LICENSE
README.md
pyproject.toml
setup.py
lobster/__main__.py
lobster/cli.py
lobster/main.py
lobster/version.py
lobster/version_cli.py
lobster/agents/graph.py
lobster/agents/state.py
lobster/agents/supervisor.py
lobster/cli_internal/__init__.py
lobster/cli_internal/commands/__init__.py
lobster/cli_internal/commands/output_adapter.py
lobster/cli_internal/commands/heavy/__init__.py
lobster/cli_internal/commands/heavy/data_commands.py
lobster/cli_internal/commands/heavy/modality_commands.py
lobster/cli_internal/commands/heavy/visualization_commands.py
lobster/cli_internal/commands/light/__init__.py
lobster/cli_internal/commands/light/agent_commands.py
lobster/cli_internal/commands/light/config_commands.py
lobster/cli_internal/commands/light/file_commands.py
lobster/cli_internal/commands/light/metadata_commands.py
lobster/cli_internal/commands/light/pipeline_commands.py
lobster/cli_internal/commands/light/purge_commands.py
lobster/cli_internal/commands/light/queue_commands.py
lobster/cli_internal/commands/light/workspace_commands.py
lobster/cli_internal/utils/__init__.py
lobster/cli_internal/utils/path_resolution.py
lobster/config/__init__.py
lobster/config/agent_capabilities.py
lobster/config/agent_config.py
lobster/config/agent_config_endpoint.py
lobster/config/agent_config_resolver.py
lobster/config/agent_presets.py
lobster/config/agent_registry.py
lobster/config/base_config.py
lobster/config/config_manager.py
lobster/config/constants.py
lobster/config/disease_ontology.json
lobster/config/global_config.py
lobster/config/llm_factory.py
lobster/config/model_service.py
lobster/config/ollama_service.py
lobster/config/premium_agent_configs.py
lobster/config/provider_setup.py
lobster/config/settings.py
lobster/config/ssl_setup.py
lobster/config/subscription_tiers.py
lobster/config/supervisor_config.py
lobster/config/version_check.py
lobster/config/workspace_agent_config.py
lobster/config/workspace_config.py
lobster/config/providers/__init__.py
lobster/config/providers/anthropic_provider.py
lobster/config/providers/azure_provider.py
lobster/config/providers/base_provider.py
lobster/config/providers/bedrock_provider.py
lobster/config/providers/gemini_provider.py
lobster/config/providers/ollama_provider.py
lobster/config/providers/registry.py
lobster/core/__init__.py
lobster/core/analysis_ir.py
lobster/core/archive_utils.py
lobster/core/client.py
lobster/core/component_registry.py
lobster/core/config_resolver.py
lobster/core/data_manager_v2.py
lobster/core/download_queue.py
lobster/core/exceptions.py
lobster/core/extraction_cache.py
lobster/core/ir_coverage.py
lobster/core/license_manager.py
lobster/core/lineage.py
lobster/core/notebook_executor.py
lobster/core/notebook_exporter.py
lobster/core/notebook_validator.py
lobster/core/plot_manager.py
lobster/core/plugin_loader.py
lobster/core/protocols.py
lobster/core/provenance.py
lobster/core/publication_queue.py
lobster/core/queue_storage.py
lobster/core/ris_parser.py
lobster/core/uv_tool_env.py
lobster/core/workspace.py
lobster/core/adapters/__init__.py
lobster/core/adapters/base.py
lobster/core/adapters/protein_structure_adapter.py
lobster/core/adapters/proteomics_adapter.py
lobster/core/adapters/pseudobulk_adapter.py
lobster/core/adapters/transcriptomics_adapter.py
lobster/core/adapters/genomics/__init__.py
lobster/core/adapters/genomics/plink_adapter.py
lobster/core/adapters/genomics/vcf_adapter.py
lobster/core/backends/__init__.py
lobster/core/backends/base.py
lobster/core/backends/h5ad_backend.py
lobster/core/backends/mudata_backend.py
lobster/core/identifiers/__init__.py
