Mutation Clinical Trial Matching MCP

[project] name = "mutation-clinical-trial-matching-mcp" version = "0.2.1" description = "A Model Context Protocol (MCP) server that enables Claude Desktop to search for clinical trials based on genetic mutations" readme = "README.md" requires-python = ">=3.11" authors = [ {name = "Clinical Trials MCP", email = "noreply@example.com"} ] keywords = ["mcp", "clinical-trials", "mutations", "claude", "healthcare"] classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", "Topic :: Scientific/Engineering :: Medical Science Apps.", "Topic :: Software Development :: Libraries :: Python Modules", ] dependencies = [ "fastmcp>=2.10.2", "httpx>=0.28.1", "mcp[cli]>=1.0.0", "pocketflow>=0.0.1", "python-dotenv==1.1.0", "redis>=6.2.0", "requests==2.31.0", ] [project.optional-dependencies] dev = [ "pytest>=7.0.0", "pytest-cov>=4.0.0", "mypy>=1.0.0", "ruff>=0.1.0", "requests==2.31.0", # temporary for legacy test compatibility ] [project.urls] Homepage = "https://github.com/pickleton89/mutation-clinical-trial-matching-mcp" Repository = "https://github.com/pickleton89/mutation-clinical-trial-matching-mcp" Documentation = "https://github.com/pickleton89/mutation-clinical-trial-matching-mcp#readme" Issues = "https://github.com/pickleton89/mutation-clinical-trial-matching-mcp/issues" [project.scripts] clinicaltrials-mcp-server = "servers.primary:main" clinicaltrials-cli = "scripts.cli:main" [tool.setuptools.packages.find] include = ["clinicaltrials*", "llm*", "utils*", "servers*", "scripts*"] exclude = ["tests*", "docs*", "assets*"] [build-system] requires = ["setuptools>=61.0", "wheel"] build-backend = "setuptools.build_meta" [dependency-groups] dev = [ "pytest>=8.4.1", "pytest-asyncio>=1.1.0", "pytest-cov>=6.2.1", "ty>=0.0.1a14", ] # Ruff configuration [tool.ruff] target-version = "py311" line-length = 100 [tool.ruff.lint] select = ["E", "F", "W", "I", "N", "UP", "B", "A", "C4", "PIE", "T20"] ignore = ["E501"] # Line too long [tool.ruff.lint.per-file-ignores] "tests/*" = ["T20"] # Allow print statements in tests # MyPy configuration [tool.mypy] python_version = "3.11" warn_return_any = true warn_unused_configs = true disallow_untyped_defs = true disallow_incomplete_defs = true check_untyped_defs = true strict_optional = true no_implicit_optional = true warn_redundant_casts = true warn_unused_ignores = true show_error_codes = true # Pytest configuration [tool.pytest.ini_options] testpaths = ["tests"] python_files = ["test_*.py"] python_classes = ["Test*"] python_functions = ["test_*"] addopts = "--strict-markers --strict-config --verbose" markers = [ "slow: marks tests as slow (deselect with '-m \"not slow\"')", "integration: marks tests as integration tests", "asyncio: marks tests as async", ] # Coverage configuration [tool.coverage.run] source = ["clinicaltrials", "llm", "utils"] omit = ["tests/*", "*/conftest.py"] [tool.coverage.report] exclude_lines = [ "pragma: no cover", "def __repr__", "raise AssertionError", "raise NotImplementedError", "if __name__ == .__main__.:", "if TYPE_CHECKING:", ] [tool.coverage.html] directory = "coverage_html_report"