Made basic-infection and births-deaths into libraries so they could s…

…hare code with the benchmarks.

.gitignore

@@ -7,7 +7,7 @@ profile.json
 # Generated by Cargo
 # will have compiled files and executables
 debug/
-target/
+**/target/
 
 # Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
 # More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html

Cargo.toml

@@ -34,6 +34,11 @@ rand_distr = "^0.4.3"
 tempfile = "^3.15.0"
 ordered-float = "^4.6.0"
 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]
 pedantic = { level = "warn", priority = -1 }
@@ -47,6 +52,11 @@ path = "tests/bin/runner_test_custom_args.rs"
 name = "runner_test_debug"
 path = "tests/bin/runner_test_debug.rs"
 
+[[bench]]
+name = "example_basic_infection"
+path = "benches/example_basic_infection/example_basic_infection.rs"
+harness = false
+
 [[bench]]
 name = "example_births_deaths"
 path = "benches/example_births_deaths/example_births_deaths.rs"

benches/README.md

@@ -4,7 +4,8 @@ For general Rust profiling information, see: https://nnethercote.github.io/perf-
 
 # Generating Flamegraphs
 
-You can use `samply` (Linux and macOS) to capture stack samples from your application and generate a flamegraph, helping you quickly identify and analyze performance hotspots.
+You can use `samply` (Linux and macOS) to capture stack samples from your application and generate
+a flamegraph, helping you quickly identify and analyze performance hotspots.
 
 ## Prerequisites
 
@@ -36,10 +37,10 @@ cargo build --example basic-infection --release && samply record -- target/relea
 
 When it completes, `samply` will automatically open a browser with the generated report.
 
-
 ## `flamegraph` Alternative
 
-You can use `flamegraph` if you prefer. It requires root privileges, but don't use `sudo cargo...`. Do this:
+You can use `flamegraph` if you prefer. It requires root privileges, but don't use
+`sudo cargo...`. Do this:
 
 ```bash
 cargo flamegraph --root --example basic-infection
@@ -49,12 +50,16 @@ This will generate an SVG of the flamegraph in the current directory.
 
 # Benchmarking Ixa
 
-Ixa uses [Criterion.rs](https://bheisler.github.io/criterion.rs/book/index.html) for statistical benchmarking.
+Ixa uses [Criterion.rs](https://bheisler.github.io/criterion.rs/book/index.html) for statistical
+benchmarking.
 
 ## Optional Prerequisites
 
- - [`gnuplot`](http://www.gnuplot.info/): The [plotters crate](https://github.com/38/plotters) will be used as a fallback if `gnuplot` is not found.
- - [cargo-criterion](https://bheisler.github.io/criterion.rs/book/cargo_criterion/cargo_criterion.html): This is the upcoming "next generation" of Criterion.rs. Eventually it will reduce compilation times and offer more features, but for now it only has feature parity.
+- [`gnuplot`](http://www.gnuplot.info/): The [plotters crate](https://github.com/38/plotters) will
+  be used as a fallback if `gnuplot` is not found.
+- [cargo-criterion](https://bheisler.github.io/criterion.rs/book/cargo_criterion/cargo_criterion.html):
+  This is the upcoming "next generation" of Criterion.rs. Eventually it will reduce compilation
+  times and offer more features, but for now it only has feature parity.
 
