LICENSE
MANIFEST.in
README.md
pyproject.toml
benchmarks/bixbench/__init__.py
benchmarks/bixbench/adapter.py
benchmarks/bixbench/batch_learn.py
benchmarks/bixbench/cli.py
benchmarks/bixbench/compare.py
benchmarks/bixbench/grader.py
benchmarks/bixbench/prepare_capsules.py
benchmarks/bixbench/run.py
benchmarks/bixbench/supervised_learn.py
benchmarks/bixbench/test_supervised_learn.py
benchmarks/common/supervised_learn.py
benchmarks/single_cell_benchmark/adapter.py
benchmarks/single_cell_benchmark/batch_learn.py
benchmarks/single_cell_benchmark/regrade.py
benchmarks/single_cell_benchmark/run_benchmark.py
pantheon/__init__.py
pantheon/__main__.py
pantheon/agent.py
pantheon/constant.py
pantheon/memory.py
pantheon/packages.py
pantheon/providers.py
pantheon/settings.py
pantheon/smart_func.py
pantheon/toolset.py
pantheon/chatroom/__init__.py
pantheon/chatroom/__main__.py
pantheon/chatroom/nats_manager.py
pantheon/chatroom/room.py
pantheon/chatroom/special_agents.py
pantheon/chatroom/start.py
pantheon/chatroom/stream.py
pantheon/chatroom/thread.py
pantheon/endpoint/__init__.py
pantheon/endpoint/__main__.py
pantheon/endpoint/core.py
pantheon/endpoint/gateway.py
pantheon/endpoint/hub.py
pantheon/endpoint/mcp.py
pantheon/endpoint/toolset_proxy.py
pantheon/endpoint/toolsets.py
pantheon/evolution/__init__.py
pantheon/evolution/__main__.py
pantheon/evolution/config.py
pantheon/evolution/database.py
pantheon/evolution/evaluator.py
pantheon/evolution/program.py
pantheon/evolution/prompt_builder.py
pantheon/evolution/result.py
pantheon/evolution/team.py
pantheon/evolution/visualizer.py
pantheon/evolution/utils/__init__.py
pantheon/evolution/utils/diff.py
pantheon/evolution/utils/metrics.py
pantheon/factory/__init__.py
pantheon/factory/models.py
pantheon/factory/template_io.py
pantheon/factory/template_manager.py
pantheon/factory/templates/mcp.json
pantheon/factory/templates/settings.json
pantheon/factory/templates/agents/package_developer.md
pantheon/factory/templates/agents/researcher.md
pantheon/factory/templates/agents/scientific_illustrator.md
pantheon/factory/templates/agents/single_cell/analysis_expert.md
pantheon/factory/templates/agents/single_cell/biologist.md
pantheon/factory/templates/agents/single_cell/browser_use.md
pantheon/factory/templates/agents/single_cell/fm_router.md
pantheon/factory/templates/agents/single_cell/leader.md
pantheon/factory/templates/agents/single_cell/reporter.md
pantheon/factory/templates/agents/single_cell/system_manager.md
pantheon/factory/templates/agents/skill_learning_v1/developer.md
pantheon/factory/templates/agents/skill_learning_v1/reflector.md
pantheon/factory/templates/agents/skill_learning_v1/skill_manager.md
pantheon/factory/templates/agents/skill_learning_v2/reflector.md
pantheon/factory/templates/agents/skill_learning_v2/skill_manager.md
pantheon/factory/templates/agents/skill_learning_v3/coordinator.md
pantheon/factory/templates/agents/skill_learning_v3/reflector.md
pantheon/factory/templates/agents/skill_learning_v3/skill_manager.md
pantheon/factory/templates/agents/skill_learning_v4/coordinator.md
pantheon/factory/templates/agents/skill_learning_v4/executor.md
pantheon/factory/templates/agents/skill_learning_v4/extractor.md
pantheon/factory/templates/agents/skill_learning_v4/reflector.md
pantheon/factory/templates/agents/skill_learning_v4/skill_manager.md
pantheon/factory/templates/prompts/agentic_general.md
pantheon/factory/templates/prompts/delegation.md
pantheon/factory/templates/prompts/output_format.md
pantheon/factory/templates/prompts/package_developer.md
pantheon/factory/templates/prompts/packages.md
pantheon/factory/templates/prompts/skills.md
pantheon/factory/templates/prompts/subagent_strategy.md
pantheon/factory/templates/prompts/web_dev.md
pantheon/factory/templates/prompts/work_strategy.md
pantheon/factory/templates/prompts/work_tracking.md
pantheon/factory/templates/skills/SKILLS.md
