Merge pull request #9 from umccr/issues-8/conda #7
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| 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: '0.1.1' # 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: Miniconda setup | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| add-pip-as-python-dependency: false # conda-lock goes crazy if pip pre-installed | |
| activate-environment: env1 | |
| mamba-version: "*" | |
| channels: "umccr,conda-forge,bioconda" | |
| - name: 🐍 Conda pkg build and upload | |
| run: | | |
| conda activate | |
| mamba create --name cbuildenv conda-build conda-verify anaconda-client boa | |
| conda activate cbuildenv | |
| conda mambabuild --R 4.2 ${recipe_path} --token ${atoken} | |
| - name: 🔒 Conda lock | |
| run: | | |
| conda activate | |
| mamba create --name lockenv conda-lock pip | |
| conda activate lockenv | |
| conda-lock --file ${env_yaml_path}/sigrap.yaml --platform linux-64 | |
| mv conda-lock.yml ${env_lock_path}/conda-lock.yml | |
| - name: 💾 Commit lockfile | |
| run: | | |
| # TODO: the version bumping guarantees there will be changes, | |
| # but during testing this can be problematic - need to | |
| # commit only if changes exist. | |
| git status | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| MSG="[bot] Updating conda-lock file (v${VERSION})" | |
| git add . | |
| git commit -m "${MSG}" | |
| git push | |
| - name: 🌐 Website publish | |
| run: | | |
| conda activate | |
| mamba env create -n pkgdownenv -f ${env_yaml_path}/pkgdown.yaml | |
| conda activate pkgdownenv | |
| sigrap.R --version | |
| Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://umccr.github.io/sigrap/'), branch = 'gh-pages', new_process = FALSE)" | |
| - name: 📥 Pull lock commit | |
| id: pull_lock_commit | |
| run: | | |
| git pull --no-rebase | |
| git --no-pager log --decorate=short --pretty=oneline -n3 | |
| LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')" | |
| echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> $GITHUB_OUTPUT | |
| - name: 🔖 Create tag | |
| uses: actions/github-script@v6 | |
| 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: . | |
| push: true | |
| platforms: linux/amd64 |