Add integration testing for default flags

Author: sirno

src/core/haplotype.rs

@@ -35,10 +35,17 @@ use super::fitness::FitnessProvider;
 pub static N_FITNESS_TABLES: OnceLock<usize> = OnceLock::new();
 
 pub fn set_number_of_fitness_tables(value: usize) -> Result<(), usize> {
+    if N_FITNESS_TABLES.get().is_some() {
+        eprintln!("Trying to set `N_FITNESS_TABLES`, which has already been set.");
+    }
     N_FITNESS_TABLES.set(value)
 }
 
 fn make_fitness_cache() -> Vec<OnceLock<f64>> {
+    // warn if the number of fitness providers has not been explicitly set at runtime
+    if N_FITNESS_TABLES.get().is_none() {
+        eprintln!("`N_FITNESS_TABLES` is not set, using default value of 1.");
+    }
     std::iter::repeat_with(OnceLock::new)
         .take(*N_FITNESS_TABLES.get_or_init(|| 1))
         .collect()

src/main.rs

@@ -10,18 +10,129 @@ use virolution::args::Args;
 use virolution::runner::Runner;
 
 fn main() {
+    let args = Args::parse();
+
     if cfg!(feature = "parallel") {
         println!("Running in parallel mode.");
     } else {
         println!("Running in serial mode.");
     }
 
-    let args = Args::parse();
-
     let mut runner = Runner::new(args).unwrap_or_else(|err| {
         eprintln!("Unable to init simulation: {err}.");
         std::process::exit(1);
     });
 
     runner.start();
 }
+
+/// TODO: These tests should run for multiple feature flags
+#[cfg(test)]
+mod tests {
+    use std::process::Command;
+
+    struct Cleanup<'a> {
+        dir: &'a str,
+    }
+
+    impl<'a> Drop for Cleanup<'a> {
+        fn drop(&mut self) {
+            std::fs::remove_dir_all(self.dir).unwrap();
+        }
+    }
+
+    /// Test invocation of program for singlehost setup with 1 generation
+    #[test]
+    fn test_singlehost() {
+        let tmp_dir = ".tmp_singlehost";
+        let _cleanup = Cleanup { dir: tmp_dir };
+        let output = Command::new("cargo")
+            .args([
+                "run",
+                "--",
+                "--disable-progress-bar",
+                "--settings",
+                "test/singlehost/singlehost.yaml",
+                "--sequence",
+                "test/singlehost/ref.fasta",
+                "--generations",
+                "1",
+                "--n-compartments",
+                "2",
+                "--outdir",
+                tmp_dir,
+            ])
+            .output()
+            .expect("Failed to execute command");
+
+        assert!(output.status.success());
+
+        // Check if output files are created
+        assert!(std::path::Path::new(&format!("{}/fitness_table_0.npy", tmp_dir)).exists());
+        assert!(std::path::Path::new(&format!("{}/virolution.log", tmp_dir)).exists());
+    }
+
+    /// Test invocation of program for multihost setup with 1 generation
+    #[test]
+    fn test_multihost() {
+        let tmp_dir = ".tmp_multihost";
+        let _cleanup = Cleanup { dir: tmp_dir };
+
+        let output = Command::new("cargo")
+            .args([
+                "run",
+                "--",
+                "--disable-progress-bar",
+                "--settings",
+                "test/multihost/multihost.yaml",
+                "--sequence",
+                "test/multihost/ref.fasta",
+                "--generations",
+                "1",
+                "--n-compartments",
+                "2",
+                "--outdir",
+                tmp_dir,
+            ])
+            .output()
+            .expect("Failed to execute command");
+
+        assert!(output.status.success());
+
+        // Check if output files are created
+        assert!(std::path::Path::new(&format!("{}/fitness_table_0.npy", tmp_dir)).exists());
+        assert!(std::path::Path::new(&format!("{}/fitness_table_1.npy", tmp_dir)).exists());
+        assert!(std::path::Path::new(&format!("{}/virolution.log", tmp_dir)).exists());
+    }
+
+    /// Test invocation of program for epistasis setup with 1 generation
+    #[test]
+    fn test_epistasis() {
+        let tmp_dir = ".tmp_epistasis";
+        let output = Command::new("cargo")
+            .args([
+                "run",
+                "--",
+                "--disable-progress-bar",
+                "--settings",
+                "test/epistasis/epistasis.yaml",
+                "--sequence",
+                "test/epistasis/ref.fasta",
+                "--generations",
+                "1",
+                "--n-compartments",
+                "2",
+                "--outdir",
+                tmp_dir,
+            ])
+            .output()
+            .expect("Failed to execute command");
+
+        assert!(output.status.success());
+
+        // Check if output files are created
+        assert!(std::path::Path::new(&format!("{}/fitness_table_0.npy", tmp_dir)).exists());
+        assert!(std::path::Path::new(&format!("{}/epistasis_table_0.npy", tmp_dir)).exists());
+        assert!(std::path::Path::new(&format!("{}/virolution.log", tmp_dir)).exists());
+    }
+}

src/simulation.rs

@@ -194,6 +194,10 @@ impl Simulation for BasicSimulation {
         self.population = population;
     }
 
+    /// Set the parameters for the simulation
+    ///
+    /// WARNING: Currently this method does only reinitialize part of the simulation. Do not use
+    /// without revising its implementation.
     fn set_parameters(&mut self, parameters: Parameters) {
         self.parameters = parameters;
         self.mutation_sampler = Binomial::new(