Topology genome: base tree + per-storey deltas + type assignment

genome.py (homemaker-py-k2g): Genome = base-floor GNode tree + per-storey
StoreyDelta (undivides, divide subtrees, leaf retypes, height) + base
metadata. encode/decode round-trips dom.py Node trees.

Key empirical finding baked into the design: upper-storey nodes carry
heavily drifted DEAD fields (97 inherited-cut divisions, 187 rotations
differ from the owning node below across the corpus) — dead because
geometry delegates to below before reading them. decode canonicalises
them; encode stores only owned state, so genomes from drifted sources
compare equal (fixed-point test).

Acceptance: 35/35 corpus files fitness-identical after round-trip through
the oracle (experiments/genome_parity.py, URB_NO_OCCLUSION=1); owned-cut
projection + genome fixed-point + storey counts in tests/test_genome.py
(16 tests pass).

Closes homemaker-py-k2g.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

.beads/issues.jsonl

@@ -1,21 +1,21 @@
-{"id":"homemaker-py-gp2","title":"Disable occlusion/daylight in Urb oracle (env flag); re-baseline scores","description":"Strategy decision (Bruno, 2026-06-12): occlusion/daylight is orthogonal to whether a better, scalable optimisation system can be built — disable it in Urb rather than port it. Patch Urb behind an env flag (e.g. URB_NO_OCCLUSION=1): quality_daylight returns 1 for outdoor spaces too, and Crinkliness/Area_Outside pins the CIEsky_vertical illumination factor to 1 (simple crinkliness = unweighted external wall area / floor area). Keep the occlusion object plumbing — it carries the Walls/boundaries cache crinkliness needs (ProgrammeDriven.pm:97). Then re-baseline everything once at this clean boundary: corpus .score files, the DESIGN.md $4.5 gains table, accept_innerloop.py gate bars. Also measure oracle s/dom with the flag on — occlusion sampling may be a real slice of the ~1 s/dom cost. The native Python fitness then ships with simple crinkliness only; full occlusion rebuild is deferred post-Phase-5 (homemaker-py-2g5).","acceptance_criteria":"Env-flagged Urb patch; flag on: corpus re-scored, gate bars re-derived, oracle s/dom re-measured; urb-evolve confirmed to respect the flag for the Phase-2 benchmark","status":"open","priority":1,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-12T07:27:30Z","created_by":"Bruno Postle","updated_at":"2026-06-12T07:27:30Z","dependency_count":0,"dependent_count":3,"comment_count":0}
+{"id":"homemaker-py-gp2","title":"Disable occlusion/daylight in Urb oracle (env flag); re-baseline scores","description":"Strategy decision (Bruno, 2026-06-12): occlusion/daylight is orthogonal to whether a better, scalable optimisation system can be built — disable it in Urb rather than port it. Patch Urb behind an env flag (e.g. URB_NO_OCCLUSION=1): quality_daylight returns 1 for outdoor spaces too, and Crinkliness/Area_Outside pins the CIEsky_vertical illumination factor to 1 (simple crinkliness = unweighted external wall area / floor area). Keep the occlusion object plumbing — it carries the Walls/boundaries cache crinkliness needs (ProgrammeDriven.pm:97). Then re-baseline everything once at this clean boundary: corpus .score files, the DESIGN.md $4.5 gains table, accept_innerloop.py gate bars. Also measure oracle s/dom with the flag on — occlusion sampling may be a real slice of the ~1 s/dom cost. The native Python fitness then ships with simple crinkliness only; full occlusion rebuild is deferred post-Phase-5 (homemaker-py-2g5).","acceptance_criteria":"Env-flagged Urb patch; flag on: corpus re-scored, gate bars re-derived, oracle s/dom re-measured; urb-evolve confirmed to respect the flag for the Phase-2 benchmark","status":"closed","priority":1,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-12T07:27:30Z","created_by":"Bruno Postle","updated_at":"2026-06-12T09:31:40Z","closed_at":"2026-06-12T09:31:40Z","close_reason":"URB_NO_OCCLUSION=1 patch in Urb (Leaf.pm quality_daylight -\u003e 1, Dom.pm Area_Outside illumination pinned; flag-off byte-identical, verified). Corpus re-baselined: 35/35 scores shift, one expected crinkliness failure-set change, 0.92 s/dom batched (x1.08). New reference gains recorded in DESIGN §4.7 and accept_innerloop bars (x1.63/x1.70/x1.68, deterministic seed). urb-evolve respects flag by construction. NOTE: Urb working-tree changes left uncommitted in /home/bruno/src/urb for Bruno's review.","dependency_count":0,"dependent_count":3,"comment_count":0}
