gnosis-morph-bench 0.1.0

Benchmark-first starter package for neutral route scoring, replay, and stability checks.

Gnosis Morph Bench

Live window into the Zer0pa lab. Benchmark methods are useful now, with live Indus replay blockers kept visible.

What This Is

Morph-Bench is a Gnosis benchmark-method lane: neutral route scoring, null metrics, stability battery, deterministic replay, and explicit Indus replay blockers.

gnosis-morph-bench is the benchmark-first methods lane of the Gnosis extraction program. It owns neutral route scoring, permutation-null metrics, a five-mode stability battery, deterministic replay, and SHA-256 reference-freeze helpers — without owning Indus or cuneiform scientific verdicts. Domain corpora connect through admitted adapters; the Indus Phase 4 v1 adapter is the first in-scope family.

Headline metric (repo-custody, clone-reproducible): 37 passed pytest in a clean Python 3.11 venv + byte-equality cross-environment smoke (macOS 3.11.15 ↔ Linux/RunPod 3.11.13) + 0/6 forbidden-monorepo-pattern lint hits + 9/9 ADAPTER_CONTRACT_v1 MUST-clause coverage. Evidence path: artifacts/blind_clone/ and tests/. Live Indus Phase 4 measured values (NMI 0.5793, Sigma 5.65, Jaccard 0.4351, Replay 3/3) are source-authority citations only — see docs/PROMOTION_READINESS.md trust boundary.

Honest blocker: Live Indus Phase 4 reproduction is blocked on admitted Phase 3c manifest access (Blocked-1); heavy-data release policy for image-bearing assets is open (Blocked-3). The synthetic smoke is what runs end-to-end today. See ## Readiness below and docs/PROMOTION_READINESS.md.

Method Mechanics

Field	Value
Architecture	GNOSIS_BENCHMARK_METHOD
Method	BenchmarkManifest route scoring, permutation nulls, stability battery, deterministic replay
Adapter	Indus Phase 4 v1 adapter
Runtime Surface	src/gnosis_morph_bench/ + CLI smoke/replay commands
Trust Boundary	synthetic smoke runs end-to-end; live Indus Phase 4 rerun remains blocked

Key Metrics

Metric	Value	Baseline
Pytest surface	37 passed	clean Python 3.11 venv
Forbidden-monorepo-pattern lint	0 / 6 hits	adapter-contract lint
Adapter contract coverage	9 / 9 MUST clauses	ADAPTER_CONTRACT_v1.md
Cross-environment smoke byte-equality	PASS	macOS 3.11.15 vs Linux/RunPod 3.11.13

Source: artifacts/blind_clone/, tests/, docs/family/ADAPTER_CONTRACT_v1.md, and docs/PROMOTION_READINESS.md.

Repo Identity

Field	Value
Identifier	Morph-Bench
Repository	https://github.com/Zer0pa/Morph-Bench
Portfolio	Gnosis
Visibility	PUBLIC
Default Branch	main
Authority Source	docs/PROMOTION_READINESS.md; artifacts/blind_clone/
License	Apache-2.0 code; CC-BY-4.0 docs

Readiness

Field	Value
Verdict	STAGED
Posture	benchmark_methods_active_with_named_blockers
Checks	37 pytest checks; lint-clean adapter contract
Authority	docs/PROMOTION_READINESS.md

Honest Blocker

Live Indus Phase 4 reproduction is blocked on admitted Phase 3c manifest access, and heavy-data image-bearing release policy remains open.

What We Prove

• The neutral benchmark contract (BenchmarkManifest) round-trips cleanly through load_manifest / evaluate_route / freeze_reference / deterministic_replay / leave_fraction_out / the four added stability modes.
• The Indus Phase 4 v1 adapter satisfies every MUST clause of docs/family/ADAPTER_CONTRACT_v1.md, enforced by tests/test_adapter_contract_coverage.py.
• The forbidden-pattern lint catches the hidden-import / path-coupling patterns named by the adapter contract, self-tested via a positive control in tests/test_forbidden_patterns.py.
• The smoke and replay outputs are byte-identical across macOS and Linux at the documented Python 3.11 floor — verified end-to-end through fresh-clone install, see artifacts/blind_clone/.

What We Don't Claim

• That the live Indus Phase 4 measured values have been reproduced from repo custody. They have not. Live rerun is blocked on admitted Phase 3c manifest access (Blocked-1). Those values are source-authority citations, not Morph-Bench-proven values.
• That the synthetic smoke path constitutes proof of any live finding.
• That the heavy-data image-bearing asset release is unblocked. It is not; Blocked-3 (heavy-data release policy) remains open. See ## Readiness and docs/PROMOTION_READINESS.md.
• That the cuneiform benchmark family is in scope for the v1 adapter contract. It is explicitly deferred to a separate future contract once the first real Indus replay lands.
• That this repo carries any descriptor, kernel, image-preprocessing, or domain-verdict ownership. Those belong to other Gnosis lanes.

