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page_id: component-component:src page_type: component generation_mode: inferred freshness_status: reused updated_at: 2026-07-06T01:44:37.349Z

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    "ingest:file:src/helix/studio/offtargets/__init__.py",
    "ingest:file:src/helix/studio/offtargets/bulge_provider.py",
    "ingest:file:src/helix/studio/offtargets/mismatch_provider.py",
    "ingest:file:src/helix/studio/offtargets/noop.py",
    "ingest:file:src/helix/studio/offtargets/rloks_provider.py",
    "ingest:file:src/helix/studio/outcomes/base_edit_model.py",
    "ingest:file:src/helix/studio/outcomes/dynamic_cut_model.py",
    "ingest:file:src/helix/studio/outcomes/noop.py",
    "ingest:file:src/helix/studio/outcomes/prime_model.py",
    "ingest:file:src/helix/studio/plugins/__init__.py",
    "ingest:file:src/helix/studio/plugins/installer.py",
    "ingest:file:src/helix/studio/render/__init__.py",
    "ingest:file:src/helix/studio/reports/__init__.py",
    "ingest:file:src/helix/studio/results_adapters/__init__.py",
    "ingest:file:src/helix/studio/semantic_audit.py",
    "ingest:file:src/helix/studio/systems/__init__.py",
    "ingest:file:src/helix/studio/systems/loader.py",
    "ingest:file:src/helix/studio/systems/panels/__init__.py",
    "ingest:file:src/helix/studio/terminal/__init__.py",
    "ingest:file:src/helix/studio/terminal/dock.py",
    "ingest:file:src/helix/studio/web_panel_policy.py",
    "ingest:file:src/helix/support/doctor.py",
    "ingest:file:src/helix/systems/__init__.py",
    "ingest:file:src/helix/systems/bundle_loader.py",
    "ingest:file:src/helix/systems/cli.py",
    "ingest:file:src/helix/systems/drift.py",
    "ingest:file:src/helix/systems/observables.py",
    "ingest:file:src/helix/systems/propagation.py",
    "ingest:file:src/helix/systems/reviewer_summary.py",
    "ingest:file:src/helix/systems/scoring.py",
    "ingest:file:src/helix/teams/blob_store_s3.py",
    "ingest:file:src/helix/teams/blob_store.py",
    "ingest:file:src/helix/teams/systems_acceptance.py",
    "ingest:file:src/helix/teams/systems_cli.py",
    "ingest:file:src/helix/triage.py",
    "ingest:file:src/helix/validation/__init__.py",
    "ingest:file:src/helix/veribiota/__init__.py",
    "ingest:file:src/helix/visualization/__init__.py",
    "ingest:file:src/helix/visualization/_dag_utils.py",
    "ingest:file:src/helix/visualization/animate.py",
    "ingest:file:src/helix/visualization/diff_view.py",
    "ingest:file:src/helix/viz/__init__.py",
    "ingest:file:src/helix/viz/alignment.py",
    "ingest:file:src/helix/viz/crispr_track.py",
    "ingest:file:src/helix/viz/distance.py",
    "ingest:file:src/helix/viz/minimizers.py",
    "ingest:file:src/helix/viz/motif.py",
    "ingest:file:src/helix/viz/rna.py",
    "ingest:file:src/helix/viz/seed_chain.py",
    "ingest:file:src/helix/viz/seed.py",
    "ingest:file:src/helix/wetlab/__init__.py",
    "ingest:file:src/helix/wetlab/preflight_migration.py",
    "ingest:file:src/helix/workflows.py",
    "ingest:file:src/helixspec/__init__.py",
    "ingest:file:src/helixspec/compare.py",
    "ingest:file:src/helixspec/diff.py",
    "ingest:file:src/helixspec/ir_v1.py",
    "ingest:file:src/helixspec/typecheck.py",
    "ingest:file:src/helixspec/types.py",
    "workflow:Makefile",
    "workflow:pyproject.toml"
  ],
  "qualityWarnings": []
}

</details>

src

Source module rooted at src.