 ```bash
 cargo install cargo-criterion
@@ -110,4 +115,5 @@ An HTML report is created at `target/criterion/report/index.html`. On macOS:
 open target/criterion/report/index.html
 ```
 
-On Linux platforms, replace `open` with `xdg-open`, `gnome-open`, or `kde-open`, depending on your system configuration, or just open the file in a browser.
+On Linux platforms, replace `open` with `xdg-open`, `gnome-open`, or `kde-open`, depending on your
+system configuration, or just open the file in a browser.

benches/example_basic_infection/example_basic_infection.rs

@@ -2,10 +2,9 @@ use criterion::{criterion_group, criterion_main, Criterion};
 use ixa::context::Context;
 use ixa::random::ContextRandomExt;
 
-mod incidence_report;
-mod infection_manager;
-mod people;
-mod transmission_manager;
+use ixa_example_basic_infection::{
+    incidence_report, infection_manager, people, transmission_manager,
+};
 
 static POPULATION: u64 = 1000;
 static SEED: u64 = 123;

benches/example_births_deaths/example_births_deaths.rs

@@ -1,14 +1,11 @@
-use crate::parameters_loader::Parameters;
 use criterion::{criterion_group, criterion_main, Criterion};
 use ixa::{Context, ContextGlobalPropertiesExt, ContextRandomExt};
 use std::path::Path;
 
-mod demographics_report;
-mod incidence_report;
-mod infection_manager;
-mod parameters_loader;
-mod population_manager;
-mod transmission_manager;
+use ixa_example_births_deaths::{
+    demographics_report, incidence_report, infection_manager, parameters_loader,
+    population_manager, transmission_manager,
+};
 
 fn births_deaths() -> Context {
     let mut context = Context::new();
@@ -19,7 +16,7 @@ fn births_deaths() -> Context {
         .expect("failed to load parameters");
 
     let parameters = context
-        .get_global_property_value(Parameters)
+        .get_global_property_value(parameters_loader::Parameters)
         .unwrap()
         .clone();
     context.init_random(parameters.seed);

benches/example_births_deaths/input.json

@@ -0,0 +1,15 @@
+{
+    "population": 100,
+    "max_time": 780.0,
+    "seed": 123,
+    "birth_rate": 0.1,
+    "death_rate": 0.1,
+    "foi_groups": [
+        {"group_name": "NewBorn", "foi": 0.2},
+        {"group_name": "General", "foi": 0.1},
+        {"group_name": "OldAdult", "foi": 0.15}
+    ],
+    "infection_duration": 5.0,
+    "output_file": "incidence",
+    "demographic_output_file": "people_report.csv"
+}

criterion.toml

@@ -19,7 +19,7 @@
 # This is used to configure the plotting backend used by cargo-criterion.
 # Options are "gnuplot" and "plotters", or "auto", which will use gnuplot if it's
 # available or plotters if it isn't.
-ploting_backend = "auto"
+plotting_backend = "auto"
 
 # The colors table allows users to configure the colors used by the charts
 # cargo-criterion generates.

examples/basic-infection/Cargo.toml

@@ -0,0 +1,21 @@
+[package]
+name = "ixa_example_basic_infection"
+version = "0.1.0"
+edition = "2021"
+
+publish = false
+
+[dependencies]
+
+ixa = { path = "../../../ixa" }
+ixa-derive = { path = "../../ixa-derive" }
+
+csv = "^1.3.1"
+serde = "^1.0.217"
+rand = "^0.8.5"
+rand_distr = "^0.4.3"
+paste = "^1.0.15"
+
+[[bin]]
+name = "basic_infection"
+path = "main.rs"

examples/basic-infection/main.rs

@@ -1,33 +1,4 @@
-use ixa::context::Context;
-use ixa::error::IxaError;
-use ixa::random::ContextRandomExt;
-
-mod incidence_report;
-mod infection_manager;
-mod people;
-mod transmission_manager;
-
-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;
-
-fn initialize() -> Result<Context, IxaError> {
-    let mut context = Context::new();
-
-    context.init_random(SEED);
-
-    people::init(&mut context);
-    transmission_manager::init(&mut context);
-    infection_manager::init(&mut context);
-    incidence_report::init(&mut context)?;
-
-    context.add_plan(MAX_TIME, |context| {
-        context.shutdown();
-    });
-    Ok(context)
-}
+use ixa_example_basic_infection::initialize;
 
 fn main() {
     let mut context = initialize().expect("Error adding report.");

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

