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 (?), exclude (!), or relative directional
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    /// All coordinates strictly above source on this axis
176    DirectionPositive, // "?+"
177    /// All coordinates strictly below source on this axis
178    DirectionNegative, // "?-"
179    /// All coordinates at or above source on this axis
180    DirectionPositiveInclusive, // "?+="
181    /// All coordinates at or below source on this axis
182    DirectionNegativeInclusive, // "?-="
183    /// Single coordinate at offset from source
184    Offset(i32), // "?+N" or "?-N"
185    /// Inclusive range relative to source [src+lo, src+hi]
186    Range(i32, i32), // "?-A:?+B"
187}
188
189// Custom serialization to convert PatternElement back to JSON properly
190impl Serialize for PatternElement {
191    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
192    where
193        S: serde::Serializer,
194    {
195        match self {
196            PatternElement::Value(v) => serializer.serialize_i32(*v),
197            PatternElement::Wildcard => serializer.serialize_str("*"),
198            PatternElement::Skip => serializer.serialize_str("?"),
199            PatternElement::Exclude => serializer.serialize_str("!"),
200            PatternElement::DirectionPositive => serializer.serialize_str("?+"),
201            PatternElement::DirectionNegative => serializer.serialize_str("?-"),
202            PatternElement::DirectionPositiveInclusive => serializer.serialize_str("?+="),
203            PatternElement::DirectionNegativeInclusive => serializer.serialize_str("?-="),
204            PatternElement::Offset(off) => {
205                if *off >= 0 {
206                    serializer.serialize_str(&format!("?+{}", off))
207                } else {
208                    serializer.serialize_str(&format!("?{}", off))
209                }
210            }
211            PatternElement::Range(lo, hi) => {
212                let lo_str = if *lo >= 0 {
213                    format!("?+{}", lo)
214                } else {
215                    format!("?{}", lo)
216                };
217                let hi_str = if *hi >= 0 {
218                    format!("?+{}", hi)
219                } else {
220                    format!("?{}", hi)
221                };
222                serializer.serialize_str(&format!("{}:{}", lo_str, hi_str))
223            }
224        }
225    }
226}
227
228// Custom deserialization to parse JSON into PatternElement
229impl<'de> Deserialize<'de> for PatternElement {
230    fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>
231    where
232        D: serde::Deserializer<'de>,
233    {
234        let value = serde_json::Value::deserialize(deserializer)?;
235        match value {
236            serde_json::Value::Number(n) => {
237                if let Some(i) = n.as_i64() {
238                    Ok(PatternElement::Value(i as i32))
239                } else {
240                    Err(serde::de::Error::custom(
241                        "Pattern element must be an integer",
242                    ))
243                }
244            }
245            serde_json::Value::String(s) => Self::parse_string(&s)
246                .ok_or_else(|| serde::de::Error::custom(format!("Unknown pattern element: {}", s))),
247            _ => Err(serde::de::Error::custom(
248                "Pattern element must be number or string",
249            )),
250        }
251    }
252}
253
254impl PatternElement {
255    /// Parse a pattern element from its string representation.
