feagi_evolutionary/
runtime.rs

1// Copyright 2025 Neuraville Inc.
2// SPDX-License-Identifier: Apache-2.0
3
4/*!
5Runtime genome representation for FEAGI.
6
7This module defines the in-memory Rust objects that represent a loaded genome.
8These objects are created by the genome parser and consumed by neuroembryogenesis.
9
10Copyright 2025 Neuraville Inc.
11Licensed under the Apache License, Version 2.0
12*/
13
14use feagi_structures::genomic::cortical_area::CorticalArea;
15use feagi_structures::genomic::cortical_area::CorticalID;
16use feagi_structures::genomic::BrainRegion;
17use serde::{Deserialize, Serialize};
18use std::collections::HashMap;
19
20/// Complete runtime genome representation
21#[derive(Debug, Clone)]
22pub struct RuntimeGenome {
23    /// Genome metadata
24    pub metadata: GenomeMetadata,
25
26    /// Cortical areas (by cortical_id as CorticalID)
27    pub cortical_areas: HashMap<CorticalID, CorticalArea>,
28
29    /// Brain regions (by region_id)
30    pub brain_regions: HashMap<String, BrainRegion>,
31
32    /// Morphology registry
33    pub morphologies: MorphologyRegistry,
34
35    /// Physiology configuration
36    pub physiology: PhysiologyConfig,
37
38    /// Genome signatures
39    pub signatures: GenomeSignatures,
40
41    /// Statistics
42    pub stats: GenomeStats,
43}
44
45/// Genome metadata
46#[derive(Debug, Clone, Serialize, Deserialize)]
47pub struct GenomeMetadata {
48    pub genome_id: String,
49    pub genome_title: String,
50    pub genome_description: String,
51    pub version: String,
52    pub timestamp: f64, // Unix timestamp
53
54    /// Root brain region ID (UUID string) - explicit identification for O(1) lookup
55    /// This eliminates the need to search through all regions to find which has no parent
56    #[serde(skip_serializing_if = "Option::is_none")]
57    pub brain_regions_root: Option<String>,
58}
59
60/// Neuron morphology registry
61#[derive(Debug, Clone, Default)]
62pub struct MorphologyRegistry {
63    /// All morphologies by morphology_id
64    morphologies: HashMap<String, Morphology>,
65}
66
67impl MorphologyRegistry {
68    /// Create empty registry
69    pub fn new() -> Self {
70        Self::default()
71    }
72
73    /// Add a morphology
74    pub fn add_morphology(&mut self, id: String, morphology: Morphology) {
75        self.morphologies.insert(id, morphology);
76    }
77
78    /// Get a morphology by ID
79    pub fn get(&self, id: &str) -> Option<&Morphology> {
80        self.morphologies.get(id)
81    }
82
83    /// Check if morphology exists
84    pub fn contains(&self, id: &str) -> bool {
85        self.morphologies.contains_key(id)
86    }
87
88    /// Get all morphology IDs
89    pub fn morphology_ids(&self) -> Vec<String> {
90        self.morphologies.keys().cloned().collect()
91    }
92
93    /// Remove a morphology by ID.
94    ///
95    /// Returns true if the morphology existed and was removed.
96    pub fn remove_morphology(&mut self, id: &str) -> bool {
97        self.morphologies.remove(id).is_some()
98    }
99
100    /// Get count of morphologies
101    pub fn count(&self) -> usize {
102        self.morphologies.len()
103    }
104
105    /// Iterate over all morphologies
106    pub fn iter(&self) -> impl Iterator<Item = (&String, &Morphology)> {
107        self.morphologies.iter()
108    }
109}
110
111/// Neuron morphology definition
112#[derive(Debug, Clone, Serialize, Deserialize)]
113pub struct Morphology {
114    /// Morphology type: "vectors", "patterns", "functions", or "composite"
115    pub morphology_type: MorphologyType,
116
117    /// Morphology parameters
118    pub parameters: MorphologyParameters,
119
120    /// Morphology class: "core", "custom", etc.
121    pub class: String,
122}
123
124/// Morphology type enum
125#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq)]
126#[serde(rename_all = "lowercase")]
127pub enum MorphologyType {
128    /// Vector-based morphology (3D offset vectors)
129    Vectors,
130
131    /// Pattern-based morphology (source → destination patterns)
132    Patterns,
133
134    /// Function-based morphology (built-in algorithms)
135    Functions,
136
137    /// Composite morphology (combines multiple morphologies)
138    Composite,
139}
140
141/// Morphology parameters (type-specific)
142#[derive(Debug, Clone, Serialize, Deserialize)]
143#[serde(untagged)]
144pub enum MorphologyParameters {
145    /// Vector parameters: list of [x, y, z] offsets
146    Vectors { vectors: Vec<[i32; 3]> },
147
148    /// Pattern parameters: list of [source_pattern, dest_pattern] pairs
149    Patterns {
150        patterns: Vec<[Vec<PatternElement>; 2]>,
151    },
152
153    /// Function parameters: empty for built-in functions
154    Functions {},
155
156    /// Composite parameters: combines seed + pattern + mapper
157    Composite {
158        src_seed: [u32; 3],
159        src_pattern: Vec<[i32; 2]>,
160        mapper_morphology: String,
161    },
162}
163
164/// Pattern element: exact value, wildcard (*), skip (?), or exclude (!)