Related Pages

• components
• workflows
• interfaces
• dependencies

Implementation Roles

src/helix/cli.py

Role classification: inferred execution boundary. Proved signals:

• Defines execution-like symbols main, run_bench.
• Imports 88 repository-local paths.
• Participates in 723 connected call edges.
• Exports 25 symbols on the visible component surface. Why this role fits: These proved signals suggest this unit is a first-hop execution boundary that receives control and hands it into component logic. Supporting implementation citations:
• src/helix/cli.py:7761
• src/helix/cli.py:1301

src/helix/gui/simbuilder/app.py

Role classification: inferred execution boundary. Proved signals:

• Defines execution-like symbols main, run_active_tab.
• Defines state-change or persistence-like symbols save_state, save_state.
• Defines boundary-oriented symbols load_from_model, load_from_run_model.
• Imports 41 repository-local paths.
• Participates in 528 connected call edges.
• Exports 124 symbols on the visible component surface. Why this role fits: These proved signals suggest this unit is a first-hop execution boundary that receives control and hands it into component logic. Supporting implementation citations:
• src/helix/gui/simbuilder/app.py:6004
• src/helix/gui/simbuilder/app.py:5747

src/helix/studio/session.py

Role classification: inferred state owner. Proved signals:

• Defines execution-like symbols RunKind.
• Defines state-change or persistence-like symbols set_experiment_intent_spec, set_helixspec.
• Defines boundary-oriented symbols connect, load_payload.
• Imports 9 repository-local paths.
• Participates in 519 connected call edges.
• Exports 27 symbols on the visible component surface. Why this role fits: These proved signals suggest this unit owns durable, cached, or mutation-heavy state transitions inside the component. Supporting implementation citations:
• src/helix/studio/session.py:341
• src/helix/studio/session.py:331

src/helix/studio/extension_host/jsonrpc.py

Role classification: inferred state owner. Proved signals:

• Defines state-change or persistence-like symbols write_frame.
• Participates in 424 connected call edges.
• Exports 13 symbols on the visible component surface. Why this role fits: These proved signals suggest this unit owns durable, cached, or mutation-heavy state transitions inside the component. Supporting implementation citations:
• src/helix/studio/extension_host/jsonrpc.py:140

<details> <summary>Related files:</summary>

• src/helix/cli.py
• src/helix/gui/simbuilder/app.py
• src/helix/studio/session.py
• src/helix/studio/extension_host/jsonrpc.py

</details> <details> <summary>Citations:</summary>

• src/helix/cli.py:7761
• src/helix/cli.py:1301
• src/helix/gui/simbuilder/app.py:6004
• src/helix/gui/simbuilder/app.py:5747
• src/helix/studio/session.py:341
• src/helix/studio/session.py:331
• src/helix/studio/extension_host/jsonrpc.py:140

</details>

Module Responsibilities

src/helix/studio/outcome_explorer.py

Role: Core implementation module. Primary behavior: Exports intended_functional_auditability (function), ProbabilityMassMeter (class), set_values (function), which makes this one of the visible implementation surfaces for src. Why this module matters: 145 exported symbols make this file part of the component's public surface. 1084 connected call edges mark this file as implementation-active. Imports 31 distinct paths, which suggests orchestration or integration work. Supporting implementation citations:

• src/helix/studio/outcome_explorer.py:245
• src/helix/studio/outcome_explorer.py:594
• src/helix/studio/outcome_explorer.py:608

src/helix/studio/main_window.py

Role: Core implementation module. Primary behavior: Exports window (function), keyPressEvent (function), focusNextPrevChild (function), which makes this one of the visible implementation surfaces for src. Why this module matters: 36 exported symbols make this file part of the component's public surface. 1200 connected call edges mark this file as implementation-active. Imports 88 distinct paths, which suggests orchestration or integration work. Supporting implementation citations:

• src/helix/studio/main_window.py:349
• src/helix/studio/main_window.py:352
• src/helix/studio/main_window.py:369

src/helix/gui/simbuilder/app.py

Role: Public orchestration module. Primary behavior: Exports FlowLayout (class), addItem (function), addWidget (function), which makes this one of the visible implementation surfaces for src. Why this module matters: 124 exported symbols make this file part of the component's public surface. 528 connected call edges mark this file as implementation-active. Imports 41 distinct paths, which suggests orchestration or integration work. Supporting implementation citations:

• src/helix/gui/simbuilder/app.py:112
• src/helix/gui/simbuilder/app.py:122
• src/helix/gui/simbuilder/app.py:125

<details> <summary>Related files:</summary>

• src/helix/studio/outcome_explorer.py
• src/helix/studio/main_window.py
• src/helix/gui/simbuilder/app.py

</details> <details> <summary>Citations:</summary>

• src/helix/studio/outcome_explorer.py:245
• src/helix/studio/outcome_explorer.py:594
• src/helix/studio/outcome_explorer.py:608
• src/helix/studio/main_window.py:349
• src/helix/studio/main_window.py:352
• src/helix/studio/main_window.py:369
• src/helix/gui/simbuilder/app.py:112
• src/helix/gui/simbuilder/app.py:122
• src/helix/gui/simbuilder/app.py:125

