refactor: lint

Author: ivan-aksamentov

packages/treetime-utils/src/assert.rs

@@ -42,3 +42,12 @@ pub fn format_array(s: impl AsRef<str>) -> String {
   let re = regex::Regex::new(r", shape=.*").unwrap();
   re.replace(&format_newlines(s), "").into_owned()
 }
+
+#[macro_export]
+macro_rules! assert_error {
+  ($result:expr, $expected_message:expr) => {{
+    let error = $result.unwrap_err();
+    let actual_message = $crate::error::report_to_string(&error);
+    pretty_assertions::assert_eq!(actual_message, $expected_message);
+  }};
+}

packages/treetime/src/commands/clock/clock_model.rs

@@ -35,7 +35,7 @@ impl ClockModel {
     let det = clock_set.determinant();
     if det <= 0.0 {
       debug!("ClockSet: {}", json_write_str(clock_set, JsonPretty(true))?);
-      debug!("ClockSet determinant: {}", det);
+      debug!("ClockSet determinant: {det}");
       return make_error!("No variation in sampling dates! Please specify your clock rate explicitly.");
     }
 

packages/treetime/src/commands/timetree/inference/runner.rs

@@ -1,5 +1,6 @@
 use crate::commands::clock::clock_model::ClockModel;
 use crate::commands::clock::clock_regression::{ClockOptions, estimate_clock_model_with_reroot};
+use crate::commands::clock::clock_set::ClockSet;
 use crate::commands::clock::find_best_root::params::BranchPointOptimizationParams;
 use crate::commands::optimize::optimize_unified::OptimizationContribution;
 use crate::commands::timetree::inference::backward_pass::propagate_distributions_backward;
@@ -33,15 +34,15 @@ pub fn run_timetree(
       }
     }
     // Reset clock set to ensure clean state for each iteration
-    node.clock_total = Default::default();
+    node.clock_total = ClockSet::default();
   }
 
   // Reset edge clock sets as well
   for edge_ref in graph.get_edges() {
     let mut edge = edge_ref.write_arc().payload().write_arc();
-    edge.clock_to_parent = Default::default();
-    edge.clock_to_child = Default::default();
-    edge.clock_from_child = Default::default();
+    edge.clock_to_parent = ClockSet::default();
+    edge.clock_to_child = ClockSet::default();
+    edge.clock_from_child = ClockSet::default();
   }
 
   log::info!("## Estimating clock rate from root-to-tip regression");

packages/treetime/src/distribution/distribution_convolution.rs

@@ -412,8 +412,10 @@ mod tests {
     let uniform_x = array![0.0, 1.0, 2.0];
     let uniform = Distribution::function(uniform_x, y).unwrap();
 
-    let result = distribution_convolution(&non_uniform, &uniform);
-    result.unwrap_err();
+    assert_error!(
+      distribution_convolution(&non_uniform, &uniform),
+      "Function distributions must use uniform grids for convolution"
+    );
   }
 
   #[test]

packages/treetime/src/distribution/distribution_division.rs

@@ -101,6 +101,7 @@ mod tests {
   use super::*;
   use approx::assert_ulps_eq;
   use ndarray::array;
+  use treetime_utils::assert_error;
 
   #[test]
   fn test_divide_empty_by_any() {
@@ -114,8 +115,10 @@ mod tests {
   fn test_divide_by_empty_fails() {
     let point = Distribution::point(1.0, 2.0);
     let empty = Distribution::empty();
-    let result = distribution_division(&point, &empty);
-    result.unwrap_err();
+    assert_error!(
+      distribution_division(&point, &empty),
+      "Cannot divide by empty distribution"
+    );
   }
 
   #[test]