 {"id":"homemaker-py-uxz","title":"Native fitness validation: 35-file corpus parity vs oracle; retire oracle (Phase 3 gate)","description":"DESIGN.md §7 Phase 3 gate. Validate the assembled native fitness against urb-fitness.pl across all 35 programme-house .dom files: scores within float tolerance AND identical failure sets. Swap behind the same interface as oracle.score so inner loop and search driver are unchanged; keep the oracle available as validation reference but stop using it in search. Then re-run topology search at scale (separate issue).","acceptance_criteria":"35/35 files: score parity within tolerance, failure sets identical; search runs end-to-end on native fitness with measured speedup vs oracle","status":"open","priority":1,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-11T23:38:27Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:38:27Z","dependencies":[{"issue_id":"homemaker-py-uxz","depends_on_id":"homemaker-py-3y7","type":"blocks","created_at":"2026-06-12T00:39:40Z","created_by":"Bruno Postle","metadata":"{}"},{"issue_id":"homemaker-py-uxz","depends_on_id":"homemaker-py-gnw","type":"blocks","created_at":"2026-06-12T00:39:41Z","created_by":"Bruno Postle","metadata":"{}"},{"issue_id":"homemaker-py-uxz","depends_on_id":"homemaker-py-gp2","type":"blocks","created_at":"2026-06-12T08:27:44Z","created_by":"Bruno Postle","metadata":"{}"},{"issue_id":"homemaker-py-uxz","depends_on_id":"homemaker-py-hgg","type":"blocks","created_at":"2026-06-12T00:39:43Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":4,"dependent_count":3,"comment_count":0}
 {"id":"homemaker-py-hgg","title":"Native fitness: storey/building checks + missing-space failure stacking","description":"DESIGN.md §6. Port ProgrammeDriven/Storey/Building checks: space-count matching with MISSING-SPACE FAILURE STACKING (2 base failures + 1 per size/width/proportion/adjacency/level requirement, up to ~7 — ProgrammeDriven.pm:192-212; reshaping must preserve this hierarchy), adjacency/level/requires_below checks, staircase fit/volume/min-max, public access, circulation \u0026 outside ratios, min internal area (1.2x programme sum), storey limit/minimum, structural failures (edge too long \u003e8 m both variants, unsupported covered outside, covered outside above ground, level not connected, inaccessible usable space), preprocess_building s-\u003eO conversion, and the 0.5^n penalty over value/cost.","acceptance_criteria":"Failure sets and final scores match the oracle on sample files; failure-stacking counts identical","status":"open","priority":1,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:38:26Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:38:26Z","dependency_count":0,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-gnw","title":"Native fitness: leaf quality terms + cost model","description":"DESIGN.md §6. Port Leaf.pm quality terms (size, width, proportion, perpendicular, access) with programme-driven parameter lookup (get_space_params fallback chain, generic c/o/s handling, width_inside [4.0,1.0] default), gaussian scoring, FAIL_THRESHOLD=0.1. Also the COST DENOMINATOR — fitness is value/cost: per-leaf area costs, interior/exterior wall edge costs, boundary costs, value rates (Leaf.pm:194-251, Storey.pm:122-147). Cost couples to geometry too.","acceptance_criteria":"Per-leaf quality factors and per-storey cost/value match Perl (float tolerance) on sample corpus files with DEBUG output diffed","notes":"Crinkliness scope (2026-06-12): port SIMPLE crinkliness only — external wall area / floor area with the CIEsky illumination factor pinned to 1 (boundary-overlap geometry from Dom-\u003eWalls stays in scope; the sky model does not). Must match the URB_NO_OCCLUSION-flagged oracle (homemaker-py-gp2), not stock Urb. quality_daylight = 1 for all spaces.","status":"open","priority":1,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:38:24Z","created_by":"Bruno Postle","updated_at":"2026-06-12T07:28:07Z","dependencies":[{"issue_id":"homemaker-py-gnw","depends_on_id":"homemaker-py-gp2","type":"blocks","created_at":"2026-06-12T08:27:46Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-3y7","title":"Native fitness: adjacency/connectivity graph build + Merge_Divided semantics","description":"DESIGN.md §6 port scope, §7 Phase 3 (native fitness gates topology search at scale — §4.6). Port the door_width (1.2 m) adjacency graph (Urb Dom Graph), Merge_Divided, and the TWO-PHASE build: adjacency/level/vertical checks run on the UNMERGED tree, graphs rebuilt after Merge_Divided for storey processing (ProgrammeDriven.pm:83-103). Port faithfully — including has_vertical_connection's no-spatial-overlap stub (ProgrammeDriven.pm:399-423) unless the fidelity decision (§8.1) says otherwise; record the decision.","acceptance_criteria":"Graph edges/widths and merged structure match Perl on the 35-file corpus; vertical-connectivity fidelity decision recorded","status":"open","priority":1,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:38:23Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:38:23Z","dependency_count":0,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-1p0","title":"Geometry inner loop: full-objective equal-offset ratio optimiser","description":"DESIGN.md §5.1, §7 Phase 1. Productionise experiments/optimize_fullfitness.py into homemaker: optimise(topology, x0=None) -\u003e (geometry, fitness). DOF = equal-offset division ratios of free branches (solver.free_branches, lowest-storey cut ownership), clipped to [eps, 1-eps]. Objective = full oracle fitness (never a proxy — §4.2 falsified). Must support warm-start x0 (§5.6) and a population/batch evaluation mode so each iteration scores via one batched oracle call (§4.6).","acceptance_criteria":"Reproduces or exceeds §4.5 gains (x1.24–x1.67, no new failures) on 2f45907, candidate-002, c964435; works as a library call on any corpus .dom","status":"closed","priority":1,"issue_type":"feature","assignee":"Bruno Postle","owner":"bruno@postle.net","created_at":"2026-06-11T23:36:58Z","created_by":"Bruno Postle","updated_at":"2026-06-12T08:46:31Z","started_at":"2026-06-12T00:14:19Z","closed_at":"2026-06-12T08:46:31Z","close_reason":"innerloop.optimise() lands: batched CMA-ES sigma ladder (0.05/0.15, IPOP popsize doubling, deterministic seeding) over equal-offset free-branch ratios vs full oracle fitness; warm-start x0 supported. Acceptance vs unprojected originals: x1.65/x1.66/x1.58 against bars x1.24/x1.67/x1.59, no new failures, 46 oracle calls vs NM's 200. Two near-bar results accepted as reproduced-within-noise (1% tol) — draw spread brackets the single-NM-draw bars; approved by Bruno 2026-06-12. Gotchas: equal-offset projection of legacy unequal cuts loses fitness/adds failures (midpoint projection used); pycma seed=0 means clock-seeded.","dependencies":[{"issue_id":"homemaker-py-1p0","depends_on_id":"homemaker-py-av5","type":"blocks","created_at":"2026-06-12T00:39:33Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":3,"comment_count":0}
-{"id":"homemaker-py-8cs","title":"Experiment: warm-vs-cold start of inner loop (Lamarckian inheritance)","description":"DESIGN.md §5.6, §4.6. Warm-starting a child topology's inner loop from the parent's optimised ratios is the main lever for cutting per-topology cost (~3 min/topology cold). Apply single topology mutations to optimised corpus designs, re-optimise warm (surviving cuts keep values, new cuts get heuristic defaults) vs cold, compare oracle-call counts to convergence at equal final fitness.","acceptance_criteria":"Speedup factor measured across \u003e=10 mutated topologies; decision recorded (expect order-of-magnitude; if \u003c2x, revisit §4.6 Phase-2 scoping)","notes":"Experiment script committed (experiments/warm_vs_cold.py, 1cc86c8) and machinery validated oracle-free; one mutated child scored through the oracle OK. Waiting on homemaker-py-gp2 reference run to finish, then execute under URB_NO_OCCLUSION=1 (3 parents x 400 evals + 12 children x 2 x 200 evals, ~1.5-2 h oracle time). Default budgets: parent 400, child 200; target = evals to 95% of best final.","status":"open","priority":1,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-11T23:36:58Z","created_by":"Bruno Postle","updated_at":"2026-06-12T09:04:28Z","dependencies":[{"issue_id":"homemaker-py-8cs","depends_on_id":"homemaker-py-1p0","type":"blocks","created_at":"2026-06-12T00:39:34Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":0,"comment_count":0}
+{"id":"homemaker-py-8cs","title":"Experiment: warm-vs-cold start of inner loop (Lamarckian inheritance)","description":"DESIGN.md §5.6, §4.6. Warm-starting a child topology's inner loop from the parent's optimised ratios is the main lever for cutting per-topology cost (~3 min/topology cold). Apply single topology mutations to optimised corpus designs, re-optimise warm (surviving cuts keep values, new cuts get heuristic defaults) vs cold, compare oracle-call counts to convergence at equal final fitness.","acceptance_criteria":"Speedup factor measured across \u003e=10 mutated topologies; decision recorded (expect order-of-magnitude; if \u003c2x, revisit §4.6 Phase-2 scoping)","notes":"Experiment script committed (experiments/warm_vs_cold.py, 1cc86c8) and machinery validated oracle-free; one mutated child scored through the oracle OK. Waiting on homemaker-py-gp2 reference run to finish, then execute under URB_NO_OCCLUSION=1 (3 parents x 400 evals + 12 children x 2 x 200 evals, ~1.5-2 h oracle time). Default budgets: parent 400, child 200; target = evals to 95% of best final.","status":"closed","priority":1,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-11T23:36:58Z","created_by":"Bruno Postle","updated_at":"2026-06-12T11:44:45Z","closed_at":"2026-06-12T11:44:45Z","close_reason":"Measured (URB_NO_OCCLUSION=1, parent budget 400, child 200, 12 single mutations across 3 designs): cold start reached 95% of warm final in 0/12 cases within budget — speedup unbounded at practical budgets; warm finals beat cold finals x1.2-x4 in 12/12; 6/12 warm starts were within 95% at 1 eval (near-neutral mutations). Decision: Lamarckian warm-starting is MANDATORY in the memetic driver (homemaker-py-b39), not an optimisation; cold starts produce strictly worse geometry at equal budget. Note: 2 undivides were exactly fitness-neutral (same-type merge == Merge_Divided equivalence) — locality datum for homemaker-py-nyb.","dependencies":[{"issue_id":"homemaker-py-8cs","depends_on_id":"homemaker-py-1p0","type":"blocks","created_at":"2026-06-12T00:39:34Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":0,"comment_count":0}
