update the release yaml file #112
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| name: CI/CD | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - '*\@[0-9]+.[0-9]+.[0-9]+*' # package development branch | |
| jobs: | |
| build: | |
| if: ${{ !contains(github.event.head_commit.message, '[no ci]') }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| branch: ${{ steps.get_pkg_info.outputs.branch }} | |
| pkg_name: ${{ steps.get_pkg_info.outputs.pkg_name }} | |
| pkg_ver: ${{ steps.get_pkg_info.outputs.pkg_ver }} | |
| docker_file: ${{ steps.get_pkg_info.outputs.docker_file }} | |
| repo_lowercase: ${{ steps.repo_lowercase.outputs.lowercase }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| architecture: "x64" | |
| env: | |
| AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache | |
| - name: Extract package name and version from branch name | |
| id: get_pkg_info | |
| shell: bash | |
| run: | | |
| echo "::set-output name=branch::$(echo ${GITHUB_REF#refs/heads/})" | |
| PKG_NAME=$(echo ${GITHUB_REF#refs/heads/} | awk -F'@' '{print $1}') | |
| PKG_VER=$(echo ${GITHUB_REF#refs/heads/} | awk -F'@' '{print $2}') | |
| echo "::set-output name=pkg_name::$(echo $PKG_NAME)" | |
| echo "::set-output name=pkg_ver::$(echo $PKG_VER)" | |
| if [[ -f "./$PKG_NAME/Dockerfile" ]]; then | |
| echo "::set-output name=docker_file::$(echo ./$PKG_NAME/Dockerfile)" | |
| else | |
| echo "::set-output name=docker_file::" | |
| fi | |
| - name: Login to GitHub Container Registry | |
| if: ${{ steps.get_pkg_info.outputs.branch != 'main' && steps.get_pkg_info.outputs.docker_file != ''}} | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.CR_PAT }} | |
| - id: repo_lowercase | |
| uses: ASzc/change-string-case-action@v1 | |
| with: | |
| string: ${{ github.repository }} | |
| - name: Build image | |
| if: ${{ steps.get_pkg_info.outputs.branch != 'main' && steps.get_pkg_info.outputs.docker_file != ''}} | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: "./${{steps.get_pkg_info.outputs.pkg_name}}" | |
| file: "${{steps.get_pkg_info.outputs.docker_file}}" | |
| platforms: linux/amd64 | |
| load: true | |
| tags: | | |
| ghcr.io/${{ steps.repo_lowercase.outputs.lowercase }}.${{ steps.get_pkg_info.outputs.pkg_name }}:${{ steps.get_pkg_info.outputs.pkg_ver }} | |
| - name: Push image to ghcr.io | |
| id: push_to_ghcr | |
| if: ${{ steps.get_pkg_info.outputs.branch != 'main' && steps.get_pkg_info.outputs.docker_file != ''}} | |
| shell: bash | |
| run: | | |
| docker push ghcr.io/${{ steps.repo_lowercase.outputs.lowercase }}.${{ steps.get_pkg_info.outputs.pkg_name }}:${{ steps.get_pkg_info.outputs.pkg_ver }} | tee ./ghcr.io.stdout | |
| IMAGE_SHA=$(cat ./ghcr.io.stdout | tr ' ' '\n' | grep 'sha256:' | awk -F':' '{print $2}') | |
| echo "::set-output name=image_sha256::$(echo ${IMAGE_SHA})" | |
| echo "::set-output name=created_at::$(date -u +%FT%TZ)" | |
| test-and-release: | |
| runs-on: ubuntu-latest | |
| needs: [build] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| architecture: "x64" | |
| env: | |
| AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wfpm | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| if [ -f requirements-test.txt ]; then pip install -r requirements-test.txt; fi | |
| if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi | |
| - name: Install Nextflow | |
| run: | | |
| wget --tries=10 -qO- https://get.nextflow.io | bash | |
| sudo chmod 755 nextflow | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: "Login to GitHub Container Registry" # normally shouldn't need to login, but new image when just created is private | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.CR_PAT }} | |
| - name: Run tests for all packages | |
| if: ${{ needs.build.outputs.branch == 'main' }} | |
| run: | | |
| wfpm test | |
| - name: Run tests for the current package only | |
| if: ${{ needs.build.outputs.branch != 'main' }} | |
| run: | | |
| cd ./${{needs.build.outputs.pkg_name}} | |
| wfpm test | |
| - name: Check whether to proceed with release | |
| id: to_release | |
| run: | | |
| if [[ \ | |
| "${{ github.event.head_commit.message }}" = "Merge"[[:space:]]"pull"[[:space:]]"request"* && \ | |
| "${{ github.event.head_commit.message }}" = *"@"* && \ | |
| "${{ github.event.head_commit.message }}" = *"[release]"* && \ | |
| "${{ needs.build.outputs.branch }}" = 'main' | |
| ]]; then | |
| echo "::set-output name=release::$(echo Y)" | |
| else | |
| echo "::set-output name=release::$(echo N)" | |
| fi | |
| - name: Extract package name and version from commit message | |
| if: ${{ steps.to_release.outputs.release == 'Y' }} | |