pantheon/factory/templates/skills/omics/SKILL.md
pantheon/factory/templates/skills/omics/cell_type_annotation.md
pantheon/factory/templates/skills/omics/environment_management.md
pantheon/factory/templates/skills/omics/parallel_computing.md
pantheon/factory/templates/skills/omics/quality_control.md
pantheon/factory/templates/skills/omics/scfm-models.md
pantheon/factory/templates/skills/omics/scfm-workflow.md
pantheon/factory/templates/skills/omics/single_cell_spatial_mapping.md
pantheon/factory/templates/skills/omics/trajectory_inference.md
pantheon/factory/templates/skills/omics/visualize_3d_spatial.md
pantheon/factory/templates/skills/omics/_scfm_docs/README.md
pantheon/factory/templates/skills/omics/_scfm_docs/SPEC_TEMPLATE.md
pantheon/factory/templates/skills/omics/_scfm_docs/checkpoint_layout.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/aidocell.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/atacformer.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/cell2sentence.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/cellfm.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/cellplm.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/chatcell.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/genecompass.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/genept.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/langcell.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/nicheformer.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/pulsar.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/scbert.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/sccello.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/scmulan.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/scplantllm.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/scprint.md
pantheon/factory/templates/skills/omics/_scfm_docs/models/tgpt.md
pantheon/factory/templates/skills/omics/database_access/SKILL.md
pantheon/factory/templates/skills/omics/database_access/cellxgene_census.md
pantheon/factory/templates/skills/omics/database_access/gget.md
pantheon/factory/templates/skills/omics/database_access/iseq.md
pantheon/factory/templates/skills/omics/sc_best_practices/SKILL.md
pantheon/factory/templates/skills/omics/sc_best_practices/bulk_deconvolution.md
pantheon/factory/templates/skills/omics/sc_best_practices/chromatin_accessibility.md
pantheon/factory/templates/skills/omics/sc_best_practices/clustering_and_annotation.md
pantheon/factory/templates/skills/omics/sc_best_practices/differential_and_condition.md
pantheon/factory/templates/skills/omics/sc_best_practices/immune_repertoire.md
pantheon/factory/templates/skills/omics/sc_best_practices/introduction.md
pantheon/factory/templates/skills/omics/sc_best_practices/multimodal_integration.md
pantheon/factory/templates/skills/omics/sc_best_practices/preprocessing.md
pantheon/factory/templates/skills/omics/sc_best_practices/regulatory_and_communication.md
pantheon/factory/templates/skills/omics/sc_best_practices/reproducibility.md
pantheon/factory/templates/skills/omics/sc_best_practices/spatial_omics.md
pantheon/factory/templates/skills/omics/sc_best_practices/surface_protein.md
pantheon/factory/templates/skills/omics/sc_best_practices/trajectory_analysis.md
pantheon/factory/templates/skills/omics/upstream_processing/SKILL.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/SKILL.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_dynamic_discovery.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_epigenomics.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_hic.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_spatial.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_transcriptomics.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_usage.md
pantheon/factory/templates/skills/omics/upstream_processing/nfcore/nfcore_variant_calling.md
