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infrastructure for QC and publishing to PyPI
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‎.github/workflows/ci.yml‎

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name: Test and Install Package
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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workflow_dispatch:
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "latest"
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- name: Install dependencies
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run: uv sync --group dev
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- name: Build and test
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run: make all

‎.github/workflows/publish.yml‎

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name: Build and Publish to PyPI
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on:
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push:
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tags:
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- 'v*' # Trigger on version tags (v1.0.0, v0.8.1, etc.)
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workflow_dispatch: # Allow manual triggering
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "latest"
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- name: Install dependencies
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run: uv sync --group dev
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- name: Run tests
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run: uv run pytest tests/
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build-and-publish:
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needs: test
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runs-on: ubuntu-latest
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permissions:
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contents: read
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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with:
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fetch-depth: 0 # Required for hatch-vcs versioning
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "latest"
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- name: Install hatch
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run: uv tool install hatch
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- name: Build package with hatch
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run: uv tool run hatch build
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- name: Check package
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run: |
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uv tool install twine
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uv tool run twine check dist/*
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- name: Verify version matches tag
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run: |
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TAG_VERSION=${GITHUB_REF#refs/tags/v}
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PACKAGE_VERSION=$(uv tool run hatch version)
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echo "Tag version: $TAG_VERSION"
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echo "Package version: $PACKAGE_VERSION"
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if [ "$TAG_VERSION" != "$PACKAGE_VERSION" ]; then
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echo "Version mismatch! Tag: $TAG_VERSION, Package: $PACKAGE_VERSION"
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exit 1
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fi
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- name: Publish to PyPI (using token-based auth)
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if: "!contains(github.ref, 'test') && !contains(github.ref, 'dryrun')"
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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verify-metadata: true
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verbose: true
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password: ${{ secrets.PYPI_API_TOKEN }}
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- name: Publish to TestPyPI (using token-based auth)
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if: "contains(github.ref, 'test') && !contains(github.ref, 'dryrun')"
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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verify-metadata: true
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verbose: true
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password: ${{ secrets.TEST_PYPI_API_TOKEN }}
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- name: Dry run (build only)
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if: "contains(github.ref, 'dryrun')"
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run: |
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echo "Dry run mode - would publish these files:"
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ls -la dist/
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echo "Package contents:"
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uv tool run twine check dist/* --verbose
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- name: Upload build artifacts
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uses: actions/upload-artifact@v4
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if: always()
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with:
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name: build-artifacts-${{ github.ref_name }}
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path: dist/

‎Makefile‎

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.PHONY: test-coverage clean install dev format lint all server build upload-test upload release deptry mypy test-mcp test-mcp-extended test-integration
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# Default target
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all: clean install dev test-coverage format lint mypy deptry build test-mcp test-mcp-extended test-integration
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# Install everything for development
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dev:
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uv sync --group dev
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# Install production only
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install:
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uv sync
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# Run tests with coverage
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test-coverage:
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uv run pytest --cov=ols_mcp --cov-report=html --cov-report=term tests/
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# Clean up build artifacts
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clean:
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rm -rf build/
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rm -rf dist/
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rm -rf *.egg-info
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find . -type d -name __pycache__ -exec rm -rf {} +
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find . -type f -name "*.pyc" -delete
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rm -rf src/*.egg-info
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# Run server mode
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server:
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uv run python src/ols_mcp/main.py
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# Format code with black
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format:
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uv run black src/ tests/
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lint:
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uv run ruff check --fix src/ tests/
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# Check for unused dependencies
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deptry:
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uvx deptry .
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# Type checking
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mypy:
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uv run mypy src/
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# Build package with hatch
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build:
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uv run hatch build
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# Upload to TestPyPI (using token-based auth)
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upload-test:
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uv run twine upload --repository testpypi dist/*
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# Upload to PyPI (using token-based auth - set TWINE_PASSWORD environment variable first)
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upload:
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uv run twine upload dist/*
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# Complete release workflow
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release: clean test-coverage build upload
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# Integration Testing
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test-integration:
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@echo "🔬 Testing OLS integration..."
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uv run pytest tests/test_api.py -v
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# MCP Server testing
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test-mcp:
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@echo "Testing MCP protocol handshake..."
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echo '{"jsonrpc": "2.0", "method": "initialize", "params": {"protocolVersion": "1.0", "capabilities": {"tools": {}}, "clientInfo": {"name": "test-client", "version": "1.0.0"}}, "id": 1}' | timeout 3 uv run python src/ols_mcp/main.py 2>/dev/null | head -1
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test-mcp-extended:
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@echo "Testing MCP protocol initialization..."
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@(echo '{"jsonrpc": "2.0", "method": "initialize", "params": {"protocolVersion": "2025-03-26", "capabilities": {"tools": {}}, "clientInfo": {"name": "test-client", "version": "1.0.0"}}, "id": 1}'; \
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sleep 0.1; \
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echo '{"jsonrpc": "2.0", "method": "tools/list", "id": 2}'; \
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sleep 0.1; \
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echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "search_ontologies", "arguments": {"term": "cancer", "ontology": "mondo", "n": 2}}, "id": 3}') | \
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timeout 5 uv run python src/ols_mcp/main.py 2>/dev/null | head -10
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# OLS MCP - Claude Desktop config:
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# Add to ~/Library/Application Support/Claude/claude_desktop_config.json:
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# {
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# "mcpServers": {
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# "ols-mcp": {
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# "command": "uv",
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# "args": ["run", "python", "src/ols_mcp/main.py"],
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# "cwd": "/path/to/ols-mcp"
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# }
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# }
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# }
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#
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# Claude Code MCP setup:
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# claude mcp add -s project ols-mcp uv run python src/ols_mcp/main.py
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#
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# Goose setup:
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# goose session --with-extension "uv run python src/ols_mcp/main.py"

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