Helix CLI docs

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page_id: diagrams page_type: diagrams generation_mode: inferred freshness_status: updated updated_at: 2026-07-06T01:47:44.114Z

<details> <summary>Build metadata</summary>

{
  "freshnessKey": "033b54d5a973e7390ca5938a3c4f41892abacfc2",
  "plannerReason": "Generated to provide a compact architecture and dependency overview.",
  "changedPaths": [],
  "dependencyPaths": [],
  "dependencyEvidenceIds": [],
  "evidenceIds": [],
  "qualityWarnings": []
}

</details>

Diagrams

Generated 4 diagrams.

Component Overview (component-overview; 9 nodes; 8 edges; omitted 126 nodes / 126 edges)
Dependency Graph (dependency-graph; 19 nodes; 16 edges; omitted 0 nodes / 26534 edges)
Directory Map (directory-map; 11 nodes; 10 edges; omitted 34 nodes / 34 edges)
Subsystem Clusters (component-overview; 5 nodes; 6 edges; omitted 0 nodes / 26544 edges)

Component Overview

Shows the most prominent inferred components connected to the repository root.

Explained in:

Interpretation note:

Interpretation: use this view to see the main repository-owned components and their highest-level relationships before drilling into page-level details. Favor it when you need a fast inventory of the system surface.

Rendered surface:

rendered nodes: 9, rendered edges: 8

Node mix:

component: 8, repository: 1

Omitted surface:

omitted nodes: 126
omitted edges: 126

graph LR
  repository["Helix"] --> component_docs["Documentation"]
  repository["Helix"] --> component_engine_src["engine/src"]
  repository["Helix"] --> component_examples_offscreen_webrtc_demo_signaling_package_json["offscreen-webrtc-signaling"]
  repository["Helix"] --> component_external_node_express["express"]
  repository["Helix"] --> component_external_node_ws["ws"]
  repository["Helix"] --> component_external_python_annotated_types["annotated-types"]
  repository["Helix"] --> component_external_python_attrs["attrs"]
  repository["Helix"] --> component_external_python_backports_tarfile["backports-tarfile"]

digraph RepoIntel {
  label="Component Overview";
  labelloc=t;
  rankdir=LR;
  node [shape=box];
  "repository" [label="Helix", shape=box];
  "component:docs" [label="Documentation", shape=box];
  "component:engine/src" [label="engine/src", shape=box];
  "component:examples/offscreen_webrtc_demo/signaling/package.json" [label="offscreen-webrtc-signaling", shape=box];
  "component:external:node:express" [label="express", shape=box];
  "component:external:node:ws" [label="ws", shape=box];
  "component:external:python:annotated-types" [label="annotated-types", shape=box];
  "component:external:python:attrs" [label="attrs", shape=box];
  "component:external:python:backports-tarfile" [label="backports-tarfile", shape=box];
  "repository" -> "component:docs" [label="contains"];
  "repository" -> "component:engine/src" [label="contains"];
  "repository" -> "component:examples/offscreen_webrtc_demo/signaling/package.json" [label="contains"];
  "repository" -> "component:external:node:express" [label="contains"];
  "repository" -> "component:external:node:ws" [label="contains"];
  "repository" -> "component:external:python:annotated-types" [label="contains"];
  "repository" -> "component:external:python:attrs" [label="contains"];
  "repository" -> "component:external:python:backports-tarfile" [label="contains"];
}

Structured graph:

nodes: 9
edges: 8

Layout:

direction: LR
strategy: root-spoke

Simplification:

simplified: yes
rendered nodes: 9
rendered edges: 8
omitted nodes: 126
omitted edges: 126
Omitted 126 lower-priority components to keep the overview readable.
Switched to a left-to-right root-spoke layout to keep the largest components scannable.

Why these edges:

Repository contains Helix as a prominent component.
Repository contains Helix as a prominent component.
Repository contains Helix as a prominent component.
Repository contains Helix as a prominent component.
Repository contains Helix as a prominent component.
Repository contains Helix as a prominent component.

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

benchmarks/README.md
deliver_workbench/README.md
deploy/helm/helix-teams/README.md
deploy/k8s/README.md
deploy/README.md
deploy/vastai/README.md
design_partner/README.md
design_partner/sessions/README.md
docs/adr/0001-gui-monolith-refactor.md
docs/artifacts.md
docs/assets/viz/alignment-ribbon.json
docs/assets/viz/alignment-ribbon.viz.json

</details>

Dependency Graph

Shows a sampled set of dependency and call relationships across indexed entities.

