codontrace 0.3.0a1__py3-none-any.whl

codontrace/__init__.py

@@ -0,0 +1,768 @@
+"""Public API for CodonTrace v0.3.0a1 alpha research release."""
+
+from codontrace.actions import (
+    ActionContext,
+    ActionHandler,
+    ActionRegistry,
+    ActionResult,
+    ActionRuntimeConfig,
+    ActionStatus,
+    EnergyEffect,
+    WorldView,
+    default_action_registry,
+)
+from codontrace.agent import Agent, RunResult, WhiteBoxAgent
+from codontrace.codon import Action, ActionName, Codon, CodonTable
+from codontrace.energy import ATPAccount, ATPBudget, ATPLedgerEntry
+from codontrace.errors import (
+    CodonTraceError,
+    ConfigurationError,
+    InsufficientATPError,
+    InvalidDensityError,
+    InvalidWorldSizeError,
+    PlacementError,
+    PluginError,
+    ReplayError,
+    ScenarioValidationError,
+    UnsupportedActionError,
+)
+from codontrace.experiment import Experiment
+from codontrace.genesis import (
+    AblationComparisonResult,
+    AblationEvidenceSummary,
+    AblationFactor,
+    AblationRunner,
+    AblationRunRecord,
+    ActionStatusDefinition,
+    ActionStatusRegistry,
+    ADFCompressionScore,
+    ADFDetectionResult,
+    ADFExpansionResult,
+    ADFMacro,
+    ADFPattern,
+    ADFProposal,
+    AgeLayeredSelection,
+    AgentSnapshot,
+    AliveGateConfig,
+    AliveGateResult,
+    AllowedOutputSchema,
+    AnalystInputBundle,
+    APIAuditResult,
+    APIDeprecationAuditResult,
+    APIStabilityLevel,
+    AppliedSubstrateRuleRecord,
+    ApprovalStatus,
+    ApprovedRuleSet,
+    ArtifactDigest,
+    ArtifactExporterProtocol,
+    ArtifactHygieneRecord,
+    BehaviorBin,
+    BehaviorDescriptor,
+    BehaviorDescriptorBuilder,
+    BehaviorDescriptorSchema,
+    BehaviorMetricRegistry,
+    BrainStepResult,
+    CapsuleEmissionConfig,
+    CapsuleEmissionResult,
+    CausalCapsule,
+    CausalCapsuleAdoptionPolicy,
+    CausalEdge,
+    CausalGraph,
+    CausalGraphConfig,
+    CausalGraphUpdateResult,
+    CausalNode,
+    CausalPrediction,
+    CausalPredictionEvaluation,
+    CausalUpdateInput,
+    CausalUpdateResult,
+    ClaimAuditFinding,
+    ClaimAuditResult,
+    ClaimDowngradeResult,
+    ClaimDowngradeRule,
+    ClaimReview,
+    ClaimType,
+    CodonActionCompatibilityCheck,
+    CompatibilitySnapshot,
+    CompiledBrain,
+    CompiledToken,
+    ComponentToggle,
+    ComponentToggleMatrix,
+    ConfigHash,
+    ConservationCheck,
+    D0BaselineRun,
+    D0BaselineRunner,
+    D0BaselineSet,
+    D0CalibrationResult,
+    D0DistanceMetricConfig,
+    D0EvidenceSummary,
+    DeprecatedAPISymbol,
+    DeterminismCheck,
+    DiscoveryCandidate,
+    DiscoveryCandidateQueue,
+    DiscoveryDetectionResult,
+    DiscoveryDetector,
+    DiscoveryRecord,
+    DiscoveryReview,
+    DiscoveryReviewPack,
+    DiscoveryWitness,
+    DiscoveryWitnessConfig,
+    DistanceToD0Result,
+    DocsConsistencyRecord,
+    DualATPBudget,
+    DynamicVocabularyConfig,
+    DynamicVocabularyState,
+    EffectSizeResult,
+    ElementCell,
+    ElementDefinition,
+    ElementGrid,
+    ElementGridConfig,
+    ElementKind,
+    ElementOrigin,
+    ElementRegistry,
+    ElementRuleConfig,
+    ElementSpec,
+    ElementStepResult,
+    ElitismSelection,
+    EpisodicEvent,
+    EpisodicMemory,
+    EpisodicMemoryConfig,
+    EvidenceBundleValidationResult,
+    EvidenceCompletenessScore,
