Add n_hits to config in preparation

Author: sirno

examples/compartments.rs

@@ -50,6 +50,7 @@ fn main() {
         max_population: 1_000_000,
         dilution: 0.02,
         host_model: HostModel::SingleHost(host_fitness),
+        n_hits: 1,
     };
 
     let (mut attribute_definition, host_specs) =

examples/simulation.rs

@@ -67,6 +67,7 @@ fn main() {
         max_population: 1_000_000,
         dilution: 0.02,
         host_model: HostModel::SingleHost(HostFitness::new(Some(fitness_model), None)),
+        n_hits: 1,
     };
     simulation_settings
         .write_to_file("parameters_example.yaml")

src/config/parameters.rs

@@ -13,14 +13,41 @@ use crate::simulation::BasicHost;
 
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq)]
 pub struct Parameters {
+    /// The mutation rate represents the probability of a mutation occurring in a virus at each
+    /// time step.
     pub mutation_rate: f64,
+
+    /// The recombination rate represents the probability of recombination occurring between two
+    /// viruses in the population.
     pub recombination_rate: f64,
+
+    /// The size of the host population in the simulation.
     pub host_population_size: usize,
+
+    /// The basic reproductive number represents the average burst size of a virus in the population.
     pub basic_reproductive_number: f64,
+
+    /// The maximum population size for number of viruses in the simulation.
     pub max_population: usize,
+
+    /// The dilution factor represents the fraction of the population that is diluted at each
+    /// time step.
     pub dilution: f64,
+
+    /// The substitution matrix is a 4x4 matrix representing the probabilities of nucleotide
+    /// substitutions.
     pub substitution_matrix: [[f64; 4]; 4],
+
+    /// The host model defines host population structure and fitness characteristics.
     pub host_model: HostModel,
+
+    /// The number of times a virus can hit hosts before it fails to infect.
+    #[serde(default = "default_n_hits")]
+    pub n_hits: usize,
+}
+
+fn default_n_hits() -> usize {
+    1
 }
 
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq)]
@@ -188,6 +215,7 @@ mod tests {
                 )),
                 None,
             )),
+            n_hits: 1,
         };
         settings.write(&mut buffer).unwrap();
         let read_settings = Parameters::read(&mut buffer.as_slice()).unwrap();
@@ -226,6 +254,7 @@ mod tests {
                 )),
                 None,
             )),
+            n_hits: 1,
         };
         settings.write(&mut buffer).unwrap();
         let read_settings = Parameters::read(&mut buffer.as_slice()).unwrap();
@@ -256,6 +285,7 @@ mod tests {
                 )),
                 None,
             )),
+            n_hits: 1,
         };
         settings.write_to_file(path).unwrap();
         let read_settings = Parameters::read_from_file(path).unwrap();

src/config/settings.rs

@@ -73,6 +73,7 @@ mod tests {
                     )),
                     None,
                 )),
+                n_hits: 1,
             }],
             schedule: Schedule::from_vec(vec![
                 ScheduleRecord::new("0", "transmission", "migration_fwd"),

src/providers/fitness.rs

@@ -217,7 +217,7 @@ impl<S: Symbol> FitnessProvider<S> {
                         .try_get_ancestor()
                         .expect("Could not find ancestor during fitness update...")
                         .get_or_compute_attribute_raw(self.name)
-                        .unwrap()
+                        .unwrap(),
                 )
                 .unwrap();
                 let update = self.update_fitness(haplotype);

src/simulation.rs

@@ -579,6 +579,7 @@ mod tests {
         max_population: POPULATION_SIZE,
         dilution: 1.,
         host_model: HostModel::SingleHost(FITNESS_MODEL),
+        n_hits: 1,
     };
 
     fn setup_test_simulation() -> BasicSimulation<Nt> {