Explained in:

Interpretation note:

Interpretation: use this graph to spot concentrated dependency hubs and outward package pressure across the repository. Favor it when you need to reason about coupling, likely blast radius, or external dependency concentration.

Rendered surface:

rendered nodes: 19, rendered edges: 16

Node mix:

symbol: 19

Omitted surface:

omitted nodes: 0
omitted edges: 26534

graph LR
  symbol_baselines_h0_baseline_py_baseline_h0_score_14 --> symbol_baselines_h0_baseline_py_BaselineH0Config_9
  symbol_benchmark_real_genome_py_benchmark_fm_index_88 --> symbol_src_helix_clock_py_perf_counter_72
  symbol_benchmark_real_genome_py_benchmark_fm_index_88 --> symbol_src_helix_genome_fm_index_py_build_genome_fm_index_116
  symbol_benchmark_real_genome_py_benchmark_fm_index_88 --> symbol_src_helix_genome_fm_index_py_search_exact_50
  symbol_benchmark_real_genome_py_benchmark_fm_index_88 --> symbol_src_helix_temp_py_TemporaryDirectory_117
  symbol_benchmark_real_genome_py_main_256 --> symbol_benchmark_real_genome_py_benchmark_cpu_baseline_220
  symbol_benchmark_real_genome_py_main_256 --> symbol_benchmark_real_genome_py_benchmark_fm_index_88
  symbol_benchmark_real_genome_py_main_256 --> symbol_benchmark_real_genome_py_benchmark_gpu_validation_131
  symbol_benchmark_real_genome_py_main_256 --> symbol_benchmark_real_genome_py_generate_realistic_guides_53
  symbol_benchmark_real_genome_py_main_256 --> symbol_benchmark_real_genome_py_load_fasta_30
  symbol_benchmark_real_genome_py_main_256 --> symbol_docs_playground_js_realtime_worker_js_bases_302
  symbol_benchmark_real_genome_py_main_256 --> symbol_src_helix_clinical_schema_py_Baseline_66
  symbol_benchmark_real_genome_py_main_256 --> symbol_src_helix_clock_py_perf_counter_72
  symbol_benchmarks_api_benchmarks_py__cmd_374 --> symbol_src_helix_studio_extension_host_jsonrpc_py_decode_31
  symbol_benchmarks_api_benchmarks_py__configure_datasets_228 --> symbol_benchmarks_api_benchmarks_py__prepare_protein_file_198
  symbol_benchmarks_api_benchmarks_py__configure_datasets_228 --> symbol_benchmarks_api_benchmarks_py__refresh_metadata_256

