neat

type ActivationType func(input float64, params ...float64) float64

type AggregationType func(inputs []float64) float64

type Config struct {
	Neat         NeatConfig
	Genome       GenomeConfig
	Reproduction ReproductionConfig
	SpeciesSet   SpeciesSetConfig
	Stagnation   StagnationConfig
}

type ConnectionGene struct {
	Key     ConnectionKey // Represents the (in_node_id, out_node_id) tuple
	Weight  float64
	Enabled bool
}

type ConnectionKey struct {
	InNodeID  int
	OutNodeID int
}

type FitnessFunc func(genomes map[int]*Genome) error

type GeneType int

type Genome struct {
	Key         int                               // Unique identifier for this genome.
	Nodes       map[int]*NodeGene                 // Map node ID -> NodeGene
	Connections map[ConnectionKey]*ConnectionGene // Map connection key -> ConnectionGene
	Fitness     float64                           // Fitness score of the genome.
	// Config holds a reference to the configuration for easy access to parameters.
	// Note: Storing the whole config might be overkill; maybe just GenomeConfig?
	// Let's start with GenomeConfig.
	Config *GenomeConfig
}

type GenomeConfig struct {
	// --- Top-level Genome parameters ---
	NumInputs                        int     `ini:"num_inputs"`
	NumOutputs                       int     `ini:"num_outputs"`
	NumHidden                        int     `ini:"num_hidden"`
	FeedForward                      bool    `ini:"feed_forward"` // If true, recurrent connections are disallowed
	CompatibilityDisjointCoefficient float64 `ini:"compatibility_disjoint_coefficient"`
	CompatibilityWeightCoefficient   float64 `ini:"compatibility_weight_coefficient"`
	ConnAddProb                      float64 `ini:"conn_add_prob"`
	ConnDeleteProb                   float64 `ini:"conn_delete_prob"`
	NodeAddProb                      float64 `ini:"node_add_prob"`
	NodeDeleteProb                   float64 `ini:"node_delete_prob"`
	SingleStructuralMutation         bool    `ini:"single_structural_mutation"` // Python default: false
	StructuralMutationSurer          string  `ini:"structural_mutation_surer"`  // Python default: 'default'
	InitialConnection                string  `ini:"initial_connection"`         // Python default: 'unconnected'

	// --- Node Gene parameters ---
	BiasInitMean    float64 `ini:"bias_init_mean"`
	BiasInitStdev   float64 `ini:"bias_init_stdev"`
	BiasInitType    string  `ini:"bias_init_type"` // Default: 'gaussian'
	BiasReplaceRate float64 `ini:"bias_replace_rate"`
	BiasMutateRate  float64 `ini:"bias_mutate_rate"`
	BiasMutatePower float64 `ini:"bias_mutate_power"`
	BiasMaxValue    float64 `ini:"bias_max_value"`
	BiasMinValue    float64 `ini:"bias_min_value"`

	ResponseInitMean    float64 `ini:"response_init_mean"`
	ResponseInitStdev   float64 `ini:"response_init_stdev"`
	ResponseInitType    string  `ini:"response_init_type"` // Default: 'gaussian'
	ResponseReplaceRate float64 `ini:"response_replace_rate"`
	ResponseMutateRate  float64 `ini:"response_mutate_rate"`
	ResponseMutatePower float64 `ini:"response_mutate_power"`
	ResponseMaxValue    float64 `ini:"response_max_value"`
	ResponseMinValue    float64 `ini:"response_min_value"`

	ActivationDefault    string   `ini:"activation_default"`           // Default: 'random'
	ActivationOptions    []string `ini:"activation_options" delim:" "` // Space-separated list
	ActivationMutateRate float64  `ini:"activation_mutate_rate"`

	AggregationDefault    string   `ini:"aggregation_default"`           // Default: 'random'
	AggregationOptions    []string `ini:"aggregation_options" delim:" "` // Space-separated list
	AggregationMutateRate float64  `ini:"aggregation_mutate_rate"`

	// --- Connection Gene parameters ---
	WeightInitMean    float64 `ini:"weight_init_mean"`
	WeightInitStdev   float64 `ini:"weight_init_stdev"`
	WeightInitType    string  `ini:"weight_init_type"` // Default: 'gaussian'
	WeightReplaceRate float64 `ini:"weight_replace_rate"`
	WeightMutateRate  float64 `ini:"weight_mutate_rate"`
	WeightMutatePower float64 `ini:"weight_mutate_power"`
	WeightMaxValue    float64 `ini:"weight_max_value"`
	WeightMinValue    float64 `ini:"weight_min_value"`

