Bump version: 1.4.1.9020 → 1.4.1.9021 #305
Workflow file for this run
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name: deploy | |
on: | |
push: | |
branches: | |
- master | |
- bundle_update_2023 | |
- locale | |
env: | |
atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} | |
recipe_path: conda/recipe | |
env_yml_path: conda/env/yml | |
env_lock_path: conda/env/lock | |
VERSION: '1.4.1.9021' # 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 | |
if: github.ref_name == 'master' | |
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: ${{ secrets.DOCKERHUB_TOKEN }} | |
# use the outputs=docker with dest to directly save to tar for apptainer | |
- name: 🐳 Docker img build, tar and push to Docker Hub | |
uses: docker/build-push-action@v6 | |
with: | |
context: . | |
push: true | |
platforms: linux/amd64 | |
tags: | | |
sigven/pcgr:${{ env.VERSION }} | |
outputs: type=docker,dest=pcgr_${{ env.VERSION }}.tar | |
# Apptainer | |
- name: Apptainer setup | |
uses: eWaterCycle/setup-apptainer@v2 | |
- name: 🕹️ Apptainer build | |
run: | | |
ls -lSha | |
df -h | |
echo "Building Apptainer SIF" | |
echo "---------------------------------" | |
apptainer build pcgr_singularity_${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 |