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Merge pull request #23 from msk-access/filter_duplicates_set_to_true
Update small_variants.py
2 parents b61adce + 5ef8921 commit 5e29129

24 files changed

Lines changed: 789 additions & 519 deletions

‎.github/workflows/publish-pypi.yml‎

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name: Publish Python Package
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on:
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release:
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types: [published]
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workflow_dispatch:
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inputs:
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version:
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description: 'Version to publish (e.g., 1.0.0)'
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required: false
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env:
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PYTHON_VERSION: '3.9'
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jobs:
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deploy:
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name: Build and Publish
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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submodules: recursive
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- name: Set up Python ${{ env.PYTHON_VERSION }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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cache: 'pip'
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cache-dependency-path: 'pyproject.toml'
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package
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run: |
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python -m build --sdist --wheel --outdir dist/
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- name: Verify package
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run: |
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twine check dist/*
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- name: Publish to PyPI
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if: github.event_name == 'release' && github.event.action == 'published'
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true
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verbose: true
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- name: Show package info
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run: |
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echo "Package built for version: ${{ github.event.release.tag_name }}"
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ls -la dist/

‎.github/workflows/publish_docker.yaml‎

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name: Publish Docker image to ghcr.io
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name: Publish Docker Image
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on:
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push:
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tags:
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- "*"
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push:
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branches: [ main, master ]
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tags: [ '*', '!*-*' ] # Match v1.2.3 but not v1.2.3-rc1
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pull_request:
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branches: [ main, master ]
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workflow_dispatch:
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inputs:
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version:
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description: 'Version to build (e.g., v1.2.3)'
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required: false
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# Set job-level environment variables
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ${{ github.repository }}
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DOCKERFILE_PATH: ./Dockerfile
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BUILDX_CACHE_DIR: /tmp/.buildx-cache
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BUILDX_CACHE_KEY: ${{ github.ref }}-${{ github.sha }}
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jobs:
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push_to_registries:
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name: Build and publish Docker image
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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- name: Prepare
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# In this preparation step, a few configurations are made
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# according to tags that will be used to export the image
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# for Docker Hub, as well as the name of the image itself
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id: prep
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run: |
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DOCKER_IMAGE=ghcr.io/msk-access/genotype_variants
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VERSION=noop
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if [ "${{ github.event_name }}" = "schedule" ]; then
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VERSION=nightly
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elif [[ $GITHUB_REF == refs/tags/* ]]; then
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VERSION=${GITHUB_REF#refs/tags/}
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elif [[ $GITHUB_REF == refs/heads/* ]]; then
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VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
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fi
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TAGS="${DOCKER_IMAGE}:${VERSION}"
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if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
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MINOR=${VERSION%.*}
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MAJOR=${MINOR%.*}
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TAGS="$TAGS,${DOCKER_IMAGE}:latest"
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elif [[ $VERSION =~ ^v[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
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VERSION=$(echo ${VERSION#v})
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TAGS="${DOCKER_IMAGE}:${VERSION}"
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elif [ "${{ github.event_name }}" = "push" ]; then
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TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}"
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fi
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echo ::set-output name=version::${VERSION}
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echo ::set-output name=tags::${TAGS}
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- name: Login to GitHub Container Registry
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#if: github.event_name != 'pull_request'
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.RS_PAT }}
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- name: Push to GitHub Packages
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uses: docker/build-push-action@v3
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with:
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context: .
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file: ./Dockerfile
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push: true
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tags: ${{ steps.prep.outputs.tags }}
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build-args: |
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GENOTYPE_VARIANTS_VERSION=${{ steps.prep.outputs.version }}
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labels: |
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org.opencontainers.image.title=${{ github.event.repository.name }}
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org.opencontainers.image.description=${{ github.event.repository.description }}
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org.opencontainers.image.version=${{ steps.prep.outputs.version }}
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build-and-push:
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name: Build and Push Docker Image
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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security-events: write # For Trivy SARIF upload
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strategy:
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fail-fast: false
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matrix:
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platform: [linux/amd64, linux/arm64]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0 # Needed for version detection
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submodules: recursive
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v3
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with:
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platforms: arm64,amd64
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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with:
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install: true
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driver-opts: |
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image=moby/buildkit:latest
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network=host
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buildkitd-config-inline: |
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[worker.oci]
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max-parallelism = 4
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- name: Get current date
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id: date
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run: echo "date=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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tags: |
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type=schedule,pattern=nightly
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type=ref,event=branch
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type=ref,event=pr
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type=semver,pattern={{version}}
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type=semver,pattern={{major}}.{{minor}}
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type=semver,pattern={{major}}
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type=sha,format=long,prefix=sha-
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type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', github.event.repository.default_branch) }}
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flavor: |
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latest=${{ github.ref == format('refs/heads/{0}', github.event.repository.default_branch) }}
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labels: |
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org.opencontainers.image.title=${{ github.event.repository.name }}
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org.opencontainers.image.description=${{ github.event.repository.description }}
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org.opencontainers.image.url=${{ github.server_url }}/${{ github.repository }}
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org.opencontainers.image.source=${{ github.server_url }}/${{ github.repository }}
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org.opencontainers.image.created=${{ steps.date.outputs.date }}
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org.opencontainers.image.revision=${{ github.sha }}
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org.opencontainers.image.version=${{ github.ref_name }}
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- name: Log in to GitHub Container Registry
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if: github.event_name != 'pull_request'
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Set up Docker Buildx cache
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uses: actions/cache@v3
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with:
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path: ${{ env.BUILDX_CACHE_DIR }}
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key: buildx-${{ runner.os }}-${{ matrix.platform }}-${{ env.BUILDX_CACHE_KEY }}
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restore-keys: |
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buildx-${{ runner.os }}-${{ matrix.platform }}-
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buildx-${{ runner.os }}-
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- name: Build and push Docker image
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uses: docker/build-push-action@v5
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with:
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context: .
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file: ${{ env.DOCKERFILE_PATH }}
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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platforms: ${{ matrix.platform }}
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cache-from: type=local,src=${{ env.BUILDX_CACHE_DIR }}
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cache-to: type=local,dest=${{ env.BUILDX_CACHE_DIR }}-new,mode=max
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build-args: |
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BUILDKIT_INLINE_CACHE=1
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GENOTYPE_VARIANTS_VERSION=${{ github.ref_name }}
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BUILD_VERSION=${{ github.ref_name }}
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BUILD_DATE=${{ steps.date.outputs.date }}
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VCS_REF=${{ github.sha }}
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provenance: ${{ github.event_name != 'pull_request' }}
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sbom: true
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secrets: |
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GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }}
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- name: Run Trivy vulnerability scanner
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if: github.event_name != 'pull_request'
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uses: aquasecurity/trivy-action@master
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with:
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image-ref: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}@${{ steps.meta.outputs.version }}
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format: 'sarif'
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output: 'trivy-results.sarif'
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severity: 'CRITICAL,HIGH'
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ignore-unfixed: true
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vuln-type: 'os,library'
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exit-code: '1'
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timeout: '5m'
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- name: Upload Trivy scan results to GitHub Security tab
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if: always() && (github.event_name != 'pull_request')
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uses: github/codeql-action/upload-sarif@v2
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with:
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sarif_file: 'trivy-results.sarif'
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category: 'container-scan'
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- name: Update Buildx cache
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if: github.event_name != 'pull_request'
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run: |
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rm -rf ${{ env.BUILDX_CACHE_DIR }}
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mv ${{ env.BUILDX_CACHE_DIR }}-new ${{ env.BUILDX_CACHE_DIR }}
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echo "Updated build cache"
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- name: Show image details
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if: always()
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run: |
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echo "Built image: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}"
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echo "Tags: ${{ steps.meta.outputs.tags }}"
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echo "Labels: ${{ steps.meta.outputs.labels }}"