</details>

Key Symbols

write_text (function)

Behavior: Persists or emits downstream effects from src/helix/studio/extension_host/remote_api.py. Receives: Called by _run_workflow, _write_limited_sequence, main. Produces or triggers: Exports write_text as part of the component's callable surface. Connected symbols:

• Callers: _run_workflow, _write_limited_sequence, main. Supporting implementation citations:
• src/helix/studio/extension_host/remote_api.py:223
• benchmarks/api_benchmarks.py:137

encode (function)

Behavior: Defines a visible implementation unit in src/helix/studio/extension_host/jsonrpc.py without strong downstream call evidence. Receives: Called by _canonical_json_bytes, _sha256_hex_text, compute_spec_hash. Produces or triggers: Exports encode as part of the component's callable surface. Connected symbols:

• Callers: _canonical_json_bytes, _sha256_hex_text, compute_spec_hash. Supporting implementation citations:
• src/helix/studio/extension_host/jsonrpc.py:27
• benchmarks/ctmc_tau_leap_perf.py:87

SessionModel (class)

Behavior: Defines a class boundary in src/helix/studio/session.py for component-owned behavior. Receives: Called by run_simulate, main, run_sim_builder. Produces or triggers: Exports SessionModel as part of the component's callable surface. Connected symbols:

• Callers: run_simulate, main, run_sim_builder. Supporting implementation citations:
• src/helix/studio/session.py:126
• src/helix/cli.py:946

<details> <summary>Related files:</summary>

• src/helix/studio/extension_host/remote_api.py
• src/helix/studio/extension_host/jsonrpc.py
• src/helix/studio/session.py

</details> <details> <summary>Citations:</summary>

• src/helix/studio/extension_host/remote_api.py:223
• benchmarks/api_benchmarks.py:137
• src/helix/studio/extension_host/jsonrpc.py:27
• benchmarks/ctmc_tau_leap_perf.py:87
• src/helix/studio/session.py:126
• src/helix/cli.py:946

</details>

State Boundaries

Validated at:

• Likely validated at normalize_sequence in src/helix/bioinformatics.py; this is inferred from validation-like naming rather than proved full program semantics. Validate with Run make (build) from .. Run helix-pilot-verify (run) from ..

Mutated in:

• Likely mutated in build_calibration_bundle in src/helix/calibration/bundle.py; this marks an inferred state-change boundary, not a formal dataflow proof. Nearby interface context: src/helix/contracts/crispr_decision_v1.schema.json (schema) via src/helix/contracts/crispr_decision_v1.schema.json; src/helix/contracts/crispr_decision_v2.schema.json (schema) via src/helix/contracts/crispr_decision_v2.schema.json.

Persisted or emitted through:

• Likely persisted or emitted through write_calibration_bundle in src/helix/calibration/bundle.py; this is inferred from persistence/emission naming and nearby implementation context. Recheck with Run make (build) from ..

<details> <summary>Supporting citations:</summary>

• src/helix/bioinformatics.py:38
• src/helix/calibration/bundle.py:238
• src/helix/calibration/bundle.py:326
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json

