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madhavajaymadhavajay
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Merge branch 'main' into madhava/wasm-fixes
2 parents e66040a + 2509e30 commit bd8a5c6

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‎.github/workflows/docker-build.yml‎

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name: Build Docker Image
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on:
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workflow_call:
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inputs:
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version:
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description: 'Image version tag, without v prefix. Defaults to VERSION.'
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required: false
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type: string
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push:
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branches: [main]
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tags:
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- 'v*'
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paths:
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- 'rust/**'
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- 'docker/**'
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- 'VERSION'
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- '.github/workflows/docker-build.yml'
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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: 'Image version tag, without v prefix. Defaults to VERSION.'
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required: false
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type: string
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: openmined/bioscript
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jobs:
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build-and-push:
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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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attestations: write
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id-token: write
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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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submodules: recursive
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Log in to GitHub Container Registry
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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: Resolve version
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id: version
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shell: bash
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env:
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VERSION_INPUT: ${{ inputs.version || '' }}
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run: |
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if [[ -n "${VERSION_INPUT}" ]]; then
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VERSION="${VERSION_INPUT#v}"
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elif [[ "${GITHUB_REF_TYPE}" == "tag" && "${GITHUB_REF_NAME}" == v* ]]; then
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VERSION="${GITHUB_REF_NAME#v}"
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else
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VERSION="$(tr -d '[:space:]' < VERSION)"
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fi
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if [[ ! "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+(-[0-9A-Za-z.-]+)?$ ]]; then
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echo "Invalid version: $VERSION" >&2
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exit 1
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fi
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echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
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echo "Resolved version: ${VERSION}"
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- name: Extract metadata 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=semver,pattern={{version}},value=v${{ steps.version.outputs.version }}
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type=semver,pattern={{major}}.{{minor}},value=v${{ steps.version.outputs.version }}
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type=semver,pattern={{major}},value=v${{ steps.version.outputs.version }}
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type=raw,value=${{ steps.version.outputs.version }}
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type=raw,value=latest,enable={{is_default_branch}}
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type=sha,prefix={{branch}}-
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- name: Build and push Docker image
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id: build
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uses: docker/build-push-action@v6
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with:
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context: .
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file: ./docker/Dockerfile
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platforms: linux/amd64,linux/arm64
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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cache-from: type=gha
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cache-to: type=gha,mode=max
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- name: Generate artifact attestation
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uses: actions/attest-build-provenance@v2
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continue-on-error: true
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with:
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subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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subject-digest: ${{ steps.build.outputs.digest }}
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push-to-registry: true

‎.github/workflows/release.yml‎

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name: Release Docker Image
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on:
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workflow_dispatch:
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inputs:
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bump:
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description: 'Version bump type'
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required: true
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type: choice
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options:
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- patch
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- minor
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- major
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- custom
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default: 'minor'
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custom_version:
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description: 'Custom version, without v prefix. Required when bump=custom.'
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required: false
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type: string
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permissions:
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contents: write
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packages: write
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attestations: write
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id-token: write
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jobs:
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version:
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runs-on: ubuntu-latest
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outputs:
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version: ${{ steps.new.outputs.version }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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submodules: recursive
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- name: Resolve new version
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id: new
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shell: bash
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run: |
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CURRENT="$(tr -d '[:space:]' < VERSION)"
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IFS='.' read -r MAJOR MINOR PATCH <<< "$CURRENT"
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case "${{ inputs.bump }}" in
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major)
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NEW_VERSION="$((MAJOR + 1)).0.0"
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;;
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minor)
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NEW_VERSION="${MAJOR}.$((MINOR + 1)).0"
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;;
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patch)
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NEW_VERSION="${MAJOR}.${MINOR}.$((PATCH + 1))"
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;;
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custom)
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NEW_VERSION="${{ inputs.custom_version }}"
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;;
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esac
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if [[ ! "$NEW_VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+(-[0-9A-Za-z.-]+)?$ ]]; then
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echo "Invalid version: $NEW_VERSION" >&2
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exit 1
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fi
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echo "version=${NEW_VERSION}" >> "$GITHUB_OUTPUT"
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echo "New version: ${NEW_VERSION}"
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- name: Bump version
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run: ./bump_version.sh "${{ steps.new.outputs.version }}"
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- name: Run tests
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run: ./test.sh
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- name: Commit version bump and tag
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shell: bash
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run: |
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VERSION="${{ steps.new.outputs.version }}"
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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git add VERSION rust/bioscript-*/Cargo.toml rust/Cargo.lock
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if git diff --cached --quiet; then
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echo "Version files already at ${VERSION}"
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else
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git commit -m "Bump version to ${VERSION}"
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fi
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git tag "v${VERSION}"
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git push origin main --tags
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docker:
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needs: version
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uses: ./.github/workflows/docker-build.yml
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secrets: inherit
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with:
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version: ${{ needs.version.outputs.version }}