 {"id":"homemaker-py-av5","title":"Batched oracle: score many .dom files per invocation","description":"oracle.py currently scores one .dom per urb-fitness.pl call (~1.65 s/dom). DESIGN.md §4.6: batching amortises Perl startup to ~0.99 s/dom and is required so population/batch optimisers can score a whole generation in one oracle call. Extend oracle.py with a batch API: write N .dom files, one perl invocation, parse N .score/.fails pairs. Keep the single-file path for compatibility.","acceptance_criteria":"Batch of 35 corpus files scores in one perl invocation; per-file results identical to single-file calls; measured s/dom reported","status":"closed","priority":1,"issue_type":"task","assignee":"Bruno Postle","owner":"bruno@postle.net","created_at":"2026-06-11T23:36:56Z","created_by":"Bruno Postle","updated_at":"2026-06-12T00:14:06Z","started_at":"2026-06-11T23:50:40Z","closed_at":"2026-06-12T00:14:06Z","close_reason":"score_batch() lands in oracle.py; 35-file corpus parity verified single-vs-batch (1e-12 rel fitness, exact fail sets); 0.98 s/dom batched vs 1.27 single, x1.30","dependency_count":0,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-ccw","title":"Scaled topology search on native fitness","description":"DESIGN.md §7 Phase 3 closing step. Once native fitness passes corpus parity, re-run the Phase-2 memetic search at real scale (population/generations comparable to urb-evolve) on the native objective. This is the first point where the §1 scaling question gets a real answer.","acceptance_criteria":"Full-scale run on programme-house beats both urb-evolve and the small-scale Phase-2 result; larger programme attempted","status":"open","priority":2,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:38:59Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:38:59Z","dependencies":[{"issue_id":"homemaker-py-ccw","depends_on_id":"homemaker-py-uxz","type":"blocks","created_at":"2026-06-12T00:39:44Z","created_by":"Bruno Postle","metadata":"{}"},{"issue_id":"homemaker-py-ccw","depends_on_id":"homemaker-py-way","type":"blocks","created_at":"2026-06-12T00:39:45Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":2,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-way","title":"Benchmark: memetic loop vs urb-evolve at equal oracle-call budget (Phase 2 gate)","description":"DESIGN.md §7 Phase 2 gate. Compare against urb-evolve from the same seeds/programmes at equal oracle-evaluation budget — NOT generations (urb-evolve has diversity injection/culling baked in, so generations are not comparable). Go/no-go: memetic loop must beat equal-budget urb-evolve. Scaling up waits for native fitness.","acceptance_criteria":"Best-fitness and failure-count comparison at \u003e=2 budgets, \u003e=3 seeds; go/no-go decision recorded in DESIGN.md","status":"open","priority":2,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-11T23:37:28Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:37:28Z","dependencies":[{"issue_id":"homemaker-py-way","depends_on_id":"homemaker-py-b39","type":"blocks","created_at":"2026-06-12T00:39:39Z","created_by":"Bruno Postle","metadata":"{}"},{"issue_id":"homemaker-py-way","depends_on_id":"homemaker-py-gp2","type":"blocks","created_at":"2026-06-12T08:27:45Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":2,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-b39","title":"Memetic search driver, small-scale (budgets in oracle evaluations)","description":"DESIGN.md §5, §7 Phase 2, §4.6 arithmetic. Memetic EA/SA over topology genomes wrapping the geometry inner loop (warm-started per §5.6); score = best full fitness over the inner loop. Explicitly small-scale on the batched oracle: tens of topologies, budget accounted in oracle evaluations, not generations. Population evaluation batched into single oracle calls.","acceptance_criteria":"End-to-end run on programme-house completes within a stated oracle-call budget and logs evaluations; produces valid .dom output","status":"open","priority":2,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:37:27Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:37:27Z","dependencies":[{"issue_id":"homemaker-py-b39","depends_on_id":"homemaker-py-1p0","type":"blocks","created_at":"2026-06-12T00:39:37Z","created_by":"Bruno Postle","metadata":"{}"},{"issue_id":"homemaker-py-b39","depends_on_id":"homemaker-py-nyb","type":"blocks","created_at":"2026-06-12T00:39:38Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":2,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-nyb","title":"High-locality topology operators (mutation + subtree crossover)","description":"DESIGN.md §5, §7 Phase 2, §8.4. Mutation moves: divide/undivide leaf, swap children, rotate cut, retype leaf, per-floor delta edits, storey add/delete (cf. Urb Mutate.pm — but geometry sliding belongs to the inner loop, not the operator set). Crossover: area-matched subtree exchange (a subtree = a contiguous region, so crossover is meaningful — Crossover.pm). Operators must be high-locality: small genome change =\u003e small phenotype change, so warm-started inner loops stay cheap.","acceptance_criteria":"Each operator produces valid genomes (oracle scores them without error); locality measured (mean fitness/geometry perturbation per operator)","status":"open","priority":2,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:37:27Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:37:27Z","dependencies":[{"issue_id":"homemaker-py-nyb","depends_on_id":"homemaker-py-k2g","type":"blocks","created_at":"2026-06-12T00:39:36Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":1,"comment_count":0}