@@ -32,7 +32,7 @@ pub fn init(context: &mut Context) -> Result<(), IxaError> {
     // examples.
     context
         .report_options()
-        .directory(PathBuf::from("./examples/basic-infection/"))
+        .directory(PathBuf::from("../"))
         .overwrite(true);
     context.add_report::<IncidenceReportItem>("incidence")?;
     context.subscribe_to_event::<InfectionStatusEvent>(handle_infection_status_change);

examples/basic-infection/src/lib.rs

@@ -0,0 +1,30 @@
+use ixa::context::Context;
+use ixa::error::IxaError;
+use ixa::random::ContextRandomExt;
+
+pub mod incidence_report;
+pub mod infection_manager;
+pub mod people;
+pub mod transmission_manager;
+
+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() -> Result<Context, IxaError> {
+    let mut context = Context::new();
+
+    context.init_random(SEED);
+
+    people::init(&mut context);
+    transmission_manager::init(&mut context);
+    infection_manager::init(&mut context);
+    incidence_report::init(&mut context)?;
+
+    context.add_plan(MAX_TIME, |context| {
+        context.shutdown();
+    });
+    Ok(context)
+}

examples/births-deaths/Cargo.toml

@@ -0,0 +1,22 @@
+[package]
+name = "ixa_example_births_deaths"
+version = "0.1.0"
+edition = "2021"
+
+publish = false
+
+[dependencies]
+
+ixa = { path = "../../../ixa" }
+ixa-derive = { path = "../../ixa-derive" }
+
+csv = "^1.3.1"
+ctor = "^0.2.8"
+serde = "^1.0.217"
+rand = "^0.8.5"
+rand_distr = "^0.4.3"
+paste = "^1.0.15"
+
+[[bin]]
+name = "births_deaths"
+path = "main.rs"

examples/births-deaths/main.rs

@@ -1,46 +1,6 @@
-use ixa::error::IxaError;
-use ixa::random::ContextRandomExt;
-use ixa::{context::Context, global_properties::ContextGlobalPropertiesExt};
-use std::path::Path;
-
-mod demographics_report;
-mod incidence_report;
-mod infection_manager;
-mod parameters_loader;
-mod population_manager;
-mod transmission_manager;
-
-use crate::parameters_loader::Parameters;
-
-fn initialize() -> Result<Context, IxaError> {
-    let mut context = Context::new();
-    let current_dir = Path::new(file!()).parent().unwrap();
-    let file_path = current_dir.join("input.json");
-
-    parameters_loader::init_parameters(&mut context, &file_path)?;
-
-    let parameters = context
-        .get_global_property_value(Parameters)
-        .unwrap()
-        .clone();
-    context.init_random(parameters.seed);
-
-    demographics_report::init(&mut context)?;
-    incidence_report::init(&mut context)?;
-
-    population_manager::init(&mut context);
-    transmission_manager::init(&mut context);
-    infection_manager::init(&mut context);
-
-    context.add_plan(parameters.max_time, |context| {
-        context.shutdown();
-    });
-    println!("{parameters:?}");
-    Ok(context)
-}
+use ixa_example_births_deaths::initialize;
 
 fn main() {
     let mut context = initialize().expect("Could not initialize context.");
-
     context.execute();
 }

examples/births-deaths/demographics_report.rs → examples/births-deaths/src/demographics_report.rs

@@ -10,7 +10,6 @@ use ixa::{
 };
 use serde::{Deserialize, Serialize};
 use std::path::Path;
-use std::path::PathBuf;
 
 #[derive(Serialize, Deserialize, Clone)]
 struct PersonReportItem {
@@ -72,9 +71,10 @@ pub fn init(context: &mut Context) -> Result<(), IxaError> {
         .clone();
 
     let current_dir = Path::new(file!()).parent().unwrap();
+    let current_dir = current_dir.join(Path::new(".."));
     context
         .report_options()
-        .directory(PathBuf::from(current_dir))
+        .directory(current_dir)
         .overwrite(true); // Not recommended for production. See `basic-infection/incidence-report`.
 
     context.add_report::<PersonReportItem>(&parameters.demographic_output_file)?;

examples/births-deaths/incidence_report.rs → examples/births-deaths/src/incidence_report.rs

@@ -47,6 +47,7 @@ pub fn init(context: &mut Context) -> Result<(), IxaError> {
         .unwrap()
         .clone();
     let current_dir = Path::new(file!()).parent().unwrap();
+    let current_dir = current_dir.join(Path::new(".."));
     context
         .report_options()
         .directory(PathBuf::from(current_dir))