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Re-Attach to running alignment chunks on retry (#372) #2099

Re-Attach to running alignment chunks on retry (#372)

Re-Attach to running alignment chunks on retry (#372) #2099

Workflow file for this run

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 }}