Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

0.3.0 - 2026-11-03

Compare with 0.2.0

Features

Support Python 3.14 (82fb47e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replace deeptime with pydtmc and cap xgi below 1.0 (42b4515 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Bug Fixes

Spawn no Rerun viewer on a Linux machine without a display (3995301 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Stop a run hanging on a Rerun viewer that cannot be reached (844c906 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the doctest group of the test session (48bb54a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move to xgi 1.0, which copies hypergraphs on Python 3.14 (c7e42f6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Docs

Record the result of the full test run on Python 3.14 (9a4d0ea by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give every model its own page and remove the coverage page (38680c8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show every registered model on the field pages (eb7200e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Tests

Widen the Lorenz delay band to what the method resolves (0173774 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave out the annotations function of Python 3.14 from magic methods (0d8a370 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the wall-clock tests as benchmarks (d359eb8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

0.2.0 - 2026-11-03

Compare with 0.1.0

Features

Build a sample of the gallery by default and fix its folders (8ab2211 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give the nematic gel the turbulent parameters of Giomi et al. 2012 (90b8093 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add mandelbrot_least_effort and the package of language models (a9c0674 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add gravity_urban_scaling (afac84a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add evolutionary_optimisers (a45ad33 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add perceptron_satisfiability (0775c54 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add oligopoly_equilibria with its static and fictitious-play dynamics (2989f6b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add von_thunen (c606c97 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add random_energy_model and continuum_percolation (e037ebf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add lq_cell_survival (93d9b6b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add kinetic equations, kinetic flocking, phase-space visuals, and their documentation (28db6d6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the dry active nematic and the active nematic and polar gels (49ec9eb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add phase spaces, class coordinates, moments over axes, collisions, and split solvers (8c5ef50 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add SatisfiabilityInteraction, OptimizationInteraction, and cooling of SamplingInteraction (3e71504 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the static form, RootSolver, log_sum_exp, contact clusters, and pymoo (66af6ab by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add principal axes, defects, and the axis visual (eab0d80 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add tensor states, tensor law utilities, and the Leray projection (9e0118a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Accept functions on every numeric law, call options, and object agent states (4fc2a69 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the random Lotka-Volterra community with third-order interactions (55663cd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the partner spec and the settlement, and rebuild the obesity meal on them (2e9e6bc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name equations, generators, and dissipators as symbolic only when given a function (20e511f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the active viscoelastic gel, whose velocity solves a force balance at every step (5d47db0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gas-kinetic-based traffic model with its look-ahead braking (710ab38 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add agent schedules and ties, declare view members, and replace silent results with errors (734c836 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Accept named values, specs, and functions in variant arguments (c5c04fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name edge ends and pair members from the interaction's roles (1282825 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the quasi-geostrophic double gyre with its streamfunction observable (1ac2c70 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read parameters through _get_parameter with an attribute fallback (6af812a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read renamed roles in the symbolic forms through _get_member (bd11ff4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Register the Elman network with its gallery example (1c2654e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw trained matrices as heat maps and lead with the loss (84d35b3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Train the parameters of nested systems by gradient steps (e80bcf5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the Amari neural field (df629d1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give inversions a boundary and shifted reads cubic interpolation (b0d3105 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lower couplings on fields to the Laplacian and to shifted reads (c759636 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compute finite-volume wave speeds from closed-form eigenvalues and slice the reconstruction (3afebe7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the JAX backend for discrete maps and ordinary differential equations (7f6ca1c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Couple groups through shaped parameters and contract coupling tensors (1593383 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add nonlocal field operators (d9309f8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add InvariantAnalysis for Poisson brackets, conservation, symmetries, and Noether charges (6e7e12f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add parameters shaped by the groups of roles (f891658 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild Hénon-Heiles on HamiltonianInteraction with canonical momenta (11d3572 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the Kepler and restricted three-body problems on HamiltonianInteraction (2547440 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add Yoshida4Solver, a fourth-order symplectic composition of velocity Verlet steps (87c1bad by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add HamiltonianInteraction deriving Hamilton's equations as rate laws (a36ca98 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document hyperedge coupling, connected components, growth by hyperedges, and ordered phases (7d83aa1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the hypergraph public goods, simplicial dilemmas, and exposure SIS models (c6c754a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Count network motifs with igraph RAND-ESU (4726afa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spawn the dynamics' stream from the seed and use library generators (08f1cde by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run symbolic update laws in ordered phases within a step (c707ff5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Resolve the target of imitation through the subclass, and record the meadow rebuild (caaf4c7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Resolve the roles of general interactions through their subclasses (55b434c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add triadic percolation on the edge role of hyperedge interactions (475b4cb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the symbolic form of GroupingInteraction on the hyperedge path (1059776 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the connected-components reduction over the active links of a group (e89045f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add heat-bath proposals, vector agent maps, periodic phases, and occupancy by cell (f6c7ae0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Grow networks by hyperedges and add the growing simplicial complex (000f362 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the reduction over hyperedges and the hyperedge mode of CouplingInteraction (e4143b6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the agent form of CouplingInteraction over radii with priorities and clamps (44c339c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Transfer amounts along group edges in both directions with shared draws (cc7b254 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run hyperedge interaction laws per hyperedge on XGI hypergraphs (375466e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add visits drawn with replacement, compositions, and observable histories to agent rules (8bb62ae by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Couple separate elements and hub elements in CouplingInteraction (a504f4d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Accept parametric coefficients and the agent form in ReactionInteraction (9e5f97d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replicate systems that hold interactions and rebuild the named maps on MapInteraction (89152a1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add shared kinetics and pharmacokinetics families and decompose Kirschner-Panetta (1538463 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add reference states, referenced transfer legs, group entries of variadic roles, source sets of transitions, and sign adjustments (28fe187 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Cumulative and vector reinforcement, agent imitation, and the learning models rebuilt on them (1d55a94 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add life cycle variants, optional roles, and growth from outside a network (cb8664b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Truncation, proportional selection, mutation rules, period, evaluation, and best-mutant climbing in evolution (2c9d870 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run agent interactions member by member and act on cells, fields, and sight (bc33807 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name transfer flows, pair disjoint neighbours, and fall back to a second group (06cd7e5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Couple conservation laws, add advection, sum Lagrangians, and widen divisors, resets, and Hurst indices (cddb301 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Extend coupling with a source group, extremes, normalized and circular means, callable weights, and joint pair states (138db6d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
React per member of a group or field and bind species under renamed roles (c068f39 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add agent forms, schedules, residence times, cluster moves, combined updates, and member events (512428e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add map, local rule, jump, transition, encounter, crossing, impulse, and sampling interactions (510be58 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Generalize coupling, add pair coupling and points (bebec96 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add movement, transfer, life cycle, grouping, and topology interactions and greedy matching (322d62a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add rate, relaxation, gradient, Euler-Lagrange, conservation, and diffusion interactions (dfa14ef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add agent choice, Fermi imitation, reinforcement, and overlapping evolution (dcedbe0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add pointwise, delay, keyed, and circular utilities to the law namespace (d33946b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add spreading, coupling, threshold, and imitation interactions (9a7a6a0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Extend neighbour edge kernels and reductions (84a6ebc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move matching and feedback to the core (f8d759c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add Ornstein-Uhlenbeck, pair force, damping, and constant force interactions to the core (06237d6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add AlignmentInteraction, polar and nematic, with noise and zones (3c976e4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add compartment, density, and oscillator elements and reaction and growth interactions (a34abbc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add ChoiceInteraction and EvolutionInteraction to the core (c6ae3a0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add ForagingInteraction and RegrowthInteraction (0b89bdb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add RandomWalkInteraction with neighbour, Gaussian, and Lévy steps (a342a6d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the agents of the social models with a view class per group (d9fd6a4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let an agent element name the typed view class of its agents (26530e5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the physics and social realizations of the dissolved field measures (3b4b76d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the field realizations of alignment, rolling, and event analyses (0a2e7dd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read feedback loops from the signed dependency graph of any system (3879482 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add DiscoveryAnalysis, which lists the analyses that apply to a source (9125d96 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Restore the conditions, histories, signals, and lookups that laws are written with to the core (c55d656 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the states every law changes targets on the law base (9c9571e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Report backend substitutions, Numba fallbacks, and invalid spaces (866d3c8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the import codemod that rewrites imports