Bio-Semantics Integration Contract — Gate 1

Version: bio-semantics/1.0.0 Status: Gate 1 candidate — contract specification only. Not implemented or tested.

Integration Pipeline

Python → Validation → Normalization → Model Inputs → Stan → MiniZinc → Quipper → Artifact Validation → Visualization/Reporting

Each stage result carries:

Field	Type
run_id, stage_id, semantic_stage	identifiers
status	blocked / not_run / running / succeeded / failed / timeout
reason	string
input_artifact_ids[], output_artifact_ids[]	references
tool_name, tool_version, command_arguments[], working_directory	execution
started_at, ended_at, exit_code	timing
stdout_artifact_id, stderr_artifact_id	logs
random_seed	value / not_applicable / unavailable

Solver outcome is separate from process status:

solver_outcome: feasible | optimal | infeasible | unknown | timeout | failed | not_run

A successful process exit is insufficient evidence of successful inference, a feasible solution, convergence, or quantum execution.

Kind	Meaning
observed	Measurement with source record locator
inferred	Posterior quantity with model/run references and uncertainty
derived	Deterministic transformation with algorithm and input references
predicted	Unobserved modeled quantity with model/run references
constrained	Declared permitted relation or solver result
encoded	Representation with semantic source, codec identifier, and bit length
executed	Actual execution event with run evidence

Reject unsupported versions, unknown discriminants, contradictory variants, empty identifiers, duplicate observation IDs
Require exactly one of present value or missing reason
Raw counts: canonical unsigned decimal only (no negatives, fractions, exponents, whitespace)
Decimal quantities: reject NaN/infinity, require declared units
Require sample/gene references to resolve
Reject inferred/predicted/constrained quantities labeled observed
Preserve excluded rows with explicit inclusion map
Missing source bytes block verified-ingestion claims
Synthetic-origin propagation through every descendant artifact
Never create model-result objects merely because a process was scheduled

u32-checked/1: unsigned 32-bit, big-endian, range 0..4294967295; overflow traps
i32-checked/1: signed two's-complement, big-endian; overflow traps; MIN_INT/-1 traps

Input alphabet: {0,1}. Tape alphabet: {0,1,_}. States: {q_even, q_odd, q_accept, q_reject}.

State	Read	Write	Move	Next
q_even	0	0	R	q_even
q_even	1	1	R	q_odd
q_odd	0	0	R	q_odd
q_odd	1	1	R	q_even
q_even	_	0	Stay	q_accept
q_odd	_	1	Stay	q_accept

For input length n: exactly n+1 transitions, n+1 tape cells, constant auxiliary storage.

Contract gate: Contracts and validators accepted; encodings/arithmetic/PTM documented; provenance validated
Engine gate: Stan/MiniZinc/Quipper sources exist; native validation evidence recorded; failures preserved
Integration/release gate: All panels rendered with lineage; WORM loaded first; governance checks preserved

Case	Expected
Present raw count "0"	Valid observed zero
Missing count with not_measured	Valid missing; never zero-filled
Missing variant also contains value	Invalid
Raw count "-1", "1.5", "1e3"	Invalid
Count above native backend range	Adapter rejects conversion
Normalized measurement labeled observed	Invalid
Posterior relabeled observed	Invalid
Missing source/hash	Provenance incomplete
Synthetic input -> posterior -> report	Synthetic marker propagated
Two records with duplicate identity	Invalid
u32 maximum plus one	Overflow fault
Integer divide by zero	Arithmetic fault
Encode/decode present zero versus missing	Distinct round trips
PTM "", "0", "1", "1011"	Output 0, 0, 1, 1; transitions 1, 2, 2, 5
Fortran summation	Expected sum=5050