[Bugfix] Fix subsample depth (#379) #2116
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| name: WDL CI | |
| on: | |
| push | |
| env: | |
| LC_ALL: C.UTF-8 | |
| LANG: C.UTF-8 | |
| DEBIAN_FRONTEND: noninteractive | |
| jobs: | |
| linters: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ${{runner.os}}-cache | |
| - name: dependencies | |
| run: | | |
| source /etc/profile | |
| sudo apt-get -qq update | |
| sudo apt-get -qq install --yes jq moreutils make virtualenv zip unzip httpie git shellcheck | |
| virtualenv --python=python3.10 .venv | |
| source .venv/bin/activate | |
| pip install -r requirements-dev.txt | |
| - name: linters | |
| run: | | |
| source .venv/bin/activate | |
| make lint | |
| - uses: andymckay/[email protected] | |
| if: ${{ failure() }} | |
| cancel-previous: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| list-workflow-dirs: | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| matrix: ${{steps.list_dirs.outputs.matrix}} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 2 | |
| - id: list_dirs | |
| run: echo "matrix=$(./scripts/diff-workflows.sh |jq -cnR '[inputs|select(length>0)]')" >> $GITHUB_OUTPUT | |
| wdl-ci: | |
| runs-on: ubuntu-22.04 | |
| needs: list-workflow-dirs | |
| if: ${{ needs['list-workflow-dirs'].outputs.matrix != '[]' && needs['list-workflow-dirs'].outputs.matrix != '' }} | |
| strategy: | |
| matrix: | |
| workflow_dir: ${{fromJson(needs['list-workflow-dirs'].outputs.matrix)}} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: docker login ghcr.io | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: docker build + push to ghcr.io | |
| run: | | |
| TAG=$(git describe --long --tags --always --dirty) | |
| IMAGE_NAME=czid-${{ matrix.workflow_dir }}-public | |
| IMAGE_URI="ghcr.io/${GITHUB_REPOSITORY}/${IMAGE_NAME}" | |
| CACHE_FROM=""; docker pull "$IMAGE_URI" && CACHE_FROM="--cache-from $IMAGE_URI" | |
| ./scripts/docker-build.sh "workflows/${{ matrix.workflow_dir }}" --tag "${IMAGE_URI}:${TAG}" $CACHE_FROM \ | |
| || ./scripts/docker-build.sh "workflows/${{ matrix.workflow_dir }}" --tag "${IMAGE_URI}:${TAG}" | |
| docker push "${IMAGE_URI}:${TAG}" | |
| if [[ ${GITHUB_REF##*/} == "main" ]]; then | |
| docker tag "${IMAGE_URI}:${TAG}" "${IMAGE_URI}:latest" | |
| docker push "${IMAGE_URI}:latest" | |
| fi | |
| echo "IMAGE_URI=${IMAGE_URI}" >> $GITHUB_ENV | |
| echo "TAG=${TAG}" >> $GITHUB_ENV | |
| - name: run tests | |
| run: | | |
| # explicitly block EC2 IMDS endpoint to work around awscli issue: | |
| # https://github.com/aws/aws-cli/issues/5234#issuecomment-635459464 | |
| # https://github.com/aws/aws-cli/issues/5262 | |
| sudo ip route add blackhole 169.254.169.254 | |
| # configure miniwdl to auto-delete task working directories, to reduce chance of worker | |
| # running out of space | |
| export MINIWDL__FILE_IO__OUTPUT_HARDLINKS=true | |
| export MINIWDL__FILE_IO__DELETE_WORK=success | |
| export MINIWDL__DOWNLOAD_CACHE__GET=true | |
| export MINIWDL__DOWNLOAD_CACHE__PUT=true | |
| export MINIWDL__DOWNLOAD_CACHE__DIR="$(mktemp -d --tmpdir miniwdl_download_cache_XXXXXX)" | |
| source /etc/profile | |
| sudo apt-get -qq update | |
| sudo apt-get -qq install --yes jq moreutils make virtualenv zip unzip httpie git shellcheck | |
| virtualenv --python=python3.10 .venv | |
| source .venv/bin/activate | |
| pip install -r requirements-dev.txt | |
| export DOCKER_IMAGE_ID="${IMAGE_URI}:${TAG}" | |
| make test-${{ matrix.workflow_dir }} |