from move tables (860946d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Register formalisms and law classes explicitly (b5f770f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the size, value names, and value rows of a group at creation (2e2cbfd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add network, flocking, and adaptive network models (0bea509 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add Active Model B+ and thermal noise of Cahn-Hilliard (e80383a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the nonreciprocal Vicsek model and fix cached Numba neighbour searches (01f3f0c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add conserved noise on lattice fields (9b4b630 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Validate topology requests and record and draw changing networks (776493a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run variable groups of networks with capacity layouts and apply topology requests (accdb31 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run interactions over neighbours once per edge and read edge states (c35f763 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add network layers, array views of networks, and network generators (590fc29 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add Metaphoria and Wilhite's trade networks (5080117 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the surveyed physiology, tipping, and flow models (0aa0983 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the surveyed stochastic and collective models (73571b1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the surveyed lattice field models (66c217c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Register the group automata models and record them in the inventory (270fa89 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the evolutionary Sherrington-Kirkpatrick game (4a66148 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add feedback controllers and control models (5449d2c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add chemical Langevin reactions and correlated asset prices (76a4c90 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add named and correlated Wiener processes to noise laws (305912f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the fractional dynamics models (f4947d7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the Mittag-Leffler function and the exact fractional relaxation (e8626a3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add Grünwald-Letnikov, L1, and predictor-corrector schemes of Caputo derivatives (4ff0eaf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Accept fractional orders of states and validate them (a2dfa94 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the echo state network (e248e97 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add kinetic models of active particles (b4d0ddc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the repeated agent economy models (8adfbed by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add group spaces, group constructors, and automata theory (b461dc6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add bounded controls, objectives, and optimal control solvers (52ac705 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fit surrogate systems to series by DMD, SINDy, and reservoirs (cec512a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Log the states of a group without a space with the traits visual (459da77 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Convert between group members and distributions over activities (81cf786 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add encounter laws, moments, and the particle solver (cc85c26 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add epsilon-machine reconstruction by causal-state splitting (13001a5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add integrated information criteria of emergence and closure of coarse-grainings (277d62f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add local entropy, mutual information, and transfer entropy (fca0cd0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add effective information, causal emergence, and ergodicity breaking (f44396e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add total correlations, O-information, partial information, and surrogate tests (096d6fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check invariants of interactions over the agents they bind (ea97447 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compile neighbourhood reductions on the Numba backend (2636989 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lower neighbourhood reductions and validate their neighbourhoods (58cccc8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Generalise neighbors to reductions over neighbourhoods (b0d9d44 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add radius, nearest, and cone neighbourhoods to the space layer (b702ee1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the Kinouchi-Copelli excitable network (e14d5dc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the nonreciprocal Cahn-Hilliard model (4d32b5f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the tipping cascade network (ae80737 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add cloning, the thermodynamic uncertainty relation, and dispersion relations (5db7dbe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port the agent models to elements with rule laws (d02ca1f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make agents ordinary elements and Mesa a backend with declared support (4518b5b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replace QuantumSystem with simulation initial states and solver limits (5b37a0f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move rule codes to the automata models and record realization decisions (e02d32d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move quantum species to the physics realizations (0c69406 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move named particle forces to the physics realizations (509e126 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move economic realizations to the library and check member invariants (5bd71ae by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rename Hamiltonian to Generator and generalize distributed delays (53772b0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add transfers, invariants, matching, and adaptive parameters (81fb3ba by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fold renewals into jumps on clocks and Monte Carlo parts into Sample (6fd2d66 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Bind interaction laws over members, pairs, neighbours, or hyperedges (e44ca45 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Declare quantum and rewritten states by their domains (c29cd9e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let groups vary in size and live on sites, edges, and hyperedges (8ce14a5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Unify spaces so boundaries belong to the space and agents share its kinds (bfeca72 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Define systems by their components, interactions, space, and time (046afb5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tag the inventory with the system vocabulary and validate systems before compilation (20ea234 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Log stock-flow outputs under their element, give extra entities their own sanitised namespace, and list trajectory names (f2f73a4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Warn when a gallery thumbnail lacks a series its caption names (3d5f6c8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fail strict documentation builds on models without examples and examples without screenshots (cc3c6e5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Report the waiting times of priority queues and show the task ages (0888831 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Print the thumbnail paths from the gallery run (ba382d3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw agents in continuous spaces y-up within the space, and start point colors at a visible blue (bca2c65 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave lag states out of scalar series and let scalar visuals pick vector components (7610fe0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run orbit diagrams and basins as one replicated simulation and read members as trajectories (65152c0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replicate systems of single elements into vectorised ensembles (4942be8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record hidden events in fix-core-defects-3 and move the stall test to a group of tubs (820cf42 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compile state conditions of laws into hidden events that restart integrators (fee225d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add cocoa, hilsa, food security, and net energy models and rebuild Meadows' resource models on flows (b5a86d4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw bodies in three dimensions and curate the Stormer problem (6160772 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw oscillator phases against their place on a ring and curate the ring chimera (ae5f12c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw fields on networks as colored graphs by default and drop the network diffusion workaround (241d804 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw one-dimensional agent positions as a space-time diagram and curate Charbonneau traffic (b1fb424 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw agents at a position state, on a line for one coordinate (5c1a800 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Size histogram bars to their bins, let traits show the histogram first, and curate the Deffuant example (5642ae5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Log distinct values and per-agent series of traits and drop the Bernoulli process workaround (59309b6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw the traits of agents without a space as histograms and statistics (0a8cd7a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw pendulums, billiards, and planar orbits as bodies and drop their observer workarounds (c679763 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add a visual of bodies, rods, fading trails, and outlines (1c1a3bd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add phases, markets, institutions, and learning blocks for agent economies (ab8bd15 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add quantum systems with QuTiP unitary, Lindblad, and trajectory solvers (f34b8a8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add stocks and flows with conserved quantities, delays, loop analysis, and agent ledgers (acb276c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Extend the analysis toolkit with data kinds, adapters, signatures, and seven families of measures (e31c9e9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add triangular and graph lattices, colored schedules, and extremal updates (b413072 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add renewal laws, fractional noise, and anomalous diffusion models (0ad11d4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add rewriting systems and the substitution fractals (191aa7c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add stochastic maps with named random draws and Markov laws (7407a96 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass sparse Jacobians derived from the laws to the implicit SciPy methods (1e03c7e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add complex states and the Mandelbrot and Julia sets (1c733f9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the cancer, systems biology, and statistical physics models of four references (75356de by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw 1-D lattices as space-time diagrams and scale points and agents to their space (6b4bc98 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the model gallery with Rerun thumbnails and ten curated examples (681e652 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Extend interaction roles with variadic roles, several groups, and member offsets (9c915bf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add reductions over groups and element sets to laws (1b3dc2e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Implement the surveyed models of every field on the core interface (4f05bcf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add spectral, finite-volume, and finite-element fields with stiff and exponential solvers (3e8aa04 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add spatial fields with differential operators, boundary conditions, and agent coupling (263c30a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add lattice dynamics with local rules, relaxation, and Monte Carlo sampling (4f95f3e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add hybrid dynamics with delays, events, drivers, noise conventions, and sections (8a98194 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the analysis toolkit for stability, chaos, distributions, series, information, space, and networks (1a6c9ff by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add experiments with designs, scenarios, ensembles, sensitivity, and calibration (3193d21 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add equations and difference equations of any order (c690ced by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the general model interface with defined components, domains, observables, and a model catalog (a7d7ee1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add co-simulation of partitions with different forms (9c9b086 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add agent-based models on Mesa and wrapped Mesa models (d81bd83 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the LAMMPS backend and standard particle potentials (3782c22 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add Numba backend, compiled stepper loops, and velocity Verlet (7b7e6f3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add element groups, pair interactions, and boundary laws (8cf8e90 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Change API to support creation of systems (ca1eec1 by georgedouzas).
Add math module (adb5c7b by georgedouzas).

