build_conda_recipes.yaml

name: deploy

on:
  push:
    branches:
      - master
      - bundle_update_2023
      - apptainer
env:
  atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
  recipe_path: conda/recipe
  env_yml_path: conda/env/yml
  env_lock_path: conda/env/lock
  VERSION: '1.4.1.9006' # 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 ${env_lock_path}
      - name: Commit changes
        run: |
          git status
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          MSG="[bot] Updating conda-lock files (v${VERSION})"
          git add .
          git commit -m "${MSG}"
          git push
      - name: 🌐 Website publish
        run: |
          micromamba env create -n pkgdownenv -f ${env_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
            })

      # 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: ${{ secrets.DOCKERHUB_TOKEN }}
      - name: 🐳 Docker img build and push to DockerHub
        uses: docker/build-push-action@v5
        with:
          context: . # yes, dot
          push: true
          platforms: linux/amd64
          tags: |
            sigven/pcgr:${{ env.VERSION }}

      - name: Apptainer setup
        uses: eWaterCycle/setup-apptainer@v2

      - name: Apptainer build
        run: |
          docker image ls -a
          docker save sigven/pcgr:${VERSION} -o pcgr_${VERSION}.tar
          apptainer build pcgr_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar
          apptainer push pcgr_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION}