fix getting the length of a generator (#377) #2059
Workflow file for this run
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name: Integration Tests | |
on: | |
push | |
env: | |
LC_ALL: C.UTF-8 | |
LANG: C.UTF-8 | |
DEBIAN_FRONTEND: noninteractive | |
jobs: | |
cancel-previous: | |
runs-on: [self-hosted, idseq-dev] | |
steps: | |
- uses: styfle/[email protected] | |
with: | |
access_token: ${{ github.token }} | |
list-workflow-dirs: | |
runs-on: [self-hosted, idseq-dev] | |
outputs: | |
matrix: ${{steps.list_dirs.outputs.matrix}} | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
fetch-depth: 2 | |
- id: list_dirs | |
# only run on wdl dirs with diff | |
run: echo "matrix=$(./scripts/diff-workflows.sh |jq -cnR '[inputs|select(length>0)]')" >> $GITHUB_OUTPUT | |
wdl-ci: | |
runs-on: [self-hosted, idseq-dev] | |
needs: list-workflow-dirs | |
if: ${{ needs['list-workflow-dirs'].outputs.matrix != '[]' && needs['list-workflow-dirs'].outputs.matrix != '' }} | |
strategy: | |
matrix: | |
workflow_dir: ${{fromJson(needs['list-workflow-dirs'].outputs.matrix)}} | |
steps: | |
- uses: actions/checkout@v2 | |
- name: docker build + push to ghcr.io | |
run: | | |
TAG=$(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}" don't push while testing | |
if [[ ${GITHUB_REF##*/} == "main" ]]; then | |
docker tag "${IMAGE_URI}:${TAG}" "${IMAGE_URI}:latest" | |
# docker push "${IMAGE_URI}:latest" don't push while testing | |
fi | |
echo "IMAGE_URI=${IMAGE_URI}" >> $GITHUB_ENV | |
echo "TAG=${TAG}" >> $GITHUB_ENV | |
- name: run tests | |
run: | | |
[ -d "${{ matrix.workflow_dir }}/integration_test" ] || exit 0 | |
source /etc/profile | |
# 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 | |
# 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=/tmp/miniwdl_download_cache_workflows/ | |
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 integration-test-${{ matrix.workflow_dir }} |