Merge pull request #33 from TravisWheelerLab/dev

nail 0.6.0

Author: jackroddy

libnail/CHANGELOG.md

@@ -16,6 +16,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+
+## [0.5.1] - 2026-7-10
+
+### Changed
+- struct `Profile` now derives `PartialEq`
+
 ## [0.5.0] - 2026-3-19
 
 ### Added

libnail/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "libnail"
-version = "0.5.0"
+version = "0.5.1"
 authors = ["Jack Roddy <jack.w.roddy@gmail.com>"]
 edition = "2021"
 license = "BSD-3-Clause"

libnail/src/structs/profile.rs

@@ -346,7 +346,7 @@ mod serialize {
     }
 }
 
-#[derive(Clone, Default, DataSize)]
+#[derive(Clone, PartialEq, Default, DataSize)]
 pub struct Profile {
     /// The name of the profile
     pub name: String,

nail/CHANGELOG.md

@@ -16,6 +16,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.6.0] - 2026-7-10
+
+### Added
+- added CLI param `--mmseqs-path` 
+- added error Structs `io::index::{Offset, IndexCollisionError}`
+- added warning for `--mmseqs-max-seqs` saturation
+- added CLI params `-f`, `-a` for controlling cloud search retries in the event of a failed cloud intersection
+- added CLI params `--seed-mode`, `--max-seeds`
+- added flag `-hz` for printing help in "zebra" format
+
+### Changed
+- trait `IndexInner` is no longer generic over offset type
+- trait method `IndexInner::extend()` now returns an error on key collisions
+- method `Index::build_chunk()` now panics on key collisions
+- renamed function `pipeline::seed_stage::seed_max_seqs()` to `seed_static()`
+- renamed  `MmseqsArgs` to `SeedArgs`
+- `Seeds::from_path()` now takes parameter `max_seeds: Option<usize>`
+- changed CLI flag `--tmp-dir` behavior to use Unix epoch timestamps
+
+### Removed
+- removed structs `io::fasta::FastaOffset`, `io::p7hmm::P7HmmOffset`, `io::seeds::SeedOffset`
+- removed struct `io::seeds::SeedsIndexInner`
+- removed CLI param `--prog-seed`
 
 ## [0.5.0] - 2026-3-19
 

nail/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nail"
-version = "0.5.0"
+version = "0.6.0"
 authors = ["Jack Roddy <jack.w.roddy@gmail.com>"]
 edition = "2021"
 license = "BSD-3-Clause"
@@ -19,8 +19,8 @@ jemalloc = ["jemallocator"]
 
 [dependencies]
 jemallocator = { version = "0.3", optional = true }
-clap = { version = "4.5.23", features = ["derive", "wrap_help"] }
-libnail = { path = "../libnail", version = "0.5.0" }
+clap = { version = "4.6.1", features = ["derive", "wrap_help"] }
+libnail = { path = "../libnail", version = "0.5.1" }
 anyhow = "1.0.66"
 thiserror = "1.0.37"
 rayon = "1.7.0"