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nj_py-0.0.12/Cargo.lock

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+checksum = "05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed"
+dependencies = [
+ "tap",
+]
+
+[[package]]
+name = "zmij"
+version = "1.0.21"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b8848ee67ecc8aedbaf3e4122217aff892639231befc6a1b58d29fff4c2cabaa"

nj_py-0.0.12/Cargo.toml

@@ -0,0 +1,11 @@
+[workspace]
+members = ["nj", "python"]
+resolver = "3"
+
+[workspace.package]
+version = "0.0.12"
+edition = "2024"
+authors = ["Rens Holmer"]
+license = "MIT"
+repository = "https://github.com/holmrenser/nj.rs"
+description = "Neighbor Joining, fast phylogenetic tree construction. Library and CLI."

nj_py-0.0.12/PKG-INFO

@@ -0,0 +1,7 @@
+Metadata-Version: 2.4
+Name: nj_py
+Version: 0.0.12
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10

nj_py-0.0.12/nj/Cargo.toml

@@ -0,0 +1,38 @@
+[package]
+name = "nj"
+description = "Neighbor Joining, fast phylogenetic tree construction. Library and CLI."
+version.workspace = true
+edition.workspace = true
+license.workspace = true
+authors.workspace = true
+repository.workspace = true
+
+
+[lib]
+crate-type = ["rlib"]
+path = "src/lib.rs"
+
+[[bin]]
+name = "nj"
+path = "src/main.rs"
+
+[dependencies]
+bitvec = "1.0.1"
+getrandom = "0.2"
+nanorand = "0.8.0"
+serde = { version = "1.0.228", features = ["derive"] }
+ts-rs = "11.1.0"
+
+# CLI-only dependencies
+[dependencies.clap]
+version = "4"
+features = ["derive"]
+optional = true
+
+
+[features]
+# default build only builds the library
+default = []
+
+# feature to build CLI
+cli = ["clap"]

nj_py-0.0.12/nj/Makefile

@@ -0,0 +1,6 @@
+all:
+	CARGO_TARGET_DIR=target cargo build --release
+	CARGO_TARGET_DIR=target cargo build --release --features cli --bin nj
+
+clean:
+	CARGO_TARGET_DIR=target cargo clean

nj_py-0.0.12/nj/bindings/SubstitutionModel.ts

@@ -0,0 +1,15 @@
+// This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually.
+
+/**
+ * Available substitution models.
+ *
+ * | Variant | Alphabet | Formula |
+ * |---------|----------|---------|
+ * | `PDiff` | DNA, Protein | `p` |
+ * | `JukesCantor` | DNA only | `-0.75 · ln(1 - 4p/3)` |
+ * | `Kimura2P` | DNA only | `-0.5 · ln(1-2p-q) - 0.25 · ln(1-2q)` |
+ * | `Poisson` | Protein only | `-ln(1 - p)` |
+ *
+ * Model–alphabet compatibility is enforced at runtime in [`crate::nj`].
+ */
+export type SubstitutionModel = "PDiff" | "JukesCantor" | "Kimura2P" | "Poisson";