digraph RepoIntel {
  label="Dependency Graph";
  labelloc=t;
  rankdir=LR;
  node [shape=box];
  "symbol:baselines/h0/baseline.py:baseline_h0_score:14" [label="baseline_h0_score", shape=box];
  "symbol:baselines/h0/baseline.py:BaselineH0Config:9" [label="BaselineH0Config", shape=box];
  "symbol:benchmark_real_genome.py:benchmark_fm_index:88" [label="benchmark_fm_index", shape=box];
  "symbol:src/helix/clock.py:perf_counter:72" [label="perf_counter", shape=box];
  "symbol:src/helix/genome/fm_index.py:build_genome_fm_index:116" [label="build_genome_fm_index", shape=box];
  "symbol:src/helix/genome/fm_index.py:search_exact:50" [label="search_exact", shape=box];
  "symbol:src/helix/temp.py:TemporaryDirectory:117" [label="TemporaryDirectory", shape=box];
  "symbol:benchmark_real_genome.py:main:256" [label="main", shape=box];
  "symbol:benchmark_real_genome.py:benchmark_cpu_baseline:220" [label="benchmark_cpu_baseline", shape=box];
  "symbol:benchmark_real_genome.py:benchmark_gpu_validation:131" [label="benchmark_gpu_validation", shape=box];
  "symbol:benchmark_real_genome.py:generate_realistic_guides:53" [label="generate_realistic_guides", shape=box];
  "symbol:benchmark_real_genome.py:load_fasta:30" [label="load_fasta", shape=box];
  "symbol:docs/playground/js/realtime_worker.js:bases:302" [label="bases", shape=box];
  "symbol:src/helix/clinical/schema.py:Baseline:66" [label="Baseline", shape=box];
  "symbol:benchmarks/api_benchmarks.py:_cmd:374" [label="_cmd", shape=box];
  "symbol:src/helix/studio/extension_host/jsonrpc.py:decode:31" [label="decode", shape=box];
  "symbol:benchmarks/api_benchmarks.py:_configure_datasets:228" [label="_configure_datasets", shape=box];
  "symbol:benchmarks/api_benchmarks.py:_prepare_protein_file:198" [label="_prepare_protein_file", shape=box];
  "symbol:benchmarks/api_benchmarks.py:_refresh_metadata:256" [label="_refresh_metadata", shape=box];
  "symbol:baselines/h0/baseline.py:baseline_h0_score:14" -> "symbol:baselines/h0/baseline.py:BaselineH0Config:9" [label="calls"];
  "symbol:benchmark_real_genome.py:benchmark_fm_index:88" -> "symbol:src/helix/clock.py:perf_counter:72" [label="calls"];
  "symbol:benchmark_real_genome.py:benchmark_fm_index:88" -> "symbol:src/helix/genome/fm_index.py:build_genome_fm_index:116" [label="calls"];
  "symbol:benchmark_real_genome.py:benchmark_fm_index:88" -> "symbol:src/helix/genome/fm_index.py:search_exact:50" [label="calls"];
  "symbol:benchmark_real_genome.py:benchmark_fm_index:88" -> "symbol:src/helix/temp.py:TemporaryDirectory:117" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:benchmark_real_genome.py:benchmark_cpu_baseline:220" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:benchmark_real_genome.py:benchmark_fm_index:88" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:benchmark_real_genome.py:benchmark_gpu_validation:131" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:benchmark_real_genome.py:generate_realistic_guides:53" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:benchmark_real_genome.py:load_fasta:30" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:docs/playground/js/realtime_worker.js:bases:302" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:src/helix/clinical/schema.py:Baseline:66" [label="calls"];
  "symbol:benchmark_real_genome.py:main:256" -> "symbol:src/helix/clock.py:perf_counter:72" [label="calls"];
  "symbol:benchmarks/api_benchmarks.py:_cmd:374" -> "symbol:src/helix/studio/extension_host/jsonrpc.py:decode:31" [label="calls"];
  "symbol:benchmarks/api_benchmarks.py:_configure_datasets:228" -> "symbol:benchmarks/api_benchmarks.py:_prepare_protein_file:198" [label="calls"];
  "symbol:benchmarks/api_benchmarks.py:_configure_datasets:228" -> "symbol:benchmarks/api_benchmarks.py:_refresh_metadata:256" [label="calls"];
}

Structured graph:

nodes: 19
edges: 16

Layout:

direction: LR
strategy: edge-ranked

Simplification:

simplified: yes
rendered nodes: 19
rendered edges: 16
omitted nodes: 0
omitted edges: 26534
Omitted 26534 lower-priority dependency edges to avoid an unreadable graph.
Kept a rank-ordered sample of stronger edges and switched to a left-to-right layout for denser graphs.

Why these edges:

symbol:baselines/h0/baseline.py:baseline_h0_score:14 calls symbol:baselines/h0/baseline.py:BaselineH0Config:9 via baselines/h0/baseline.py.
symbol:benchmark_real_genome.py:benchmark_fm_index:88 calls symbol:src/helix/clock.py:perf_counter:72 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:benchmark_fm_index:88 calls symbol:src/helix/genome/fm_index.py:build_genome_fm_index:116 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:benchmark_fm_index:88 calls symbol:src/helix/genome/fm_index.py:search_exact:50 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:benchmark_fm_index:88 calls symbol:src/helix/temp.py:TemporaryDirectory:117 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:main:256 calls symbol:benchmark_real_genome.py:benchmark_cpu_baseline:220 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:main:256 calls symbol:benchmark_real_genome.py:benchmark_fm_index:88 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:main:256 calls symbol:benchmark_real_genome.py:benchmark_gpu_validation:131 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:main:256 calls symbol:benchmark_real_genome.py:generate_realistic_guides:53 via benchmark_real_genome.py.
symbol:benchmark_real_genome.py:main:256 calls symbol:benchmark_real_genome.py:load_fasta:30 via benchmark_real_genome.py.