</details> <details> <summary>Related files:</summary>

• src/helix/bioinformatics.py
• src/helix/core/invariants.py
• src/helix/crispr/guide_objectives.py
• src/helix/crispr/guide_sweep.py
• src/helix/decision_support/check_registry.py
• src/helix/decision_support/offline_validate.py
• src/helix/decision_support/schema_validate.py
• src/helix/edge/run_descriptor.py
• src/helix/enzyme/schema.py
• src/helix/evidence_runtime.py
• src/helix/governance/gates.py
• src/helix/licensing/license.py
• src/helix/licensing/seats.py
• src/helix/lightcone/outcomes.py
• src/helix/live/cli_utils.py
• src/helix/live/realtime.py
• src/helix/metrics/roi.py
• src/helix/motif/core.py
• src/helix/schema/__init__.py
• src/helix/sim/evidence.py
• src/helix/sim/structural_risk.py
• src/helix/species/core.py
• src/helix/studio/base_position_calibration.py
• src/helix/studio/batch/model.py
• src/helix/studio/delivery/contract.py
• src/helix/studio/export_provenance.py
• src/helix/studio/governance_stamp.py
• src/helix/studio/iterated_dynamics.py
• src/helix/studio/lightcone_live.py
• src/helix/studio/offtargets/model.py
• src/helix/studio/outcomes/cell_context.py
• src/helix/studio/outcomes/intent_eval.py
• src/helix/studio/plugins/manifest.py
• src/helix/studio/plugins/registry.py
• src/helix/studio/png_provenance.py
• src/helix/studio/results_adapters/crispresso2.py
• src/helix/studio/results_io.py
• src/helix/studio/semantic_schema.py
• src/helix/studio/suggested_priors.py
• src/helix/studio/suggestions.py
• src/helix/studio/summary_contract_v2.py
• src/helix/studio/target_field.py
• src/helix/studio/target_resolution.py
• src/helix/studio/ui_dispatcher.py
• src/helix/systems/disease_models.py
• src/helix/teams/digest.py
• src/helix/teams/release_integrity.py
• src/helix/teams/systems_enforcement.py
• src/helix/veribiota/checks.py
• src/helixspec/ast.py
• src/helixspec/canon.py
• src/helixspec/verify_fs.py
• src/helix/calibration/bundle.py
• src/helix/clinical/mechanisms/registry.py
• src/helix/clock.py
• src/helix/compute/backends/registry.py
• src/helix/core/graph.py
• src/helix/core/scheduler.py
• src/helix/crispr/cut_spectrum.py
• src/helix/crispr/dag_api.py
• src/helix/crispr/dynamic/repair.py
• src/helix/crispr/interaction_proxy.py
• src/helix/crispr/offtarget_parity.py
• src/helix/crispr/pam.py
• src/helix/crispr/physics.py
• src/helix/decision_support/dataset_version.py
• src/helix/decision_support/run_manifest.py
• src/helix/determinism/guard.py
• src/helix/dsl/hgx.py
• src/helix/edge/bundle.py
• src/helix/edge/ion_receiver.py
• src/helix/edge/run_registry.py
• src/helix/edge/translators/basespace.py
• src/helix/edge/translators/thermo_connect.py
• src/helix/edit/simulate.py
• src/helix/entropy.py
• src/helix/enzyme/bundle.py
• src/helix/eval/azimuth_mlp_phase3.py
• src/helix/evaluation/auroc_metric.py
• src/helix/evaluation/offtarget_pack_builder.py
• src/helix/evaluation/pack_manifest.py
• src/helix/genome/diff.py
• src/helix/genome/digital.py
• src/helix/genome/fm_index.py
• src/helix/genome/fm_registry.py
• src/helix/governance/ledger.py
• src/helix/graphs/colored.py
• src/helix/graphs/dbg.py
• src/helix/gui/modern/builders_2p5d.py
• src/helix/gui/modern/builders.py
• src/helix/gui/modern/engine.py
• src/helix/gui/modern/export.py
• src/helix/gui/modern/qt.py
• src/helix/gui/modern/selection_utils.py
• src/helix/gui/railbands/widget.py
• src/helix/gui/simbuilder/app.py
• src/helix/gui/theme.py
• src/helix/hub/decision_export.py
• src/helix/hub/decision_store.py
• src/helix/lightcone/allele_ops.py
• src/helix/lightcone/branch_tree.py
• src/helix/lightcone/builders/base_v0.py
• src/helix/lightcone/builders/crispr_v0.py
• src/helix/lightcone/builders/prime_v0.py
• src/helix/lightcone/contract.py
• src/helix/lightcone/metadata.py
• src/helix/lightcone/picking.py
• src/helix/lightcone/render.py
• src/helix/lightcone/stress.py
• src/helix/live/hot_swap.py
• src/helix/live/livelab.py
• src/helix/live/viz/feed.py
• src/helix/live/viz/hud.py
• src/helix/live/viz/renderer.py
• src/helix/nodes/base.py
• src/helix/ogn/ingest_status_client.py
• src/helix/pilot_package_cli.py
• src/helix/predictors/receipt.py
• src/helix/prime/dag_api.py
• src/helix/prime/simulator.py
• src/helix/repro/bundle.py
• src/helix/scientific_contract.py
• src/helix/seed/syncmer.py
• src/helix/server/instrument_runs_api.py
• src/helix/sim/experiment_planner.py
• src/helix/sim/posterior.py
• src/helix/species/builder.py
• src/helix/species/bundle.py
• src/helix/string/fm.py
• src/helix/studio/assays/assay_chooser.py
• src/helix/studio/assays/primer_design.py
• src/helix/studio/batch/bundle.py
• src/helix/studio/calibration_coverage.py
• src/helix/studio/calibration.py
• src/helix/studio/center_panel.py
• src/helix/studio/demo_loader.py
• src/helix/studio/edit_dag_panel.py
• src/helix/studio/evaluation_access.py
• src/helix/studio/evidence_view_model.py
• src/helix/studio/evs_view_models.py
• src/helix/studio/experiment_intent_spec_panel.py
• src/helix/studio/experiment_setup_dialog.py
• src/helix/studio/experiment_setup_model.py
• src/helix/studio/experiment_spec_panel.py
• src/helix/studio/experimental/run_history_mv/run_history_model.py
• src/helix/studio/export_clip.py
