updated to make ci pass #6
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| # 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: 60 | |
| 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 | |
| timeout-minutes: 20 | |
| 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://$(pwd)@g" -e "s@[email protected]+dockerbuild$(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 | |
| timeout-minutes: 20 | |
| 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 | |
| timeout-minutes: 20 | |
| 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 simulator_run/figures | |
| - | |
| name: Archive figures | |
| uses: actions/upload-artifact@v3 | |
| timeout-minutes: 10 | |
| with: | |
| name: usecase-figures | |
| path: figures.tar.gz |