Bug Fixes

Keep MPI off InfiniBand devices in the LAMMPS solver (420e0f8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Load the MPI library of the mpich wheel for LAMMPS on Linux (61edf43 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep one copy of the parameters across frames while they stay the same (4176f12 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the Rerun update notice out of web captures (74f718e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave the states of variable groups out of the default series (afa7227 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Align velocities along a line by their sign (a0f47eb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read group states as series and phases by their role (8c83a72 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Apply the turbulent defaults of active_gels to the nematic order only (d2187a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lower the default step of the double gyre below its stability limit (ffa377c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Derive the Jacobian of log_sum_exp, fall back from an unparsable exact solve, and keep a converged search (7b97e98 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Resolve the conflict markers left in the active matter exports (a3f92bc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Resolve the active matter surface after the rebase (e6decdf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Clear the pydoclint, mypy, and docformatter findings of the merged static and phase-space work (95a5f65 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the Target alias, record the gel primitives, and describe the bursts of the gel (c359174 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave coupling tensors out of the parameters a Rerun observer logs (485eb13 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Raise for spec variants without an override and fire every tied crossing (8358a0f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read a parameter declared outside the interaction from the namespace (5b04070 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw initial values from the seed's own stream now that runs spawn theirs (55fc921 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Join periodic clusters across every wrapped neighbour offset (8fd1baa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the parameters to the offset reads of flow observables (4324bc3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Combine updates of one group member without visiting every member (93ae8ce by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fix the typing, docstring, and security findings of the checks (791abb4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep agent rules in the declared order of plain interactions (9c3481a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let a reference state name no member in a model without the referenced group (2f01dbc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read the interactions bound to a field in its dispersion relation (bfe26fb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the increment mode of the rewritten maps by its new name (9014eac by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep Verhulst's logistic free of the crowding exponent and test every population form (b1bd93f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Export the energy sector element so its example imports the public surface (1788c45 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the increment mode of map interactions by its new name (9498fa6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Drop the import of the renamed clearing spec from the interactions surface (2edc20c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the compiled printer function and give in-place kernels an empty result (cdc6926 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Remove the last suppressions and pass the checks session (ccf35ed by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the remaining findings of mypy without suppressions (f5a73d3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fix the type, docstring, and suppression findings of the core, analysis, experiments, specs, root, tests, and docs (7cbb602 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the engine's hooks and results and remove its suppressions (a498157 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the checks in the physics models (47902e7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the social model tests and gallery examples without suppressions (cafbe49 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the checks in the biology and chemistry models (b4074e4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the model catalog's run settings and registered tuples without suppressions (693477e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the gallery examples that broke under earlier API changes (4a33789 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Discover only the general analyses, not the realizations of the models (1249058 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read the swept values of orbit diagrams and seed the Ising domain growth test (f82e70f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Size the coupling observable of the origin-fixation walk by its prepared genome (ea03a33 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Report laws on fractional states that no fractional solver runs (60024a1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Report bindings over neighbours and hyperedges by interaction class, and too large Cayley balls (f480c22 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read the prepared values of a group when validating its variables (f8b8d28 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Declare that Cayley spaces lack image visuals (318d1df by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the label of a generator neighbourhood to its base by keyword (2d9c4ff by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Size the couplings of origin-fixation walks from the prepared genome, and convert the remaining model tests (7276fb7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give spins one half and lattice particles the operators of the converted quantum models (8b116fa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the moves of spin models with MoveSpec kinds, and keep the defaults of institution phases (db72ee2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Store the values of finite sets of numbers instead of their indices (2946557 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Match the laws a passed solver supports by subclass in planning (7224576 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the arguments of the conservation hooks and leave init docstrings out of tests (199aa73 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read slow-test trajectories by name, ignore test law kinds in the inventory, and rewrap long lines (f4b1292 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep attribute access of agents in the market realizations (833ac9e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Repair the tests and checks broken by merging the verb families (a71a78d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Print plain floats in the control solver doctests (f277d92 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the test formalism out of collection and follow the engine split in tests and the gallery cache (5714b4b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the gate on Python 3.12 and keep docstrings and tests current (2a61869 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Release the threads of finished Rerun recordings (3452075 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Clean up type and lint issues after merging add-adaptive-networks (3f78337 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Share network spaces across clones, keep reductions undecided in conditions, and type the edge kernels (2a5d9d0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Default the fractional Lorenz flow to the chaotic order 0.995 (5f4a3ca by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run a call with a vector target once per evaluation in NumPy kernels (d6ad724 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Skip time breakpoints of a modulo nested inside another function (1f39b87 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compile Laplacians on networks without edges (0f7c81b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the redesigned core for mypy and pass the checks (a0d481c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Redeclare the domain of a symbol whose name was declared before (e9db036 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mirror the bounds of binary_collision_flocking now that agents are drawn y-up (9f298b7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw gallery runs on Agg and silence plt.show even when pyplot is already imported (8517f3e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the gallery tooling for both the checks and the full environment (404f6fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let fixed-step integrators step over switches of the drift instead of firing hidden events (ea21ec6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the Burridge-Knopoff fault with a fixed-step RK4 by default (7cb3b84 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Seed catalog runs and factory initial conditions by default (846d1f5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give LEGION a default time scale that fires both objects in a short run (b4b91d8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give the speckle field a default strength that shows anomalous diffusion (9aa674e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Start the restricted three-body problem on a chaotic orbit (9b33657 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Time whole gallery scripts and give each run its own recording folder (27670ce by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave LSODA after too many steps in a frame, name integrators stuck on a sliding switch, and name blow-ups (a7b37ad by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Remove the checksums of failed gallery examples (d955260 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Include the core code in the gallery cache key (cb925bf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Silence the warnings of powerlaw during power-law fits (ff1aeb7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Accept single-channel images in the gallery capture checks (2c029a4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Feed obesity eaters without nearby restaurants and add an activity factor (c3bf887 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compile Lyapunov tangent dynamics once with signs for absolute values, name dead worker pools, and keep hidden events to flows (55716c1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Silence plt.show while the gallery runs examples on Agg (c174551 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Retry connecting to the headless viewer until it listens (77b96b7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Damp the Nyquist mode of the spectral Laplacian, seed both parts of the CGL amplitude, and curate it (723230b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the group of a stigmergic offspring positionally for the type checker (a8841c3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give the offspring of stigmergic animals their parent's hunger (c5f16c9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Size single particles by the whole drawing and curate the spring chain (54ed232 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Start the Huygens clocks away from the escapement switch (82210fa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the sessions that install with pdm on the newest supported Python (8d397b3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the bounds of binary_collision_flocking, whose birds are agents drawn without the y-up flip (5398d87 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mirror the vertical bounds of point examples drawn y-up, and silence mkdocs-gallery's own deprecation warnings (f9d9b2c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Scale the Schlögl defaults so noise switches and set the hodgepodge infection rate to 34 (f3b1d9c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Total rows of numbers in trait visuals, such as inventories of known words (70d89bf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Flip social impact opinions under net pressure (982c34e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Declare the lazily imported analysis libraries to deptry and document the return of the quantum solver stub (5e60684 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show trait statistics first, one bar per integer value, and distinct statistic colors (774f878 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Widen color ranges that are not given instead of fixing them from the first frame (b892055 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw 2D points with the vertical axis up (f39c441 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give the series of scalar visuals distinct colors (5239417 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Color angle images cyclically and keep wrapped angles exact (4f0855a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show the sugarscape landscape example as plain floats, independent of NumPy's print options (b6615fc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Project a state resting on its boundary at the end of the step, and start every loop at its first stock (44543a9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Continue with RK45 when LSODA stalls on a state resting on a discontinuity of the drift (4d587e0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Choose LSODA only while its dense matrix fits, and RK45 or BDF for larger systems (f04a6ec by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep LSODA's own first step unless the drift vanishes, and pin solver tolerances in tests of RK45 values (c64170c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Declare hidden states at running offsets and start LSODA from a trial step when the drift vanishes (f948002 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Wrap angles into (-pi, pi] and apply boundary laws after lattice steps (c80aa83 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run rosenzweig_macarthur with relative error control through its deep prey collapse (1f48e63 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import heavy analysis libraries on first use and annotate the analysis tests for mypy (b461b26 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fix the second round of core defects and make LSODA the default ODE solver (fce79fd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the chaos game type ignore valid without NumPy stubs and mark the draw pickle test for bandit (445d859 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fix the core defects found while building the model library (f8742e3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make two doctests independent of NumPy print options and mark seeded draws for bandit (dc4e17e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spawn the Rerun viewer installed with the running interpreter (b1f808c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Docs