Verification Status

Code	Check	Verdict
V_01	Clean Python 3.11 pytest: 37 passed	PASS
V_02	Adapter contract coverage: 9/9 MUST clauses	PASS
V_03	Forbidden-pattern lint with positive control	PASS
V_04	Cross-environment blind-clone byte equality	PASS
V_05	Live Indus Phase 4 rerun from repo custody	BLOCKED

Proof Anchors

Path	State
PRD_GNOSIS_MORPH_BENCH_2026-04-23.md	VERIFIED
docs/family/ADAPTER_CONTRACT_v1.md	VERIFIED
docs/family/STABILITY_BATTERY_v1.md	VERIFIED
docs/PROMOTION_READINESS.md	VERIFIED
artifacts/blind_clone/03-01_transcript.md	VERIFIED
tests/test_adapter_contract_coverage.py	VERIFIED

Repo Shape

Field	Value
Proof Anchors	6 display anchors
Portfolio	Gnosis
Package	gnosis-morph-bench
Primary Source	src/gnosis_morph_bench/
Tests	tests/
Artifacts	artifacts/blind_clone/; artifacts/smoke/
Support Sections	Licensing; Quick Start; Upcoming Workstreams

Field	Value
Proof Anchors	6 display anchors
Portfolio	Gnosis
Package	gnosis-morph-bench
Primary Source	src/gnosis_morph_bench/
Tests	tests/
Artifacts	artifacts/blind_clone/; artifacts/smoke/
Support Sections	Licensing; Quick Start; Upcoming Workstreams

.
├── NOTICE                          # Apache-2.0 code and CC-BY-4.0 docs posture
├── PRD_GNOSIS_MORPH_BENCH_2026-04-23.md
├── README.md
├── pyproject.toml                     # Python ≥ 3.10, deps: numpy, scikit-learn
├── .github/workflows/ci.yml           # pytest on Ubuntu / Python 3.11
├── .gpd/                              # GPD orchestration state, plans, summaries
├── src/gnosis_morph_bench/
│   ├── adapters/indus_phase4.py       # v1 adapter (CLI: gnosis-morph-bench-adapter-indus-phase4)
│   ├── benchmark.py                   # route scoring, NMI + null + sigma + silhouette
│   ├── stability.py                   # 5-mode stability battery
│   ├── replay.py                      # ReplayRecord emission
│   ├── schema.py                      # BenchmarkManifest, freeze_reference
│   ├── cli.py / __main__.py           # smoke + replay subcommands
│   ├── hf_cache.py                    # SHA-pinned HF dataset fetch
│   └── _utils.py                      # repo-local JSON / hash helpers
├── tests/                             # 37 tests across 9 files
├── fixtures/tiny_benchmark_manifest.json
├── artifacts/
│   ├── smoke/smoke_report.json        # committed byte-reference (SHA-pinned)
│   ├── replay/                        # default replay output dir (gitignored content)
│   └── blind_clone/                   # cross-env blind-clone transcripts
├── docs/                              # promotion readiness, HF custody, legal prep, family contracts
└── code/                              # code-facing surface notes and current limits

Licensing

This repository is part of the Zer0pa Gnosis Portfolio.

Code in this repository is licensed under the Apache License 2.0. See LICENSE for the full text. SPDX identifier: Apache-2.0.

Documentation, reports, and written materials are licensed under Creative Commons Attribution 4.0 International. SPDX identifier: CC-BY-4.0. Canonical terms: https://creativecommons.org/licenses/by/4.0/.

Data and fixtures are handled per dataset and artifact family. See DATA_POLICY.md for this repository's data boundary. The code license does not license raw corpora, image-bearing cultural-heritage assets, private HF artifacts, model weights, endpoint logs, or operational transcripts.

Trademarks - "Gnosis", "Zer0pa Gnosis", and distinctive sub-marks are trademarks of Zer0pa. Apache-2.0 and CC-BY-4.0 do not grant trademark rights. See TRADEMARKS.md.

Public visibility is a separate repository-setting action. The license files in this repo define the intended open-source/open-documentation terms for released Gnosis code and written materials; they do not publish rights-gated data.

Quick Start

git clone https://github.com/Zer0pa/Morph-Bench.git
cd Morph-Bench
python3.11 -m venv .venv
source .venv/bin/activate
pip install -e '.[dev]'

# repo-local pytest suite
pytest -q

# synthetic smoke (deterministic, byte-stable)
python -m gnosis_morph_bench smoke fixtures/tiny_benchmark_manifest.json \
    --output artifacts/smoke/smoke_report.json

# full 5-mode stability + replay
python -m gnosis_morph_bench replay fixtures/tiny_benchmark_manifest.json \
    --output artifacts/replay/replay_record.json

# Indus Phase 4 v1 adapter (against fixture inputs only until Blocked-1 clears)
gnosis-morph-bench-adapter-indus-phase4 --help

For the full audit walkthrough: AUDITOR_PLAYBOOK.md.

For what is and is not promotable today: docs/PROMOTION_READINESS.md.

For governance and status semantics: GOVERNANCE.md.

For release protocol and owner inputs: RELEASING.md.

Upcoming Workstreams

Open work across four categories. "Useful now, improving continuously" — every item here is surfaced honestly, not an apology.

Operations / External Dependency

• Blocked-1 — Phase 3c manifest admission: live Indus Phase 4 rerun from repo custody cannot proceed without an admitted Phase 3c feature manifest JSON with SHA-256. Owner-gated. When clear: produces artifacts/replay/indus_phase4_live_<date>.json.
• Blocked-3 — Heavy-data release policy: image-bearing benchmark payloads cannot enter the repo until the release boundary is written (which asset classes, under what terms, storage location and size bound). Owner-gated. When clear: produces DATA_POLICY.md §Image-Bearing Release appendix.

Active Engineering

• Cuneiform benchmark family adapter: deferred to a separate future contract per current scope decision; no active engineering until Blocked-1 live rerun lands and the v1 adapter is validated against a second source family.
• Smoke byte-reference re-freeze: local housekeeping only; re-run smoke and commit the new byte-reference when convenient. Not a promotion gate.

Research-Deferred — Investigation Underway

(none currently — all research surface is defined by the v1 adapter contract and the 5-mode stability battery)

Zero-Base Scientific Thinking — GPD Research and Planning Pending

(none currently — the Phase 04 cuneiform contract is the next planned GPD unit; not yet initiated)