• src/helix/studio/export_gate.py
• src/helix/studio/export_image_settings.py
• src/helix/studio/export_labels.py
• src/helix/studio/extension_host/remote_api.py
• src/helix/studio/gl_panel.py
• src/helix/studio/guide_compare.py
• src/helix/studio/guide_inspector.py
• src/helix/studio/helixspec_editor.py
• src/helix/studio/hint_banner.py
• src/helix/studio/instrument_runs_view.py
• src/helix/studio/lightcone_audit_pack.py
• src/helix/studio/lightcone_panel.py
• src/helix/studio/main_window.py
• src/helix/studio/offtarget_heat_widget.py
• src/helix/studio/offtargets/reference_accessor.py
• src/helix/studio/offtargets/rloks_ui_helpers.py
• src/helix/studio/offtargets/tail_risk_helpers.py
• src/helix/studio/offtargets/validation_plan.py
• src/helix/studio/outcome_explorer.py
• src/helix/studio/outcome_space_map.py
• src/helix/studio/outcomes/base_overlay.py
• src/helix/studio/outcomes/clone_yield.py
• src/helix/studio/outcomes/hotspots.py
• src/helix/studio/outcomes/model.py
• src/helix/studio/outcomes/outcome_spectrum_panel.py
• src/helix/studio/outcomes/prime_overlay.py
• src/helix/studio/pcr_workflow.py
• src/helix/studio/pilot_handoff.py
• src/helix/studio/plugins/manager.py
• src/helix/studio/plugins/plugin_package.py
• src/helix/studio/plugins/studio_host.py
• src/helix/studio/policy_patches.py
• src/helix/studio/prime_inspector.py
• src/helix/studio/prime_multiplex_calibration.py
• src/helix/studio/prime_multiplex_leaderboard.py
• src/helix/studio/provenance_header.py
• src/helix/studio/qtconcurrent_compat.py
• src/helix/studio/rail_model.py
• src/helix/studio/rail_state.py
• src/helix/studio/rail_widget.py
• src/helix/studio/render/scene.py
• src/helix/studio/repair_pathways.py
• src/helix/studio/reports/session_report.py
• src/helix/studio/results_adapters/csv_counts.py
• src/helix/studio/results_adapters/indel_profile.py
• src/helix/studio/results_adapters/pileup.py
• src/helix/studio/run_artifact.py
• src/helix/studio/run_compare.py
• src/helix/studio/run_metrics.py
• src/helix/studio/run_status_panel.py
• src/helix/studio/semantic_proof.py
• src/helix/studio/session_inspector.py
• src/helix/studio/session.py
• src/helix/studio/simulation_diagnostics_panel.py
• src/helix/studio/simulation_diagnostics.py
• src/helix/studio/spatial_review_panel.py
• src/helix/studio/systems/acceptance_detail_panel.py
• src/helix/studio/systems/acceptance_status_widget.py
• src/helix/studio/systems/acceptance_viewer.py
• src/helix/studio/systems/panels/cascade_panel.py
• src/helix/studio/systems/panels/compare_panel.py
• src/helix/studio/systems/panels/feasibility_panel.py
• src/helix/studio/systems/panels/summary_panel.py
• src/helix/studio/systems/panels/uncertainty_panel.py
• src/helix/studio/systems/systems_viewer.py
• src/helix/studio/target_refine_drawer.py
• src/helix/studio/terminal/ansi_parser.py
• src/helix/studio/terminal/process_backend.py
• src/helix/studio/terminal/session_widget.py
• src/helix/studio/ui/evidence_dialog.py
• src/helix/studio/ui/text_preview_dialog.py
• src/helix/studio/visualization_review_panel.py
• src/helix/studio/web_panel_csp.py
• src/helix/studio/web_panels.py
• src/helix/studio/welcome.py
• src/helix/studio/workflow_panel.py
• src/helix/support/build_meta.py
• src/helix/systems/bundle.py
• src/helix/systems/perturbation_program.py
• src/helix/systems/reviewer_summary_qualified.py
• src/helix/teams/backup.py
• src/helix/teams/client.py
• src/helix/teams/db.py
• src/helix/teams/server.py
• src/helix/teams/systems_db.py
• src/helix/teams/systems_policy.py
• src/helix/temp.py
• src/helix/viz/_utils.py
• src/helix/wetlab/lint_badge.py
• src/helixspec/manifest.py
• src/helixspec/run_graph.py
• src/helix/campaigns/bundle.py
• src/helix/campaigns/corpus.py
• src/helix/campaigns/receipt.py
• src/helix/campaigns/streaming.py
• src/helix/campaigns/topology.py
• src/helix/campaigns/verify.py
• src/helix/compute/batch.py
• src/helix/compute/binary_results.py
• src/helix/compute/harness.py
• src/helix/crispr/guide_export.py
• src/helix/crispr/ontargetx/bundle_io.py
• src/helix/enzyme/report.py
• src/helix/enzyme/schema_pack.py
• src/helix/experiments/campaign.py
• src/helix/experiments/corpus.py
• src/helix/experiments/verify.py
• src/helix/gui/bridge.py
• src/helix/lightcone/png.py
• src/helix/live/event_bus.py
• src/helix/live/state_reducer.py
• src/helix/live/viz/channel.py
• src/helix/ogn/analysis_store.py
• src/helix/studio/backend_commit.py
• src/helix/studio/experiment_presets.py
• src/helix/studio/export_evidence.py
• src/helix/studio/extension_host/host_process.py
• src/helix/studio/extension_host/jsonrpc.py
• src/helix/studio/layout_presets.py
• src/helix/studio/plugins/install_txn.py
• src/helix/studio/plugins/trust_store.py
• src/helix/studio/predictor_evidence_panel.py
• src/helix/studio/project.py
• src/helix/studio/reports/run_report.py
• src/helix/studio/results_adapters/batch_ingest.py
• src/helix/studio/session_io.py
• src/helix/studio/systems/publish_blocked_banner.py
• src/helix/studio/terminal/manager.py
• src/helix/support/bundle.py
• src/helix/support/crash.py
• src/helix/user_config.py
• src/helix/visualization/dag_viz.py
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json