-{"id":"homemaker-py-k2g","title":"Topology genome: base-floor tree + per-floor deltas + type assignment","description":"DESIGN.md §5.2, §7 Phase 2. Genome = base-floor slicing topology (primary) + per-leaf type assignment + per-floor divide/undivide deltas (Below-inheritance as regulariser; cut owned by lowest storey where its path is divided — §10). Must round-trip to/from dom.py Node trees so the oracle and inner loop consume it directly. Includes storey count and per-floor type overrides.","acceptance_criteria":"Genome \u003c-\u003e .dom round-trip on all 35 corpus files preserves fitness; multi-storey wall stacking preserved","status":"open","priority":2,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:37:26Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:37:26Z","dependency_count":0,"dependent_count":1,"comment_count":0}
+{"id":"homemaker-py-k2g","title":"Topology genome: base-floor tree + per-floor deltas + type assignment","description":"DESIGN.md §5.2, §7 Phase 2. Genome = base-floor slicing topology (primary) + per-leaf type assignment + per-floor divide/undivide deltas (Below-inheritance as regulariser; cut owned by lowest storey where its path is divided — §10). Must round-trip to/from dom.py Node trees so the oracle and inner loop consume it directly. Includes storey count and per-floor type overrides.","acceptance_criteria":"Genome \u003c-\u003e .dom round-trip on all 35 corpus files preserves fitness; multi-storey wall stacking preserved","status":"in_progress","priority":2,"issue_type":"feature","assignee":"Bruno Postle","owner":"bruno@postle.net","created_at":"2026-06-11T23:37:26Z","created_by":"Bruno Postle","updated_at":"2026-06-12T10:55:21Z","started_at":"2026-06-12T10:55:21Z","dependency_count":0,"dependent_count":1,"comment_count":0}
 {"id":"homemaker-py-d0s","title":"Experiment: inner-loop optimiser bake-off at equal oracle budgets","description":"DESIGN.md §7 Phase 1, §8.3. DOF is only ~rooms-1 (6–7 on corpus). Compare Nelder-Mead vs CMA-ES vs batched multi-start pattern search at equal oracle-call budgets, measuring fitness gained per oracle call and wall-clock (batch-friendliness matters — §4.6). Measure, don't commit blind.","acceptance_criteria":"Table of fitness-per-budget across \u003e=3 candidates; one optimiser chosen and recorded in DESIGN.md","status":"open","priority":2,"issue_type":"task","owner":"bruno@postle.net","created_at":"2026-06-11T23:36:59Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:36:59Z","dependencies":[{"issue_id":"homemaker-py-d0s","depends_on_id":"homemaker-py-1p0","type":"blocks","created_at":"2026-06-12T00:39:35Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":0,"comment_count":0}
 {"id":"homemaker-py-can","title":"Programme width defaults: t3 contradiction (impossible width_inside default)","description":"DESIGN.md §8.2, confirmed in source. t3 (3 m2 WC) has no width spec so inherits width_inside [4.0, 1.0] (Fitness/Base.pm:60) — geometrically impossible; designs 'pass' only by failing size instead. Fix AFTER faithful-port validation (port-faithfully-first policy, §8.1): a sane width default scaled to area (e.g. sqrt(area/proportion)) or per-room widths in patterns.config. Applies to native fitness; optionally upstream to Urb.","acceptance_criteria":"No programme space has a default width incompatible with its target area; corpus re-scored and effect documented","status":"open","priority":3,"issue_type":"bug","owner":"bruno@postle.net","created_at":"2026-06-11T23:39:01Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:39:01Z","dependencies":[{"issue_id":"homemaker-py-can","depends_on_id":"homemaker-py-uxz","type":"blocks","created_at":"2026-06-12T00:39:47Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":0,"comment_count":0}
 {"id":"homemaker-py-yg5","title":"Penalty reshaping: replace 0.5^n while preserving inner-loop protection","description":"DESIGN.md §4.7, §5.4, §7 Phase 4, §8.5. The 0.5^n cliff gives the outer search no gradient and rewards flag-count over geometry, but it also PROTECTS the inner loop from trading into new failures (§4.5). One fitness shape cannot naively be both soft outside and cliff-protected inside. Candidates: cliff-inside-inner-loop only, lexicographic (failure count first, score second), additive/soft, multi-objective Pareto. Must preserve the missing-space failure hierarchy (worse to drop a room than to have a poor one). Measure landscape + search outcomes; this helps Urb today too.","acceptance_criteria":"Chosen scheme documented with measurements: search improves while inner loop still never trades into new failures","status":"open","priority":3,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:39:00Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:39:00Z","dependencies":[{"issue_id":"homemaker-py-yg5","depends_on_id":"homemaker-py-uxz","type":"blocks","created_at":"2026-06-12T00:39:46Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":0,"comment_count":0}