lobster/core/identifiers/accession_resolver.py
lobster/core/interfaces/__init__.py
lobster/core/interfaces/adapter.py
lobster/core/interfaces/backend.py
lobster/core/interfaces/base_client.py
lobster/core/interfaces/download_service.py
lobster/core/interfaces/validator.py
lobster/core/schemas/__init__.py
lobster/core/schemas/clinical_schema.py
lobster/core/schemas/database_mappings.py
lobster/core/schemas/database_registry.py
lobster/core/schemas/download_queue.py
lobster/core/schemas/download_urls.py
lobster/core/schemas/export_schemas.py
lobster/core/schemas/genomics.py
lobster/core/schemas/metabolomics.py
lobster/core/schemas/metagenomics.py
lobster/core/schemas/ontology.py
lobster/core/schemas/protein_structure.py
lobster/core/schemas/proteomics.py
lobster/core/schemas/publication_queue.py
lobster/core/schemas/sra.py
lobster/core/schemas/transcriptomics.py
lobster/core/schemas/validation.py
lobster/core/utils/__init__.py
lobster/core/utils/h5ad_utils.py
lobster/lobster_cloud/__init__.py
lobster/lobster_cloud/client.py
lobster/prompts/__init__.py
lobster/prompts/composer.py
lobster/prompts/config.py
lobster/prompts/loader.py
lobster/prompts/registry.py
lobster/services/analysis/bulk_rnaseq_service.py
lobster/services/analysis/clustering_service.py
lobster/services/analysis/pathway_enrichment_bridge_service.py
lobster/services/analysis/pathway_enrichment_service.py
lobster/services/data_access/content_access_service.py
lobster/services/data_access/docling_service.py
lobster/services/data_access/geo_download_service.py
lobster/services/data_access/geo_fallback_service.py
lobster/services/data_access/geo_service.py
lobster/services/data_access/massive_download_service.py
lobster/services/data_access/pride_download_service.py
lobster/services/data_access/sra_download_service.py
lobster/services/data_access/workspace_content_service.py
lobster/services/data_access/geo/constants.py
lobster/services/data_access/geo/downloader.py
lobster/services/data_access/geo/facade.py
lobster/services/data_access/geo/parser.py
lobster/services/data_access/geo/strategy.py
lobster/services/data_access/geo/loaders/tenx.py
lobster/services/data_access/proteomics_parsers/__init__.py
lobster/services/data_access/proteomics_parsers/base_parser.py
lobster/services/data_management/concatenation_service.py
lobster/services/data_management/modality_management_service.py
lobster/services/data_management/strategy_recommendation_service.py
lobster/services/execution/custom_code_execution_service.py
lobster/services/execution/execution_context_builder.py
lobster/services/execution/registry.py
lobster/services/execution/sdk_delegation_service.py
lobster/services/metadata/identifier_provenance_service.py
lobster/services/metadata/metadata_overview_service.py
lobster/services/metadata/metadata_validation_service.py
lobster/services/metadata/protocol_extraction/base.py
lobster/services/metadata/protocol_extraction/registry.py
lobster/services/metadata/protocol_extraction/amplicon/details.py
lobster/services/metadata/protocol_extraction/amplicon/service.py
lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json
lobster/services/metadata/protocol_extraction/mass_spec/details.py
lobster/services/metadata/protocol_extraction/mass_spec/service.py
lobster/services/metadata/protocol_extraction/rnaseq/details.py
lobster/services/metadata/protocol_extraction/rnaseq/service.py
lobster/services/orchestration/publication_processing_service.py
lobster/testing/__init__.py
lobster/testing/contract_mixins.py
lobster/testing/fixtures.py