</details> <details> <summary>Citations:</summary>

• src/helix/bioinformatics.py:38
• src/helix/calibration/bundle.py:238
• src/helix/calibration/bundle.py:326
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json

</details>

State Ownership and Handoffs

Insufficient evidence to infer state ownership and handoffs confidently.

<details> <summary>Supporting citations:</summary>

• none

</details>

Request Lifecycle

Insufficient evidence to infer a bounded request lifecycle confidently.

<details> <summary>Supporting citations:</summary>

• none

</details>

Responsibilities

Source module rooted at src.

Type: module Root path: src Ecosystem: unknown

<details> <summary>Related files:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• src/helix_engine/include/helix/ctmc_tau_leap_cuda.hpp
• src/helix_engine/include/helix/l0_thermo_cuda.hpp
• src/helix_engine/include/helix/physics_cuda.hpp
• src/helix_engine/include/helix/physics.hpp

</details> <details> <summary>Citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt

</details>

Entrypoints and Runtime Surface

• none

Interfaces and Config

• src/helix/contracts/crispr_decision_v1.schema.json (schema) from src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json (schema) from src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json (schema) from src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json (schema) from src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json (schema) from src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json (schema) from src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json (schema) from src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json (schema) from src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json (schema) from src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json (schema) from src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json (schema) from src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json (schema) from src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json (schema) from src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json (schema) from src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json (schema) from src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json (schema) from src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json (schema) from src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json (schema) from src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json (schema) from src/helix/schema/run_descriptor.schema.json

<details> <summary>Related files:</summary>

• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json

</details> <details> <summary>Citations:</summary>

• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json

</details>

Dependencies and Relationships

Repository-owned edges:

• component:src depends_on src/helix/api.py (medium)
• component:src depends_on src/helix/helix_cuda_fields.py (medium)
• component:src depends_on src/helix_engine/__init__.py (medium)
• component:src depends_on src/helix_engine/species_detect.py (medium)
• component:src depends_on src/helix_engine/__init__.py (medium)
• component:src depends_on src/helix/crispr/kmm.py (medium)
• component:src depends_on src/helix/crispr/physics.py (medium)
• component:src depends_on src/helix_engine/__init__.py (medium)
• component:src depends_on src/helix/species/detect.py (medium)
• component:src depends_on src/helix_workflows.py (medium)
• component:src depends_on src/helix/__init__.py (medium)
• component:src depends_on src/helix/crispr/simulate.py (medium)
• 2015 more repository-owned dependency edges omitted from this page. External dependency edges (bounded):
• component:src depends_on component:external:python:numpy (medium)
• component:src depends_on component:external:python:matplotlib (medium)
• component:src depends_on component:external:python:numpy (medium)
• component:src depends_on component:external:python:cryptography (medium)
• component:src depends_on component:external:python:jsonschema (medium)
• component:src depends_on component:external:python:matplotlib (medium)
• component:src depends_on component:external:python:requests (medium)
• component:src depends_on component:external:python:numpy (medium)
• component:src depends_on component:external:python:numpy (medium)
• component:src depends_on component:external:python:numpy (medium)
• component:src depends_on component:external:python:numpy (medium)
• component:src depends_on component:external:python:numpy (medium)
• 138 more external dependency edges omitted from this page.

