Merge pull request #81 from umccr/cancer_report_fixes #48
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: conda-docker-docs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| env: | |
| atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} | |
| recipe_path: conda/recipe | |
| env_yaml_path: conda/env/yaml | |
| env_lock_path: conda/env/lock | |
| VERSION: '2.0.0' # versioned by bump2version | |
| GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }} | |
| 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: | | |
| dvc pull | |
| ls -l inst/extdata/* | |
| conda mambabuild --R 4.2 ${recipe_path} --token ${atoken} | |
| - name: 🔒 Conda lock | |
| run: | | |
| conda-lock lock --file ${env_yaml_path}/gpgr.yaml --platform linux-64 | |
| conda-lock render --kind explicit -p linux-64 conda-lock.yml --filename-template 'gpgr-{platform}.lock' && rm conda-lock.yml | |
| mv gpgr-*.lock ${env_lock_path}/ | |
| - name: 💾 Commit lockfile | |
| run: | | |
| # TODO: the version bumping guarantees there will be changes, | |
| # but during testing this can be problematic - need to | |
| # commit only if changes exist. | |
| git status | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| MSG="[bot] Updating conda-lock file (v${VERSION})" | |
| git add . | |
| git commit -m "${MSG}" | |
| git push | |
| - name: 🌐 Website publish | |
| run: | | |
| micromamba env create -n pkgdownenv -f ${env_yaml_path}/pkgdown.yaml | |
| micromamba activate pkgdownenv | |
| gpgr.R --version | |
| Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://umccr.github.io/gpgr/'), branch = 'gh-pages', new_process = FALSE)" | |
| - name: 📥 Pull lock commit | |
| id: pull_lock_commit | |
| run: | | |
| git pull --no-rebase | |
| git --no-pager log --decorate=short --pretty=oneline -n3 | |
| LATEST_COMMIT_HASH="$(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: ${{ secrets.GITHUB_TOKEN }} | |
| - name: 🐳 Docker img build and push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| tags: ghcr.io/${{ github.repository }}:${{ env.VERSION }} | |
| context: . # yes, dot | |
| push: true | |
| platforms: linux/amd64 |