	EnabledDefault        string  `ini:"enabled_default"` // Default: 'True'
	EnabledMutateRate     float64 `ini:"enabled_mutate_rate"`
	EnabledRateToTrueAdd  float64 `ini:"enabled_rate_to_true_add"`  // Python default: 0.0
	EnabledRateToFalseAdd float64 `ini:"enabled_rate_to_false_add"` // Python default: 0.0

	// --- Calculated/Derived ---
	InputKeys    []int // Derived
	OutputKeys   []int // Derived
	NodeKeyIndex int   // Derived, used for assigning new node keys
}

type GenomeDistanceCache struct {
	Distances map[ConnectionKey]float64 // Using ConnectionKey as a proxy for genome pair (g1.Key, g2.Key)
	Hits      int
	Misses    int
	Config    *GenomeConfig // Needed for the Distance function
}

type NeatConfig struct {
	PopSize              int     `ini:"pop_size"`
	FitnessCriterion     string  `ini:"fitness_criterion"` // e.g., "max", "min", "mean"
	FitnessThreshold     float64 `ini:"fitness_threshold"`
	ResetOnExtinction    bool    `ini:"reset_on_extinction"`
	NoFitnessTermination bool    `ini:"no_fitness_termination"`
}

type NodeGene struct {
	Key         int // Unique identifier for this node gene (negative for inputs, >=0 for outputs/hidden)
	Bias        float64
	Response    float64
	Activation  string // Name of the activation function
	Aggregation string // Name of the aggregation function
}

type Population struct {
	Config       *Config
	Population   map[int]*Genome // Current generation of genomes (maps genome key -> genome)
	SpeciesSet   *SpeciesSet
	Reproduction *Reproduction
	Stagnation   *Stagnation
	Generation   int
	BestGenome   *Genome // Best genome found so far

}

type PopulationSaveData struct {
	Population   map[int]*Genome
	SpeciesSet   *SpeciesSet
	Reproduction *Reproduction // Includes NextGenomeKey and Ancestors
	Generation   int
	BestGenome   *Genome
}

type Reproduction struct {
	Config *ReproductionConfig
	// GenomeIndexer func() int // Function removed, state stored in NextGenomeKey
	NextGenomeKey int           // State for the next genome key
	Ancestors     map[int][]int // Map genome key -> parent keys (for tracking lineage)
	// Reporters   *reporting.ReporterSet // TODO: Add reporters later
	Stagnation *Stagnation // Reference to stagnation info for filtering
}

type ReproductionConfig struct {
	Elitism           int     `ini:"elitism"`            // Python default: 0
	SurvivalThreshold float64 `ini:"survival_threshold"` // Python default: 0.2
	MinSpeciesSize    int     `ini:"min_species_size"`   // Python default: 1
}

type Species struct {
	Key             int             // Unique identifier for the species.
	Created         int             // Generation number when the species was created.
	LastImproved    int             // Last generation where fitness improved.
	Representative  *Genome         // The representative genome for this species.
	Members         map[int]*Genome // Genomes belonging to this species (maps genome key -> genome).
	Fitness         float64         // Calculated fitness for the species (e.g., mean fitness of members).
	AdjustedFitness float64         // Fitness adjusted by sharing.
	FitnessHistory  []float64       // History of fitness values for stagnation detection.
}

type SpeciesSet struct {
	Species         map[int]*Species  // Map species key -> Species
	GenomeToSpecies map[int]int       // Map genome key -> species key
	Indexer         int               // Counter for assigning new species keys (start at 1)
	Config          *SpeciesSetConfig // Reference to speciation config

}

type SpeciesSetConfig struct {
	CompatibilityThreshold float64 `ini:"compatibility_threshold"`
}

type Stagnation struct {
	Config             *StagnationConfig
	SpeciesFitnessFunc func([]float64) float64
}

type StagnationConfig struct {
	SpeciesFitnessFunc string `ini:"species_fitness_func"` // Python default: 'mean'
	MaxStagnation      int    `ini:"max_stagnation"`       // Python default: 15
	SpeciesElitism     int    `ini:"species_elitism"`      // Python default: 0
}

type StagnationInfo struct {
	SpeciesID  int
	Species    *Species
	IsStagnant bool
}