<details> <summary>Related files:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• src/helix_engine/include/helix/ctmc_tau_leap_cuda.hpp
• src/helix_engine/include/helix/l0_thermo_cuda.hpp
• src/helix_engine/include/helix/physics_cuda.hpp
• src/helix_engine/include/helix/physics.hpp
• src/helix_engine/native.py
• src/helix_engine/species_detect.py
• src/helix/api.py
• src/helix/bioinformatics.py
• src/helix/campaigns/receipt.py
• src/helix/cli.py
• src/helix/compute/backends/cpu_backend.py
• src/helix/compute/backends/cuda_backend.py
• src/helix/compute/cuda_physics.py

</details> <details> <summary>Citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt

</details>

Why This Hotspot Matters

Architectural role: Hotspot score 93609 with 16933 inbound and 14267 outbound inferred edges marks src as a coordination-heavy component. It bridges external, root, tools.

Main coupling surfaces:

• Coupled components: helix-governance, numpy, matplotlib, cryptography.
• Owned interfaces: src/helix/contracts/crispr_decision_v1.schema.json, src/helix/contracts/crispr_decision_v2.schema.json, src/helix/contracts/design_verdict_v1.schema.json.
• Call-heavy surface with 29026 inferred call edges.
• Dependency-heavy surface with 2174 inferred dependency edges.

Likely failure modes:

• Upstream breakage risk: 16933 inbound edges suggest downstream callers depend on this boundary staying stable.
• Coordination risk: 14267 outbound edges mean changes can ripple into neighboring components.
• Cross-subsystem regression risk: changes can disrupt handoffs across external, root, tools.

<details> <summary>Supporting citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json

</details> <details> <summary>Related files:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json

</details> <details> <summary>Citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json

</details>

Operational Risk Surface

Likely fault domains:

• External dependency boundaries: numpy, matplotlib, cryptography, jsonschema.
• Cross-subsystem handoffs: external, root, tools.

High-cost dependencies:

• numpy acts as a external dependency boundary.
• matplotlib acts as a external dependency boundary.
• cryptography acts as a external dependency boundary.
• jsonschema acts as a external dependency boundary.

First validation checks:

• Run make (build) from ..
• Run helix-pilot-verify (run) from ..

<details> <summary>Supporting citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• Makefile
• pyproject.toml

</details> <details> <summary>Related files:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• Makefile
• pyproject.toml

</details> <details> <summary>Citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• Makefile
• pyproject.toml

</details>

Invariants and Failure Handling

require

Guard condition: require in src/helix/cli.py is an explicit validation or guard-like symbol that likely enforces a precondition before downstream work proceeds. Failure trigger: if the condition enforced by require is not met, downstream callers are likely blocked or forced onto an error path; this is inferred from the guard-like symbol name rather than proved full-program control flow.

<details> <summary>Supporting citations:</summary>

• src/helix/cli.py:1037

</details>

validate_edge_units

Guard condition: validate_edge_units in src/helix/core/invariants.py is an explicit validation or guard-like symbol that likely enforces a precondition before downstream work proceeds. Failure trigger: if the condition enforced by validate_edge_units is not met, downstream callers are likely blocked or forced onto an error path; this is inferred from the guard-like symbol name rather than proved full-program control flow.

<details> <summary>Supporting citations:</summary>

• src/helix/core/invariants.py:22

</details>

validate_snapshot

Guard condition: validate_snapshot in src/helix/core/invariants.py is an explicit validation or guard-like symbol that likely enforces a precondition before downstream work proceeds. Failure trigger: if the condition enforced by validate_snapshot is not met, downstream callers are likely blocked or forced onto an error path; this is inferred from the guard-like symbol name rather than proved full-program control flow.