Show the catalog entry on example pages and sample three models per field (bab8500 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Hide the gallery subsections without examples (6c7c60f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive neutralize-core-names and link the README images absolutely (c9a6dff by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Plan the analysis data, the particle results, and the remaining names (4c45313 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name operator dynamics in the user guide and the constitution (61fbb63 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State the operation in the docstrings of operator dynamics (7f279ca by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show screenshots of ready-made models in the README (73d2129 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name operator dynamics for their mathematics instead of moving them to physics (bb007c8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Drop the bold from the README prose (ff9a9ce by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Shorten the README titles and lead its usage with building a model (f9cbaf2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show how to browse the model catalog in the README (281819a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Align the README gallery images at the top of their cells (f57f861 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the badge table of the README in its place (c6e217c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the README around the models of every field (2aeeee5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the position role and the remaining renames of neutralize-core-names (0df5a48 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive and complete add-tensor-fields (72e2add by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive and complete add-static-models (12c0697 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document log_sum_exp, contact clusters, satisfiability, optimisation, and annealing (2862461 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery of the static models and mark them implemented in the inventory (657244f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery example of the Bertin-Droz-Gregoire kinetic flock (ac98227 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery example of the Enskog equation (1ea8859 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery example of the Boltzmann equation (fd77657 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery example of the BGK equation (ae42f23 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery example of the Vlasov equation (ad600dc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose neutralize-core-names from the core audit (960b017 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the measured references of add-static-models (dbd786f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the anchoring, turbulence, and operator cache decisions of add-tensor-fields (c86ae9b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Restore the generated changelog of the last release (37fd476 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave the changelog to the entries generated from the commits (6c0d54e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the changelog entry of tensor states and the new models (c640ee9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the gallery examples of the five higher-order models without one (48dc2d0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive and complete add-phase-space-fields (9eb0c18 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Say disorder averages sweep the seed throughout the add-static-models design (d8917d7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the disorder averages and the cooling check of add-static-models (a3c4fcc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive and complete make-core-extensible (1b7d2b1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document hooks, partners, functions, and object states, and tick make-core-extensible (b61cc36 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
List the movement arguments in the order of its signature (c1c228b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive and complete the higher-order, variational, finite-volume, learning, and nonlocal changes (7af2001 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the matching defaults and tick the silent results of make-core-extensible (1d37c71 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the partner selection tasks (932af3f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the nonlocal operators and couplings on fields in the user guide (a8ce32f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the nonlocal field models to the inventory and the gallery (08b8bef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Follow the sources for the higher-order Lotka-Volterra model and the GKT front speed (cf63e46 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the LEGION check, the variant rule, and the trajectory names (0a089af by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Require boundary= for mixed-boundary inversions in add-nonlocal-operators (a6a31b8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the variadic expressions of contraction in its docstring (d18a999 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document training interactions, shaped parameters, and the JAX backend in the user guide (452b355 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the learning-dynamics decisions and save the Elman blueprint (c12f613 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show the shares of customers in the perishables example and fit the higher-order examples in the gallery budget (b1a55bb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the changelog task of the faster finite-volume kernel (6599ecc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the finite-volume timings before and after the faster kernel (7edf0ba by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the decisions of the nonlocal and learning changes (caeced2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document HamiltonianInteraction, Yoshida4Solver, and InvariantAnalysis in the user guide (24d3ed2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the variational-mechanics primitive of the Hamiltonian models (ca58de9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive complete-general-model-rewrites and sync its specs (d1d2d0b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Schedule the intensity of choice in the standardized agents example (b86f2d1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the arguments and returns that pydoclint asks for (a2b2de7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 3.3 of complete-general-model-rewrites (47c3c79 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose make-core-extensible from the extensibility audit (0b31ebb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Point the higher-order Lotka-Volterra entry at add-learning-dynamics (d2ba1aa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fold the library audit into the planned OpenSpec changes (0887a44 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the library audit in complete-general-model-rewrites (55d736a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Plan independent random streams in complete-general-model-rewrites (c0e1fcf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the third round of decisions in the rewrite and higher-order changes (646a557 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Note that the hyperedges reduction of task 2.3 is merged (bf5203b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the core extensions and social rebuilds in complete-general-model-rewrites (5077a4f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the observables and the economics transfers in complete-general-model-rewrites (20a9ee6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the open points of the public goods rebuilds in add-higher-order-interactions (5ea5986 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the new tasks to their group (c8601a7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the second round of decisions in the rewrite and higher-order changes (9fb5626 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the transfers along edges in complete-general-model-rewrites (5ee18a8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the couplings and the gallery budget in complete-general-model-rewrites (f67c02f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document hypergraphs and record the XGI survey (39b3d9b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record visits, compositions, and histories in complete-general-model-rewrites (efdf0fd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the biology ODE decompositions in complete-general-model-rewrites (0464497 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the ecology rebuilds and the herders in complete-general-model-rewrites (b67ce11 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the social rebuilds and the classes that stay in complete-general-model-rewrites (8cd538c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record parametric coefficients and agent reactions in complete-general-model-rewrites (5eae586 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the replication of interactions in complete-general-model-rewrites (d6b7a5b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive general-elements-and-interactions and sync its specs (76b9dd9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the open design decisions in the OpenSpec changes (eb2f928 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the documentation, checks, and merge tasks of general-elements-and-interactions done (369d6c0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fix the README and the gallery examples for moved names and states (4d3e44b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Align the add-acausal-components change with the revised add-static-models (529c5d4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-constraint-based-models change to the current core (58e8e77 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-static-models change to the current core (8e54029 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-learning-dynamics change to the current core (e866628 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-multiscale-networks change to the current core (a9cfc3f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-unblocked-models change to the current core (804a1d4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-acausal-components change to the current core (f9c3bda by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Generate the model equations and the compatibility page from the current API (5848095 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the extend-agent-spaces change to the current core (2563ade by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-molecular-structures change to the current core (5c3b8a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-nonlocal-operators change to the current core (6aea700 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-phase-space-fields change to the current core (62bb951 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-link-fields change to the current core (238d00f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the import-system-dynamics change to the current core (da6649c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-tensor-fields change to the current core (64c40ed by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-higher-order-interactions change to the current core (c35409f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the laws and bindings every model uses on the general classes (2425db7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the adopt-pyclaw-finite-volumes change to the current core (3f7ade4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Revise the add-variational-mechanics change to the current core (dd0597a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the general elements, interactions, and law utilities (cde0c37 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record what the general rewrite delivered and move its leftovers to complete-general-model-rewrites (0e9afc3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off the engine extensions and the fields and mechanics (57964c8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Resolve the merge of the transfer and life-cycle catalog rows (dfb545e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State what enters the core: fundamental paradigms usable across domains (8470d6d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the learning and evolution variants in the catalog and the spec (f1426ef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the core capabilities the model rewrites need (96e0842 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fit the shared family docstrings to the line length (f705cb9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
List every shared physics family (13c1236 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the earth elements and keep their law helpers as private methods (1863185 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the excitable family of the shared biology code (7c3bcbd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the flows the process elements return (5ba17bd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off coupling and points (eee6cdc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off events and discrete states and add the engine extensions they need (4c7bade by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off the agents, groups, and exchange interactions (c205277 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off the continuous-time interactions (a0b9e32 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Choose the agent lowering by a form argument and check off choice and learning (405dbb3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the law utilities as done and the compartment state as renamed by subclasses (595017c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Redesign the general-elements change around operations instead of field mechanisms (8581cb9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off the merged core, force, and matching tasks (3144d77 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let mechanisms lower to agent rules on agent groups (002724e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off the choice and evolution tasks (2d8cdac by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Extend neighbour interactions and reductions in the general-mechanisms change (31ec8e0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record that hyperedge laws do not compile per hyperedge yet (c5a3d71 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose the general-elements-and-interactions change (be4fbfe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the restore-abstract-hooks-and-fitted-results change (85bbce3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check off the integration tasks of restore-abstract-hooks-and-fitted-results (63b43a1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State the abstract hooks and fitted results in the Project Profile (c7945a1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose the restore-abstract-hooks-and-fitted-results change (2bd8f5c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the pass-checks-session change (7481141 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the real arguments of the engineering, mathematics, and computer science models (7b43964 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the real arguments of the social models and the model catalog (18ae77c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the simplify-base, restructure-downstream-packages, unify-root-hierarchy, and pluggable-compilers changes (c64547e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose the pluggable-compilers change (d59722e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
List the specs, core, and engine sources of a model in the gallery tools (eeed68e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read ProblemSpec and SignatureSpec in the gallery tools (9e7bcf7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import ObservableSpec in four gallery examples and name ScenarioSpec in the restructure change (88f1456 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose the unify-root-hierarchy change (7645160 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import LocalOperator from the problems package in a doctest (ecb3b78 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name MemberLowering in its doctest (202a22a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass the factory of a model to the orbit diagrams of the gallery (99eff5d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Specify the engine's common API, the model catalog in the models library, and experiments of systems (ef1baec by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the user's engine decisions and the common API of every engine class (24f343a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the engine helper and module tasks done (34263a3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the engine concept model written (9801b5d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Write the engine's concept model for review (89b03c6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the realization placement task done (624f450 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the engine design tasks to the restructure (2008cb0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State in the constitution where model code shared by a field lives (33a594b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Specify that specialized code moves to the model library and add the realization placement task (e24f399 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Place each realization with the one package that uses it, or in the field's shared families (ee61add by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the general operations and field realizations done (80592dc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Convert the user guide and gallery to the general kinds and realizations (1cc8a4f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the loop generalisation and the naming audit done (3fe2a24 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Describe the loops of any system in the user guide (32011b6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep specialized analyses as model realizations instead of removing them (8c5888f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Audit field names in the core, the engine, and experiments (cb993fa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Specify general operations in library packages and field measures as model realizations (e04db96 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the engine helper and module tasks to the restructure (d923205 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the guide and README tasks done (21e7037 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Bring agents, rewriting, quantum, experiments, and analyses in the guide to the current API (0634dc7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Bring lattices, networks, kinetics, fields, and backends in the guide to the current API (3f3555d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Describe the current package layout and kinds of dynamics in the guide (6ef48b3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Bring stochastic maps, observables, and flows in the guide to the current API (cf34889 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Write the README and the guide's basics with annotated specs (2245fd2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the analysis surface and layering tasks done (a40534e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the series and criticality families done (437773d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the merged analysis, experiments, and engine tasks done (5aa798f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Specify the restructure of the engine, analysis, and experiments as estimators (74ea1ef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Nest the subsystems of the co-simulation example and print the Laplacian trace as a float (4e56135 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Update the model examples to the new core (c32f38c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Write the doctests of the engine and the analysis with the new core, and partition co-simulations on the default backend (4a79f71 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Describe parts and their verbs in the guide and the constitution (f460661 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the objectives and aggregates of the base change (66a5662 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec a part base with three verbs for elements, interactions, laws, and systems (37c78bb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the removal of quantities, observables, and invariants (fab9278 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Limit the base to elements, interactions, and laws in the constitution, and map auxiliaries to expressions (0f3e204 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec a base of elements, interactions, and laws only (ac5f705 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the class relations change (d94b10a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the gate of the class relations (97e102c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State the purpose of the base interfaces spec (b58ec32 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the base classes, base interfaces, and test speed changes (ef6628d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Count the voters of a snapshot by their ids (aa01651 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Note the current names of the related classes (4556a06 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Settle the names and the open questions of the class relations (f2d2c15 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the shared fields of the value bases (8fd264f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the finished tasks of the base interfaces (83f977a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
List the integrations that follow the system dynamics readers by area and order (4817168 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Join the roadmap to the list of changes (5646872 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Order the integrations that follow the system dynamics readers (76a1385 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read trajectories with values in the gallery (a9a8b27 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec reading Vensim and XMILE models into systems (f1a1061 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import the formalisms package from its new place (14ba273 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the preparing verb prepare instead of fit (3e53fd3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Amend the constitution with the shared verbs, trivial constructors, and no magic methods (1d06128 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the surrogates as estimators (cb5cb7d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read collections and symbols without magic methods (2afec1b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give every configurable base the verbs check, fit, and run (70b2800 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec bases that define the public API of their families (50ce61b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Settle where the problem, backend, and system compiler bases live (078b33b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name classes after what they are and regroup the core base by concept (40e7819 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the relations of the base classes and of the classes that derive wrongly (e6c1835 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec gathering the base classes into the base packages (025ca99 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the package requirement of package-layout (bfb3af5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose speed-up-imports-and-tests (d046e20 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 3.2 (5975dea by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrap the dependency placement entry (eb1fb72 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Amend the Project Profile for the core, engine, and formalisms packages (e7fea15 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Amend the Project Profile for strictly mirrored tests and import contracts (69deb76 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the model inventory in the docs build (b88c0eb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 2.1 (08305b9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 7.1 (17ba554 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 5.3 (a4e8df6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 6.1 (035b503 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