pantheon/factory/templates/skills/omics/upstream_processing/openst/SKILL.md
pantheon/factory/templates/skills/omics/upstream_processing/openst/openst_computational.md
pantheon/factory/templates/teams/default.md
pantheon/factory/templates/teams/evolution_team.md
pantheon/factory/templates/teams/single_cell_team.md
pantheon/factory/templates/teams/learning/skill_learning_team_v1.md
pantheon/factory/templates/teams/learning/skill_learning_team_v2.md
pantheon/factory/templates/teams/learning/skill_learning_team_v3.md
pantheon/factory/templates/teams/learning/skill_learning_team_v4.md
pantheon/internal/__init__.py
pantheon/internal/injector.py
pantheon/internal/compression/__init__.py
pantheon/internal/compression/compressor.py
pantheon/internal/compression/plugin.py
pantheon/internal/compression/prompts.py
pantheon/internal/learning/__init__.py
pantheon/internal/learning/json_parser.py
pantheon/internal/learning/pipeline.py
pantheon/internal/learning/plugin.py
pantheon/internal/learning/reflector.py
pantheon/internal/learning/skill_injector.py
pantheon/internal/learning/skill_loader.py
pantheon/internal/learning/skill_manager.py
pantheon/internal/learning/skillbook.py
pantheon/internal/message/attachment_detection.py
pantheon/internal/message/attachment_pipeline.py
pantheon/internal/package_runtime/__init__.py
pantheon/internal/package_runtime/context.py
pantheon/internal/package_runtime/manager.py
pantheon/internal/package_runtime/runtime.py
pantheon/remote/__init__.py
pantheon/remote/factory.py
pantheon/remote/remote.py
pantheon/remote/backend/__init__.py
pantheon/remote/backend/base.py
pantheon/remote/backend/nats.py
pantheon/remote/backend/registry.py
pantheon/repl/__init__.py
pantheon/repl/__main__.py
pantheon/repl/core.py
pantheon/repl/prompt_app.py
pantheon/repl/renderers.py
pantheon/repl/setup_wizard.py
pantheon/repl/task_renderers.py
pantheon/repl/ui.py
pantheon/repl/utils.py
pantheon/repl/handlers/__init__.py
pantheon/repl/handlers/base.py
pantheon/repl/handlers/template_handler.py
pantheon/repl/handlers/builtin/__init__.py
pantheon/repl/handlers/builtin/bash.py
pantheon/repl/handlers/builtin/edit.py
pantheon/repl/handlers/builtin/mcp.py
pantheon/repl/handlers/builtin/revert.py
pantheon/repl/handlers/builtin/view.py
pantheon/repl/viewers/__init__.py
pantheon/repl/viewers/file_viewer_ptk.py
pantheon/repl/viewers/notify_dialog.py
pantheon/slack/__init__.py
pantheon/slack/__main__.py
pantheon/slack/app.py
pantheon/team/__init__.py
pantheon/team/aat.py
pantheon/team/base.py
pantheon/team/moa.py
pantheon/team/pantheon.py
pantheon/team/plugin.py
pantheon/team/sequential.py
pantheon/team/swarm.py
pantheon/toolsets/__init__.py
pantheon/toolsets/__main__.py
pantheon/toolsets/package.py
pantheon/toolsets/scraper.py
pantheon/toolsets/skillbook.py
pantheon/toolsets/web.py
pantheon/toolsets/web_urllib.py
pantheon/toolsets/code/__init__.py
pantheon/toolsets/code/code_toolset.py
pantheon/toolsets/code/tree_sitter_parser.py
pantheon/toolsets/database_api/__init__.py
pantheon/toolsets/database_api/database_api_query.py
pantheon/toolsets/database_api/schema_manager.py
pantheon/toolsets/database_api/schemas/cbioportal.json
pantheon/toolsets/database_api/schemas/clinvar.json
pantheon/toolsets/database_api/schemas/dbsnp.json
pantheon/toolsets/database_api/schemas/emdb.json
pantheon/toolsets/database_api/schemas/ensembl.json
pantheon/toolsets/database_api/schemas/geo.json
pantheon/toolsets/database_api/schemas/gnomad.json
pantheon/toolsets/database_api/schemas/gtopdb.json
pantheon/toolsets/database_api/schemas/gwas_catalog.json
pantheon/toolsets/database_api/schemas/interpro.json
pantheon/toolsets/database_api/schemas/iucn.json
pantheon/toolsets/database_api/schemas/jaspar.json
pantheon/toolsets/database_api/schemas/kegg.json
pantheon/toolsets/database_api/schemas/monarch.json
pantheon/toolsets/database_api/schemas/mpd.json
