Genotype-Phenotype Covariance

# Blind Machine curated protocol bundle — genotype_phenotype_covariance.## The v1 encrypted×encrypted anchor: a genuine ciphertext×ciphertext product# (depth 1) under multiplication-supporting BFV params. This manifest is the ONLY# file the Rails platform parses. The author's pure functions in server.py /# local_project_owner.py / local_data_owner.py own the computation; the numbered# stage files are kit-owned shims that call them (see docs/rfcs/0002). This file# owns the governance + review surface (display metadata + the gate values that# let compute be authorized without unpacking the tarball). See# docs/protocol_structure.md for the schema and docs/protocol_catalog.md §6.name: genotype_phenotype_covarianceversion: 1.0.0builder:  type: uv  project: envcrypto: tenseal-bfv              # display hint; real deps live in env/uv.lockcomputation: multiplicative_bfv  # depth-1 ciphertext×ciphertext product (relin)min_contributors: 30# The published definition: the variant coordinate list PLUS the phenotype coding# scheme, both folded into the bundle SHA-256. Every contributor MUST encode# against the identical definition or the blind moments are meaningless — that# invariant is what folding this manifest into the digest enforces. For the# synthetic v1 demo the coordinate list is generated deterministically from `seed`# rather than enumerated inline (see docs/protocol_structure.md).input:  genotype:    type: integer_vector    length: 1000    value_domain: [0, 1, 2]      # alt-allele dosage per coordinate; missing -> 0    coordinates:      kind: synthetic_variants      seed: blind-v1-demo-coordinates      fields: [chrom, pos, ref, alt]  phenotype:    type: integer_scalar    coding: case_control         # binary; broadcast to all L slots at encode time    value_domain: [0, 1]         # a quantized trait uses [0, Q] + a larger t  # Each contributor uploads ONE packed blob co-packing that owner's (cipher_g,  # cipher_y) pair into a single deterministic BMCT1 container (magic b"BMCT1\n",  # names {g, y}); stage 30 unpacks it and forms enc(g) * enc(y) itself (catalog  # §6). One blob per contributor is the platform's canonical contribution shape:  # it keeps the (g, y) pair inseparable through the hosted worker's digest-sorting  # Stager, which would otherwise reorder two separate ciphertexts and silently  # mis-pair them. See SECURITY.md § "Pairing integrity".  submitted_as: one_packed_pair_ciphertextoutput:  shape: covariance_moment_vectors  # sum_g, sum_gy, sum_y, sum_y2 (+ N sentinel)  exactness: exact                  # BFV is exact in Z_t; moment sums never overflow t  tolerance: 0  # Stage 30 writes ONE opaque result.bin FILE (the worker content-addresses a  # single artifact). All four moment ciphertexts are packed into a deterministic  # BMCT1 container (magic b"BMCT1\n"; shared verbatim with  # allele_frequency_with_variance). max_ciphertext_mb below bounds the WHOLE  # packed container.release_policy:  aggregate_only: true           # only the summed moment set is ever decrypted  allowed_runs_per_project: 1    # run cap (differencing mitigation, not a defense)# Larger ring (poly 16384) + one packed (g, y) blob per contributor (two# ciphertexts) + four output ciphertexts => the additive flagship's 8192/3600/512# budget is bumped.resources:  max_memory_mb: 16384  max_wall_seconds: 7200  max_ciphertext_mb: 2048# Collaboration scenario (docs/rfcs/0002 §4.1): who runs which role's functions.# The author writes pure functions grouped BY ROLE into the files below; the# numbered stage shims that call them are kit-owned framework code, materialized# at run time (never signed into the bundle). `aggregate` = 1 project owner + N# data owners.scenario:  name: aggregate  roles:    project_owner: { file: local_project_owner.py, functions: [ keygen, decrypt, decode ] }    data_owner:    { file: local_data_owner.py,    functions: [ encode, encrypt ] }    server:        { file: server.py,              functions: [ compute ] }# Content-addressing digests. Computed at registry ingest — `bundle` by# protocols/hash_bundle.py, `env_lock` over env/uv.lock + env/.python-version +# pinned runner metadata. Left null in the committed bundle ON PURPOSE: the# canonical bundle digest is computed over the raw bytes of every signed file# INCLUDING this manifest, so a computed `bundle` value here would be# self-referential (its own input). The authoritative digest instead NAMES the# bundle (protocol-<name>@<digest>) and is recorded out-of-band# (.blind-signature / DB), never inside the file it would have to hash. See# protocols/README.md § "Why the manifest ships null hash placeholders".hashes:  bundle: null  env_lock: null