List formalism contributions on the compatibility page (4a21557 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the user guide for components, laws, layout, and formalisms (c1ed059 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 5.4 (2dce750 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Amend the Project Profile for the formalisms and the component contract (ad32016 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 2.8 (693e211 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the removal of tools and the mirrored test tree to redesign-core-concepts (d8fea74 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the planner's need for both a form and a solver (fe3f32d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 2.6 (6b283e1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 4.2 (37ed94e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the shared step count and tick task 4.1 (e896e71 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Order the pass pipeline before the moves buried in the compiler (c17f40a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick tasks 2.1 and 2.2 of redesign-core-concepts (4a815ef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose redesign-core-concepts (4422ad5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the correlated geometric Brownian motion example within the frame budget (1eccdce by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Measure the redundancy of Ising spins with the O-information (ded39f1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the decisions of add-adaptive-networks and tick its tasks (8c0ad73 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document network generators, layers, interactions over edges, reductions, and topology requests (48eef3c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the reservoir forecast from shadowing run in the user guide (6c7f613 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the library task of add-conserved-noise and record its choices (8e49d97 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the Active Model B+ gallery example and conserved noise to the compatibility page (e398a31 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Review the nonreciprocal Vicsek example (bef81b9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the nonreciprocal Vicsek example within the frame budget (86ea23f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick task 2.1 of add-adaptive-networks (0e42466 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the surveyed models implemented and record their reviews (17936cb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the reviews of the group automata thumbnails (50c7bc2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document control and record the optimal control decisions (9bc806f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document group spaces and automata theory, and add the group automata gallery (cf63bfa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add gallery examples of the control models (1025895 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record how the evacuation model holds a distribution on network nodes (e8144d1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add gallery examples of the kinetic models (5823044 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add gallery examples of the agent economy models (b3d4e76 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document fractional orders, schemes, and memory, with gallery examples (8236ca8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document kinetic models of active particles in the user guide (5d0e919 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document shared and correlated noise (91b477c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document surrogates fitted to data (5cb3914 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the decisions of the agent economy models (a9ab464 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document coarse-graining, causal emergence, and ergodicity breaking (87bd768 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document higher-order information and emergence, and add causal states to the Markov source example (70d9121 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document cloning, the uncertainty relation, and dispersion relations (670568a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Survey the thinly cited textbooks and the papers into the inventory (95601c7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the system redesign and sync its specs (e6b5f8e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the gate of the system redesign (7d0f3cb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tag implemented models with the laws their systems contain (bbe16a1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the migration of the library against the baseline (be8b1f4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record why Source and Sink stay as labelled transfer ends (4c10028 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the split of the core packages (e620b32 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import the README examples from the restructured core (93a5c99 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Amend the constitution to the restructured core (1.6.0) (8cd879c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Plan the constitution amendment of the restructured core (c6cc7f1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port the Mesa section of the user guide and record agent recognition (f6854b1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the rebase of the pending changes (824cdb0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebase noise, fractional, and analysis changes onto the redesigned vocabulary (aaf0d6a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebase field, kinetic, and finite-volume changes onto the redesigned vocabulary (855b7db by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebase learning, agent, and group-automata changes onto the redesigned vocabulary (0befb52 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebase network, link-field, and tensor changes onto the redesigned vocabulary (520e003 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebase static, molecular-structure, and acausal changes onto the redesigned vocabulary (27c5433 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebase constraint-based, optimal-control, and variational changes onto the redesigned vocabulary (a316be4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mirror the system definition in the core packages (464a5d9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Reflow the form requirement (b0bdc4b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the form table as a lowering detail of the compiler (af15f21 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the redesign of systems as components, interactions, space, and time with declarative validation (73093d9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec higher-order interactions, information decomposition, data-driven dynamics, multiscale networks, and dynamics analyses from recent papers (a0487bb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec emergence analysis, gauge networks, von Thünen land use, and the survey of thin references (aa68a53 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive add-model-gallery and fix-core-defects-3 and sync their specs (f9a59c5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the arguments and result of the LSODA stall check (5f9fe07 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Specify the model defaults of the model checks and close task 9.5 (ada0b6c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State the dealiasing cut of the Kuramoto-Sivashinsky spectrum (a147de4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State when the Faraday disk charges its battery and when its current oscillates (bdffedc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the solver findings and name the stable step of Rayleigh-Benard convection (2da9f07 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Close the capture spike with the CI gallery job as its Linux leg (1e0cc75 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the gallery tooling decisions and complete task 9.6 (d4933d3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive fix-core-defects-2, add-agent-economies, and add-stocks-and-flows and sync their specs (ad54584 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the gates of fix-core-defects-2, add-agent-economies, and add-stocks-and-flows (2a1052f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the social science gallery batch (3de7b8f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the blueprint clutter task and defer grouping by magnitude (11f4aef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State that the sandpile budget is not met and name the compiled relaxation loop (c29481d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the physics, biology, and engineering gallery batches (c7d47a9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate cocoa, hilsa fishery, food security, and energy return gallery examples (7813448 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the cause of the Nyquist defect of the spectral Laplacian (7303de5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the light-sensitive robots and record the model checks (c0dadf8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the XY model gallery example (e50d520 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State the carrying capacity and the die-off of the meadow model (3514d29 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the 3D bodies and the shared point radius in fix-core-defects-3 (e8c194b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the Kuramoto-Sakaguchi chimera gallery example (bb65a5b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the space-time diagram of one-dimensional agents in fix-core-defects-3 (0de3be2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the model checks of fix-core-defects-3 (523f4ae by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
State that a sensory delay drives light-sensitive robots out of the light (79d4870 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Correct the docstrings of the circadian clock, hypercycles, wealth, and living crystals models (4a58c62 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the prisoner's dilemma tournament gallery example (265f384 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the naming game gallery example (f4d7bdc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the Galam majority gallery example (425c062 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the Tangled Nature gallery example (56d3cf5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the Moran process, NK landscape, and adaptive climbing gallery examples (d5b15bb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the Bonabeau hierarchies gallery example (c3a670d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the real-time benchmarks of the gas and the Game of Life after the fixes (afe98e0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the angle tasks of fix-core-defects-3 after their regression run (105c422 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the mathematics gallery batch (34d2b68 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show the whole run in the dynamical systems time series views (f48d40d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the model gallery in the contributing guide (bfee9fd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run fewer Galton-Watson replicas (6da4f17 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the last stochastic process gallery examples (4c2212d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the social gallery review (aac20d6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate stochastic process gallery examples (b6802d9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fold the second curation log into fix-core-defects-3 (bab4c7e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fix the trafficking review row (7051bbd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the trafficking gallery example (9c971a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate social organization gallery examples (c18e26c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate social gallery examples (7dbf074 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Update reviewed mathematics thumbnail rows (e484898 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make mathematics thumbnails show their captions (4332494 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate social spreading gallery examples (a8f8cbf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the computer science gallery batch (61fda4c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate the Bernoulli process example and review new mathematics examples (52da9c7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate mathematics network gallery examples (b706d0c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the economics gallery batch (76cecb9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate mathematics gallery examples (b6b2e73 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Update the process review rows (8ffbf3f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show the whole run in the process thumbnails (7c24800 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate ring road drivers and complete the engineering review (d775c78 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Brighten fractal thumbnails and describe reviewed thumbnails (456e0f5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate engineering gallery examples (9d011e3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Show every captioned series in the economics thumbnails (df5d22c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add mathematics gallery review (0814dee by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate social gallery examples and review economics examples (2ac1804 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add computer science gallery review and fit the Takens-Bogdanov view (b6dcc1a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate computer science gallery examples (e177e60 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate economics gallery examples (776be32 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate turbulence, convection, and living crystals gallery examples (b898602 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Complete the chemistry and earth science gallery batches (3994e4f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate fluids gallery examples (f2477a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate earth gallery examples (67280c3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate Lennard-Jones, MIPS, and Toner-Tu gallery examples (e16bb12 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate statistical mechanics and active matter gallery examples (979201d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add review rows for curated physics examples (bf3799b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate economics gallery examples (WIP) (3526f0a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate rotating mechanics gallery examples (4eb07ad by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate mechanics gallery examples (25a36d1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add chemistry gallery review (bdc6a82 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the registered ODE models, the documentation, and the docstrings on the default solver (1364bf2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate soft matter, active matter, and criticality gallery examples (b5f84df by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Describe the new biology examples in the review list (d07e602 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Extend the biology gallery review list (581491b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate biology gallery examples (77f8030 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark gallery observer workarounds for removal (ecf73e6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Review curated physics examples by other authors (84067f6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate restricted three-body gallery example (4274168 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the biology gallery review list (dd26637 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate mechanics and celestial mechanics gallery examples (59aa20e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate synchronization gallery examples (6f7d8ca by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add physics gallery review list (149062d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive organize-model-library and add-quantum-systems and sync their specs (0df64c7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the primitives and priority of every inventory entry and report coverage by primitive (e6cfdaa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Propose the third round of core defect fixes (18ed8b8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate celestial mechanics, waves, cosmology, heat, and pattern formation gallery examples (6d8bff6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate sandpile gallery examples (7cdb741 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate criticality gallery examples (352a9bc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate statistical mechanics gallery examples (7ac9a26 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate mechanics and nonlinear oscillators gallery examples (5d03c1f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Curate chemistry gallery examples (49c7628 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive extend-analysis-toolkit and sync its specs (76836ef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec models as probes of the core, with primitives and priorities in the inventory (079a586 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive add-lattice-geometries and sync its specs (0a1b57c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive add-anomalous-processes and sync its specs (7f5ec8a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive nine applied changes and sync their specs (0e44bc4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the gate of add-complex-states (9a93d4f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the second round of core defects found while building the model library (22b87df by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave no surveyed model out of scope (051ef5c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the Bertin models, the analysis toolkit, and changes for every out-of-scope model (1ff5589 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Survey three systems biology and cancer references and spec their models (8a1ef00 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the model screenshots the gallery thumbnails (c45a803 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec a gallery with a runnable example and a Rerun screenshot for every model (b892a06 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the fixes of the core defects found while building the model library (5a51bed by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec correlated noise, extended interaction roles, and group reductions (e1a94e6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Record the numerics audit and spec its follow-ups (51747bc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the core and models layout, the taxonomy, the model pattern, and the moved paths (1082ba4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the pending changes to the core paths and record their models in the inventory (69d4aa6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the model inventory, its check, the coverage page, and the field pattern pages (2c6670f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the missing features that block surveyed models (d5a0717 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Amend the constitution to build on mature libraries and the core and models layout (79a632b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the organization of the model library by scientific field (dae5b05 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the lattice dynamics, spatial fields, and PDE solvers changes and sync their specs (7d39d4e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the hybrid dynamics change and sync its specs (527b635 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the analysis toolkit change and sync its specs (d9c61da by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the experiments change and sync its spec (b165df3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the general model interface and higher-order equations changes and sync their specs (c47f38e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec equations and difference equations of any order (025ca2b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spec the general model interface and fifteen changes drawn from the references (d5b922f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the Sage change, sync its specs, and remove the equivalence baseline (27f228e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the co-simulation change and sync its specs (bfdffb6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the Mesa agents change and sync its specs (c7a800a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Match the Mesa agents design to the implementation (963ac7e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the LAMMPS backend change and sync its specs (0c5c659 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the Numba acceleration change and sync its specs (b630272 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the element groups change and sync its specs (4037e3a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Plan the co-simulation change (c00dda7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Plan element groups, Numba, LAMMPS, and Mesa changes (8824479 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive the framework kernel change and sync its specs (2773358 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fill the Project Profile and record the kernel change progress (b16d36e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Plan the framework kernel change (c3cfaba by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Modify usage instructions (b3ee83b by georgedouzas).

