Release v0.0.25

Author: willchet

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file. The format
 is roughly based on [Keep a Changelog], and this project tries to adheres to
 [Semantic Versioning].
 
-## [0.0.25] - TBD
+## [0.0.25] - 2026-02-04
 
 ### Added
 
@@ -18,7 +18,6 @@ is roughly based on [Keep a Changelog], and this project tries to adheres to
 
 - Fixes Zoe to use the latest sync'd portable SIMD in Rust nightly 1.95. For earlier versions, try Rust nightly 1.94.
 
-
 ## [0.0.24] - 2026-01-26
 
 ### Added

Cargo.lock

@@ -1,7 +1,7 @@
 [package]
 edition = "2024"
 name = "zoe"
-version = "0.0.25-dev"
+version = "0.0.25"
 rust-version = "1.95"
 description = "A nightly library for viral genomics"
 license = "Apache-2.0"

Cargo.toml

@@ -189,8 +189,8 @@ impl<'a, const S: usize> ScalarProfile<'a, S> {
 /// - `T` - The numeric type used for scores. `i8`, `i16`, `i32`, and `i64` use
 ///   the signed algorithm, which is the most common. `u8`, `u16`, `u32`, and
 ///   `u64` use the unsigned algorithm.
-/// - `N` - The number of SIMD lanes (usually 16, 32 or 64)
-/// - `S` - The size of the alphabet (usually 5 for DNA including `N`)
+/// - `N` - The number of SIMD lanes (usually 16, 32 or 64).
+/// - `S` - The size of the alphabet (usually 5 for DNA including `N`).
 #[derive(Debug, Clone, PartialEq, Eq, Hash)]
 pub struct StripedProfile<'a, T, const N: usize, const S: usize>
 where
@@ -268,7 +268,7 @@ where
     where
         T: From<U>,
         U: AnyInt, {
-        // SupportedLaneCount cannot presently be zero.
+        // A SIMD vector cannot presently be of length 0
         let number_vectors = seq.len().div_ceil(N);
         let total_lanes = N * number_vectors;
 

src/alignment/profile.rs

@@ -12,10 +12,10 @@ use std::{cell::OnceCell, sync::OnceLock};
 ///
 /// ## Type Parameters
 ///
-/// - `M` - The number of SIMD lanes for i8 profiles
-/// - `N` - The number of SIMD lanes for i16 profiles
-/// - `O` - The number of SIMD lanes for i32 profiles
-/// - `S` - The size of the alphabet (usually 5 for DNA including *N*)
+/// - `M` - The number of SIMD lanes for `i8` profiles.
+/// - `N` - The number of SIMD lanes for `i16` profiles.
+/// - `O` - The number of SIMD lanes for `i32` profiles.
+/// - `S` - The size of the alphabet (usually 5 for DNA including `N`).
 pub trait ProfileSets<'a, const M: usize, const N: usize, const O: usize, const S: usize>: Sized {
     /// Gets or initializes [`StripedProfile`] with elements of `i8` and `M`
     /// SIMD lanes and returns a reference to the field.
@@ -370,10 +370,10 @@ pub trait ProfileSets<'a, const M: usize, const N: usize, const O: usize, const
 ///
 /// ## Type Parameters
 ///
-/// - `M` - The number of SIMD lanes for `i8` profiles
-/// - `N` - The number of SIMD lanes for `i16` profiles
-/// - `O` - The number of SIMD lanes for `i32` profiles
-/// - `S` - The size of the alphabet (usually 5 for DNA including *N*)
+/// - `M` - The number of SIMD lanes for `i8` profiles.
+/// - `N` - The number of SIMD lanes for `i16` profiles.
+/// - `O` - The number of SIMD lanes for `i32` profiles.
+/// - `S` - The size of the alphabet (usually 5 for DNA including `N`).
 #[derive(Debug, Clone)]
 pub struct LocalProfiles<'a, const M: usize, const N: usize, const O: usize, const S: usize> {
     pub(crate) seq:         &'a [u8],

src/alignment/profile_set.rs

@@ -94,7 +94,9 @@ impl AminoAcids {
     }
 
     /// Cuts the N-terminus of the [`AminoAcids`] just prior to the new starting
-    /// index (0-based). Be aware that this clones the internal buffer!
+    /// index (0-based).
+    ///
+    /// This method clones the internal buffer.
     #[inline]
     pub fn cut_to_start(&mut self, new_start: usize) {
         *self = Self(self.0.drain(new_start..).collect());
@@ -107,7 +109,8 @@ impl AminoAcids {
     }
 