+    EvidenceRecord,
+    EvolutionConfig,
+    EvolutionSelectionResult,
+    ExperimentSummary,
+    ExternalReviewRecord,
+    FailureModeRecord,
+    FitnessBreakdown,
+    FitnessComponent,
+    FitnessConfig,
+    FitnessExploitCheck,
+    FitnessProportionalSelection,
+    FitnessResult,
+    FitnessSignal,
+    FitnessSignalProtocol,
+    FitnessSignalRegistry,
+    ForbiddenClaimPolicy,
+    GenerationResult,
+    GenesisATPState,
+    GenesisCodonTable,
+    GenesisEngine,
+    GenesisEngineConfig,
+    GenesisEngineRunResult,
+    GenesisExperimentSpec,
+    GenesisFitnessV1,
+    GenesisOrganism,
+    GenesisRun,
+    GenesisRunResult,
+    GenesisRunSummary,
+    GenesisSnapshot,
+    GenesisTickResult,
+    HumanApprovalRecord,
+    HumanReviewDecision,
+    JsonArtifactExporter,
+    LearningATPConfig,
+    LearningUpdateDecision,
+    LimitationRecord,
+    LimitationsAuditResult,
+    LimitationSeverity,
+    LineageRecord,
+    LLMReviewRequest,
+    LLMReviewResult,
+    LocalityCheck,
+    MemoryConsolidationResult,
+    MemoryWriteResult,
+    MultiSeedProtocol,
+    MutationConfig,
+    MutationResult,
+    NamespaceCheck,
+    NexusSignal,
+    NoveltyWeightedSelection,
+    OffspringPlacementPolicy,
+    OrganismStepRecord,
+    OrganismTickResult,
+    PersistenceChecker,
+    PopulationCausalSummary,
+    PopulationConfigs,
+    PopulationRunner,
+    PopulationSnapshot,
+    PopulationState,
+    PopulationTickResult,
+    PublicAPISymbol,
+    QDArchive,
+    QDArchiveBatchUpdateResult,
+    QDArchiveConfig,
+    QDArchiveItemUpdateRecord,
+    QDArchivePolicy,
+    QDArchiveRejectedCandidate,
+    QDArchiveSummary,
+    QDArchiveUpdateResult,
+    QDElite,
+    QDEvidenceSummary,
+    RawEventSchema,
+    ReactionCycleCheck,
+    ReleaseCandidateChecklist,
+    ReleaseCandidateDecision,
+    ReleaseGateException,
+    ReleaseGateRecord,
+    ReleaseGateStatus,
+    ReleaseReadinessProfile,
+    ReplayBundle,
+    ReplayVerificationResult,
+    ReproductionConfig,
+    ReproductionDecision,
+    ReproductionResult,
+    ReviewArtifact,
+    ReviewArtifactType,
+    ReviewerInstructionSet,
+    ReviewerProtocol,
+    ReviewFinding,
+    ReviewSeverity,
+    ReviewStatus,
+    Ribosome,
+    RuleProposal,
+    RuleProposalReview,
+    RuleProposalSource,
+    RuleRiskReport,
+    RuleSetDiff,
+    RuleValidationResult,
+    RuleValidator,
+    RunArtifactSchema,
+    RunId,
+    RunManifest,
+    ScenarioComponentRequirement,
+    ScenarioSuite,
+    ScenarioSuiteValidationResult,
+    ScientificEvidencePack,
+    SeedMatrix,
+    SelectionPolicy,
+    StatisticalProtocolConfig,
+    SubstratePhysicsConfig,
+    SubstrateRule,
+    SubstrateRuleConfig,
+    SupplyChainAuditResult,
+    SupplyChainCheck,
+    TournamentSelection,
+    TranslationResult,
+    ValidationBundle,
+    ValidationIssue,
+    ValidationMatrixConfig,
+    ValidationMatrixResult,
+    ValidationResult,
+    ValidationRunRecord,
+    ValidationScenario,
+    WitnessEvidenceSummary,
+    WitnessValidationResult,
+    apply_approved_rule_set,
+    apply_claim_downgrade_rules,
+    apply_human_review,
+    assign_behavior_bin,
+    attach_review_result,
+    audit_claim_text,
+    audit_deprecations,
+    audit_docs_claims,
+    audit_limitations,
+    build_compatibility_snapshot,
+    build_discovery_witness,
