adding cli, other fixes #3
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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://$(pwd)@g" -e "s@[email protected]+dockerbuild$(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 | |
| 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 |