Update Cargo.toml

Author: Paururo

Cargo.toml

@@ -1,32 +1,44 @@
 [package]
 name = "pathotypr"
-version = "0.1.0"
+version = "0.2.0"
 authors = ["Paula Ruiz Rodriguez <paula.ruiz.rodriguez@csic.es>"]
 edition = "2021"
-description = "Pathotypr is a tool to classify genomes using the train, predict, and classify subcommands."
+description = "A high-performance tool for genome classification and variant genotyping."
 license = "GPL-3"
 repository = "https://github.com/PathoGenOmics-Lab/pathotypr"
 
 [dependencies]
-anyhow = "1.0.98"
-bio = "2.0.3"
-bincode = "1.3"
-chrono = "0.4.39"
+# CLI and UI
 clap = { version = "4.5.28", features = ["derive"] }
-csv = "1.3.1"
-env_logger = "0.11.6"
-flate2 = "1.0"
 indicatif = "0.17.0"
 log = "0.4"
-nalgebra = "0.33.2"
-rand = "0.8.0"
+env_logger = "0.11.6"
+chrono = "0.4.39"
+
+# Core Logic & ML
+smartcore = { version = "0.4.1", features = ["serde"] }
+rand = { version = "0.8.5", features = ["small_rng"] }
 rayon = "1.10.0"
+
+# Data Handling & Serialization
 serde = { version = "1.0", features = ["derive"] }
+bincode = "1.3.3"
+zstd = "0.13.1"
+
+# Bioinformatics
+# CORRECTED: The simplest declaration is the correct one.
+# No features are needed to access the bit_kmers functionality.
 needletail = "0.6.3"
-fxhash = "0.2.1"
+rustc-hash = "2.0.0"
+
+# Other utilities from the original project
+anyhow = "1.0.98"
+bio = "2.0.3"
+csv = "1.3.1"
+nalgebra = "0.33.2"
 tempfile = "3.20.0"
 ndarray = { version = "0.15", features = ["serde"] }
-smartcore   = { version = "0.4.1", features = ["serde"] }
 gff = "0.1.0"
 rust-lapper = "1.1.0"
 bio-types = "1.0.4"
+fxhash = "0.2.1"