     /// Prepends the amino acid sequence with the given slice.
-    /// This method always allocates.
+    ///
+    /// This method allocates.
     #[inline]
     pub fn prepend_from_slice(&mut self, slice: impl AsRef<[u8]>) {
         let slice = slice.as_ref();
@@ -120,14 +123,17 @@ impl AminoAcids {
         *self = AminoAcids(new);
     }
 
-    /// Pads the C-terminus (end) of the [`AminoAcids`] by `aa` for `count` times.
+    /// Pads the C-terminus (end) of the [`AminoAcids`] by `aa` for `count`
+    /// times.
     #[inline]
     pub fn pad_end(&mut self, aa: u8, count: usize) {
         self.0.extend(std::iter::repeat_n(aa, count));
     }
 
     /// Pads the N-terminus (start) of the [`AminoAcids`] by `aa` for `count`
-    /// times. This method always allocates.
+    /// times.
+    ///
+    /// This method allocates.
     #[inline]
     pub fn pad_start(&mut self, aa: u8, count: usize) {
         if count == 0 {
@@ -140,8 +146,9 @@ impl AminoAcids {
     }
 
     /// Pads the [`AminoAcids`] on both flanking sides by `aa` for
-    /// `amount_before` and `amount_after` respectively. This method always
-    /// allocates.
+    /// `amount_before` and `amount_after` respectively.
+    ///
+    /// This method allocates.
     #[inline]
     pub fn pad_both_sides(&mut self, aa: u8, amount_before: usize, amount_after: usize) {
         if amount_before == 0 && amount_after == 0 {

src/data/types/amino_acids/mod.rs

@@ -126,7 +126,9 @@ impl Nucleotides {
     }
 
     /// Cuts the 5' end of the [`Nucleotides`] just prior to the new starting
-    /// index (0-based). Be aware that this clones the internal buffer!
+    /// index (0-based).
+    ///
+    /// This method clones the internal buffer.
     #[inline]
     pub fn cut_to_start(&mut self, new_start: usize) {
         *self = Nucleotides(self.0.drain(new_start..).collect());
@@ -139,7 +141,8 @@ impl Nucleotides {
     }
 
     /// Prepends the nucleotide sequence with the given slice.
-    /// This method always allocates.
+    ///
+    /// This method allocates.
     #[inline]
     pub fn prepend_from_slice(&mut self, slice: impl AsRef<[u8]>) {
         let slice = slice.as_ref();
@@ -152,14 +155,17 @@ impl Nucleotides {
         *self = Nucleotides(new);
     }
 
-    /// Pads the end or 3' end of the [`Nucleotides`] by `base` for `count` times.
+    /// Pads the end or 3' end of the [`Nucleotides`] by `base` for `count`
+    /// times.
     #[inline]
     pub fn pad_end(&mut self, base: u8, count: usize) {
         self.0.extend(std::iter::repeat_n(base, count));
     }
 
     /// Pads the start or 5' end of the [`Nucleotides`] by `base` for `count`
-    /// times. This method always allocates.
+    /// times.
+    ///
+    /// This method allocates.
     #[inline]
     pub fn pad_start(&mut self, base: u8, count: usize) {
         if count == 0 {
@@ -172,8 +178,9 @@ impl Nucleotides {
     }
 
     /// Pads the [`Nucleotides`] on both flanking sides by `base` for
-    /// `amount_before` and `amount_after` respectively. This method always
-    /// allocates.
+    /// `amount_before` and `amount_after` respectively.
+    ///
+    /// This method allocates.
     #[inline]
     pub fn pad_both_sides(&mut self, base: u8, amount_before: usize, amount_after: usize) {
         if amount_before == 0 && amount_after == 0 {

src/data/types/nucleotides/mod.rs

@@ -164,8 +164,8 @@ pub fn position_by_byte3<const N: usize>(haystack: &[u8], b1: u8, b2: u8, b3: u8
 ///
 /// The following parameters can be used to adjust performance characteristics:
 ///
-/// - `N` - The number of SIMD lanes
-/// - `UF` - The unroll factor
+/// - `N` - The number of SIMD lanes to use.
+/// - `UF` - The unroll factor.
 #[inline]
 #[must_use]
 #[allow(clippy::needless_range_loop)]

src/search/bytes/search.rs

@@ -71,8 +71,8 @@ const fn create_masks<const N: usize>() -> [Simd<u8, N>; 256] {
 ///
 /// ## Parameters
 ///
-/// - `N` - The number of SIMD lanes to use
-/// - `K` - The number of differences allowed
+/// - `N` - The number of SIMD lanes to use.
+/// - `K` - The number of differences allowed.
 ///
 /// ## Limitations
 ///