Cleaned up basic-infection. Fixes #239.

Cargo.toml

@@ -41,7 +41,6 @@ assert_cmd = "^2.0.16"
 criterion = "^0.5.1"
 
 # Example Libraries
-ixa_example_basic_infection = { path = "examples/basic-infection" }
 ixa_example_births_deaths = { path = "examples/births-deaths" }
 
 [lints.clippy]

benches/example_basic_infection/example_basic_infection.rs

@@ -1,6 +1,30 @@
+pub mod incidence_report;
+pub mod infection_manager;
+pub mod people;
+pub mod transmission_manager;
+
 use criterion::{criterion_group, criterion_main, Criterion};
-use ixa::Context;
-use ixa_example_basic_infection::initialize;
+use ixa::{Context, ContextRandomExt};
+
+static POPULATION: u64 = 1000;
+static SEED: u64 = 123;
+static MAX_TIME: f64 = 303.0;
+static FOI: f64 = 0.1;
+static INFECTION_DURATION: f64 = 5.0;
+
+pub fn initialize(context: &mut Context) {
+    context.init_random(SEED);
+
+    people::init(context);
+    transmission_manager::init(context);
+    infection_manager::init(context);
+    incidence_report::init(context).unwrap_or_else(|e| {
+        eprintln!("failed to init incidence_report: {e}");
+    });
+    context.add_plan(MAX_TIME, |context| {
+        context.shutdown();
+    });
+}
 
 pub fn criterion_benchmark(c: &mut Criterion) {
     c.bench_function("example basic-infection", |bencher| {

examples/basic-infection/src/incidence_report.rs → benches/example_basic_infection/incidence_report.rs

@@ -31,6 +31,7 @@ fn handle_infection_status_change(context: &mut Context, event: InfectionStatusE
     });
 }
 
+#[allow(clippy::missing_errors_doc)]
 pub fn init(context: &mut Context) -> Result<(), IxaError> {
     trace!("Initializing incidence_report");
 

examples/basic-infection/src/infection_manager.rs → benches/example_basic_infection/infection_manager.rs

@@ -48,6 +48,8 @@ pub fn init(context: &mut Context) {
 
 #[cfg(test)]
 mod test {
+    #![allow(clippy::all)] // False positives
+    #![allow(unused_imports)] // False positives
     use crate::infection_manager::InfectionStatusEvent;
     use crate::people::InfectionStatus;
     use crate::people::InfectionStatusValue;
@@ -57,6 +59,7 @@ mod test {
 
     define_data_plugin!(RecoveryPlugin, usize, 0);
 
+    #[allow(dead_code)] // False positive
     fn handle_recovery_event(context: &mut Context, event: InfectionStatusEvent) {
         if event.current == InfectionStatusValue::R {
             *context.get_data_container_mut(RecoveryPlugin) += 1;

examples/basic-infection/src/people.rs → benches/example_basic_infection/people.rs

@@ -21,6 +21,7 @@ define_person_property_with_default!(
 );
 
 /// Populates the "world" with the `POPULATION` number of people.
+#[allow(clippy::missing_panics_doc)]
 pub fn init(context: &mut Context) {
     trace!("Initializing people");
     for _ in 0..POPULATION {

examples/basic-infection/src/transmission_manager.rs → benches/example_basic_infection/transmission_manager.rs

@@ -51,6 +51,8 @@ pub fn init(context: &mut Context) {
 
 #[cfg(test)]
 mod test {
+    #![allow(clippy::all)] // False positives
+    #![allow(unused_imports)] // False positives
     use super::*;
     use crate::people::{InfectionStatus, InfectionStatusValue};
     use crate::SEED;

docs/book/models/disease_model

@@ -0,0 +1 @@
+../../../examples/disease_model