Style

Wrap two docstring lines of the analysis base to the line limit (fbec3b0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give the gallery time limit variable a string default (bd78f68 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Word a test docstring so the formatter leaves it alone (6cd7887 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Wrap the docstring of SamplingInteraction at the line limit (25b2c6d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Wrap a long assertion in the field lowering tests (3f04343 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the higher-order docstrings on one line under docformatter (7021e3a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the Hamiltonian interaction tests (536daef by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the docstrings with docformatter (ced0674 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the settings docstring last among the invariant constants (eea9e4f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the corrected gallery examples (1af9e50 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Shorten a docstring line of the transfer leg check (c40f66b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the expansion potential (438bd5f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the merged biology models (10797ad by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the billiard visual default (b2ed95c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the merged interaction tests (f391e68 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the tree with black (8e82720 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Clean the lint of the ported engine (6ff13f5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Reflow the domain base docstring (acedd02 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Apply docformatter wrapping (6f15349 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Format the spectral Laplacian field tests with black (2327bd7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Code Refactoring

Couple LEGION oscillators and exchanging cells with CouplingInteraction (319fdd4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Hold the generalized Lotka-Volterra matrix as a parameter (ae55c20 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the social model modules into one class per module (0234e52 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the Q2R spin and Rosenzweig-MacArthur modules as their models are written (9b5473e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the biology model modules into one class per module (7346592 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the physics model modules into one class per module (2c64854 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the mathematics model modules into one class per module (257b05e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the engineering model modules into one class per module (a2373ad by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the economics model modules into one class per module (9fc5d63 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the earth model modules into one class per module (36c3039 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the computer science model modules into one class per module (fe28ae2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the chemistry model modules into one class per module (d8a257a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild standardization, segregation blocks, beliefs, the employee, and trafficking bills on general classes (57e71be by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep only the transfer legs in the economics transfer interactions (bd372a8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read the catalog observables instead of reporter-only interactions (bc94d22 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Decompose single-element ODE models of oncology, neuroscience, physiology, and systems biology (16a38e7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build agent predation, trails, ants, angiogenesis, and stigmergic plants and animals on member interactions (33e8e38 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Buy and sell the herders' cows by a member life cycle (bcb1c90 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the perishables market and tangled nature on visits and general agent interactions (7a1e124 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the wandering of the sabotage supervisors to a member movement (74bdc63 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the system traps on transfers and the employment takeover on local rules (1e27a07 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the spatial games on local rule interactions (9b156af by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild crowding, walls, and recruitment on encounter, gradient, and rate interactions (26cb5f7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the coevolving voters and club members on maps and topology interactions (2a1e310 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the transitions of the epidemiology PersonElement on TransitionInteraction (332f1b5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the degree-class mean fields on callable coupling weights (9f53b31 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move times and neighbourhoods to their own core packages (5641d40 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pay and repay at the referenced banks by transfers in fractional-reserve banking (f9845c6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name parents, employers, and owners by reference states and pay the bank's dividends by a transfer with a fallback in metaphoria (5f1f287 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the sugarscape foragers on a best step with vision, transfers, and a life cycle (bf55c43 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the owner of a cow by a reference state in the commons (d28a8bf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read credit partners by reference, separate workers by a transition, and step shop prices by sign adjustment (591fd46 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Bring riders as arrivals of a life cycle (3d979fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Grow networks, branch, and fragment by topology and life cycle interactions (20b3245 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the wolf-sheep animals from member movements, transfers, and life cycles (e0ba2e4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the chemistry kinetics as reactions in chemistry/common/kinetics (dc09cfa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild shallow water, traffic continua, KS, vorticity, Boussinesq, walkers, pendulum springs, and spring-dampers on general interactions (7344adf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Quote, post, search, plan, open, settle, appraise, regrow, and respond in the markets by agent maps (cd6c03e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the Hopfield neurons by a random-sequential agent map (1435c5c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the Nagel-Schreckenberg rules and the rider waiting on local-rule and agent map interactions (616efab by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the Kinouchi-Copelli elements by transitions (5a861ab by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build reducing jumps, Bernoulli trials, and ageing walks on agent maps (41fc60b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run investing firms, credit plans, settlements, and bank quotes as agent maps, and share the regrowth of resources (f7d3a7c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Grow Gibrat and Kesten firms, floor their sizes, account traders, and adopt phones by agent maps (7665301 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build voting, Watts activation, social impact, and threshold adoption on map, transition, and movement interactions (71986cd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the probabilistic Boolean function on MapInteraction (2e8020c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the activity-driven hosts by two discrete-time transitions (d038ee8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild pulse firing, Q2R, FHP, and billiard walls on crossing, local-rule, and reflection interactions (8616504 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the oncology growth laws from the shared populations family and drop transitional re-exports (39c6c6a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Turn the matching protocols into rule specs run by MatchingInteraction (a0abe96 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild fluids on conservation and variational gradient interactions (8ec011c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Relocate Schelling residents with the core MovementInteraction (1bf39f1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Play the tournament as a grouping and drop the imitate helper (f98a44a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild soft matter on gradient, rate, relaxation, jump, map, and local-rule interactions (8bef48f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build kinetic encounters on EncounterInteraction and the drive on RelaxationInteraction (596be13 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild mangrove succession growth as rate interactions (d3f9bed by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild spins, sandpiles, and forest fires on the general core with shared spin sampling (5624f7e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the opinion group mechanisms on the core GroupingInteraction (85c2f16 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild generalized Lotka-Volterra growth as a rate interaction (3c00665 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Step Jensen's unstable populations by maps and document the Fisher-KPP site (14c8314 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the network models on topology, map, coupling, diffusion, and movement interactions (ddb00f0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild waves on rate interactions and a moving harmonic anchor (cd3ced8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Switch intermittent hormone therapy by TherapySwitchInteraction crossings (d6f37f8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild active matter and pattern formation on the general core with shared active and field realizations (91ee4e8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Deliver radiation fractions by an ImpulseInteraction instead of a counter state (52cd3aa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the markets agent models on choice, reinforcement, greedy matching, and movement (3327968 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild heat and cosmology on relaxation, diffusion, and gradient interactions (cc4a624 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build growth on RateInteraction, encounters on EncounterInteraction, and use core utilities (02139a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the resources models on the general core (65b333a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild celestial mechanics on Euler-Lagrange and gradient interactions (1202922 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild ecology maps, jumps, and predator-prey events on general interactions (d0fe020 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fire spiking neurons by a crossing reset and use the core sigmoids (d89d7bc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Draw the chaos game by a random affine map interaction (0cf3bd4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild mechanics on Euler-Lagrange, gradient, rate, and reflection interactions (b14213e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild synchronization and nonlinear oscillators on the general core with shared oscillators (a830de1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the stochastic processes on jump, transition, map, and rate interactions (9d56ce3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build car following, Langevin driving, and LWR on the core interactions (06b6892 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the creative phase transition on MapInteraction and document the Bass market (513349c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Derive the fractional element types from their integer-order elements (4efd3d2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build flows, pharmacokinetics, and excitable media on core transfers, reactions, and diffusion (7ed49a5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild macroeconomics on general rate, map, and greedy matching interactions (6aee988 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the wealth class encounters on EncounterInteraction (d16e9af by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Share the Lorenz flow and drive the Rössler flow by core interactions (8daa28b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the arbitrage transport on RateInteraction and quote order book forecasts with the shared heuristics (b8ee27c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Send El Farol patrons to the bar with a best-rule choice (edfd603 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rebuild the cobweb and price markets on map and rate interactions (ac27f3f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Choose the minority game strategy with a best-rule choice (a33c717 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build gene circuits, cascades, and Boolean maps on core reactions and maps (ba32590 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the Kolkata restaurant problem on choice and grouping (73e9d33 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the econophysics wealth exchanges on transfers (f3c5203 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Write dry friction with the core sign (60bf670 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Kick the impulsive circuit with the core ImpulseInteraction (f2307a0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build finance asset and wealth motions on rate and coupling interactions (3e9343f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build the controllers on the core clip and sign (4ed541b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build processes on the core delays, transfers, and pointwise utilities (2b73a26 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rename ThresholdInteraction to CascadeInteraction and RelaxationLaw to CascadeLaw (92aa08a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replace typing.Any with concrete types (7df2123 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the readings of the data kinds inside their property (0a95ce8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import generated source from the cache directory instead of running it with exec (cf45e58 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the agents of the economics models with view classes and remove the suppressions of earth and economics (3c4aaec by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the values of Chua's circuit without Any (3e51de1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Apply a catalog model's run settings with set_params (d81b3e4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the rewriting plug-in, the fractional types, and the tests against the engine bases (aefe83f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the agents of the engineering, mathematics, and computer science models with views (bf66e69 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the traffic agents with views and replace the suppressions of the models (e0b55b7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Document the arguments of the earth and economics models and type the shared economics blocks (601b145 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the context and input types of the engine's bases (dc77c06 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the verbs of BaseConfig by context and input, and _get_laws by namespace and parts (3482e31 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Stop compile passes from mutating kernel specs (c45c529 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rename the model elements that reused core element names (b700c4e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the work of the compile specs into their callers and make the compile working data frozen specs (bb3a48b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Merge SplitOperator and its spectral blocks into SplitSolver, and the LAMMPS atoms into LammpsSolver (6f4a4c9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the methods of the problem, reference, patch, and control problem specs into the classes that use them (3333624 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the scenario a spec, move the composed rule into the automaton analysis, and make the group expansion a configurable class (db90a40 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move every frozen dataclass into the specs package as a Spec, and the kinds and protocols into types (a5e8906 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Derive