upgrade to pyproject.toml #1097
Workflow file for this run
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
| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| target: | |
| strategy: | |
| matrix: | |
| ci_target: | |
| - ci_housekeeping | |
| - ci_unit_tests | |
| - integration_tests | |
| - viral_refbased | |
| - viral_assemble | |
| # disabled due to test data bitrot (Apr 2023) | |
| # - skylab_bulk_rna | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Maximize build space | |
| uses: AdityaGarg8/remove-unwanted-software@v3 | |
| with: | |
| remove-dotnet: 'true' | |
| remove-android: 'true' | |
| remove-haskell: 'true' | |
| remove-codeql: 'true' | |
| if: ${{ matrix.ci_target == 'viral_assemble' }} | |
| - name: Login to GitHub Packages Docker Registry | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: docker.pkg.github.com | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: docker build | |
| run: | | |
| # Cache the dependency-installation image layer on GitHub Packages to speed up CI. Use a | |
| # year/month tag to ensure we do refresh them occasionally. | |
| DOCKER_TAG="docker.pkg.github.com/${GITHUB_REPOSITORY}/miniwdl_ci:$(date +%Y%m)" | |
| echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV | |
| if docker pull "$DOCKER_TAG"; then | |
| docker build -t "$DOCKER_TAG" --cache-from "$DOCKER_TAG" . | |
| else | |
| docker build -t "$DOCKER_TAG" . | |
| fi | |
| if [ "${{ matrix.ci_target }}" == "ci_housekeeping" ]; then | |
| docker push "$DOCKER_TAG" || true # allow failure for third-party PRs | |
| fi | |
| - name: make ${{ matrix.ci_target }} | |
| run: | | |
| chmod -R ugo+rw . | |
| # AWS_EC2_METADATA_DISABLED needed on Azure: https://github.com/aws/aws-cli/issues/5623 | |
| docker run \ | |
| --group-add $(stat -c %g /var/run/docker.sock) -v /var/run/docker.sock:/var/run/docker.sock \ | |
| -v $(pwd):/home/wdler/miniwdl -v /tmp:/tmp \ | |
| -e AWS_EC2_METADATA_DISABLED=true -e CI=true \ | |
| "$DOCKER_TAG" make -C miniwdl ${{ matrix.ci_target }} | |
| - name: Coveralls | |
| if: ${{ matrix.ci_target == 'ci_unit_tests' }} | |
| # https://github.com/coverallsapp/github-action/issues/30 | |
| # https://github.com/marketplace/actions/coveralls-python | |
| uses: AndreMiras/coveralls-python-action@develop | |
| focal_self_test: | |
| # run_self_test in a ubuntu:20.04 image with only the minimal runtime dependencies installed | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: docker build | |
| run: | | |
| # overwriting Dockerfile! | |
| cat << 'EOF' > Dockerfile | |
| FROM ubuntu:20.04 | |
| ENV LC_ALL C.UTF-8 | |
| ENV LANG C.UTF-8 | |
| RUN apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq install -y python3-pip git-core | |
| RUN useradd -ms /bin/bash -u 1337 wdler | |
| USER wdler | |
| WORKDIR /home/wdler | |
| RUN mkdir miniwdl | |
| ENV PATH $PATH:/home/wdler/.local/bin | |
| COPY . /home/wdler/miniwdl | |
| RUN cd miniwdl && pip3 install --user . | |
| CMD miniwdl run_self_test | |
| EOF | |
| docker build -t miniwdl_focal_self_test . | |
| - name: miniwdl run_self_test | |
| run: | | |
| docker run \ | |
| --group-add $(stat -c %g /var/run/docker.sock) -v /var/run/docker.sock:/var/run/docker.sock \ | |
| -v /tmp:/tmp \ | |
| -e AWS_EC2_METADATA_DISABLED=true \ | |
| miniwdl_focal_self_test |