Merge pull request #156 from umccr/piedb-comp #55
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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 |