<details> <summary>Supporting citations:</summary>

• src/helix/core/invariants.py:36

</details>

assert_invariants

Guard condition: assert_invariants in src/helix/core/invariants.py is an explicit validation or guard-like symbol that likely enforces a precondition before downstream work proceeds. Failure trigger: if the condition enforced by assert_invariants is not met, downstream callers are likely blocked or forced onto an error path; this is inferred from the guard-like symbol name rather than proved full-program control flow.

<details> <summary>Supporting citations:</summary>

• src/helix/core/invariants.py:53

</details> <details> <summary>Related files:</summary>

• src/helix/cli.py
• src/helix/core/invariants.py

</details> <details> <summary>Citations:</summary>

• src/helix/cli.py:1037
• src/helix/core/invariants.py:22
• src/helix/core/invariants.py:36
• src/helix/core/invariants.py:53

</details>

Where to Edit

Likely change entry files:

• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json

Owned interfaces:

• src/helix/contracts/crispr_decision_v1.schema.json (schema) from src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json (schema) from src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json (schema) from src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json (schema) from src/helix/schema/governance/ledger/signoff_v1.schema.json

Nearby verification surfaces:

• Validate with python -m pytest (test) from ..

<details> <summary>Supporting citations:</summary>

• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json
• pyproject.toml

</details> <details> <summary>Related files:</summary>

• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json
• pyproject.toml

</details> <details> <summary>Citations:</summary>

• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json
• pyproject.toml

</details>

Change Planning

Impacted areas:

• Downstream components likely affected: helix-governance, numpy, matplotlib, cryptography.
• Cross-subsystem risk touches external, root, tools.
• Hotspot score 93609 with 16933 inbound and 14267 outbound edges suggests higher coordination risk.

Suggested verification steps:

• Validate with python -m pytest (test) from ..

<details> <summary>Supporting citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• pyproject.toml

</details> <details> <summary>Related files:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• pyproject.toml

</details> <details> <summary>Citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• pyproject.toml

</details>

Nearby Workflows

• none

Citations

<details> <summary>Citations:</summary>

• src/helix/cli.py:7761
• src/helix/cli.py:1301
• src/helix/gui/simbuilder/app.py:6004
• src/helix/gui/simbuilder/app.py:5747
• src/helix/studio/session.py:341
• src/helix/studio/session.py:331
• src/helix/studio/extension_host/jsonrpc.py:140
• src/helix/studio/outcome_explorer.py:245
• src/helix/studio/outcome_explorer.py:594
• src/helix/studio/outcome_explorer.py:608
• src/helix/studio/main_window.py:349
• src/helix/studio/main_window.py:352
• src/helix/studio/main_window.py:369
• src/helix/gui/simbuilder/app.py:112
• src/helix/gui/simbuilder/app.py:122
• src/helix/gui/simbuilder/app.py:125
• src/helix/studio/extension_host/remote_api.py:223
• benchmarks/api_benchmarks.py:137
• src/helix/studio/extension_host/jsonrpc.py:27
• benchmarks/ctmc_tau_leap_perf.py:87
• src/helix/studio/session.py:126
• src/helix/cli.py:946
• src/helix/bioinformatics.py:38
• src/helix/calibration/bundle.py:238
• src/helix/calibration/bundle.py:326
• src/helix/contracts/crispr_decision_v1.schema.json
• src/helix/contracts/crispr_decision_v2.schema.json
• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• src/helix/contracts/design_verdict_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v1.schema.json
• src/helix/schema/governance/ledger/signoff_v2.schema.json
• src/helix/schema/governance/ledger/transition_request_v1.schema.json
• src/helix/schema/governance/ledger/transition_request_v2.schema.json
• src/helix/schema/governance/ledger/waiver_v1.schema.json
• src/helix/schema/helix_verify_result_v1.schema.json
• src/helix/schema/hub/approval_receipt_v1.schema.json
• src/helix/schema/hub/approval_surface_v1.schema.json
• src/helix/schema/hub/audit_export_v1.schema.json
• src/helix/schema/hub/backend_fingerprint_v1.schema.json
• src/helix/schema/hub/bundle_manifest_v1.schema.json
• src/helix/schema/hub/decision_v1.schema.json
• src/helix/schema/hub/job_v1.schema.json
• src/helix/schema/hub/run_receipt_v1.schema.json
• src/helix/schema/proof_kit/replay_receipt_v1.schema.json
• src/helix/schema/run_descriptor.schema.json
• Makefile
• pyproject.toml
• src/helix/cli.py:1037
• src/helix/core/invariants.py:22
• src/helix/core/invariants.py:36
• src/helix/core/invariants.py:53

</details>