LICENSE
README.md
pyproject.toml
src/biomcp/__init__.py
src/biomcp/__main__.py
src/biomcp/cbioportal_helper.py
src/biomcp/circuit_breaker.py
src/biomcp/connection_pool.py
src/biomcp/constants.py
src/biomcp/core.py
src/biomcp/domain_handlers.py
src/biomcp/exceptions.py
src/biomcp/http_client.py
src/biomcp/http_client_simple.py
src/biomcp/individual_tools.py
src/biomcp/logging_filter.py
src/biomcp/metrics.py
src/biomcp/metrics_handler.py
src/biomcp/parameter_parser.py
src/biomcp/prefetch.py
src/biomcp/query_parser.py
src/biomcp/query_router.py
src/biomcp/rate_limiter.py
src/biomcp/render.py
src/biomcp/request_batcher.py
src/biomcp/retry.py
src/biomcp/router.py
src/biomcp/router_handlers.py
src/biomcp/shared_context.py
src/biomcp/thinking_tool.py
src/biomcp/thinking_tracker.py
src/biomcp/articles/__init__.py
src/biomcp/articles/autocomplete.py
src/biomcp/articles/fetch.py
src/biomcp/articles/preprints.py
src/biomcp/articles/search.py
src/biomcp/articles/search_optimized.py
src/biomcp/articles/unified.py
src/biomcp/biomarkers/__init__.py
src/biomcp/biomarkers/search.py
src/biomcp/cli/__init__.py
src/biomcp/cli/articles.py
src/biomcp/cli/biomarkers.py
src/biomcp/cli/diseases.py
src/biomcp/cli/health.py
src/biomcp/cli/interventions.py
src/biomcp/cli/main.py
src/biomcp/cli/openfda.py
src/biomcp/cli/organizations.py
src/biomcp/cli/server.py
src/biomcp/cli/trials.py
src/biomcp/cli/variants.py
src/biomcp/diseases/__init__.py
src/biomcp/diseases/getter.py
src/biomcp/diseases/search.py
src/biomcp/drugs/__init__.py
src/biomcp/drugs/getter.py
src/biomcp/genes/__init__.py
src/biomcp/genes/getter.py
src/biomcp/integrations/__init__.py
src/biomcp/integrations/biothings_client.py
src/biomcp/integrations/cts_api.py
src/biomcp/interventions/__init__.py
src/biomcp/interventions/getter.py
src/biomcp/interventions/search.py
src/biomcp/openfda/__init__.py
src/biomcp/openfda/adverse_events.py
src/biomcp/openfda/adverse_events_helpers.py
src/biomcp/openfda/cache.py
src/biomcp/openfda/constants.py
src/biomcp/openfda/device_events.py
src/biomcp/openfda/device_events_helpers.py
src/biomcp/openfda/drug_approvals.py
src/biomcp/openfda/drug_labels.py
src/biomcp/openfda/drug_labels_helpers.py
src/biomcp/openfda/drug_recalls.py
src/biomcp/openfda/drug_recalls_helpers.py
src/biomcp/openfda/drug_shortages.py
src/biomcp/openfda/drug_shortages_detail_helpers.py
src/biomcp/openfda/drug_shortages_helpers.py
src/biomcp/openfda/exceptions.py
src/biomcp/openfda/input_validation.py
src/biomcp/openfda/rate_limiter.py
src/biomcp/openfda/utils.py
src/biomcp/openfda/validation.py
src/biomcp/organizations/__init__.py
src/biomcp/organizations/getter.py
src/biomcp/organizations/search.py
src/biomcp/resources/__init__.py
src/biomcp/resources/getter.py
src/biomcp/resources/instructions.md
src/biomcp/resources/researcher.md
src/biomcp/thinking/__init__.py
src/biomcp/thinking/sequential.py
src/biomcp/thinking/session.py
src/biomcp/trials/__init__.py
src/biomcp/trials/getter.py
src/biomcp/trials/nci_getter.py
src/biomcp/trials/nci_search.py
src/biomcp/trials/search.py
src/biomcp/utils/__init__.py
src/biomcp/utils/cancer_types_api.py
src/biomcp/utils/cbio_http_adapter.py
src/biomcp/utils/endpoint_registry.py
src/biomcp/utils/gene_validator.py
src/biomcp/utils/metrics.py
src/biomcp/utils/mutation_filter.py
src/biomcp/utils/query_utils.py
src/biomcp/utils/rate_limiter.py
src/biomcp/utils/request_cache.py
src/biomcp/variants/__init__.py
src/biomcp/variants/alphagenome.py
src/biomcp/variants/cancer_types.py
src/biomcp/variants/cbio_external_client.py
src/biomcp/variants/cbioportal_mutations.py
src/biomcp/variants/cbioportal_search.py
src/biomcp/variants/cbioportal_search_helpers.py
src/biomcp/variants/constants.py
src/biomcp/variants/external.py
src/biomcp/variants/filters.py
src/biomcp/variants/getter.py
src/biomcp/variants/links.py
src/biomcp/variants/search.py
src/biomcp/workers/__init__.py
src/biomcp/workers/worker.py
src/biomcp_python.egg-info/PKG-INFO
src/biomcp_python.egg-info/SOURCES.txt
src/biomcp_python.egg-info/dependency_links.txt
src/biomcp_python.egg-info/entry_points.txt
src/biomcp_python.egg-info/requires.txt
src/biomcp_python.egg-info/top_level.txt
tests/test_pydantic_ai_integration.py