Make epistasis configurable

Author: sirno

src/core/fitness/epistasis.rs

@@ -25,8 +25,8 @@ pub struct EpistasisTable {
 impl EpistasisTable {
     pub fn from_model(model: &FitnessModel) -> Result<Self, VirolutionError> {
         let table = match &model.distribution {
-            FitnessDistribution::Epistatic(_, epi_params) => {
-                let entries = epi_params.load_table();
+            FitnessDistribution::Epistatic(epi_params) => {
+                let entries = epi_params.load_epistasis();
                 Self::from_vec(entries)
             }
             _ => {

src/core/fitness/init.rs

@@ -29,7 +29,7 @@ pub enum FitnessDistribution {
     Exponential(ExponentialParameters),
     File(FileParameters),
     Lognormal(LognormalParameters),
-    Epistatic(FileParameters, EpiFileParameters),
+    Epistatic(EpiFileParameters),
     // Spikes,
     // Beta,
     // Empirical,
@@ -73,6 +73,7 @@ pub struct FileParameters {
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq)]
 pub struct EpiFileParameters {
     pub path: String,
+    pub epi_path: String,
 }
 
 impl MutationCategoryWeights {
@@ -170,7 +171,16 @@ impl FileParameters {
 }
 
 impl EpiFileParameters {
-    pub fn load_table(&self) -> Vec<EpiEntry> {
+    pub fn load_table(&self) -> Vec<f64> {
+        let reader = NpyFile::new(std::fs::File::open(&self.path).unwrap()).unwrap();
+        reader
+            .data::<f64>()
+            .unwrap()
+            .map(|entry| entry.unwrap())
+            .collect()
+    }
+
+    pub fn load_epistasis(&self) -> Vec<EpiEntry> {
         let reader = NpyFile::new(std::fs::File::open(&self.path).unwrap()).unwrap();
         reader
             .data::<EpiEntry>()

src/core/fitness/provider.rs

@@ -48,7 +48,7 @@ impl FitnessProvider {
                 let table = FitnessTable::from_model(sequence, n_symbols, model)?;
                 FitnessFunction::NonEpistatic(table)
             }
-            FitnessDistribution::Epistatic(_, _) => {
+            FitnessDistribution::Epistatic(_) => {
                 let table = FitnessTable::from_model(sequence, n_symbols, model)?;
                 let epistasis = EpistasisTable::from_model(model)?;
                 FitnessFunction::SimpleEpistatic(table, epistasis)

src/core/fitness/table.rs

@@ -35,7 +35,7 @@ impl FitnessTable {
             }
             FitnessDistribution::Lognormal(ref params) => params.create_table(n_symbols, sequence),
             FitnessDistribution::File(ref params) => params.load_table(),
-            FitnessDistribution::Epistatic(ref params, _) => params.load_table(),
+            FitnessDistribution::Epistatic(ref params) => params.load_table(),
         };
 
         if table.len() != n_sites * n_symbols {