | |
| required: false | |
| env: | |
| DOCKER_IMAGE_NAME: ghcr.io/loculus-project/ena-submission | |
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | |
| BUILD_ARM: ${{ github.event.inputs.build_arm || inputs.build_arm || github.ref == 'refs/heads/main' }} | |
| sha: ${{ github.event.pull_request.head.sha || github.sha }} | |
| concurrency: | |
| group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-ena-submission-${{github.event.inputs.build_arm}} | |
| cancel-in-progress: true | |
| jobs: | |
| ena-submission-image: | |
| name: Build ena-submission Docker Image # Don't change: Referenced by .github/workflows/update-argocd-metadata.yml | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 15 | |
| permissions: | |
| contents: read | |
| packages: write | |
| checks: read | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Validate submitToEnaProduction is not true in values.yaml | |
| run: | | |
| python -c " | |
| import yaml | |
| with open('kubernetes/loculus/values.yaml', 'r') as file: | |
| values = yaml.safe_load(file) | |
| submit_to_ena_prod = values.get('submitToEnaProduction', False) | |
| if submit_to_ena_prod: | |
| print('Error: The flag submitToEnaProduction is set to true - this will submit data to ENA production. Please set it to false in values.yaml') | |
| exit(1) | |
| " | |
| - name: Shorten sha | |
| run: echo "sha=${sha::7}" >> $GITHUB_ENV | |
| - uses: actions/checkout@v4 | |
| - name: Generate files hash | |
| id: files-hash | |
| run: | | |
| DIR_HASH=$(echo -n ${{ hashFiles('ena-submission/**', '.github/workflows/ena-submission-image.yml') }}) | |
| echo "DIR_HASH=$DIR_HASH${{ env.BUILD_ARM == 'true' && '-arm' || '' }}" >> $GITHUB_ENV | |
| - name: Setup Docker metadata | |
| id: dockerMetadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_IMAGE_NAME }} | |
| tags: | | |
| type=raw,value=${{ env.DIR_HASH }} | |
| type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }} | |
| type=raw,value=${{ env.BRANCH_NAME }} | |
| type=raw,value=commit-${{ env.sha }} | |
| type=raw,value=${{ env.BRANCH_NAME }}-arm,enable=${{ env.BUILD_ARM }} | |
| - 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 ${{ env.DOCKER_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1 && echo "true" || echo "false") | |
| echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push image if input files changed | |
| if: env.CACHE_HIT == 'false' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: ./ena-submission | |
| push: true | |
| tags: ${{ steps.dockerMetadata.outputs.tags }} | |
| cache-from: type=gha,scope=ena-submission-${{ github.ref }} | |
| cache-to: type=gha,mode=max,scope=ena-submission-${{ github.ref }} | |
| platforms: ${{ env.BUILD_ARM == 'true' && 'linux/amd64,linux/arm64' || 'linux/amd64' }} | |
| - name: Retag and push existing image if cache hit | |
| if: env.CACHE_HIT == 'true' | |
| run: | | |
| TAGS=(${{ steps.dockerMetadata.outputs.tags }}) | |
| for TAG in "${TAGS[@]}"; do | |
| docker buildx imagetools create --tag $TAG ${{ env.DOCKER_IMAGE_NAME }}:${{ env.DIR_HASH }} | |
| done |