feat: derive serde::[De-]Serialize for alignment interface structs

lib_tsalign/src/a_star_aligner/alignment_geometry.rs

@@ -1,15 +1,15 @@
 use std::{fmt::Display, ops::Range};
 
 #[derive(Debug, Clone, Eq, PartialEq)]
-#[cfg_attr(feature = "serde", derive(serde::Deserialize))]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[cfg_attr(feature = "serde", serde(rename_all = "snake_case"))]
 pub struct AlignmentRange {
     offset: AlignmentCoordinates,
     limit: AlignmentCoordinates,
 }
 
 #[derive(Debug, Clone, Copy, Eq, PartialEq)]
-#[cfg_attr(feature = "serde", derive(serde::Deserialize))]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[cfg_attr(feature = "serde", serde(rename_all = "snake_case"))]
 pub struct AlignmentCoordinates {
     reference: usize,

lib_tsalign/src/a_star_aligner/configurable_a_star_align.rs

@@ -53,7 +53,7 @@ pub use compact_genome::implementation::alphabets;
 pub use compact_genome::interface::alphabet::Alphabet;
 
 #[derive(Debug, Default)]
-#[cfg_attr(feature = "serde", derive(serde::Deserialize))]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[cfg_attr(feature = "serde", serde(rename_all = "snake_case"))]
 pub enum MinLengthStrategySelector {
     None,
@@ -68,7 +68,7 @@ pub enum MinLengthStrategySelector {
 }
 
 #[derive(Debug, Default)]
-#[cfg_attr(feature = "serde", derive(serde::Deserialize))]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[cfg_attr(feature = "serde", serde(rename_all = "snake_case"))]
 pub enum ChainingStrategySelector {
     #[default]
@@ -78,7 +78,7 @@ pub enum ChainingStrategySelector {
 }
 
 #[derive(Debug, Default)]
-#[cfg_attr(feature = "serde", derive(serde::Deserialize))]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[cfg_attr(feature = "serde", serde(rename_all = "snake_case"))]
 pub enum TotalLengthStrategySelector {
     None,
@@ -97,10 +97,9 @@ struct QueryData<'a> {
     memory_limit: Option<usize>,
 }
 
-#[cfg_attr(feature = "serde", derive(serde::Deserialize))] // Mostly used for kwargs in python bindings
-#[cfg_attr(feature = "serde", serde(default))]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
+#[cfg_attr(feature = "serde", serde(default, bound = ""))]
 pub struct Aligner<AlphabetType: Alphabet = DnaAlphabetOrN> {
-    #[cfg_attr(feature = "serde", serde(skip))] // Not deserializable
     costs: TemplateSwitchConfig<AlphabetType, U64Cost>,
 
     // ↓ Settings for how the alignment (definition)

lib_tsalign/src/config.rs

@@ -13,6 +13,14 @@ use crate::{
 pub mod io;
 
 #[derive(Debug, Eq, PartialEq)]
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
+#[cfg_attr(
+    feature = "serde",
+    serde(bound(
+        deserialize = "Cost: serde::Deserialize<'de>", // omit AlphabetType
+        serialize = "Cost: serde::Serialize" // omit AlphabetType
+    ))
+)]
 pub struct TemplateSwitchConfig<AlphabetType, Cost> {
     // Limits
     pub left_flank_length: isize,
@@ -39,6 +47,7 @@ pub struct TemplateSwitchConfig<AlphabetType, Cost> {
     pub reverse_anti_primary_gap_costs: CostFunction<isize, Cost>,
 }
 
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[derive(Debug, Clone, Eq, PartialEq)]
 pub struct BaseCost<Cost> {
     /// Primary: reference; secondary: reference; direction: forward.

lib_tsalign/src/costs/cost_function.rs

@@ -17,6 +17,7 @@ pub mod io;
 /// * `f(x) = 3` for `2 <= x`.
 ///
 /// The function can be evaluated via its [`evaluate`](Self::evaluate) function.
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
 #[derive(Debug, Clone, Eq, PartialEq)]
 pub struct CostFunction<SourceType, Cost> {
     function: Vec<(SourceType, Cost)>,

lib_tsalign/src/costs/gap_affine.rs

@@ -5,13 +5,27 @@ use generic_a_star::cost::AStarCost;
 
 pub mod io;
 
+#[cfg_attr(feature = "serde", derive(serde::Deserialize, serde::Serialize))]
+#[cfg_attr(
+    feature = "serde",
+    serde(bound(
+        deserialize = "Cost: serde::Deserialize<'de>", // omit AlphabetType
+        serialize = "Cost: serde::Serialize" // omit AlphabetType
+    ))
+)]
 #[derive(Debug, Eq, PartialEq)]
 pub struct GapAffineAlignmentCostTable<AlphabetType, Cost> {
     name: String,
     substitution_cost_table: Vec<Cost>,
     gap_open_cost_vector: Vec<Cost>,
     gap_extend_cost_vector: Vec<Cost>,
-    phantom_data: PhantomData<AlphabetType>,
+
+    // Establish invariance over AlphabetType
+    // Because we don't actually store any data of type AlphabetType,
+    // we do not want to use PhantomData<AlphabetType> directly,
+    // for example so that AlphabetType does not need to be Send + Sync for
+    // this cost table to be Send + Sync.
+    phantom_data: PhantomData<fn(AlphabetType) -> AlphabetType>,
 
     // Cache some values that are potentially used often.
     min_substitution_cost: Cost,