Reformat code, resolve lint and type errors #5
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| name: Continuous Deployment (build & push docker images) | |
| on: | |
| push: | |
| branches: [ main, add-ci-cd ] | |
| tags: ['v*', 'v*.*', 'v*.*.*'] | |
| pull_request: | |
| workflow_dispatch: | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_PREFIX: ${{ github.repository_owner }}/pyigmap | |
| TOOLS: | | |
| fq-downloader | |
| fastp | |
| vidjil | |
| igblast | |
| cdr3nt-error-corrector | |
| vidjil-ref-builder | |
| igblast-ref-builder | |
| olga-ref-builder | |
| permissions: | |
| contents: read | |
| packages: write | |
| id-token: write | |
| jobs: | |
| matrix: | |
| runs-on: ubuntu-24.04 | |
| outputs: | |
| tools: ${{ steps.mkjson.outputs.tools }} | |
| steps: | |
| - name: Expand TOOLS (newline list) -> JSON | |
| id: mkjson | |
| shell: bash | |
| run: | | |
| mapfile -t arr < <(printf '%s\n' "${TOOLS}" \ | |
| | sed -E 's/^[[:space:]]+|[[:space:]]+$//g' \ | |
| | sed -E '/^($|#)/d') | |
| json_items=$(printf '"%s",' "${arr[@]}") | |
| json_array="[${json_items%,}]" | |
| printf '{"tool":%s}\n' "${json_array}" > tools.json | |
| echo "tools=$(cat tools.json)" >> "$GITHUB_OUTPUT" | |
| build: | |
| name: Build ${{ matrix.tool }} @ ${{ matrix.arch }} | |
| needs: [matrix] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tool: ${{ fromJSON(needs.matrix.outputs.tools).tool }} | |
| arch: [amd, arm] | |
| include: | |
| - arch: amd | |
| os: ubuntu-24.04 | |
| platform: linux/amd64 | |
| suffix: -amd | |
| - arch: arm | |
| os: ubuntu-24.04-arm | |
| platform: linux/arm64 | |
| suffix: -arm | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| - uses: docker/login-action@v3 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Parse version | |
| id: ver | |
| run: | | |
| FILE="./bin/${{ matrix.tool }}/pyproject.toml" | |
| V="" | |
| if [[ -f "$FILE" ]]; then | |
| V=$(awk ' | |
| /^\[project\]/ { in_p=1; next } | |
| in_p && $0 ~ /^version[[:space:]]*=/ { | |
| match($0,/"([^"]+)"/,m); if(m[1]!=""){print m[1]; exit} | |
| }' "$FILE" || true) | |
| fi | |
| echo "version=$V" >> "$GITHUB_OUTPUT" | |
| - name: Gate (skip if tag exists) | |
| id: gate | |
| if: steps.ver.outputs.version != '' | |
| run: | | |
| set -euo pipefail | |
| BASE="${{ env.REGISTRY }}/${{ env.IMAGE_PREFIX }}-${{ matrix.tool }}" | |
| TAG="${BASE}:${{ steps.ver.outputs.version }}${{ matrix.suffix }}" | |
| if docker buildx imagetools inspect "${TAG,,}" >/dev/null 2>&1; then | |
| echo "skip=true" >> "$GITHUB_OUTPUT" | |
| else | |
| echo "skip=false" >> "$GITHUB_OUTPUT" | |
| fi | |
| echo "tag=${TAG,,}" >> "$GITHUB_OUTPUT" | |
| - name: Docker metadata | |
| id: meta | |
| if: steps.ver.outputs.version != '' && steps.gate.outputs.skip != 'true' | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_PREFIX }}-${{ matrix.tool }} | |
| tags: | | |
| type=raw,value=${{ steps.ver.outputs.version }}${{ matrix.suffix }},enable=true | |
| flavor: | | |
| latest=false | |
| - name: Build & push | |
| if: steps.ver.outputs.version != '' && steps.gate.outputs.skip != 'true' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: ./bin/${{ matrix.tool }} | |
| file: ./bin/${{ matrix.tool }}/Dockerfile | |
| platforms: ${{ matrix.platform }} | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| provenance: false | |
| sbom: false | |
| manifest: | |
| name: Manifest — ${{ matrix.tool }} | |
| needs: [matrix, build] | |
| runs-on: ubuntu-24.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tool: ${{ fromJSON(needs.matrix.outputs.tools).tool }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Parse version | |
| id: ver | |
| run: | | |
| FILE="./bin/${{ matrix.tool }}/pyproject.toml" | |
| V="" | |
| if [[ -f "$FILE" ]]; then | |
| V=$(awk ' | |
| /^\[project\]/ { in_p=1; next } | |
| in_p && $0 ~ /^version[[:space:]]*=/ { | |
| match($0,/"([^"]+)"/,m); if(m[1]!=""){print m[1]; exit} | |
| }' "$FILE" || true) | |
| fi | |
| echo "version=$V" >> "$GITHUB_OUTPUT" | |
| - name: Gate manifest | |
| id: gate | |
| if: steps.ver.outputs.version != '' | |
| run: | | |
| set -euo pipefail | |
| BASE="${{ env.REGISTRY }}/${{ env.IMAGE_PREFIX }}-${{ matrix.tool }}" | |
| V="${{ steps.ver.outputs.version }}" | |
| AMD="${BASE}:${V}-amd" | |
| ARM="${BASE}:${V}-arm" | |
| TGT="${BASE}:${V}" | |
| has_multi=false; has_amd=false; has_arm=false | |
| docker buildx imagetools inspect "${TGT,,}" >/dev/null 2>&1 && has_multi=true || true | |
| docker buildx imagetools inspect "${AMD,,}" >/dev/null 2>&1 && has_amd=true || true | |
| docker buildx imagetools inspect "${ARM,,}" >/dev/null 2>&1 && has_arm=true || true | |
| echo "has_multi=$has_multi" >> "$GITHUB_OUTPUT" | |
| echo "has_amd=$has_amd" >> "$GITHUB_OUTPUT" | |
| echo "has_arm=$has_arm" >> "$GITHUB_OUTPUT" | |
| echo "target=${TGT,,}" >> "$GITHUB_OUTPUT" | |
| echo "amd=${AMD,,}" >> "$GITHUB_OUTPUT" | |
| echo "arm=${ARM,,}" >> "$GITHUB_OUTPUT" | |
| - name: Create multi-arch manifest | |
| if: steps.ver.outputs.version != '' && steps.gate.outputs.has_multi != 'true' && steps.gate.outputs.has_amd == 'true' && steps.gate.outputs.has_arm == 'true' | |
| run: | | |
| docker buildx imagetools create --tag "${{ steps.gate.outputs.target }}" \ | |
| "${{ steps.gate.outputs.amd }}" "${{ steps.gate.outputs.arm }}" | |
| docker buildx imagetools inspect "${{ steps.gate.outputs.target }}" |