docker.yaml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.

# GitHub recommends pinning actions to a commit SHA.
# To get a newer version, you will need to update the SHA.
# You can also reference a tag or branch, but the action may change without warning.

name: Create and publish a Docker image

on:
  push:
    branches:
      - feat/improve_docker_building 
  workflow_dispatch:

defaults:
  run:
    shell: bash -l {0}

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: choderalab/perses

jobs:
  build-and-push-image:
    runs-on: ubuntu-latest
    permissions:
      contents: read
      packages: write

    steps:
      - name: Free disk space
        run: |
          run: |
          sudo docker rmi $(docker image ls -aq) >/dev/null 2>&1 || true
          sudo rm -rf \
            /usr/share/dotnet /usr/local/lib/android /opt/ghc \
            /usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \
            /usr/lib/jvm || true
          echo "some directories deleted"
          sudo apt install aptitude -y >/dev/null 2>&1
          sudo aptitude purge aria2 ansible azure-cli shellcheck rpm xorriso zsync \
            esl-erlang firefox gfortran-8 gfortran-9 google-chrome-stable \
            google-cloud-sdk imagemagick \
            libmagickcore-dev libmagickwand-dev libmagic-dev ant ant-optional kubectl \
            mercurial apt-transport-https mono-complete libmysqlclient \
            unixodbc-dev yarn chrpath libssl-dev libxft-dev \
            libfreetype6 libfreetype6-dev libfontconfig1 libfontconfig1-dev \
            snmp pollinate libpq-dev postgresql-client powershell ruby-full \
            sphinxsearch subversion mongodb-org azure-cli microsoft-edge-stable \
            -y -f >/dev/null 2>&1
          sudo aptitude purge google-cloud-sdk -f -y >/dev/null 2>&1
          sudo aptitude purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
          sudo apt purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
          sudo aptitude purge '~n ^mysql' -f -y >/dev/null 2>&1
          sudo aptitude purge '~n ^php' -f -y >/dev/null 2>&1
          sudo aptitude purge '~n ^dotnet' -f -y >/dev/null 2>&1
          sudo apt-get autoremove -y >/dev/null 2>&1
          sudo apt-get autoclean -y >/dev/null 2>&1
          echo "some packages purged"

      - name: Checkout repository
        uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Get Latest Version
        id: latest-version
        run: |
          LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
          echo $LATEST_TAG
          echo "LATEST_TAG=$LATEST_TAG" >> $GITHUB_OUTPUT
          # In this case the version is the same as the latest_tag
          VERSION=$LATEST_TAG
          echo $VERSION
          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT

      - name: Print Latest Version
        run: echo ${{ steps.latest-version.outputs.VERSION }}

      - name: Create fully qualified image registry path
        id: fqirp
        run: |
          FQIRP=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}
          echo "FQIRP=$FQIRP" >> $GITHUB_OUTPUT

      - name: Print FQIRP
        run: echo ${{ steps.fqirp.outputs.FQIRP  }}

      - name: Log in to the Container registry
        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Extract metadata (tags, labels) for Docker
        id: meta
        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
        with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
          tags: |
            type=schedule,pattern=nightly,enable=true,priority=1000
            type=ref,event=branch,enable=true,priority=600
            type=ref,event=tag,enable=true,priority=600
            type=ref,event=pr,prefix=pr-,enable=true,priority=600
            type=semver,pattern={{major}}.{{minor}}
            type=semver,pattern={{version}}
            type=sha
            ${{ steps.latest-version.outputs.VERSION }}
            latest

      - name: Build and export to Docker
        uses: docker/build-push-action@v4
        with:
          context: .
          file: docker/Dockerfile
          load: true
          push: false
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}
          build-args: |
            VERSION=${{ steps.latest-version.outputs.VERSION }}

      - name: Test image
        run: |
          mkdir oe_license_dir
          # Write out license to a file
          echo "${{ secrets.OE_LICENSE }}" > oe_license_dir/oe_license.txt
          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} perses-cli --help
          # Mount oe_license_dir (which should have the license file) to /openeye on container for testing
          #docker run -e GITHUB_ACTIONS=true --mount type=bind,source=$PWD/oe_license_dir/,target=/openeye/,readonly --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs perses -a "not advanced" -n auto -m "not gpu_needed" -v

      - name: Push Docker image
        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
        with:
          context: .
          file: docker/Dockerfile
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}
          build-args: |
            VERSION=${{ steps.latest-version.outputs.VERSION }}

      - name: Setup Apptainer
        uses: eWaterCycle/setup-apptainer@v2
        with:
          apptainer-version: 1.1.2

      - name: Build Apptainer Image
        run: singularity build perses_${{ steps.latest-version.outputs.VERSION }}.sif docker-daemon:${{ steps.fqirp.outputs.FQIRP }}

      - name: Test & Push Apptainer Image
        run: |
          set -e 
          mkdir test_apptainer
          cd test_apptainer
          singularity run ../perses_${{ steps.latest-version.outputs.VERSION }}.sif perses-cli --help
          #singularity run --bind ../oe_license_dir/:/openeye/ --env "GITHUB_ACTIONS=true" ../perses_${{ steps.latest-version.outputs.VERSION }}.sif pytest --pyargs perses -a "not advanced" -n auto -m "not gpu_needed" -v
          echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
          singularity push ../perses_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}-apptainer
          singularity push ../perses_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest-apptainer