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…criptors (v4.0.0)
Replace fixed 32x32x16 grid archive with Voronoi tessellation fitted from
observed rollout distributions. No normalizers anywhere.
- archive.py: cKDTree-based CVT archive, attach_centroids(), similarity
rejection against occupied centroid subset
- loop.py: _calibration_phase() runs N_CAL rollouts before search, fits
k-means centroids, assigns creature_id="{run_id}-{seed}" at insertion;
SearchConfig gains calibration and centroids fields
- rollout.py: SIGNAL_STEPS and PRESET_CALIBRATION tables replace
signal_preset(); SIGNAL_CALIBRATION_BONUS=50 for signal runs
- descriptors.py: all 18 compute() return raw float in [0, 100]; normalizer
divisions removed; SPECTRAL_ENTROPY_FLOOR remap removed
- result.py: creature_id and parent_id replace parent_cell and CellCoord;
LegacyCellCoord alias kept for old pickle compat
- cli.py: --calibration and --centroids flags; preset-derived calibration
defaults; signal step override via SIGNAL_STEPS for all presets
- ecosystem/config.py: CreatureSource gains creature_id field; parser
accepts creature_id or cell (deprecated)
- ecosystem/run.py: load_creature looks up by creature_id first, falls
back to coords for old archives
- smoke_ecosystem.sh: CVT archive seeding, creature_id in YAML
- All tests updated; ruff clean, pyright 0 errors, 422 tests passing
Add src/biota/viz/tty.py: SearchDisplay class with two rendering modes. TTY mode: 7-line overwriting block (header, progress bar, archive stats, last-10 insertion summary, per-descriptor coverage bars). Non-TTY mode: append-only lines matching pre-v4.0.0 format plus summary every 50 rollouts. loop.py: add CalibrationProgressFn / CalibrationDoneFn callback types, thread them through _calibration_phase and search(). cli.py: wire SearchDisplay to the event stream; pass live Archive to search() so coverage bars read real descriptor distributions.
archive.html: three-panel layout replacing the fixed grid. Left panel (58%): virtual-scrolled creature cards with filter/sort and inline YAML copy. Right panel: descriptor histograms (quality-colored bars, selected- creature marker) and Pearson correlation matrix. Collapsible health header with calibration stats. All JS uses creature_id / parent_id; deep-link is render.py: remove body_inner stub, add calibration_n/survivors from manifest. ecosystem.html: coords_hash deep-links now use creature_id when available. index.html: CVT language in System tab, creature_id in Reproduce tab YAML, stat block updated (1024 centroids / CVT-MAP-Elites). build_index.py: _build_sources_context emits creature_id for deep-links.
… quality metric Replace emission_activity/receptor_sensitivity/signal_retention with signal_field_variance, signal_mass_ratio, dominant_channel_fraction -- descriptors that measure final field state and work for equilibrium solitons. Add batched signal physics to rollout_batch (was silently skipped before). Fix alive filter: exclude initial_signal_mass from conservation check since signal decays by design. Add initial_signal_mass to RolloutEvaluation for signal_activity quality term (replaces retention). Update README, index.html, tests.
…dates archive.py: persistent _occupied_tree rebuilt lazily on dirty flag instead of O(n) rebuild per insertion; similarity epsilon now operates in scaled space matching cell_for(). rollout.py: _batched_sim_step returns (new_A, U_sum) -- signal step reuses U_sum directly, eliminating a duplicate FFT per step. _build_batched_signal_ params uses build_signal_kernel_fft() without constructing B FlowLenia instances. make_signal_fields_batch() replaces per-element init loop. flowlenia.py: add build_signal_kernel_fft() and make_signal_fields_batch() module-level functions; add mass_kernels_fft and decay public properties. localized.py: remove all reportPrivateUsage suppressions; use public API. docs: archive-grid.svg and search-loop.svg updated to CVT language. README: emission_rate range corrected, render.py stale comment cleaned.
Gallery grid replaces card list; thumbnails fill card width via aspect-ratio. Filter bar moves to header row. Click opens modal directly (no preview strip). Right panel (38% width) holds 2x2 histogram grid (velocity, gyradius, d2, quality distribution) plus compact correlation matrix below. Hover highlights bins across all three descriptor histograms simultaneously.
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biota v4.0.0 — CVT-MAP-Elites, signal overhaul, archive gallery, ecosystem fixes
Replaces the fixed 32×32×16 grid archive with CVT-MAP-Elites, rebuilds the archive viewer as a gallery, overhauled signal descriptors and batched rollouts, and fixes several ecosystem bugs.
Archive
creature_idreplaces 3D coords as stable creature identity._is_too_similarnow maintains a persistent occupied-centroid tree (lazy dirty-flag rebuild); similarity epsilon operates in scaled space matchingcell_for().Search / rollouts
_batched_sim_stepreturns(new_A, U_sum); signal step reusesU_sum, eliminating a duplicate FFT per step._build_batched_signal_paramsusesbuild_signal_kernel_fft()directly without constructing BFlowLeniainstances.make_signal_fields_batch()replaces per-element init loop.FlowLeniaAPI:mass_kernels_fft,decay,build_signal_kernel_fft(),make_signal_fields_batch().localized.pydrops allreportPrivateUsagesuppressions.Signal descriptors
emission_activity,receptor_sensitivity,signal_retentionremoved -- all returned zero for equilibrium solitons. Replaced withsignal_field_variance,signal_mass_ratio,dominant_channel_fraction, which measure final field state and work correctly for stable creatures.retentionterm replaced bysignal_activity = clip(final_signal_mass / initial_signal_mass, 0, 1). Weights: compactness 0.5 / stability 0.3 / signal_activity 0.2.CLI / TTY
Archive viewer
aspect-ratio:1thumbnails), filter bar in header, 2×2 analytics panel (three descriptor histograms + quality distribution), compact Pearson correlation matrix below. Click opens modal directly. Hover highlights corresponding bin across all histograms simultaneously.Ecosystem
receptor_alignmentbug fixed:compute_ecosystemnow loads creatures eagerly so_compute_outputsalways has them, not just in the Ray dispatcher path._extract_primary_sourcehandles"cell": nullincreature_id-based summaries.Docs / diagrams
docs/archive-grid.svg,docs/search-loop.svgupdated to CVT language.