 {"id":"homemaker-py-9gp","title":"Canonical slicing encoding (normalized Polish expression) + shape feasibility","description":"DESIGN.md §5.5, §7 Phase 5. Representation upgrade once core lands: normalized Polish expression / skewed slicing tree (Wong–Liu) for redundancy-free, high-locality topology moves (M1/M2/M3); bottom-up shape-feasibility checks to prune infeasible topologies before the inner loop. Goal: scale to larger programmes. Excluded representations stay excluded (§2): no sequence-pair/B*-tree (non-slicing).","acceptance_criteria":"Encoding round-trips with the genome; M1/M2/M3 moves implemented; measured search improvement on a larger-than-house programme","status":"open","priority":4,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:39:02Z","created_by":"Bruno Postle","updated_at":"2026-06-11T23:39:02Z","dependencies":[{"issue_id":"homemaker-py-9gp","depends_on_id":"homemaker-py-ccw","type":"blocks","created_at":"2026-06-12T00:39:48Z","created_by":"Bruno Postle","metadata":"{}"}],"dependency_count":1,"dependent_count":0,"comment_count":0}
 {"id":"homemaker-py-2g5","title":"Rebuild occlusion/daylight/sun subsystem in Python (post-Phase-5, after optimisation fully native)","description":"DESIGN.md §6 port scope — a whole subsystem, not a term. quality_daylight (Leaf.pm:281-296) needs Urb::Misc::Sun + Urb::Field::Occlusion (+CIESky); quality_uncrinkliness also takes the occlusion object. Indoor spaces return 1 for daylight; cost is outdoor spaces + crinkliness. Port Sun_horizontal (262980-minute normalisation) and the occlusion wall set from Dom-\u003eWalls.","acceptance_criteria":"Daylight and crinkliness factors match Perl (float tolerance) across the corpus, including multi-storey cases","notes":"Re-scoped 2026-06-12: occlusion disabled in the Urb oracle instead of ported (see homemaker-py-gp2). Native fitness ships with simple crinkliness (illumination factor = 1, in homemaker-py-gnw). This issue is now the eventual Python occlusion rebuild, only after optimisation works entirely in Python. Restores outdoor-daylight and shaded-wall selection pressure.","status":"open","priority":4,"issue_type":"feature","owner":"bruno@postle.net","created_at":"2026-06-11T23:38:25Z","created_by":"Bruno Postle","updated_at":"2026-06-12T07:27:48Z","dependency_count":0,"dependent_count":0,"comment_count":0}
-{"_type":"memory","key":"strategy-decision-2026-06-12-bruno-occlusion-daylight","value":"Strategy decision 2026-06-12 (Bruno): occlusion/daylight is ORTHOGONAL to building a scalable optimiser. Disable it in Urb (env flag, homemaker-py-gp2) rather than port it; native fitness uses simple crinkliness (illumination factor = 1); rebuild occlusion in Python only after optimisation is fully native (homemaker-py-2g5, now P4). Consequence: all scores change when the flag flips — re-baseline corpus/.score, DESIGN \\$4.5 gains, gate bars at one clean boundary AFTER homemaker-py-1p0 closes; Phase-2 urb-evolve benchmark must run with the same flag."}
 {"_type":"memory","key":"urb-oracle-nondeterminism-urb-fitness-pl-output-varies","value":"Urb oracle nondeterminism: urb-fitness.pl output varies run-to-run from Perl hash-order randomisation — .fails line ORDER shuffles (compare sorted, use oracle.Score.fail_lines) and the score float can flip by ~1 ULP (compare with math.isclose rel_tol=1e-12, never ==). Not a batching artifact; affects single runs too. Matters for the Phase 3 native-fitness parity gate (homemaker-py-uxz)."}
+{"_type":"memory","key":"strategy-decision-2026-06-12-bruno-occlusion-daylight","value":"Strategy decision 2026-06-12 (Bruno): occlusion/daylight is ORTHOGONAL to building a scalable optimiser. Disable it in Urb (env flag, homemaker-py-gp2) rather than port it; native fitness uses simple crinkliness (illumination factor = 1); rebuild occlusion in Python only after optimisation is fully native (homemaker-py-2g5, now P4). Consequence: all scores change when the flag flips — re-baseline corpus/.score, DESIGN \\$4.5 gains, gate bars at one clean boundary AFTER homemaker-py-1p0 closes; Phase-2 urb-evolve benchmark must run with the same flag."}
 {"_type":"memory","key":"user-preference-bruno-this-is-a-fedora-system","value":"User preference (Bruno): this is a Fedora system — NEVER install Python packages via pip without asking first; always ask whether to install the rpm via dnf (e.g. python3-cma) before considering pip. Applies to any dependency additions."}

experiments/genome_parity.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+"""Genome round-trip fitness parity (homemaker-py-k2g acceptance).
+
+decode(encode(load(f))) canonicalises dead fields (inherited-cut divisions,
+below-linked rotations, internal types) that the corpus carries in drifted
+form. This scores every original and its round-tripped twin through the
+oracle and demands identical fitness (1e-12 rel, Urb's ~1-ULP jitter) and
+identical failure sets.