+    calibrate_d0_baseline,
+    can_reproduce,
+    collect_genesis_public_api,
+    compare_ablation_runs,
+    compare_compatibility_snapshots,
+    compare_public_api_snapshots,
+    consolidate_memory,
+    decide_learning_update,
+    describe_behavior,
+    descriptor_distance,
+    detect_adf_patterns,
+    element_grid_to_world2d,
+    elements_to_dicts,
+    estimate_effect_size_lite,
+    evaluate_alive,
+    evaluate_artifact_hygiene,
+    evaluate_discovery_candidate,
+    evaluate_docs_consistency,
+    evaluate_fitness,
+    evaluate_prediction,
+    evaluate_release_candidate,
+    evaluate_supply_chain_checks,
+    evaluate_validation_matrix,
+    expand_adf_macro,
+    extend_codon_table_with_adfs,
+    get_element_spec,
+    macro_from_proposal,
+    manifest_from_parts,
+    measure_distance_to_d0,
+    mutate_genome,
+    normalize_descriptor,
+    policy_from_name,
+    predict_next_outcome,
+    propose_dynamic_vocabulary,
+    reproduce,
+    score_adf_pattern,
+    score_evidence_completeness,
+    select_population,
+    step_population,
+    summarize_qd_archive,
+    update_causal_graph_from_memory,
+    update_causal_graph_from_step,
+    update_causal_graph_from_trace,
+    update_qd_archive,
+    update_qd_archive_many,
+    validate_citation_metadata,
+    validate_descriptor_against_schema,
+    validate_digest_stability,
+    validate_evidence_bundle,
+    validate_genesis_exports,
+    validate_no_app_drift_project_metadata,
+    validate_release_evidence_consistency,
+    validate_review_result,
+    validate_roundtrip,
+    validate_scenario_suite,
+    validate_witness_evidence,
+    verify_replay_bundle,
+    world2d_to_element_grid,
+)
+from codontrace.genome import Genome, SemanticGenome
+from codontrace.initialization import (
+    AgentFactory,
+    AgentProfile,
+    AgentSpec,
+    GenomeStrategy,
+    GenomeStrategyHandler,
+    InitializationConfig,
+    LineageConfig,
+    PlacementStrategy,
+)
+from codontrace.mutation import Mutation, MutationLog
+from codontrace.plugins import discover_action_plugins
+from codontrace.recorder import RunRecorder
+from codontrace.replay import (
+    CausalReplay,
+    Explanation,
+    PerturbationResult,
+    ReplayResult,
+    ReplaySnapshot,
+    TimelineReplayResult,
+)
+from codontrace.rng import RNGManager
+from codontrace.scenario import (
+    ObstacleConfig,
+    ResourceConfig,
+    Scenario,
+    ScenarioAgentProfile,
+    ScenarioConfig,
+    ScenarioFactory,
+    ScenarioResult,
+    WorldConfig,
+    WorldFactory,
+)
+from codontrace.scheduling import (
+    EnergyPriorityScheduler,
+    FitnessWeightedScheduler,
+    RandomOrderScheduler,
+    RoundRobinScheduler,
+    SchedulerProtocol,
+    SequentialScheduler,
+)
+from codontrace.simulation import Simulation, SimulationConfig, SimulationResult
+from codontrace.specs import CodonTableSpec, GenomeSpec
+from codontrace.topology import (
+    ClosedTopology,
+    CylinderTopology,
+    MobiusTopology,
+    OpenTopology,
+    TopologyProtocol,
+    TorusTopology,
+    WrapTopology,
+)
+from codontrace.trace import TimelineFrame, Trace, TraceEvent, WorldEvent
+from codontrace.world import World2D, WorldObject
+
+__version__ = "0.3.0a1"
+
+__all__ = [
+    "AgentSnapshot",
+    "ArtifactDigest",
+    "ArtifactExporterProtocol",
+    "ConfigHash",
