feat: add pairwise distance computation and phylogenetic trees

This commit introduces a new `distance` CLI subcommand that computes pairwise genomic distance matrices using configurable metrics (Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger). It optionally generates phylogenetic trees (NJ or UPGMA) in Newick format and outputs results as CSV. The implementation adds a robust distance computation backend that dynamically routes to optimized backends based on index configuration, supports parallel iteration, and gracefully handles missing data. Additionally, it adds a `dump` task for exporting k-mer to genome mappings as CSV, introduces an `InvalidInput` error variant, updates dependencies to support numerical operations and tree construction, and performs minor module reorganizations.

src/Cargo.lock

@@ -176,6 +176,21 @@ dependencies = [
  "thiserror 1.0.69",
 ]
 
+[[package]]
+name = "bit-set"
+version = "0.5.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1"
+dependencies = [
+ "bit-vec",
+]
+
+[[package]]
+name = "bit-vec"
+version = "0.6.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
+
 [[package]]
 name = "bitflags"
 version = "1.3.2"
@@ -625,6 +640,12 @@ dependencies = [
  "syn",
 ]
 
+[[package]]
+name = "dtoa"
+version = "1.0.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4c3cf4824e2d5f025c7b531afcb2325364084a16806f6d47fbc1f5fbd9960590"
+
 [[package]]
 name = "either"
 version = "1.15.0"
@@ -1102,6 +1123,15 @@ dependencies = [
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "kodama"
+version = "0.2.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7a44f3a71a44fbf49ce38152db7dc9adf959d4fe5c29344cd1858bdbda8d9091"
+dependencies = [
+ "num-traits",
+]
+
 [[package]]
 name = "lazy_static"
 version = "1.5.0"
@@ -1453,7 +1483,10 @@ name = "obikindex"
 version = "0.1.0"
 dependencies = [
  "indicatif",
+ "ndarray",
+ "obicompactvec",
  "obikpartitionner",
+ "obilayeredmap",
  "obiskio",
  "obisys",
  "rayon",
@@ -1468,6 +1501,7 @@ version = "0.1.0"
 dependencies = [
  "clap",
  "indicatif",
+ "kodama",
  "obifastwrite",
  "obikindex",
  "obikpartitionner",
@@ -1480,6 +1514,7 @@ dependencies = [
  "obisys",
  "pprof",
  "rayon",
+ "speedytree",
  "tracing",
  "tracing-subscriber",
 ]
@@ -1886,8 +1921,8 @@ dependencies = [
  "lazy_static",
  "log",
  "mem_dbg",
- "rand",
- "rand_chacha",
+ "rand 0.9.4",
+ "rand_chacha 0.9.0",
  "rayon",
  "rdst",
  "rustc-hash",
@@ -1918,14 +1953,35 @@ version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dc33ff2d4973d518d823d61aa239014831e521c75da58e3df4840d3f47749d09"
 
+[[package]]
+name = "rand"
+version = "0.8.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5ca0ecfa931c29007047d1bc58e623ab12e5590e8c7cc53200d5202b69266d8a"
+dependencies = [
+ "libc",
+ "rand_chacha 0.3.1",
+ "rand_core 0.6.4",
+]
+
 [[package]]
 name = "rand"
 version = "0.9.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "44c5af06bb1b7d3216d91932aed5265164bf384dc89cd6ba05cf59a35f5f76ea"
 dependencies = [
- "rand_chacha",
- "rand_core",
+ "rand_chacha 0.9.0",
+ "rand_core 0.9.5",
+]
+
+[[package]]
+name = "rand_chacha"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
+dependencies = [
+ "ppv-lite86",
+ "rand_core 0.6.4",
 ]
 
 [[package]]
@@ -1935,7 +1991,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb"
 dependencies = [
  "ppv-lite86",
- "rand_core",
+ "rand_core 0.9.5",
+]
+
+[[package]]
+name = "rand_core"
+version = "0.6.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c"
+dependencies = [
+ "getrandom 0.2.17",
 ]
 
 [[package]]
@@ -1973,6 +2038,12 @@ dependencies = [
  "crossbeam-utils",
 ]
 
+[[package]]
+name = "rb_tree"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6724c78e033e1c4155b4d3f76593d09ad384739c6986c1addc2bd2f55b1aefe"
+
 [[package]]
 name = "rdst"
 version = "0.20.14"
@@ -2227,6 +2298,25 @@ version = "1.15.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "67b1b7a3b5fe4f1376887184045fcf45c69e92af734b7aaddc05fb777b6fbd03"
 
+[[package]]
+name = "speedytree"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7f4522052445ce1b002c095d93e9dc545c326e9e2321c1315f1ab2a381c11666"
+dependencies = [
+ "bit-set",
+ "bit-vec",
+ "bitvec",
+ "clap",
+ "dtoa",
+ "fixedbitset",
+ "parking_lot",
+ "petgraph",
+ "rand 0.8.6",
+ "rayon",
+ "rb_tree",
+]
+
 [[package]]
 name = "stable_deref_trait"
 version = "1.2.1"