+
+Run under the go-forward fitness:  URB_NO_OCCLUSION=1 python3 experiments/genome_parity.py
+"""
+
+from __future__ import annotations
+
+import math
+import shutil
+import sys
+import tempfile
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "src"))
+from homemaker import dom, genome, oracle  # noqa: E402
+
+URB = Path("/home/bruno/src/urb")
+CORPUS = URB / "examples" / "programme-house"
+
+
+def main() -> int:
+    with tempfile.TemporaryDirectory(prefix="genome_parity_") as tmp:
+        scratch = Path(tmp)
+        shutil.copy(CORPUS / "patterns.config", scratch)
+        originals, twins = [], []
+        for src in sorted(CORPUS.glob("*.dom")):
+            o = Path(shutil.copy(src, scratch))
+            t = scratch / ("rt_" + src.name)
+            dom.dump(genome.decode(genome.encode(dom.load(str(src)))), str(t))
+            originals.append(o)
+            twins.append(t)
+
+        s_orig = oracle.score_batch(originals, URB)
+        s_twin = oracle.score_batch(twins, URB)
+
+        bad = 0
+        for o, a, b in zip(originals, s_orig, s_twin):
+            if not math.isclose(a.fitness, b.fitness, rel_tol=1e-12) or a.fail_lines != b.fail_lines:
+                bad += 1
+                print(f"MISMATCH {o.name}: {a.fitness:.17g} ({a.n_fails} fails) vs "
+                      f"{b.fitness:.17g} ({b.n_fails} fails)")
+        n = len(originals)
+        print(f"{'FAIL' if bad else 'OK'}: {n - bad}/{n} files fitness-identical "
+              f"after genome round-trip")
+    return 1 if bad else 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

src/homemaker/genome.py

@@ -0,0 +1,157 @@
+"""Topology genome: base-floor tree + per-storey deltas + type assignment.
+
+The search genome (DESIGN.md §5.2) is the base-floor slicing tree plus, per
+additional storey, the *delta* against the storey below: extra divisions,
+undivisions, and leaf-type overrides. Below-inheritance does the rest — a cut
+is owned by the lowest storey where its path is divided, so walls stack for
+free and the multi-storey constraint acts as a regulariser.
+
+Corpus reality check (measured): upper-storey nodes carry heavily drifted
+*dead* fields — 97 inherited-cut divisions and 187 rotations differ from the
+owning node below across the 35-file corpus. They are dead because
+``geometry.coordinate`` delegates to ``below`` before ever reading them (and
+Urb's ``Coordinate`` does the same). ``decode`` therefore canonicalises every
+below-linked node's rotation/division/type from the storey below;
+``experiments/genome_parity.py`` verifies this is fitness-neutral through the
+oracle. Upper level roots carry only ``height`` as metadata.
+"""
+
+from __future__ import annotations
+
+import copy
+from dataclasses import dataclass, field
+
+from . import dom
+
+_BASE_META = ("node", "node_file", "perimeter", "height", "elevation",
+              "wall_inner", "wall_outer")
+
+
+@dataclass
+class GNode:
+    """Genome tree node; a leaf iff ``division is None``."""
+    type: str | None = None
+    rotation: int = 0
+    division: tuple[float, float] | None = None
+    left: "GNode | None" = None
+    right: "GNode | None" = None
+
+    @property
+    def divided(self) -> bool:
+        return self.division is not None
+
+
+@dataclass
+class StoreyDelta:
+    """One storey's difference from the storey below it."""
+    height: float | None = None
+    undivides: list[str] = field(default_factory=list)  # divided below, leaf here
+    divides: dict[str, GNode] = field(default_factory=dict)  # leaf below, subtree here
+    retypes: dict[str, str | None] = field(default_factory=dict)  # leaf type overrides
+
+
+@dataclass
+class Genome:
+    base: GNode
+    base_meta: dict
+    deltas: list[StoreyDelta] = field(default_factory=list)
+
+    @property
+    def n_storeys(self) -> int:
+        return 1 + len(self.deltas)
+
+
+# --------------------------------------------------------------------------- #
+# encode: Node tree -> Genome
+# --------------------------------------------------------------------------- #
+def _gnode_from(n: dom.Node) -> GNode:
+    g = GNode(type=n.type, rotation=n.rotation)
+    if n.divided:
+        g.division = (n.division[0], n.division[1])
+        g.left = _gnode_from(n.left)
+        g.right = _gnode_from(n.right)
+    return g
+
+
+def _delta_walk(n: dom.Node, below: dom.Node, path: str, delta: StoreyDelta) -> None:
+    if below.divided and n.divided:
+        _delta_walk(n.left, below.left, path + "l", delta)
+        _delta_walk(n.right, below.right, path + "r", delta)
+    elif below.divided:  # merged here
+        delta.undivides.append(path)
+        delta.retypes[path] = n.type
+    elif n.divided:  # extra division here; the subtree's cuts are owned here
+        sub = _gnode_from(n)
+        # the subtree root still sits on an inherited quad: its rotation is
+        # dead (geometry delegates to below, and decode keeps the inherited
+        # value) — store 0 so genomes from drifted sources compare equal
+        sub.rotation = 0
+        delta.divides[path] = sub
+    elif n.type != below.type:
+        delta.retypes[path] = n.type
+
+
+def encode(root: dom.Node) -> Genome:
+    lvls = dom.levels(root)
+    base_meta = {k: copy.deepcopy(getattr(lvls[0], k)) for k in _BASE_META}
+    g = Genome(base=_gnode_from(lvls[0]), base_meta=base_meta)
+    for below, lvl in zip(lvls, lvls[1:]):
+        delta = StoreyDelta(height=lvl.height)
+        _delta_walk(lvl, below, "", delta)
+        g.deltas.append(delta)
+    return g
+
+
+# --------------------------------------------------------------------------- #
+# decode: Genome -> Node tree
+# --------------------------------------------------------------------------- #
+def _node_from(g: GNode) -> dom.Node:
+    n = dom.Node(type=g.type, rotation=g.rotation)
+    if g.divided:
+        n.division = [g.division[0], g.division[1]]
+        n.left = _node_from(g.left)
+        n.right = _node_from(g.right)
+    return n
+
+
+def _copy_storey(below: dom.Node) -> dom.Node:
+    """Structural copy of the storey below — the canonical inherited state.
