refine_assembly -- update to sanitize fasta headers #186
Workflow file for this run
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| name: "viral-assemble CI" | |
| on: | |
| push: | |
| merge_group: | |
| pull_request: | |
| branches: | |
| - master | |
| 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-assemble" | |
| DOCKER_REPO_DEV: "quay.io/broadinstitute/viral-assemble" | |
| #BOTO_CONFIG: /dev/null # bogus value to override config on travis | |
| _JAVA_OPTIONS: "-Xmx3g" # 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@v4 | |
| # fetch git tags (tagged releases) because | |
| # actions/checkout@v4 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@v3 | |
| with: | |
| registry: ${{ env.DOCKER_REGISTRY }} | |
| username: ${{ secrets.QUAY_USERNAME }} | |
| password: ${{ secrets.QUAY_ROBOT_TOKEN }} | |
| # cache; see: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows | |
| - name: setup cache | |
| id: docker_cache | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: old-docker-tag | |
| with: | |
| path: "$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 assembly --cov assemble" | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| # fetch git tags (tagged releases) because | |
| # actions/checkout@v4 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@v3 | |
| - 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`/.coveragerc:/opt/viral-ngs/source/.coveragerc -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@v4 | |
| # fetch git tags (tagged releases) because | |
| # actions/checkout@v4 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" >> $GITHUB_ENV | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: pull docker image | |
| run: | | |
| set -e -x | |
| DOCKER_TAG=$(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' |