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

benchmarks/README.md
deliver_workbench/README.md
deploy/helm/helix-teams/README.md
deploy/k8s/README.md
deploy/README.md
deploy/vastai/README.md
design_partner/README.md
design_partner/sessions/README.md
docs/adr/0001-gui-monolith-refactor.md
docs/artifacts.md
docs/assets/viz/alignment-ribbon.json
docs/assets/viz/alignment-ribbon.viz.json

</details>

Directory Map

Shows top-level directory layout to orient unfamiliar agents.

Interpretation note:

Interpretation: use this map to orient yourself in the repository layout before reading code. Favor it when you need to connect top-level paths to the graph surfaces shown elsewhere.

Rendered surface:

rendered nodes: 11, rendered edges: 10

Node mix:

directory: 10, repository: 1

Omitted surface:

omitted nodes: 34
omitted edges: 34

graph LR
  repository["Helix"] --> _bench[".bench/"]
  repository["Helix"] --> _githooks[".githooks/"]
  repository["Helix"] --> _github[".github/"]
  repository["Helix"] --> _helix[".helix/"]
  repository["Helix"] --> _playwright_mcp[".playwright-mcp/"]
  repository["Helix"] --> _repointel[".repointel/"]
  repository["Helix"] --> _smoke_systems[".smoke_systems/"]
  repository["Helix"] --> VeriBiota["VeriBiota/"]
  repository["Helix"] --> Visualization_Bench["Visualization_Bench/"]
  repository["Helix"] --> baselines["baselines/"]

digraph RepoIntel {
  label="Directory Map";
  labelloc=t;
  rankdir=LR;
  node [shape=box];
  "repository" [label="Helix", shape=box];
  ".bench" [label=".bench/", shape=box];
  ".githooks" [label=".githooks/", shape=box];
  ".github" [label=".github/", shape=box];
  ".helix" [label=".helix/", shape=box];
  ".playwright-mcp" [label=".playwright-mcp/", shape=box];
  ".repointel" [label=".repointel/", shape=box];
  ".smoke_systems" [label=".smoke_systems/", shape=box];
  "VeriBiota" [label="VeriBiota/", shape=box];
  "Visualization_Bench" [label="Visualization_Bench/", shape=box];
  "baselines" [label="baselines/", shape=box];
  "repository" -> ".bench" [label="contains"];
  "repository" -> ".githooks" [label="contains"];
  "repository" -> ".github" [label="contains"];
  "repository" -> ".helix" [label="contains"];
  "repository" -> ".playwright-mcp" [label="contains"];
  "repository" -> ".repointel" [label="contains"];
  "repository" -> ".smoke_systems" [label="contains"];
  "repository" -> "VeriBiota" [label="contains"];
  "repository" -> "Visualization_Bench" [label="contains"];
  "repository" -> "baselines" [label="contains"];
}

Structured graph:

nodes: 11
edges: 10

Layout:

direction: LR
strategy: linear-map

Simplification:

simplified: yes
rendered nodes: 11
rendered edges: 10
omitted nodes: 34
omitted edges: 34
Omitted 34 additional top-level directories from the diagram.
Switched to a left-to-right directory map to keep the remaining top-level layout readable.

Why these edges:

.bench/ is a top-level directory under the repository root.
.githooks/ is a top-level directory under the repository root.
.github/ is a top-level directory under the repository root.
.helix/ is a top-level directory under the repository root.
.playwright-mcp/ is a top-level directory under the repository root.
.repointel/ is a top-level directory under the repository root.
.smoke_systems/ is a top-level directory under the repository root.
VeriBiota/ is a top-level directory under the repository root.
Visualization_Bench/ is a top-level directory under the repository root.
baselines/ is a top-level directory under the repository root.

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

benchmarks/README.md
deliver_workbench/README.md
deploy/helm/helix-teams/README.md
deploy/k8s/README.md
deploy/README.md
deploy/vastai/README.md
design_partner/README.md
design_partner/sessions/README.md
docs/adr/0001-gui-monolith-refactor.md
docs/artifacts.md
docs/assets/viz/alignment-ribbon.json
docs/assets/viz/alignment-ribbon.viz.json

</details>

Subsystem Clusters

Shows a simplified subsystem graph grouped by dominant repository paths and graph-connected merges.

Explained in:

Interpretation note:

Interpretation: use this clustering view to understand which source areas act like larger architectural slices and how strongly they connect. Favor it when you need a quick map of architectural boundaries instead of individual files or packages.