+    "DiscoveryRecord",
+    "ExperimentSummary",
+    "JsonArtifactExporter",
+    "PopulationSnapshot",
+    "RawEventSchema",
+    "ReplayBundle",
+    "ReplayVerificationResult",
+    "ReviewStatus",
+    "RunArtifactSchema",
+    "RunId",
+    "RunManifest",
+    "manifest_from_parts",
+    "verify_replay_bundle",
+    "AnalystInputBundle",
+    "AblationRunner",
+    "D0BaselineRunner",
+    "DiscoveryCandidateQueue",
+    "DiscoveryDetectionResult",
+    "DiscoveryDetector",
+    "DiscoveryReviewPack",
+    "MultiSeedProtocol",
+    "PersistenceChecker",
+    "GenesisEngine",
+    "GenesisEngineConfig",
+    "GenesisExperimentSpec",
+    "GenesisRun",
+    "GenesisEngineRunResult",
+    "GenesisRunSummary",
+    "GenesisSnapshot",
+    "GenesisTickResult",
+    "attach_review_result",
+    "apply_human_review",
+    "BehaviorDescriptor",
+    "BehaviorDescriptorBuilder",
+    "BehaviorMetricRegistry",
+    "describe_behavior",
+    "FitnessBreakdown",
+    "FitnessComponent",
+    "GenesisFitnessV1",
+    "AllowedOutputSchema",
+    "ClaimReview",
+    "DiscoveryReview",
+    "ExternalReviewRecord",
+    "ForbiddenClaimPolicy",
+    "HumanReviewDecision",
+    "LLMReviewRequest",
+    "LLMReviewResult",
+    "ReviewArtifact",
+    "ReviewArtifactType",
+    "ReviewFinding",
+    "ReviewSeverity",
+    "ReviewerInstructionSet",
+    "ReviewerProtocol",
+    "RuleProposalReview",
+    "validate_review_result",
+    "ApprovalStatus",
+    "ApprovedRuleSet",
+    "CodonActionCompatibilityCheck",
+    "ConservationCheck",
+    "DeterminismCheck",
+    "FitnessExploitCheck",
+    "HumanApprovalRecord",
+    "LocalityCheck",
+    "NamespaceCheck",
+    "ReactionCycleCheck",
+    "RuleProposal",
+    "RuleProposalSource",
+    "RuleRiskReport",
+    "RuleSetDiff",
+    "RuleValidationResult",
+    "RuleValidator",
+    "apply_approved_rule_set",
+    "AgeLayeredSelection",
+    "ElitismSelection",
+    "EvolutionConfig",
+    "EvolutionSelectionResult",
+    "FitnessProportionalSelection",
+    "NoveltyWeightedSelection",
+    "SelectionPolicy",
+    "TournamentSelection",
+    "policy_from_name",
+    "select_population",
+    "APIStabilityLevel",
+    "DeprecatedAPISymbol",
+    "APIDeprecationAuditResult",
+    "audit_deprecations",
+    "EvidenceRecord",
+    "EvidenceBundleValidationResult",
+    "validate_evidence_bundle",
+    "LimitationSeverity",
+    "LimitationRecord",
+    "FailureModeRecord",
+    "LimitationsAuditResult",
+    "audit_limitations",
+    "ValidationMatrixConfig",
+    "ValidationMatrixResult",
+    "evaluate_validation_matrix",
+    "ScenarioComponentRequirement",
+    "SeedMatrix",
+    "ComponentToggle",
+    "ComponentToggleMatrix",
+    "ScenarioSuite",
+    "ScenarioSuiteValidationResult",
+    "validate_scenario_suite",
+    "ReleaseGateStatus",
+    "ReleaseGateRecord",
+    "ReleaseCandidateChecklist",
+    "ReleaseCandidateDecision",
+    "SupplyChainCheck",
+    "SupplyChainAuditResult",
+    "evaluate_release_candidate",
+    "ReleaseGateException",
+    "evaluate_supply_chain_checks",
+    "ReleaseReadinessProfile",
+    "ArtifactHygieneRecord",
+    "DocsConsistencyRecord",
+    "evaluate_artifact_hygiene",
+    "evaluate_docs_consistency",
+    "D0EvidenceSummary",
+    "QDEvidenceSummary",
+    "AblationEvidenceSummary",
+    "WitnessEvidenceSummary",
+    "ScientificEvidencePack",