165#[derive(Debug, Clone, PartialEq, Eq)]
166pub enum PatternElement {
167    /// Exact coordinate value
168    Value(i32),
169    /// Wildcard - matches any value
170    Wildcard, // "*"
171    /// Skip - don't check this coordinate
172    Skip, // "?"
173    /// Exclude - exclude this coordinate
174    Exclude, // "!"
175}
176
177// Custom serialization to convert PatternElement back to JSON properly
178impl Serialize for PatternElement {
179    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
180    where
181        S: serde::Serializer,
182    {
183        match self {
184            PatternElement::Value(v) => serializer.serialize_i32(*v),
185            PatternElement::Wildcard => serializer.serialize_str("*"),
186            PatternElement::Skip => serializer.serialize_str("?"),
187            PatternElement::Exclude => serializer.serialize_str("!"),
188        }
189    }
190}
191
192// Custom deserialization to parse JSON into PatternElement
193impl<'de> Deserialize<'de> for PatternElement {
194    fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>
195    where
196        D: serde::Deserializer<'de>,
197    {
198        let value = serde_json::Value::deserialize(deserializer)?;
199        match value {
200            serde_json::Value::Number(n) => {
201                if let Some(i) = n.as_i64() {
202                    Ok(PatternElement::Value(i as i32))
203                } else {
204                    Err(serde::de::Error::custom(
205                        "Pattern element must be an integer",
206                    ))
207                }
208            }
209            serde_json::Value::String(s) => match s.as_str() {
210                "*" => Ok(PatternElement::Wildcard),
211                "?" => Ok(PatternElement::Skip),
212                "!" => Ok(PatternElement::Exclude),
213                _ => Err(serde::de::Error::custom(format!(
214                    "Unknown pattern element: {}",
215                    s
216                ))),
217            },
218            _ => Err(serde::de::Error::custom(
219                "Pattern element must be number or string",
220            )),
221        }
222    }
223}
224
225/// Physiology configuration (runtime parameters)
226#[derive(Debug, Clone, Serialize, Deserialize)]
227pub struct PhysiologyConfig {
228    /// Simulation timestep in seconds (formerly burst_delay)
229    pub simulation_timestep: f64,
230
231    /// Maximum neuron age
232    pub max_age: u64,
233
234    /// Evolution burst count
235    pub evolution_burst_count: u64,
236
237    /// IPU idle threshold
238    pub ipu_idle_threshold: u64,
239
240    /// Plasticity queue depth
241    pub plasticity_queue_depth: usize,
242
243    /// Lifespan management interval
244    pub lifespan_mgmt_interval: u64,
245
246    /// Quantization precision for numeric values
247    /// Options: "fp32" (default), "fp16", "int8"
248    #[serde(default = "default_quantization_precision")]
249    pub quantization_precision: String,
250}
251
252pub fn default_quantization_precision() -> String {
253    "int8".to_string() // Default to INT8 for memory efficiency
254}
255
256impl Default for PhysiologyConfig {
257    fn default() -> Self {
258        Self {
259            simulation_timestep: 0.025,
260            max_age: 10_000_000,
261            evolution_burst_count: 50,
262            ipu_idle_threshold: 1000,
263            plasticity_queue_depth: 3,
264            lifespan_mgmt_interval: 10,
265            quantization_precision: default_quantization_precision(),
266        }
267    }
268}
269
270/// Genome signatures for comparison
271#[derive(Debug, Clone, Serialize, Deserialize)]
272pub struct GenomeSignatures {
273    /// Full genome signature
274    pub genome: String,
275
276    /// Blueprint signature
277    pub blueprint: String,
278
279    /// Physiology signature
280    pub physiology: String,
281
282    /// Morphologies signature (optional, for future extension)
283    #[serde(skip_serializing_if = "Option::is_none")]
284    pub morphologies: Option<String>,
285}
286
287/// Genome statistics
288#[derive(Debug, Clone, Serialize, Deserialize, Default)]
289pub struct GenomeStats {
290    /// Innate cortical area count
291    pub innate_cortical_area_count: usize,
292
293    /// Innate neuron count
294    pub innate_neuron_count: usize,
295
296    /// Innate synapse count
297    pub innate_synapse_count: usize,
298}
299
300#[cfg(test)]
301mod tests {
302    use super::*;
303
304    #[test]
305    fn test_morphology_registry_creation() {
306        let registry = MorphologyRegistry::new();
307        assert_eq!(registry.count(), 0);
308    }
309
310    #[test]
311    fn test_morphology_registry_add_and_get() {
312        let mut registry = MorphologyRegistry::new();
313
314        let morphology = Morphology {
315            morphology_type: MorphologyType::Vectors,
316            parameters: MorphologyParameters::Vectors {
317                vectors: vec![[1, 0, 0], [0, 1, 0]],
318            },
319            class: "test".to_string(),
320        };
321
322        registry.add_morphology("test_morph".to_string(), morphology);
323
324        assert_eq!(registry.count(), 1);
325        assert!(registry.contains("test_morph"));
326        assert!(registry.get("test_morph").is_some());
327    }
328
329    #[test]
330    fn test_physiology_config_default() {
331        let config = PhysiologyConfig::default();
332        assert_eq!(config.simulation_timestep, 0.025);
333        assert_eq!(config.max_age, 10_000_000);
334    }
335}
feagi_evolutionary/runtime.rs

feagi_evolutionary/
runtime.rs