Rendered surface:

rendered nodes: 5, rendered edges: 6

Node mix:

subsystem: 5

Omitted surface:

omitted nodes: 0
omitted edges: 26544

graph LR
  subgraph group_benchmarks["benchmarks/"]
    subsystem_root["root"]
  end
  subgraph group_engine["engine/"]
    subsystem_engine["engine"]
  end
  subgraph group_examples["examples/"]
    subsystem_external["external"]
    subsystem_src["src"]
  end
  subgraph group_tools["tools/"]
    subsystem_tools["tools"]
  end

  subsystem_root --> subsystem_src
  subsystem_root --> subsystem_tools
  subsystem_src --> subsystem_root
  subsystem_src --> subsystem_tools
  subsystem_tools --> subsystem_src
  subsystem_src --> subsystem_external

digraph RepoIntel {
  label="Subsystem Clusters";
  labelloc=t;
  rankdir=LR;
  node [shape=box];
  "subsystem:external" [label="external", shape=box];
  "subsystem:root" [label="root", shape=box];
  "subsystem:src" [label="src", shape=box];
  "subsystem:tools" [label="tools", shape=box];
  "subsystem:engine" [label="engine", shape=box];
  "subsystem:root" -> "subsystem:src" [label="depends_on", weight=8, penwidth=5];
  "subsystem:root" -> "subsystem:tools" [label="depends_on", weight=7, penwidth=4.5];
  "subsystem:src" -> "subsystem:root" [label="depends_on", weight=3571, penwidth=6];
  "subsystem:src" -> "subsystem:tools" [label="depends_on", weight=11, penwidth=6];
  "subsystem:tools" -> "subsystem:src" [label="depends_on"];
  "subsystem:src" -> "subsystem:external" [label="depends_on", weight=533, penwidth=6];
}

Structured graph:

nodes: 5
edges: 6

Layout:

direction: LR
strategy: hierarchy-ranked

Simplification:

simplified: yes
rendered nodes: 5
rendered edges: 6
omitted nodes: 0
omitted edges: 26544
Collapsed 26544 additional subsystem edges from the rendered view.
Grouped subsystem nodes by dominant path segment across 4 hierarchy buckets before rendering edges.
Used a left-to-right hierarchy-ranked layout so dominant path groups stay visually clustered.
Subsystem graph edges are condensed by repeated source/target pairs before sampling.

Why these edges:

root calls src via docs/playground/js/realtime_worker.js. 7 additional inferred edges reinforce this path. (8 inferred edges combined.)
root calls tools via docs/playground/js/realtime.js. 6 additional inferred edges reinforce this path. (7 inferred edges combined.)
src calls root via src/helix_engine/species_detect.py. 3570 additional inferred edges reinforce this path. (3571 inferred edges combined.)
src calls tools via src/helix/cli.py. 10 additional inferred edges reinforce this path. (11 inferred edges combined.)
tools calls src via tools/hubverifier-go/internal/hubverify/hubverify.go.
src depends_on external via deliver_workbench/tests/test_adapter_e2e.py. 532 additional inferred edges reinforce this path. (533 inferred edges combined.)

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

benchmarks/README.md
deliver_workbench/README.md
deploy/helm/helix-teams/README.md
deploy/k8s/README.md
deploy/README.md
deploy/vastai/README.md
design_partner/README.md
design_partner/sessions/README.md
docs/adr/0001-gui-monolith-refactor.md
docs/artifacts.md
docs/assets/viz/alignment-ribbon.json
docs/assets/viz/alignment-ribbon.viz.json

</details>

Citations

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

benchmarks/README.md
deliver_workbench/README.md
deploy/helm/helix-teams/README.md
deploy/k8s/README.md
deploy/README.md
deploy/vastai/README.md
design_partner/README.md
design_partner/sessions/README.md
docs/adr/0001-gui-monolith-refactor.md
docs/artifacts.md
docs/assets/viz/alignment-ribbon.json
docs/assets/viz/alignment-ribbon.viz.json

</details>

page_id: diagrams page_type: diagrams generation_mode: inferred freshness_status: updated updated_at: 2026-07-06T01:47:44.114Z

Diagrams

Diagram Navigation

Related Pages

Component Overview

Dependency Graph

Directory Map

Subsystem Clusters

Citations