+    "ClaimDowngradeRule",
+    "ClaimDowngradeResult",
+    "EvidenceCompletenessScore",
+    "apply_claim_downgrade_rules",
+    "score_evidence_completeness",
+    "APIAuditResult",
+    "ClaimAuditFinding",
+    "ClaimAuditResult",
+    "ClaimType",
+    "CompatibilitySnapshot",
+    "PublicAPISymbol",
+    "QDArchiveItemUpdateRecord",
+    "ValidationBundle",
+    "ValidationIssue",
+    "ValidationResult",
+    "ValidationRunRecord",
+    "ValidationScenario",
+    "audit_claim_text",
+    "audit_docs_claims",
+    "build_compatibility_snapshot",
+    "collect_genesis_public_api",
+    "compare_compatibility_snapshots",
+    "compare_public_api_snapshots",
+    "validate_digest_stability",
+    "validate_genesis_exports",
+    "validate_no_app_drift_project_metadata",
+    "validate_release_evidence_consistency",
+    "validate_citation_metadata",
+    "validate_roundtrip",
+    "DiscoveryWitnessConfig",
+    "WitnessValidationResult",
+    "validate_witness_evidence",
+    "QDArchivePolicy",
+    "QDArchiveRejectedCandidate",
+    "QDArchiveBatchUpdateResult",
+    "update_qd_archive_many",
+    "validate_descriptor_against_schema",
+    "normalize_descriptor",
+    "descriptor_distance",
+    "AblationFactor",
+    "AblationRunRecord",
+    "AblationComparisonResult",
+    "compare_ablation_runs",
+    "StatisticalProtocolConfig",
+    "EffectSizeResult",
+    "estimate_effect_size_lite",
+    "GenomeSpec",
+    "CodonTableSpec",
+    "ActionRuntimeConfig",
+    "ElementGridConfig",
+    "AppliedSubstrateRuleRecord",
+    "summarize_qd_archive",
+    "update_qd_archive",
+    "assign_behavior_bin",
+    "QDArchiveUpdateResult",
+    "QDArchiveSummary",
+    "QDArchive",
+    "QDArchiveConfig",
+    "QDElite",
+    "BehaviorBin",
+    "BehaviorDescriptorSchema",
+    "build_discovery_witness",
+    "evaluate_discovery_candidate",
+    "measure_distance_to_d0",
+    "calibrate_d0_baseline",
+    "DistanceToD0Result",
+    "DiscoveryWitness",
+    "DiscoveryCandidate",
+    "D0DistanceMetricConfig",
+    "D0CalibrationResult",
+    "D0BaselineSet",
+    "D0BaselineRun",
+    "ElementDefinition",
+    "ElementRegistry",
+    "SubstrateRule",
+    "SubstrateRuleConfig",
+    "SubstratePhysicsConfig",
+    "FitnessSignal",
+    "FitnessSignalProtocol",
+    "FitnessSignalRegistry",
+    "ActionStatusDefinition",
+    "ActionStatusRegistry",
+    "SchedulerProtocol",
+    "SequentialScheduler",
+    "RoundRobinScheduler",
+    "RandomOrderScheduler",
+    "EnergyPriorityScheduler",
+    "FitnessWeightedScheduler",
+    "TopologyProtocol",
+    "ClosedTopology",
+    "OpenTopology",
+    "WrapTopology",
+    "CylinderTopology",
+    "TorusTopology",
+    "MobiusTopology",
+    "score_adf_pattern",
+    "propose_dynamic_vocabulary",
+    "macro_from_proposal",
+    "extend_codon_table_with_adfs",
+    "expand_adf_macro",
+    "detect_adf_patterns",
+    "NexusSignal",
+    "DynamicVocabularyState",
+    "DynamicVocabularyConfig",
+    "CausalCapsule",
+    "CausalCapsuleAdoptionPolicy",
+    "CapsuleEmissionResult",
+    "CapsuleEmissionConfig",
+    "ADFProposal",
+    "ADFPattern",
+    "ADFMacro",
+    "ADFExpansionResult",
+    "ADFDetectionResult",
+    "ADFCompressionScore",
+    "update_causal_graph_from_trace",
+    "update_causal_graph_from_memory",
+    "update_causal_graph_from_step",
