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Merge pull request #111 from broadinstitute/dp-fasta-handling #320

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Merge pull request #111 from broadinstitute/dp-fasta-handling

Merge pull request #111 from broadinstitute/dp-fasta-handling #320

Workflow file for this run

.github/workflows/build.yml at 979583f
name: "viral-core CI"
on:
push:
pull_request:
branches:
- master
merge_group:
release:
types:
- created
env:
HOME: "${{ github.workspace }}"
CACHE_DIR: "${{ github.workspace }}/misc_cache"
MINICONDA_DIR: "${{ github.workspace }}/miniconda"
GATK_PATH: "${{ github.workspace }}/misc_cache"
PYTHONIOENCODING: UTF8
DOCKER_REGISTRY: "quay.io"
DOCKER_REPO_PROD: "quay.io/broadinstitute/viral-core"
DOCKER_REPO_DEV: "quay.io/broadinstitute/viral-core"
#BOTO_CONFIG: /dev/null # bogus value to override config on travis
_JAVA_OPTIONS: "-Xmx5g" # overrides jvm opts set elsewhere; see: https://stackoverflow.com/questions/28327620/difference-between-java-options-java-tool-options-and-java-opts
# TravisCI variables described here:
# https://docs.travis-ci.com/user/environment-variables/
# GitHub Actions environment variables and context described here:
# https://docs.github.com/en/actions/reference/environment-variables
# https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#env-context
GITHUB_ACTIONS_COMMIT: ${{ github.sha }}
GITHUB_ACTIONS_BUILD_DIR: ${{ github.workspace }}
#GITHUB_ACTIONS_BRANCH: ${{ github.base_ref }}
GITHUB_ACTIONS_BRANCH: ${{ github.ref }}
GITHUB_ACTIONS_PULL_REQUEST: ${{ github.event.number }}
GITHUB_ACTIONS_PULL_REQUEST_BRANCH: ${{ github.head_ref }}
GITHUB_ACTIONS_PULL_REQUEST_SHA : ${{ github.event.pull_request.head.sha }}
GITHUB_ACTIONS_BASE_REF: ${{ github.base_ref }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
jobs:
build_docker:
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v3
# fetch git tags (tagged releases) because
# actions/checkout@v3 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
# if GITHUB_ACTIONS_PULL_REQUEST_BRANCH is set, this is a pull request build
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: Login to docker registry
uses: docker/login-action@v2
with:
registry: ${{ env.DOCKER_REGISTRY }}
username: ${{ secrets.QUAY_USERNAME }}
password: ${{ secrets.QUAY_ROBOT_TOKEN }}
# cache; see: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows
- name: setup cache
id: docker_cache
uses: actions/cache@v3
env:
cache-name: old-docker-tag
with:
path: "$CACHE_DIR"
key: ${{ runner.os }}-${{ env.cache-name }}
# - name: Pull old docker image from cache
# if: steps.docker_cache.outputs.cache-hit != 'true'
# run: |
- name: Attempt to pull older image from cache
if: steps.docker_cache.outputs.cache-hit == 'true'
shell: bash
run: |
set -e
# restore old tag from cache if present
if [ -f "$CACHE_DIR/old-docker-tag.txt" ]; then
OLD_DOCKER_TAG=$(cat $CACHE_DIR/old-docker-tag.txt)
else
OLD_DOCKER_TAG=$DOCKER_REPO_PROD
fi
echo "old docker tag = $OLD_DOCKER_TAG"
# attempt to pull tag from cache
if docker pull $OLD_DOCKER_TAG; then
echo _CACHE_FROM="--cache-from $OLD_DOCKER_TAG" >> $GITHUB_ENV
else
echo "_CACHE_FROM=" >> $GITHUB_ENV
fi
- name: Build docker image
shell: bash
run: |
set -e -x
git describe --tags --always | tee VERSION
if [ -n "$GITHUB_ACTIONS_TAG" ]; then
echo "Release $GITHUB_ACTIONS_TAG"
elif [ -n "$GITHUB_ACTIONS_PULL_REQUEST_BRANCH" ]; then
echo "LABEL quay.expires-after=10w" >> Dockerfile
elif [[ "$GITHUB_ACTIONS_BRANCH" != "master" ]]; then
echo "LABEL quay.expires-after=10w" >> Dockerfile
fi
echo "Building with cache from: $_CACHE_FROM"
docker build -t local/build-container:build $_CACHE_FROM .
- name: Deploy docker image
run: |
github_actions_ci/deploy-docker.sh
- name: store tag ID in cache
run: |
mkdir -p $CACHE_DIR
github_actions_ci/list-docker-tags.sh | tail -1 | tee $CACHE_DIR/old-docker-tag.txt
test_in_docker:
needs: build_docker
runs-on: ubuntu-20.04
env:
GITHUB_ACTIONS_PYTHON_VERSION: "3.10"
PYTEST_ADDOPTS: "-rsxX --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-config=.coveragerc --cov-report xml:coverage.xml --cov-report= --cov broad_utils --cov illumina --cov read_utils --cov reports --cov tools --cov util --cov file_utils"
steps:
- name: checkout repository
uses: actions/checkout@v3
# fetch git tags (tagged releases) because
# actions/checkout@v3 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
# if GITHUB_ACTIONS_PULL_REQUEST_BRANCH is set, this is a pull request build
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: install python
uses: actions/setup-python@v5
with:
python-version: "${{ env.GITHUB_ACTIONS_PYTHON_VERSION }}"
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
- name: pull docker image
run: |
set -e -x
DOCKER_TAG=$(github_actions_ci/list-docker-tags.sh | tail -1)
echo "DOCKER_TAG=$DOCKER_TAG" >> $GITHUB_ENV
echo "pulling $DOCKER_TAG"
docker pull $DOCKER_TAG
mkdir coverage
- name: test with docker
run: |
docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; pytest -n $(nproc) test/unit; cp coverage.xml /coverage'
- name: Run coveralls
uses: coverallsapp/github-action@v2
with:
file: coverage/coverage.xml
## note: this test_docs job does not actually produce the output on readthedocs
## readthedocs does its own build trigger. this job exists simply to alert us
## of build failures of the docs because otherwise we would never know.
test_docs:
needs: build_docker
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v3
# fetch git tags (tagged releases) because
# actions/checkout@v3 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
# if GITHUB_ACTIONS_PULL_REQUEST_BRANCH is set, this is a pull request build
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
- name: pull docker image
run: |
set -e -x
DOCKER_TAG=$(github_actions_ci/list-docker-tags.sh | tail -1)
echo "DOCKER_TAG=$DOCKER_TAG" >> $GITHUB_ENV
echo "pulling $DOCKER_TAG"
docker pull $DOCKER_TAG
- name: test building docs
run: |
set -e -x
docker run --entrypoint /bin/bash -v `pwd`:/opt/viral-ngs/source $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; github_actions_ci/install-pip-docs.sh; cd docs; make html'