256    pub fn parse_string(s: &str) -> Option<Self> {
257        match s {
258            "*" => Some(PatternElement::Wildcard),
259            "?" => Some(PatternElement::Skip),
260            "!" => Some(PatternElement::Exclude),
261            "?+" => Some(PatternElement::DirectionPositive),
262            "?-" => Some(PatternElement::DirectionNegative),
263            "?+=" => Some(PatternElement::DirectionPositiveInclusive),
264            "?-=" => Some(PatternElement::DirectionNegativeInclusive),
265            _ => {
266                if let Some(range) = Self::try_parse_range(s) {
267                    return Some(range);
268                }
269                if let Some(offset) = Self::try_parse_offset(s) {
270                    return Some(offset);
271                }
272                None
273            }
274        }
275    }
276
277    fn try_parse_range(s: &str) -> Option<Self> {
278        let parts: Vec<&str> = s.split(':').collect();
279        if parts.len() != 2 {
280            return None;
281        }
282        let lo = Self::extract_relative_offset(parts[0])?;
283        let hi = Self::extract_relative_offset(parts[1])?;
284        Some(PatternElement::Range(lo, hi))
285    }
286
287    fn try_parse_offset(s: &str) -> Option<Self> {
288        let offset = Self::extract_relative_offset(s)?;
289        Some(PatternElement::Offset(offset))
290    }
291
292    fn extract_relative_offset(s: &str) -> Option<i32> {
293        if !s.starts_with('?') {
294            return None;
295        }
296        let rest = &s[1..];
297        if rest.is_empty() || rest == "+" || rest == "-" || rest == "+=" || rest == "-=" {
298            return None;
299        }
300        rest.parse::<i32>().ok()
301    }
302}
303
304/// Physiology configuration (runtime parameters)
305#[derive(Debug, Clone, Serialize, Deserialize)]
306pub struct PhysiologyConfig {
307    /// Simulation timestep in seconds (formerly burst_delay)
308    pub simulation_timestep: f64,
309
310    /// Maximum neuron age
311    pub max_age: u64,
312
313    /// Evolution burst count
314    pub evolution_burst_count: u64,
315
316    /// IPU idle threshold
317    pub ipu_idle_threshold: u64,
318
319    /// Plasticity queue depth
320    pub plasticity_queue_depth: usize,
321
322    /// Lifespan management interval
323    pub lifespan_mgmt_interval: u64,
324
325    /// Quantization precision for numeric values
326    /// Options: "fp32" (default), "fp16", "int8"
327    #[serde(default = "default_quantization_precision")]
328    pub quantization_precision: String,
329}
330
331pub fn default_quantization_precision() -> String {
332    "int8".to_string() // Default to INT8 for memory efficiency
333}
334
335impl Default for PhysiologyConfig {
336    fn default() -> Self {
337        Self {
338            simulation_timestep: 0.025,
339            max_age: 10_000_000,
340            evolution_burst_count: 50,
341            ipu_idle_threshold: 1000,
342            plasticity_queue_depth: 3,
343            lifespan_mgmt_interval: 10,
344            quantization_precision: default_quantization_precision(),
345        }
346    }
347}
348
349/// Genome signatures for comparison
350#[derive(Debug, Clone, Serialize, Deserialize)]
351pub struct GenomeSignatures {
352    /// Full genome signature
353    pub genome: String,
354
355    /// Blueprint signature
356    pub blueprint: String,
357
358    /// Physiology signature
359    pub physiology: String,
360
361    /// Morphologies signature (optional, for future extension)
362    #[serde(skip_serializing_if = "Option::is_none")]
363    pub morphologies: Option<String>,
364}
365
366/// Genome statistics
367#[derive(Debug, Clone, Serialize, Deserialize, Default)]
368pub struct GenomeStats {
369    /// Innate cortical area count
370    pub innate_cortical_area_count: usize,
371
372    /// Innate neuron count
373    pub innate_neuron_count: usize,
374
375    /// Innate synapse count
376    pub innate_synapse_count: usize,
377}
378
379#[cfg(test)]
380mod tests {
381    use super::*;
382
383    #[test]
384    fn test_morphology_registry_creation() {
385        let registry = MorphologyRegistry::new();
386        assert_eq!(registry.count(), 0);
387    }
388
389    #[test]
390    fn test_morphology_registry_add_and_get() {
391        let mut registry = MorphologyRegistry::new();
392
393        let morphology = Morphology {
394            morphology_type: MorphologyType::Vectors,
395            parameters: MorphologyParameters::Vectors {
396                vectors: vec![[1, 0, 0], [0, 1, 0]],
397            },
398            class: "test".to_string(),
399        };
400
401        registry.add_morphology("test_morph".to_string(), morphology);
402
403        assert_eq!(registry.count(), 1);
404        assert!(registry.contains("test_morph"));
405        assert!(registry.get("test_morph").is_some());
406    }
407
408    #[test]
409    fn test_physiology_config_default() {
410        let config = PhysiologyConfig::default();
411        assert_eq!(config.simulation_timestep, 0.025);
412        assert_eq!(config.max_age, 10_000_000);
413    }
414}
feagi_evolutionary/runtime.rs

feagi_evolutionary/
runtime.rs