every base from BaseConfig and every spec from BaseSpec in the specs package (98b27d5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Put backends and solvers under BaseConfig with the common verbs and hooks (5b2533c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move BaseConfig, the errors, the specs, and the type aliases to root modules (cd19c40 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep only classes under the bases in the public surface of the problems package (deda3aa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make every value of the problems package a frozen BaseValue (c774869 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Print expressions with ExpressionPrinter under BasePrinter (2f3fce9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Put every compiled law of the problems package under BaseKernel (037890e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Hoist the validation checks of passes into their classes and merge the lattice context's methods into its pass (c5796c0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check every simulation before running it (2ba2098 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Derive observers, clocks, visuals, and Simulation from BaseConfig, and lay out blueprints with RerunObserver settings (10dd352 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lower reductions through a ReductionLowering, events included (afca009 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Expand and lower flows through a TransferLowering prepared on the compilation (7f87db4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Delete the dead code of the engine (7784476 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lower draws through a DrawLowering prepared on the compilation (8c5d305 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lower member offsets and field operators through BaseLowering classes (8147bfc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Experiments take a system or a factory, and CoarseGrainAnalysis bins a state over given values (35e9ff3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Prepare visuals on a problem and run them on a frame, and fold the blueprint and visual lookup into RerunObserver (7497ba0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the model catalog from the engine runtime to the models library (cd6407d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give observers and clocks their runtime bases, one class per module, and the simulation one input per verb (3f9ac52 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the estimator root of the engine to engine/base.py (02a64a9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the compile modules into one module per class (186ffab by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Group the shared economics realizations by family and move barter into the markets (a39822e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the solver modules into one module per solver (ccb662c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the feedback controllers into the control models (7bd2b06 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the early warnings of tipping next to the climate models (60c6d5b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the social realizations next to the models that use them (09e32cd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the physics measures next to the models they measure (e1e92e2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move Lowering out of the backend base module (c9e5954 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the problems modules into one module per class (e246670 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the viz helpers methods of the visuals and the observer (41d9080 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the shared compile helpers methods of their owning classes (05438da by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Dissolve the Binder, fluctuation, and mixing analyses into general kinds (cff6efd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the compile helpers that one class uses its methods (8a164fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Regroup order, early warning, avalanche, and dispersion analyses into general operations (0a86d54 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the solver helpers methods of the solvers that use them (9ea159f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the backend helpers methods of the backends and the Numba source (330c64e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the problems helpers methods of the classes that use them (f6490fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the replication helpers private methods of BaseExperiment (b94e984 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Share the surrogate helpers through BaseAnalysis and SparseIdentificationAnalysis (6d07fae by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the stability, symbolic, and Mittag-Leffler helpers methods of their analyses (75cfd53 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the Markov, passage, and automaton helpers methods of their analyses (5835be3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the field, agent, and network helpers methods of their analyses (0b21aed by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the series helpers methods of their analyses (39d06c4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the entropy and information helpers methods of their analyses (3c5d25d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the shared readers and lazy imports of analysis into BaseAnalysis (20550c1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check choices and ignored settings once in the analysis base (92fd75b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Turn the remaining public functions of analysis into classes (02c98e5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replace signature_analysis with SignatureAnalysis (bb73f1c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fold the trajectory readers into the analysis base and drop the analysis registry (10c1856 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move automata, linear automata, and subshifts to the automata models (ee2b791 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the single-class helpers of engine.viz private methods (8f46ba9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the single-class helpers of engine.runtime private methods (79448b7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the single-class helpers of engine.backends private methods (1f3b672 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the single-class helpers of engine.solvers private methods (aed5491 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the single-class helpers of engine.problems private methods (c81d5c1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the single-class helpers of engine.compile private methods (c4bf1fd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port fields to the new core (764d7fa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port quantum systems to the new core (d435645 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port runtime, visualization, experiments, and analysis to the new core (087ac3d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port rewriting, Cayley spaces, and topology to the new core (f679e8f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port particles, LAMMPS, and optimal control to the new core (7d4b729 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port lattice dynamics and Monte Carlo to the new core (70eabca by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port fractional dynamics and kinetic encounters to the new core (9910915 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Port agent-based models to the new core (8400ac1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Derive elements, interactions, laws, and systems from one part base with three verbs (8c6cd29 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the space, time, and layout bases out of the base package (ad98fe3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the base into elements, interactions, laws, types, errors, and utils (806424d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Bind Wiener processes through a noise role of an interaction (0cc97fa by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the rewriting rules laws of the rewritten component (d182565 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make the schedule of an experiment a member of its task (963c7cf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the group solvers after the word problem (b2b7359 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read layouts, registries, and snapshots by name and call evaluate instead of call (db6abb1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read collections and callables through named methods (94c4713 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replace magic methods and object.setattr of values and printing (4184929 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read problems through BaseProblem and drop magic methods of components (2cb6fdb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read trajectories and sections by name with values (972b143 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the preparing verb prepare instead of fit (e9ba3a8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give spaces and times the verbs fit and run (2758570 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move solvers and clocks to the estimator verbs fit and run (ca2c629 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move backends, system compilers, passes, and components to fit and run (f0f4c4e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fit and run visuals and observers through the estimator verbs (020e0e2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Remove every post_init outside the models (9e24a4c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fit and run designs and surrogates as estimators (5eeab3c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give every configurable base the estimator verbs check, fit, and run (a27383f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check laws and neighbourhoods when they are used, not when they are built (564aa14 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Locate packages with importlib.resources instead of file (bb42eda by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make vocabulary terms strings of their value (fd89671 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Merge modules of one concept, drop legacy references, and amend the constitution (4a3388d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run any problem through the problem base (d2eabcc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Hold what a system compiles to in a core problems package (f5d651d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name the compilers of whole systems apart from the passes (72c7eeb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the problem and solver bases to the core base (98d0e7a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make components and interactions sibling bases, and the system neither (113f5a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the law, space, and time bases into the core base (2528e76 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Regroup the core base by concept and give every domain a base (3ceecb6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Name every class after what it is (5662a04 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite imports for the core, engine, and formalisms packages (a1768ec by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the core into core, engine, and formalisms, and propose split-core-engine (0826a78 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spell the flocking tags and the neighbourhood reduction key as neighborhood (4fcf8f9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fold neighbor_sum into neighbors and rename the lattice keyword to over (7fa6c22 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Spell the public neighbour names and the binding as neighbor (e917c1c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Order the definitions of analysis and the formalisms by kind and dependency (21f52c8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Find calls of mod and shift_member with the one call walker of compile (32972ea by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Order the definitions of every compile module by kind and privacy (031be13 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep compile's internals out of its surface and name the shared core's rules (925425f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make companions_of private to base, which alone uses it (0047828 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Join the stepper snapshots in one module and stop exporting the visual registry (649cadf by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move helpers that one package uses out of base and laws (5283360 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the visuals into one module per visual, with shared colors and drawing helpers (2336f9b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep the solver registry in compile, which plans partitions with it (b70dab7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the Numba backend into source, kernel, reduction, and loop generators (f75efe4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Share the array types of compile and break its guarded import cycles (f80ec77 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Order the definitions of the ODE steppers, the traits visual, and the neighbour searches (606bcc4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Delete unused constants and the unused word inverse of the formalisms (a0c07f9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Order and hoist the modelling packages and split components by concept (0e6dbe2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the experiment runner into sources, tasks, and the experiment (f0942f6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compute every Shannon entropy and divergence in analysis with scipy (f75a6fd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import deeptime and powerlaw without a type-checking guard in analysis (a7bff31 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Delete the redesign codemod and record stocks and flows in the shared core (900aa08 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the fractional formalism into skcomplex.core.formalisms (a0b2cb8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the agents formalism into skcomplex.core.formalisms (ebb0dcc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the lattices and fields formalisms into skcomplex.core.formalisms (04c2bf6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move topology and control to formalisms, and lower waiting-time jumps in the core (81a5068 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let a formalism name the default solver of each of its forms (ea77bca by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let formalisms declare stepwise forms, combined laws, owner rules, and bindings (b950274 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the compiler into a pipeline of passes over one compilation state (f65b035 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move group spaces, Cayley graphs, and their visual into the groups formalism (cee408e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Build pair kernels on the bounded grid of the neighbour search (7cd0c7d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the quantum and rewriting formalisms into skcomplex.core.formalisms (4c6a203 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split the steppers by form and share one step count (011049e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Give components one explicit constructor and one hierarchy (46b0b97 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read law values through one traversal, values_of (46f5fb3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Derive every law from one Law base with declared traits (d5cb82e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Make law kinds, forms, space kinds, and traits open vocabularies (3c0af9d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Gather the NumPy, Numba, Mesa, and LAMMPS backends in core.backends (4ff1c17 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split core.model into space, laws, components, interactions, and system (7822c04 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rename the core segregation module to mixing (4f5f694 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move Turtle to core.viz as WordGeometry (0e637c3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Organize the model library by scientific field (0d183f1 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the framework packages under skcomplex.core (78617bb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Split package into base, component and system modules (43b942e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Tests