lobster/testing/mock_data_manager.py
lobster/testing/mock_llm.py
lobster/tools/__init__.py
lobster/tools/custom_code_tool.py
lobster/tools/download_orchestrator.py
lobster/tools/enhanced_handoff_tool.py
lobster/tools/expert_handoff_manager.py
lobster/tools/expert_handoff_patterns.py
lobster/tools/geo_downloader.py
lobster/tools/geo_parser.py
lobster/tools/gpu_detector.py
lobster/tools/handoff_builder.py
lobster/tools/handoff_tool.py
lobster/tools/pipeline_strategy.py
lobster/tools/rate_limiter.py
lobster/tools/rate_limiter_arena.py
lobster/tools/todo_tools.py
lobster/tools/url_transforms.py
lobster/tools/workflow_tracker.py
lobster/tools/workspace_tool.py
lobster/tools/providers/__init__.py
lobster/tools/providers/abstract_provider.py
lobster/tools/providers/base_provider.py
lobster/tools/providers/biopython_entrez_wrapper.py
lobster/tools/providers/biorxiv_medrxiv_config.py
lobster/tools/providers/biorxiv_medrxiv_provider.py
lobster/tools/providers/geo_provider.py
lobster/tools/providers/geo_utils.py
lobster/tools/providers/massive_provider.py
lobster/tools/providers/ncbi_query_builder.py
lobster/tools/providers/organism_enum.py
lobster/tools/providers/pdb_provider.py
lobster/tools/providers/pmc_provider.py
lobster/tools/providers/pride_normalizer.py
lobster/tools/providers/pride_provider.py
lobster/tools/providers/provider_registry.py
lobster/tools/providers/publication_resolver.py
lobster/tools/providers/pubmed_provider.py
lobster/tools/providers/sra_provider.py
lobster/tools/providers/structure_provider.py
lobster/tools/providers/webpage_provider.py
lobster/ui/__init__.py
lobster/ui/commands.py
lobster/ui/console_manager.py
lobster/ui/live_dashboard.py
lobster/ui/os_app.py
lobster/ui/progress_manager.py
lobster/ui/themes.py
lobster/ui/callbacks/__init__.py
lobster/ui/callbacks/textual_callback.py
lobster/ui/components/__init__.py
lobster/ui/components/file_tree.py
lobster/ui/components/multi_progress.py
lobster/ui/components/parallel_workers_progress.py
lobster/ui/components/status_display.py
lobster/ui/formatters/__init__.py
lobster/ui/screens/__init__.py
lobster/ui/screens/analysis_screen.py
lobster/ui/services/__init__.py
lobster/ui/services/error_service.py
lobster/ui/widgets/__init__.py
lobster/ui/widgets/activity_log.py
lobster/ui/widgets/adapters_panel.py
lobster/ui/widgets/agents_panel.py
lobster/ui/widgets/chat_message.py
lobster/ui/widgets/connections_panel.py
lobster/ui/widgets/data_hub.py
lobster/ui/widgets/error_modal.py
lobster/ui/widgets/modality_list.py
lobster/ui/widgets/plot_preview.py
lobster/ui/widgets/query_prompt.py
lobster/ui/widgets/queue_panel.py
lobster/ui/widgets/queue_status_bar.py
lobster/ui/widgets/results_display.py
lobster/ui/widgets/status_bar.py
lobster/ui/widgets/system_info.py
lobster/ui/widgets/token_usage_panel.py
lobster/utils/__init__.py
lobster/utils/callbacks.py
lobster/utils/deviance.py
lobster/utils/error_handlers.py
lobster/utils/file_analyzer.py
lobster/utils/file_naming.py
lobster/utils/json_extractor.py
lobster/utils/llm_response_utils.py
lobster/utils/logger.py
lobster/utils/progress_wrapper.py
lobster/utils/ssl_utils.py
lobster/utils/statistics.py
lobster/utils/system.py
lobster_ai.egg-info/PKG-INFO
lobster_ai.egg-info/SOURCES.txt
lobster_ai.egg-info/dependency_links.txt
lobster_ai.egg-info/entry_points.txt
lobster_ai.egg-info/requires.txt
lobster_ai.egg-info/top_level.txt
tests/test_expert_handoffs.py
tests/test_kevin_bugs.py
tests/test_kevin_bugs_with_data.py
tests/test_plugin_contract.py
tests/test_scvi_integration_validation.py
tests/test_visualization_expert.py