test: add minimal example_1 test module

src/dataset/sarscov2/phylogeny.rs

@@ -301,20 +301,8 @@ pub fn compress_lineage(
 ///
 /// # Arguments
 ///
-///  * `lineage` | `String` | A String of a SARS-CoV-2 lineage name.
-///  * `alias_key` | `&BTreeMap<String, Vec<String>>` | A mapping of SARS-CoV-2 aliases to decompressed lineage paths.
-///
-/// # Basic usage:
-///
-/// ```
-/// decompress_lineage("BA.5.2", alias_key)?;
-/// ```
-///
-/// # Example
-///
-/// ```no run
-/// let alias_key = import_alias_key(".")?;
-/// decompress_lineage("BA.5.2", alias_key)?;
+///  * `lineage` | A string slice that contains a SARS-CoV-2 lineage name.
+///  * `alias_key` | A mapping of SARS-CoV-2 aliases to decompressed lineage paths.
 /// ```
 pub fn decompress_lineage(
     lineage: &str,

src/lib.rs

@@ -5,6 +5,8 @@ pub mod phylogeny;
 pub mod plot;
 pub mod recombination;
 pub mod sequence;
+#[cfg(test)]
+pub mod test;
 pub mod utils;
 
 use crate::dataset::attributes::Name;

src/test/mod.rs

@@ -0,0 +1,47 @@
+use crate::cli;
+use crate::dataset::attributes::{Name, Tag};
+use crate::dataset::download;
+use color_eyre::eyre::{Report, Result};
+use std::path::PathBuf;
+use std::str::FromStr;
+
+#[tokio::test]
+async fn example_1() -> Result<(), Report> {
+    // ------------------------------------------------------------------------
+    // Dataset Download
+
+    let name = Name::SarsCov2;
+    let tag = Tag::from_str("2023-11-17")?;
+    let output_dir = PathBuf::from("test").join("example_1").join("dataset");
+    let summary = None;
+
+    let mut args = cli::dataset::download::Args {
+        name,
+        tag,
+        output_dir: output_dir.clone(),
+        summary,
+    };
+
+    download::dataset(&mut args).await?;
+
+    // // ------------------------------------------------------------------------
+    // // Run
+
+    // let population = Some("AY.4.2*,BA.5.2,XBC.1.6*,XBB.1.5.1,XBL".to_string());
+    // let dataset_dir = output_dir;
+    // let output_dir = PathBuf::from("test").join("example_1").join("run");
+
+    // let mut args = cli::run::Args {
+    //     population,
+    //     dataset_dir: dataset_dir.clone(),
+    //     output_dir: output_dir.clone(),
+    //     ..Default::default()
+    // };
+
+    // run(&mut args)?;
+
+    // ------------------------------------------------------------------------
+    // Plot
+
+    Ok(())
+}