Merge pull request #166 from umccr/add-citation #59
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| name: conda-docker-docs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| env: | |
| atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} | |
| recipe_path: deploy/conda/recipe | |
| env_yaml_path: deploy/conda/env/yaml | |
| env_lock_path: deploy/conda/env/lock | |
| VERSION: '1.1.0' # versioned by bump2version | |
| jobs: | |
| condarise-dockerise-document: | |
| # When merging to main and the commit message starts with 'Bump version:' | |
| if: "startsWith(github.event.head_commit.message, 'Bump version:')" | |
| name: Conda Docker Docs | |
| 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_yaml_path }}/condabuild.yaml | |
| - name: 🐍 Conda pkg build and upload | |
| run: | | |
| conda mambabuild ${recipe_path} -c umccr -c conda-forge -c bioconda --token ${atoken} | |
| - name: 🔒 Conda lock | |
| run: | | |
| # 1. generate a combined lock file | |
| # 2. render platform-specific locks | |
| conda-lock lock --file ${env_yaml_path}/rnasum.yaml -p osx-64 -p linux-64 | |
| conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'rnasum-{platform}.lock' && rm conda-lock.yml | |
| mv rnasum-*.lock ${env_lock_path}/ | |
| - name: 💾 Commit lockfile | |
| run: | | |
| git status | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| MSG="[bot] Updating conda-lock files (v${VERSION})" | |
| git add . | |
| git commit -m "${MSG}" | |
| git push | |
| - name: 🌐 Website publish | |
| run: | | |
| micromamba env create -n pkgdownenv -f ${env_yaml_path}/pkgdown.yaml | |
| micromamba activate pkgdownenv | |
| rnasum.R --version | |
| Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://umccr.github.io/RNAsum/'), branch = 'gh-pages', new_process = FALSE)" | |
| - name: 📥 Pull lock commit | |
| id: pull_lock_commit | |
| run: | | |
| git pull --no-rebase | |
| git --no-pager log --decorate=short --pretty=oneline -n3 | |
| LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')" | |
| echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> ${GITHUB_OUTPUT} | |
| - name: 🔖 Create tag | |
| 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 | |
| with: | |
| install: true | |
| config-inline: | | |
| [worker.oci] | |
| max-parallelism = 2 | |
| - name: 🐙 GitHub CR login | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: 🐣 Lowercase repo | |
| env: | |
| REPO_NM: ${{ github.repository }} | |
| run: | | |
| echo "repo_nm: ${REPO_NM}" | |
| echo "REPO_NM_LC=${REPO_NM,,}" >> ${GITHUB_ENV} | |
| - name: 🐳 Docker img build and push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| tags: ghcr.io/${{ env.REPO_NM_LC }}:${{ env.VERSION }} | |
| context: . | |
| push: true | |
| platforms: linux/amd64 |