+    "predict_next_outcome",
+    "evaluate_prediction",
+    "CausalPrediction",
+    "CausalPredictionEvaluation",
+    "CausalUpdateInput",
+    "CausalUpdateResult",
+    "CausalNode",
+    "CausalGraphUpdateResult",
+    "CausalGraphConfig",
+    "CausalGraph",
+    "CausalEdge",
+    "OffspringPlacementPolicy",
+    "MemoryWriteResult",
+    "EpisodicMemoryConfig",
+    "EpisodicMemory",
+    "EpisodicEvent",
+    "decide_learning_update",
+    "consolidate_memory",
+    "MemoryConsolidationResult",
+    "LearningUpdateDecision",
+    "LearningATPConfig",
+    "describe_behavior",
+    "BehaviorDescriptor",
+    "Action",
+    "ActionContext",
+    "ActionHandler",
+    "ActionName",
+    "ActionRegistry",
+    "ActionResult",
+    "ActionStatus",
+    "Agent",
+    "AgentFactory",
+    "AgentProfile",
+    "AgentSpec",
+    "ATPAccount",
+    "ATPBudget",
+    "ATPLedgerEntry",
+    "CodonTraceError",
+    "CausalReplay",
+    "Codon",
+    "CodonTable",
+    "ConfigurationError",
+    "EnergyEffect",
+    "AliveGateConfig",
+    "AliveGateResult",
+    "CompiledBrain",
+    "CompiledToken",
+    "DualATPBudget",
+    "ElementCell",
+    "ElementGrid",
+    "ElementKind",
+    "ElementOrigin",
+    "ElementRuleConfig",
+    "ElementSpec",
+    "ElementStepResult",
+    "GenesisATPState",
+    "GenesisCodonTable",
+    "FitnessConfig",
+    "FitnessResult",
+    "GenerationResult",
+    "LineageRecord",
+    "MutationConfig",
+    "MutationResult",
+    "OrganismStepRecord",
+    "PopulationCausalSummary",
+    "PopulationConfigs",
+    "PopulationRunner",
+    "PopulationState",
+    "ReproductionConfig",
+    "ReproductionDecision",
+    "ReproductionResult",
+    "can_reproduce",
+    "evaluate_fitness",
+    "mutate_genome",
+    "reproduce",
+    "step_population",
+    "GenesisOrganism",
+    "GenesisRunResult",
+    "Ribosome",
+    "TranslationResult",
+    "element_grid_to_world2d",
+    "elements_to_dicts",
+    "evaluate_alive",
+    "get_element_spec",
+    "world2d_to_element_grid",
+    "Experiment",
+    "Explanation",
+    "Genome",
+    "GenomeStrategy",
+    "GenomeStrategyHandler",
+    "InitializationConfig",
+    "InsufficientATPError",
+    "InvalidDensityError",
+    "InvalidWorldSizeError",
+    "LineageConfig",
+    "Mutation",
+    "MutationLog",
+    "PerturbationResult",
+    "PlacementError",
+    "PlacementStrategy",
+    "PluginError",
+    "ReplayError",
+    "ReplayResult",
+    "ReplaySnapshot",
+    "ObstacleConfig",
+    "ResourceConfig",
+    "Scenario",
+    "ScenarioAgentProfile",
+    "ScenarioConfig",
+    "ScenarioFactory",
+    "ScenarioResult",
+    "ScenarioValidationError",
+    "RNGManager",
+    "RunResult",
+    "SemanticGenome",
+    "Simulation",
+    "SimulationConfig",
+    "SimulationResult",
+    "RunRecorder",
+    "TimelineFrame",
+    "TimelineReplayResult",
+    "WorldEvent",
+    "Trace",
+    "TraceEvent",
+    "UnsupportedActionError",
+    "WhiteBoxAgent",
+    "WorldConfig",
+    "WorldFactory",
+    "World2D",
+    "WorldView",
+    "WorldObject",
+    "default_action_registry",
+    "discover_action_plugins",
+    "__version__",
+]
+
+# Strong library Phase 1 convenience exports.
+from codontrace.rng import NumpyGeneratorBackend, RNGManagerBackend, RNGProtocol
+
+__all__.extend(["RNGProtocol", "RNGManagerBackend", "NumpyGeneratorBackend"])