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madhavajaymadhavajay
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Merge pull request #3 from OpenMined/madhava/call_interface
Madhava/call interface
2 parents a65a0b9 + 4e54dda commit 695f98b

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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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push:
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branches:
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- main
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paths:
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- 'python/**'
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- 'docker/**'
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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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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ${{ github.repository }}
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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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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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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: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract version from __init__.py
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id: version
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run: |
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VERSION=$(grep '^__version__ = ' python/src/bioscript/__init__.py | cut -d'"' -f2)
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echo "version=${VERSION}" >> $GITHUB_OUTPUT
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echo "Extracted 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@v5
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with:
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context: .
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file: ./docker/Dockerfile
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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@v1
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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/pr-checks.yml‎

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cd python
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uv sync --all-extras
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- name: Run ruff format check
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run: |
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cd python
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uv run ruff format --check .
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- name: Run ruff linting
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run: |
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cd python
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uv run ruff check .
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- name: Run mypy
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run: |
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cd python
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uv run mypy src/bioscript
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- name: Run linting
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run: bash lint.sh
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test:
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runs-on: ubuntu-latest
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run: |
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cd python
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uv run pytest
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test-local:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.8
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- name: Run local smoke test
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run: bash test_local.sh
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test-docker:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.8
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- name: Run Docker smoke test
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run: bash test_docker.sh

‎.github/workflows/publish.yml‎

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on:
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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., 0.1.0)'
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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: 'patch'
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custom_version:
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description: 'Custom version (only if bump=custom, e.g., 0.2.0)'
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required: false
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type: string
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jobs:
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- name: Set up Python
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run: uv python install 3.8
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- name: Update version in pyproject.toml
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- name: Get current version
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id: current
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run: |
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cd python
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sed -i 's/version = ".*"/version = "${{ inputs.version }}"/' pyproject.toml
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CURRENT=$(grep '^__version__ = ' python/src/bioscript/__init__.py | cut -d'"' -f2)
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echo "version=${CURRENT}" >> $GITHUB_OUTPUT
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echo "Current version: ${CURRENT}"
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- name: Calculate new version
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id: new
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run: |
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CURRENT="${{ steps.current.outputs.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="${{ inputs.custom_version }}"
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;;
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esac
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echo "version=${NEW_VERSION}" >> $GITHUB_OUTPUT
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echo "New version: ${NEW_VERSION}"
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- name: Update version in __init__.py
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run: |
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cd python
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sed -i 's/__version__ = ".*"/__version__ = "${{ inputs.version }}"/' src/bioscript/__init__.py
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sed -i 's/__version__ = ".*"/__version__ = "${{ steps.new.outputs.version }}"/' src/bioscript/__init__.py
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grep '__version__' src/bioscript/__init__.py
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- name: Install dependencies
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run: |
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packages-dir: python/dist/
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password: ${{ secrets.PYPI_API_TOKEN }}
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- name: Commit version bump
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- name: Commit version bump and tag
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run: |
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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 python/pyproject.toml python/src/bioscript/__init__.py
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git commit -m "Bump version to ${{ inputs.version }}"
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git tag "v${{ inputs.version }}"
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git add python/src/bioscript/__init__.py
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git commit -m "Bump version to ${{ steps.new.outputs.version }}"
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git tag "v${{ steps.new.outputs.version }}"
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git push origin main --tags

‎bump_version.sh‎

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#!/bin/bash
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set -e
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# Bump version in __init__.py
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# Usage: ./bump_version.sh <major|minor|patch|version>
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#
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# Examples:
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# ./bump_version.sh patch # 0.1.0 -> 0.1.1
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# ./bump_version.sh minor # 0.1.0 -> 0.2.0
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# ./bump_version.sh major # 0.1.0 -> 1.0.0
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# ./bump_version.sh 0.2.0 # Set to specific version
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REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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INIT_FILE="$REPO_ROOT/python/src/bioscript/__init__.py"
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if [ $# -ne 1 ]; then
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echo "Usage: $0 <major|minor|patch|version>"
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exit 1
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fi
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# Get current version
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CURRENT_VERSION=$(grep '^__version__ = ' "$INIT_FILE" | cut -d'"' -f2)
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echo "Current version: $CURRENT_VERSION"
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# Parse current version
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IFS='.' read -r MAJOR MINOR PATCH <<< "$CURRENT_VERSION"
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# Calculate new version
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case "$1" in
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major)
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NEW_VERSION="$((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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*)
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# Assume it's a specific version
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NEW_VERSION="$1"
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;;
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esac
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echo "New version: $NEW_VERSION"
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# Update __init__.py
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sed -i.bak "s/__version__ = .*/__version__ = \"${NEW_VERSION}\"/" "$INIT_FILE"
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rm "${INIT_FILE}.bak"
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echo "✓ Updated $INIT_FILE"
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echo ""
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echo "Next steps:"
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echo " git add python/src/bioscript/__init__.py"
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echo " git commit -m \"Bump version to ${NEW_VERSION}\""
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echo " git tag v${NEW_VERSION}"
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echo " git push origin main --tags"

‎docker/Dockerfile‎

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FROM python:3.13-slim
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LABEL org.opencontainers.image.source=https://github.com/OpenMined/bioscript
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LABEL org.opencontainers.image.description="BioScript - Genetic variant classification tool"
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LABEL org.opencontainers.image.licenses=Apache-2.0
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# Install uv for fast package management
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COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
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# Set working directory
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WORKDIR /app
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# Copy Python package files
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COPY python/pyproject.toml python/README.md ./
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COPY python/src ./src
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# Install bioscript
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RUN uv pip install --system --no-cache .
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# Set the default command to show help
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CMD ["bioscript", "--help"]

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