GHA: test apptainer workflow #239
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: deploy | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - bundle_update_2023 | |
| - apptainer | |
| env: | |
| atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} | |
| recipe_path: conda/recipe | |
| env_yml_path: conda/env/yml | |
| env_lock_path: conda/env/lock | |
| VERSION: '1.4.1.9006' # versioned by bump2version | |
| jobs: | |
| build_pcgrr_conda_pkg: | |
| # When merging to one of the branches above and the commit message matches | |
| if: "startsWith(github.event.head_commit.message, 'Bump version:')" | |
| name: Build pcgrr conda pkg | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Code checkout | |
| uses: actions/checkout@v4 | |
| - name: Micromamba setup | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ env.env_yml_path }}/condabuild.yml | |
| - name: 🐍 Conda pkg build and upload | |
| run: | | |
| conda mambabuild ${recipe_path}/pcgrr -c conda-forge -c bioconda --token ${atoken} | |
| build_pcgr_conda_pkg: | |
| # When merging to one of the branches above and the commit message matches | |
| if: "startsWith(github.event.head_commit.message, 'Bump version:')" | |
| name: Build pcgr conda pkg | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Code checkout | |
| uses: actions/checkout@v4 | |
| - name: Micromamba setup | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ env.env_yml_path }}/condabuild.yml | |
| - name: 🐍 Conda pkg build and upload | |
| run: | | |
| conda mambabuild ${recipe_path}/pcgr -c conda-forge -c bioconda --token ${atoken} --quiet | |
| # spin up fresh instance since conda-lock takes ages when run on previous one | |
| conda_lock: | |
| name: Conda lock | |
| runs-on: ubuntu-latest | |
| needs: [build_pcgr_conda_pkg, build_pcgrr_conda_pkg] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Code checkout | |
| uses: actions/checkout@v4 | |
| - name: Micromamba setup | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ env.env_yml_path }}/condabuild.yml | |
| - name: 🔒 Conda lock | |
| run: | | |
| # 1. generate a combined lock file | |
| # 2. render platform-specific locks | |
| conda-lock lock --file ${env_yml_path}/pcgr.yml -p osx-64 -p linux-64 | |
| conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'pcgr-{platform}.lock' && rm conda-lock.yml | |
| conda-lock lock --file ${env_yml_path}/pcgrr.yml -p osx-64 -p linux-64 | |
| conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'pcgrr-{platform}.lock' && rm conda-lock.yml | |
| mv pcgrr-*.lock ${env_lock_path} | |
| mv pcgr-*.lock ${env_lock_path} | |
| - name: Commit changes | |
| run: | | |
| git status | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| MSG="[bot] Updating conda-lock files (v${VERSION})" | |
| git add . | |
| git commit -m "${MSG}" | |
| git push | |
| - name: 🌐 Website publish | |
| run: | | |
| micromamba env create -n pkgdownenv -f ${env_yml_path}/pkgdown.yml | |
| micromamba activate pkgdownenv | |
| cp pcgrr/DESCRIPTION . # hack for pkgdown to work | |
| printf "pcgrr version:\n" | |
| Rscript -e "packageVersion('pcgrr')" | |
| Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = 'Built PCGR website: https://sigven.github.io/pcgr/', branch = 'gh-pages', new_process = FALSE)" | |
| docker_deploy: | |
| name: Build and deploy Docker | |
| runs-on: ubuntu-latest | |
| needs: conda_lock | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Code checkout | |
| uses: actions/checkout@v4 | |
| - id: pull_lock_commit | |
| name: 📥 Pull lock commit | |
| run: | | |
| git pull --no-rebase # for pulling in the changed locks | |
| git --no-pager log --decorate=short --pretty=oneline -n3 | |
| LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')" | |
| echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> $GITHUB_OUTPUT | |
| - name: 🔖 Tag creation | |
| uses: actions/github-script@v7 | |
| env: | |
| LATEST_COMMIT_HASH: ${{ steps.pull_lock_commit.outputs.latest_commit_hash }} | |
| with: | |
| script: | | |
| const the_tag_name = 'refs/tags/v' + process.env.VERSION | |
| const the_sha = process.env.LATEST_COMMIT_HASH | |
| github.rest.git.createRef({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| ref: the_tag_name, | |
| sha: the_sha | |
| }) | |
| # work with tag from above | |
| - name: Code checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: v${{ env.VERSION }} | |
| - name: 🏰 QEMU setup | |
| uses: docker/setup-qemu-action@v3 | |
| - name: 🏯 Buildx setup | |
| uses: docker/setup-buildx-action@v3 | |
| - name: DockerHub login | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: 🐳 Docker img build and push to DockerHub | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . # yes, dot | |
| push: true | |
| platforms: linux/amd64 | |
| tags: | | |
| sigven/pcgr:${{ env.VERSION }} | |
| - name: Apptainer setup | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| - name: Apptainer build | |
| run: | | |
| docker image ls -a | |
| docker save sigven/pcgr:${VERSION} -o pcgr_${VERSION}.tar | |
| apptainer build pcgr_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar | |
| apptainer push pcgr_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION} |