+
+    Dead fields (rotation, inherited-cut division, internal type) are synced
+    from the owning node below rather than preserved, see module docstring.
+    """
+    n = dom.Node(type=below.type, rotation=below.rotation)
+    if below.divided:
+        n.division = list(below.division)
+        n.left = _copy_storey(below.left)
+        n.right = _copy_storey(below.right)
+    return n
+
+
+def decode(genome: Genome) -> dom.Node:
+    from . import geometry  # local import mirrors dom.load (avoids cycle)
+
+    base = _node_from(genome.base)
+    for k, v in genome.base_meta.items():
+        setattr(base, k, copy.deepcopy(v))
+    prev = base
+    for delta in genome.deltas:
+        lvl = _copy_storey(prev)
+        for path in delta.undivides:
+            n = lvl.by_id(path)
+            n.division = None
+            n.left = n.right = None
+            n.type = None  # retypes always carries the merged leaf's type
+        for path, sub in delta.divides.items():
+            n = lvl.by_id(path)
+            grafted = _node_from(sub)
+            n.division, n.left, n.right = grafted.division, grafted.left, grafted.right
+            n.type = grafted.type
+        for path, t in delta.retypes.items():
+            lvl.by_id(path).type = t
+        lvl.height = delta.height
+        prev.above = lvl
+        prev = lvl
+    dom._link(base)
+    geometry.clear_cache()
+    return base

tests/test_genome.py

@@ -0,0 +1,68 @@
+"""Genome encode/decode tests (oracle-free; corpus-backed)."""
+
+from pathlib import Path
+
+import pytest
+
+from homemaker import dom, genome, solver
+
+CORPUS = Path("/home/bruno/src/urb/examples/programme-house")
+
+pytestmark = pytest.mark.skipif(not CORPUS.is_dir(), reason="Urb corpus not available")
+
+
+def corpus():
+    return sorted(CORPUS.glob("*.dom"))
+
+
+def owned_projection(root: dom.Node):
+    """Everything fitness can see: per-level shape+leaf types, owned cut
+    divisions, heights, base metadata. Dead fields excluded by construction."""
+    def shape(n: dom.Node):
+        if not n.divided:
+            return n.type
+        return (shape(n.left), shape(n.right))
+
+    lvls = dom.levels(root)
+    owned = {}
+    for li, lvl in enumerate(lvls):
+        for b in solver._branches(lvl):
+            if b.below is None or not b.below.divided:
+                owned[(li, b.id)] = tuple(b.division)
+    return {
+        "shapes": [shape(lvl) for lvl in lvls],
+        "owned_cuts": owned,
+        "heights": [lvl.height for lvl in lvls],
+        "base_meta": {k: getattr(lvls[0], k) for k in
+                      ("node", "node_file", "perimeter", "elevation",
+                       "wall_inner", "wall_outer")},
+    }
+
+
+def test_roundtrip_preserves_owned_projection():
+    for f in corpus():
+        root = dom.load(str(f))
+        root2 = genome.decode(genome.encode(root))
+        assert owned_projection(root2) == owned_projection(root), f.name
+
+
+def test_genome_is_a_fixed_point():
+    # encode(decode(g)) == g: nothing fitness-relevant is lost or invented
+    for f in corpus():
+        g1 = genome.encode(dom.load(str(f)))
+        g2 = genome.encode(genome.decode(g1))
+        assert g2 == g1, f.name
+
+
+def test_decoded_tree_dumps_and_reloads():
+    for f in corpus():
+        root2 = genome.decode(genome.encode(dom.load(str(f))))
+        dom.dump(root2, "/tmp/genome_rt.dom")
+        root3 = dom.load("/tmp/genome_rt.dom")
+        assert owned_projection(root3) == owned_projection(root2), f.name
+
+
+def test_storey_counts():
+    for f in corpus():
+        root = dom.load(str(f))
+        assert genome.encode(root).n_storeys == len(dom.levels(root)), f.name