‎.github/workflows/validate.yaml‎

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name: validate
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name: Validate
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on:
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push:
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branches: [ main ]
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paths-ignore:
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- 'docs/**'
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- '**.md'
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- '**.rst'
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tags-ignore:
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- v*
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- 'docs/**'
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- '**.md'
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- '**.rst'
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- '**.gitignore'
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- '.github/**'
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pull_request:
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paths-ignore:
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- 'docs/**'
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- '**.md'
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- '**.rst'
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- 'docs/**'
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- '**.md'
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- '**.rst'
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- '**.gitignore'
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- '.github/**'
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env:
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PYTHON_VERSION: '3.9'
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jobs:
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test_nucleo:
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runs-on: ${{ matrix.platform }}
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if: "!contains(github.event.head_commit.message, 'ci skip')"
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test:
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name: Test Python 3.9 on Ubuntu
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runs-on: ubuntu-latest
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if: github.event.head_commit == null || !contains(github.event.head_commit.message, 'ci skip')
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strategy:
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max-parallel: 4
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matrix:
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platform: [ubuntu-latest]
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python-version: [3.7, 3.8]
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fail-fast: false
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steps:
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- name: Checkout repo
27-
uses: actions/checkout@v2
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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ref: ${{ github.head_ref }}
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fetch-depth: 0
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submodules: recursive
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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- name: Set up Python ${{ env.PYTHON_VERSION }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Python dependencies
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python-version: ${{ env.PYTHON_VERSION }}
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cache: 'pip'
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cache-dependency-path: 'pyproject.toml'
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- name: Set up environment and install dependencies
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run: |
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# Create virtual environment
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python -m venv .venv
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# Activate and set up the environment
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source .venv/bin/activate
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# Ensure pip is up to date and install build tools
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python -m pip install --upgrade pip setuptools wheel build
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# Install package with dev dependencies from pyproject.toml
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pip install -e ".[dev]"
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- name: Build package
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run: |
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source .venv/bin/activate
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python -m build --sdist --wheel --outdir dist/ .
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- name: Run tests
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run: |
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python -m pip install --upgrade pip
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pip install tox tox-gh-actions
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- name: Test with tox
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id: run-tox
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run: tox -vv
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env:
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PLATFORM: ${{ matrix.platform }}
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source .venv/bin/activate
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python -m pytest tests/ -v

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