Force the LSODA stall within a short run (bf11329 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Stop relying on how LSODA fails on one platform (77f9468 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Widen the Mackey-Glass periodic bound to the solver noise of Linux (bebe227 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Seed the Poisson births test of LifeCycleInteraction (4846b85 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Skip static systems in the test of reductions read from a continuous system (70de316 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check that a tensor relaxes to its one fixed matrix between edges (24cc1ee by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the declared orders of every solver (523bc43 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the compile-time and closed-form speed checks as timing benchmarks (559ee3b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Compare the rebuilt LEGION and exchange couplings with the previous elements (d4c2fd8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run the Lempel-Ziv speed check as a timing benchmark (ee96097 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Broadcast the expected momentum, which NumPy 2.5 no longer does in assert_allclose (5e5132d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Update the tests that read the dynamics' random stream (975d642 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check Fermi imitation switching probabilities from both states on both backends (799ce39 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add trailing commas in the vector map tests (34e584b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Keep a pair ring for the pair Jacobian tests and compare the oscillator position as a vector (5225be0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Shorten the agent view test summary (49ca59a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the combined agent view protocol (e8c34c6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Guard the public names of the core against field terms (7103acb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Drop checks that need a new process, eval, pickle, or SymPy (bdf9af2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check that no source hides a finding or a type-checking import (56e92bb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Validate and read observables through the compiler in the catalog conformance test (ec2247e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Cover the general compiler's verbs, settings, report, and claims (8b63bb4 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Expect the shared physics code before the mechanics models among the loaded modules (89b9582 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Convert the compile and problems tests to the new core and engine API (92db50f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the tests of transfers, encounters, and the law utilities for the new core and mirror their modules (cf2c683 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Convert the solver, backend, runtime, and viz tests to the new API (7dad6cc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the tests of the laws of rates, equations, updates, jumps, noise, rules, and lattices for the new core (ef52591 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the element tests for the new core and mirror the modules of the elements (97515ab by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Pass backends as instances, fields and subsystems by keyword, in the model tests (97fc5bc by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Convert the analysis and experiments tests to the new API (f896089 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the interaction tests for the new core and mirror the modules of the interactions (1103676 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the tests of the base, specs, errors, types, and system of the core for the new API (3a6eb79 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Convert the solver choices, parts, and catalog probes of the model tests to the new core (4ecbd0a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Rewrite the space tests for the new core and mirror the modules of the spaces (16af298 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Write the noisy pair of the compilation tests as an element class (99e1237 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import the names of the tests from their new homes (6fdda14 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Move the formalism tests to mirror the engine and convert the test classes to the new core (47b5664 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Leave the init docstring out of the tally component (d40212d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Allow the design ignore to go unused when tests are checked alone (d338950 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the verbs, the absence of magic methods, trajectory values, and agent views (1d0db5e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Read trades by their buyer and seller (a945df2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the pickle round trip of terms for bandit (ae09b22 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Type the avalanche shapes and drop unused ignores (affe9f3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the tests above ten seconds as slow and shorten the ones above a minute (f94e402 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Measure coverage only in the nox session and skip slow tests by default (d6740b9 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mirror the tests on core, engine, and formalisms, and rewrite the import contracts (9646cc6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run docstring and document examples through pytest's collection (b7aca2b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Delete the test modules that do not mirror a source module, and propose mirror-tests-strictly (f3abbfd by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the pickle round-trip of terms as safe for bandit (6801165 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Remove two unused type ignores (0420794 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Enable the layout checks on the real tree (c1a5a6a by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Fail the layout test on a test module without a mirrored source module (5020c6b by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Load the backends before checking where they live (01b4a96 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mirror the test tree on the source tree (e3f87a7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the registration of the kinetics and particles formalisms (84ddf80 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mirror the lattice and field tests under their formalisms and test the declared dependency (d30b0f3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Import the package in the main thread so parallel runs rebuild its warnings (55690b5 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check module order, base imports, guards, formalism imports, and leaking exports (85548e7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Verify the damage phases of random Boolean networks (9d92f61 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Cover group spaces, their validation and visual, and the automata theory (0b8ea21 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Cover the nearest-neighbour emergence criteria of a multivariate macro feature (f5c5e15 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Verify neighbourhood reductions, Kuramoto synchronisation, and flocking (0a936e2 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Annotate the pairs the order-book test records (99f0bd0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Average seeded quenches in the aging collapse test (085f4fb by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Test agents as ordinary elements on the Mesa backend (667c22e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add the field-term and import-graph tests of the agnostic core (4308fe8 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Write the expected layout violation without implicit concatenation (a455ea0 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Let model packages import the realizations of their own field (d518b86 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Mark the subprocess run of the main-guard test as reviewed for bandit (a93ff7e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Seed the ideal gas run of the Boltzmann law test (7498336 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Check the precession rate of the gimballed gyroscope and curate its example (8478c61 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Shorten the docstring of the small-group traits test (1d5717c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add a failing test of cyclic colors for angle images (8cc1b75 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com

Chore

Release 0.2.0 (3ff34a7 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Run black after docformatter and audit the runtime dependencies (aa6771d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add JAX, Optax, and Diffrax as runtime dependencies (272b689 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Tick the checks and full-suite gate of the general model rewrites (bcfd712 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Replace suppression comments with configured exemptions (13be4a6 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Remove a Rerun recording committed by mistake (b4da630 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Ignore Rerun recordings written to the repository root (0196a69 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive split-core-engine and sync its specs (77424af by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive mirror-tests-strictly and sync its specs (c0a8ac3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive redesign-core-concepts and sync its specs (1df3e17 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Archive 14 completed changes and add add-unblocked-models (03697c3 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add PySINDy, PyDMD, and ReservoirPy as runtime dependencies (3b7af7e by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Lock dit and its dependencies (c958a58 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add dit as a runtime dependency after surveying information estimators (62d2a9d by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Exclude the gallery from docformatter and pass it elsewhere (2a081fe by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Merge development into fix-core-defects-3 (c4759e4 by georgedouzas).
Ignore references directory (90edab7 by georgedouzas).
Drop Python 3.11 and pin cysignals for the Sage extra (2a6257f by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Support Python 3.11 to 3.13 (76047da by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Initialize OpenSpec with Claude Code tooling (e27c950 by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Update copier template to 2.0.2 (621059c by georgedouzas). Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com
Add lammps dependency (2fe89a8 by georgedouzas).
Update copier template (48cb0db by georgedouzas).
Remove Python versions (474ecc5 by georgedouzas).
Remove unused import (14bc62b by georgedouzas).
Add more Python version (6d777e9 by georgedouzas).

0.1.0 - 2023-09-19

Compare with first commit

Bug Fixes

Use correct type definition (23120a1 by georgedouzas).

Code Refactoring

Prepare stable release (ceadea6 by georgedouzas).

Chore

Release 0.1.0 (076d45b by georgedouzas).
Rename to main (5b9b89d by georgedouzas).
Remove cli files (9ccc379 by georgedouzas).