file_copy with overwrite #280
Workflow file for this run
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| name: deploy | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - bundle_update_2023 | |
| env: | |
| atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} | |
| recipe_path: conda/recipe | |
| env_yml_path: conda/env/yml | |
| env_lock_path: conda/env/lock | |
| VERSION: '1.4.1.9014' # 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: ${{ steps.pull_lock_commit.outputs.latest_commit_hash }} | |
| with: | |
| script: | | |
| const the_tag_name = 'refs/tags/v' + process.env.VERSION | |
| const the_sha = process.env.LATEST_COMMIT_HASH | |
| github.rest.git.createRef({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| ref: the_tag_name, | |
| sha: the_sha | |
| }) | |
| - name: 🗑 Free Disk Space | |
| uses: jlumbroso/free-disk-space@main | |
| # work with tag from above | |
| - name: Code checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: v${{ 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: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: 🐳 Docker img build and push to DockerHub | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . # yes, dot | |
| push: true | |
| load: true | |
| platforms: linux/amd64 | |
| tags: | | |
| sigven/pcgr:${{ 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 | |
| ls -la | |
| df -h | |
| echo "Building Apptainer SIF" | |
| echo "---------------------------------" | |
| apptainer build pcgr_singularity_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar | |
| echo "---------------------------------" | |
| ls -lSha | |
| - name: Upload SIF to GHCR | |
| run: | | |
| echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io | |
| apptainer push pcgr_singularity_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION}.singularity |