| id: get_pkg_info | |
| shell: bash | |
| run: | | |
| MERGED_BR=$(echo -e '${{ github.event.head_commit.message }}' | \ | |
| { grep '^Merge pull request'||:; } | tr ' ' '\n' |{ grep '@'||:; } | awk -F'/' '{print $2}') | |
| PKG_NAME=$(echo $MERGED_BR | awk -F'@' '{print $1}') | |
| PKG_VER=$(echo $MERGED_BR | awk -F'@' '{print $2}') | |
| echo "::set-output name=pkg_name::$(echo ${PKG_NAME})" | |
| echo "::set-output name=pkg_ver::$(echo ${PKG_VER})" | |
| if [[ -f "./$PKG_NAME/Dockerfile" ]]; then | |
| echo "::set-output name=docker_file::$(echo ./$PKG_NAME/Dockerfile)" | |
| echo "::set-output name=docker_image::$(echo ghcr.io/${{ needs.build.outputs.repo_lowercase }}.$PKG_NAME:$PKG_VER)" | |
| else | |
| echo "::set-output name=docker_file::" | |
| echo "::set-output name=docker_image::" | |
| fi | |
| - name: Prepare package release tarball | |
| id: prep_assets | |
| if: ${{ steps.to_release.outputs.release == 'Y' }} | |
| shell: bash | |
| run: | | |
| ./scripts/cleanup_temp_files.sh # just in case | |
| PKG_TAR=${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}.tar.gz | |
| pushd ${{ steps.get_pkg_info.outputs.pkg_name }} | |
| tar --exclude=wfpr_modules --dereference -czvf ../$PKG_TAR . | |
| popd | |
| echo "::set-output name=pkg_tar::$(echo ${PKG_TAR})" | |
| echo "::set-output name=pkg_tar_sha::$(sha256sum ${PKG_TAR} |awk '{print $1}')" | |
| echo "::set-output name=pkg_tar_size::$(ls -l ${PKG_TAR} |awk '{print $5}')" | |
| echo "::set-output name=created_at::$(date -u +%FT%TZ)" | |
| - name: Create release | |
| id: create_release | |
| if: ${{ steps.to_release.outputs.release == 'Y' }} | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }} | |
| release_name: ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }} | |
| body: | | |
| * Release `${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}` (${{ github.sha }}) | |
| * Package `${{ steps.prep_assets.outputs.pkg_tar }}` (sha256: `${{ steps.prep_assets.outputs.pkg_tar_sha }}`) | |
| * Package URI `github.com/${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}@${{ steps.get_pkg_info.outputs.pkg_ver }}` | |
| * Run the package: `nextflow run ${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}/main.nf -r ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }} -params-file <params-json-file>` | |
| draft: false | |
| prerelease: false | |
| - name: Prepare in pkg-release.json | |
| if: ${{ steps.to_release.outputs.release == 'Y' }} | |
| shell: bash | |
| run: | | |
| WFPM_VER=$(wfpm -v | cut -d ' ' -f 2) | |
| if [[ '${{ steps.get_pkg_info.outputs.docker_file }}' != '' ]]; then | |
| docker pull ${{ steps.get_pkg_info.outputs.docker_image }} | tee image.info | |
| IMAGE_SHA=$(cat ./image.info | tr ' ' '\n' | grep 'sha256:' | awk -F':' '{print $2}') | |
| else | |
| IMAGE_SHA=$(echo) | |
| fi | |
| # temporary solution | |
| TAG="${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}" | |
| ./scripts/prepare_package_release_json.py -p ${{ steps.get_pkg_info.outputs.pkg_name }}/pkg.json -d \ | |
| " | |
| { | |
| \"_release\": { | |
| \"created\": \"${{ steps.prep_assets.outputs.created_at }}\", | |
| \"hash\": { | |
| \"checksum_type\": \"sha1\", | |
| \"checksume\": \"${{ github.sha }}\" | |
| }, | |
| \"tag\": \"$TAG\", | |
| \"assets\": [ | |
| { | |
| \"filename\": \"$TAG.tar.gz\", | |
| \"download_url\": \"https://github.com/${{ github.repository }}/releases/download/$TAG/$TAG.tar.gz\", | |
| \"checksum\": \"${{ steps.prep_assets.outputs.pkg_tar_sha }}\", | |
| \"checksum_type\": \"sha256\", | |
| \"size\": ${{ steps.prep_assets.outputs.pkg_tar_size }} | |
| }, | |
| { | |
| \"_NOTE_\": \"this file\", | |
| \"filename\": \"pkg-release.json\", | |
| \"download_url\": \"https://github.com/${{ github.repository }}/releases/download/$TAG/pkg-release.json\", | |
| \"checksum\": null, | |
| \"checksum_type\": null, | |
| \"size\": null | |
| } | |
| ] | |
| }, | |
| \"_image_digest\": { | |
| \"checksum\": \"$IMAGE_SHA\", | |
| \"checksum_type\": \"sha256\" | |
| }, | |
| \"_wfpm_ver\": \"$WFPM_VER\" | |
| } | |
| " > pkg-release.json | |
| - name: Upload package release tarball | |
| if: ${{ steps.to_release.outputs.release == 'Y' }} | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: ./${{ steps.prep_assets.outputs.pkg_tar }} | |
| asset_name: ${{ steps.prep_assets.outputs.pkg_tar }} | |
| asset_content_type: application/zip | |
| - name: Upload package release json | |
| if: ${{ steps.to_release.outputs.release == 'Y' }} | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: ./pkg-release.json | |
| asset_name: pkg-release.json | |
| asset_content_type: application/json |