‎VERSION‎

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0.2.0

‎bump_version.sh‎

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#!/usr/bin/env bash
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set -euo pipefail
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if [[ $# -ne 1 ]]; then
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echo "Usage: $0 <version>" >&2
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echo "Example: $0 0.2.0" >&2
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exit 1
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fi
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VERSION="$1"
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if [[ ! "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+(-[0-9A-Za-z.-]+)?$ ]]; then
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echo "Invalid semver version: $VERSION" >&2
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exit 1
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fi
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ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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cd "$ROOT_DIR"
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printf "%s\n" "$VERSION" > VERSION
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for manifest in \
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rust/bioscript-cli/Cargo.toml \
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rust/bioscript-core/Cargo.toml \
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rust/bioscript-ffi/Cargo.toml \
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rust/bioscript-formats/Cargo.toml \
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rust/bioscript-runtime/Cargo.toml \
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rust/bioscript-schema/Cargo.toml \
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rust/bioscript-wasm/Cargo.toml
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do
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perl -0pi -e 's/^version = ".*?"$/version = "'"$VERSION"'"/m' "$manifest"
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done
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cargo metadata --manifest-path rust/Cargo.toml --format-version 1 >/dev/null
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echo "Bumped BioScript to $VERSION"

‎docker/Dockerfile‎

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FROM rust:1-bookworm AS builder
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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bash \
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ca-certificates \
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clang \
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cmake \
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git \
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libbz2-dev \
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libclang-dev \
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libcurl4-openssl-dev \
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liblzma-dev \
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libssl-dev \
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pkg-config \
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zlib1g-dev \
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&& rm -rf /var/lib/apt/lists/*
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WORKDIR /src
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COPY . .
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RUN cargo build --release \
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--manifest-path rust/Cargo.toml \
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-p bioscript-cli
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RUN install -m 0755 rust/target/release/bioscript /usr/local/bin/bioscript
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FROM debian:bookworm-slim AS runtime
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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bash \
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ca-certificates \
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libbz2-1.0 \
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libcurl4 \
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liblzma5 \
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libssl3 \
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zlib1g \
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&& rm -rf /var/lib/apt/lists/*
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COPY --from=builder /usr/local/bin/bioscript /usr/local/bin/bioscript
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RUN ln -s /usr/local/bin/bioscript /usr/local/bin/bs
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LABEL org.opencontainers.image.source="https://github.com/OpenMined/bioscript"
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LABEL org.opencontainers.image.description="BioScript runtime"
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LABEL org.opencontainers.image.licenses="Apache-2.0"
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WORKDIR /workspace
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CMD ["bioscript"]

‎docker/build.sh‎

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#!/usr/bin/env bash
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set -euo pipefail
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ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
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cd "$ROOT_DIR"
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VERSION="${1:-$(tr -d '[:space:]' < VERSION)}"
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IMAGE="${BIOSCRIPT_IMAGE:-ghcr.io/openmined/bioscript}"
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PLATFORMS="${PLATFORMS:-linux/amd64,linux/arm64}"
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PUSH="${PUSH:-0}"
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LOAD="${LOAD:-0}"
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BUILD_ARGS=(
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docker buildx build
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--platform "$PLATFORMS"
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-f docker/Dockerfile
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-t "${IMAGE}:${VERSION}"
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-t "${IMAGE}:latest"
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.
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)
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if [[ "$PUSH" == "1" ]]; then
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BUILD_ARGS+=(--push)
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elif [[ "$LOAD" == "1" ]]; then
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if [[ "$PLATFORMS" == *,* ]]; then
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echo "LOAD=1 requires a single platform, got: $PLATFORMS" >&2
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exit 1
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fi
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BUILD_ARGS+=(--load)
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else
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BUILD_ARGS+=(--output "type=oci,dest=docker/bioscript-${VERSION}.oci.tar")
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fi
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"${BUILD_ARGS[@]}"

‎rust/Cargo.lock‎

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‎rust/bioscript-cli/Cargo.toml‎

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[package]
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name = "bioscript-cli"
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version = "0.1.0"
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version = "0.2.0"
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edition = "2024"
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[[bin]]

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