build_docker.yml

# modified from https://docs.docker.com/build/ci/github-actions/push-multi-registries/

name: build_docker

on:
  workflow_dispatch:
  push:
    # todo2: disable again
    branches:
      - "main"

    tags:
      - 'v*' # push of any tag
#   workflow_run:
#     workflows: ["run_tox"]
#     branches: [main]
#     types: 
#     - completed

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: ${{ github.repository }}
  TEST_TAG: ${{ github.repository }}_test
  BUILD_TARGET: dev # prod

concurrency:
  group: docker-${{ github.ref }}
  cancel-in-progress: true

jobs:
  docker:
    permissions: 
      packages: write
      contents: read
    runs-on: ubuntu-latest
    timeout-minutes: 45
    steps:
      -
        name: Checkout
        uses: actions/checkout@v3
        with:
          token: ${{ secrets.PAT }} # the special secrets.GITHUB_TOKEN only allows access to the current repository, so we added a personal access token with scope "repo" as a secret to this repo
          submodules: true
      -
        # qemu required if building for multiple platforms with Docker (other than the platform the docker build is executed on)
        name: Set up QEMU
        uses: docker/setup-qemu-action@v2
      -
        name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v2
    #   -
    #     name: Login to Docker Hub
    #     uses: docker/login-action@v2
    #     with:
    #       username: ${{ secrets.DOCKERHUB_USERNAME }}
    #       password: ${{ secrets.DOCKERHUB_TOKEN }}
      -
        name: Login to GitHub Container Registry
        uses: docker/login-action@v2
        with:
          registry: ${{ env.REGISTRY }}
          # ${{ github.repository_owner }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}
      - 
        name: Extract metadata (tags, labels) for Docker
        id: meta
        uses: docker/metadata-action@v4
        with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
      - 
        name: Build and export to Docker (using cache)
        uses: docker/build-push-action@v4
        timeout-minutes: 20
        with:
          context: .
          target: ${{ env.BUILD_TARGET }}
          load: true
          tags: ${{ env.TEST_TAG }}
          # todo2: disable cache eventually
          cache-from: type=gha
          cache-to: type=gha,mode=max
      - 
        name: Test docker image in python3.10
        uses: addnab/docker-run-action@v3
        with:
          image: ${{ env.TEST_TAG }}
          shell: /bin/bash
          run: |
            set -ex
            source ~/ont_project_all/ont_project_venv/bin/activate || true
            export PATH=~/ont_project_all/tools/bin:$PATH && which minimap2
            cd /root/ont_project_all/ont_project
            sed -i'.backup' -e "s@{root:uri}@file://$(pwd)@g" -e "s@unknown_version@0.0.1.dev+dockerbuild$(date +%YY%mM%dD%HH%MM%SS)@" pyproject.toml
            pip install tox
            tox run -e py310
      -
        name: Push docker image
        uses: docker/build-push-action@v4
        id: Push
        with:
          context: .
          platforms: linux/amd64 #,linux/arm64
          target: ${{ env.BUILD_TARGET }}
          push: true
          tags: ${{ steps.meta.outputs.tags }}_${{ env.BUILD_TARGET }}
          labels: ${{ steps.meta.outputs.labels }}
      - 
        name: Run full usecase (in Docker container)
        uses: addnab/docker-run-action@v3
        with:
          image: ${{ env.TEST_TAG }}
          shell: /bin/bash
          run: |
            set -ex
            cd ~/ont_project_all/ont_project
            curl https://public.bmi.inf.ethz.ch/user/mmordig/ont_project/prepackaged/usecase_data_docker.tar.gz -O
            tar -xvzf usecase_data_docker.tar.gz
            
            pwd
            ls -lR .
            
            cd runs/enrich_usecase
            source ~/ont_project_all/ont_project_venv/bin/activate || true
            export PATH=~/ont_project_all/tools/bin:$PATH && which minimap2
            mkdir chr202122_run && cd chr202122_run
            
            ln -s ../data .
            ln -s ../configs/chr202122_run/sampler_per_window configs
            python ~/ont_project_all/ont_project/usecases/enrich_usecase.py

            tar -cvzf figures.tar.gz readfish_run/figures
      - 
        name: Archive figures
        uses: actions/upload-artifact@v3
        with:
          name: usecase-figures
          path: figures.tar.gz