pantheon/toolsets/database_api/schemas/openfda.json
pantheon/toolsets/database_api/schemas/opentarget.json
pantheon/toolsets/database_api/schemas/paleobiology.json
pantheon/toolsets/database_api/schemas/pdb.json
pantheon/toolsets/database_api/schemas/pride.json
pantheon/toolsets/database_api/schemas/reactome.json
pantheon/toolsets/database_api/schemas/remap.json
pantheon/toolsets/database_api/schemas/stringdb.json
pantheon/toolsets/database_api/schemas/ucsc.json
pantheon/toolsets/database_api/schemas/uniprot.json
pantheon/toolsets/database_api/schemas/worms.json
pantheon/toolsets/evolution/__init__.py
pantheon/toolsets/evolution/evaluator_toolset.py
pantheon/toolsets/evolution/evolution_toolset.py
pantheon/toolsets/file/__init__.py
pantheon/toolsets/file/apply_patch.py
pantheon/toolsets/file/file_manager.py
pantheon/toolsets/file/grep_glob.py
pantheon/toolsets/file_transfer/__init__.py
pantheon/toolsets/file_transfer/client.py
pantheon/toolsets/file_transfer/worker.py
pantheon/toolsets/image/__init__.py
pantheon/toolsets/image/image_gen.py
pantheon/toolsets/julia/__init__.py
pantheon/toolsets/julia/_julia.py
pantheon/toolsets/julia/julia_interpreter.py
pantheon/toolsets/knowledge/__init__.py
pantheon/toolsets/knowledge/config.py
pantheon/toolsets/knowledge/knowledge_manager.py
pantheon/toolsets/knowledge/models.py
pantheon/toolsets/knowledge/vector_store.py
pantheon/toolsets/notebook/__init__.py
pantheon/toolsets/notebook/handlers.py
pantheon/toolsets/notebook/integrated_notebook.py
pantheon/toolsets/notebook/jedi_integration.py
pantheon/toolsets/notebook/jupyter_kernel.py
pantheon/toolsets/notebook/notebook_contents.py
pantheon/toolsets/python/__init__.py
pantheon/toolsets/python/python_interpreter.py
pantheon/toolsets/r/__init__.py
pantheon/toolsets/r/_rinter.py
pantheon/toolsets/r/r_interpreter.py
pantheon/toolsets/rag/__init__.py
pantheon/toolsets/rag/__main__.py
pantheon/toolsets/rag/build.py
pantheon/toolsets/rag/text.py
pantheon/toolsets/rag/toolset.py
pantheon/toolsets/rag/vectordb.py
pantheon/toolsets/rag/wrap.py
pantheon/toolsets/scfm/__init__.py
pantheon/toolsets/scfm/_conda_runner.py
pantheon/toolsets/scfm/registry.py
pantheon/toolsets/scfm/router.py
pantheon/toolsets/scfm/toolset.py
pantheon/toolsets/scfm/adapters/__init__.py
pantheon/toolsets/scfm/adapters/aidocell.py
pantheon/toolsets/scfm/adapters/atacformer.py
pantheon/toolsets/scfm/adapters/base.py
pantheon/toolsets/scfm/adapters/cell2sentence.py
pantheon/toolsets/scfm/adapters/cellfm.py
pantheon/toolsets/scfm/adapters/cellplm.py
pantheon/toolsets/scfm/adapters/chatcell.py
pantheon/toolsets/scfm/adapters/genecompass.py
pantheon/toolsets/scfm/adapters/geneformer.py
pantheon/toolsets/scfm/adapters/genept.py
pantheon/toolsets/scfm/adapters/langcell.py
pantheon/toolsets/scfm/adapters/nicheformer.py
pantheon/toolsets/scfm/adapters/pulsar.py
pantheon/toolsets/scfm/adapters/scbert.py
pantheon/toolsets/scfm/adapters/sccello.py
pantheon/toolsets/scfm/adapters/scfoundation.py
pantheon/toolsets/scfm/adapters/scgpt.py
pantheon/toolsets/scfm/adapters/scmulan.py
pantheon/toolsets/scfm/adapters/scplantllm.py
pantheon/toolsets/scfm/adapters/scprint.py
pantheon/toolsets/scfm/adapters/tabula.py
pantheon/toolsets/scfm/adapters/tgpt.py
pantheon/toolsets/scfm/adapters/uce.py
pantheon/toolsets/shell/__init__.py
pantheon/toolsets/shell/_shell.py
pantheon/toolsets/shell/shell.py
pantheon/toolsets/task/__init__.py
pantheon/toolsets/task/ephemeral.py
pantheon/toolsets/task/task_state.py
pantheon/toolsets/task/task_toolset.py
pantheon/utils/__init__.py
pantheon/utils/display.py
pantheon/utils/llm.py
pantheon/utils/llm_providers.py
pantheon/utils/log.py
pantheon/utils/memory_compress.py
pantheon/utils/message_formatter.py
pantheon/utils/misc.py
pantheon/utils/model_selector.py
pantheon/utils/process.py
pantheon/utils/template.py
pantheon/utils/truncate.py
pantheon/utils/vision.py