feat: add Sankoff parsimony model and directory locking

Implements a calibrated 16-state Sankoff substitution cost matrix and CLI pipeline for evolutionary distance computation, including empirical calibration via saturation-filtered SNP counts. Refactors the sibling scanning stage to use batched transforms for improved synchronization efficiency. Introduces an OS-level advisory directory lock across all index-modifying commands to prevent concurrent write corruption. Updates dependencies and exposes new Sankoff utilities in the public API.

src/Cargo.lock

@@ -48,6 +48,15 @@ dependencies = [
  "as-slice",
 ]
 
+[[package]]
+name = "aligned-vec"
+version = "0.6.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dc890384c8602f339876ded803c97ad529f3842aba97f6392b3dba0dd171769b"
+dependencies = [
+ "equator",
+]
+
 [[package]]
 name = "allocator-api2"
 version = "0.2.21"
@@ -497,6 +506,18 @@ dependencies = [
  "windows-sys 0.59.0",
 ]
 
+[[package]]
+name = "console"
+version = "0.16.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4fe5f465a4f6fee88fad41b85d990f84c835335e85b5d9e6e63e0d06d28cba7c"
+dependencies = [
+ "encode_unicode",
+ "libc",
+ "unicode-width",
+ "windows-sys 0.61.2",
+]
+
 [[package]]
 name = "const-oid"
 version = "0.10.2"
@@ -820,6 +841,26 @@ dependencies = [
  "syn",
 ]
 
+[[package]]
+name = "equator"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4711b213838dfee0117e3be6ac926007d7f433d7bbe33595975d4190cb07e6fc"
+dependencies = [
+ "equator-macro",
+]
+
+[[package]]
+name = "equator-macro"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "44f23cf4b44bfce11a86ace86f8a73ffdec849c9fd00a386a53d278bd9e81fb3"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "equivalent"
 version = "1.0.2"
@@ -907,6 +948,16 @@ dependencies = [
  "percent-encoding",
 ]
 
+[[package]]
+name = "fs4"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e8c6b3bd49c37d2aa3f3f2220233b29a7cd23f79d1fe70e5337d25fb390793de"
+dependencies = [
+ "rustix 0.38.44",
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "fs_at"
 version = "0.2.1"
@@ -1228,13 +1279,26 @@ version = "0.17.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "183b3088984b400f4cfac3620d5e076c84da5364016b4f49473de574b2586235"
 dependencies = [
- "console",
+ "console 0.15.11",
  "number_prefix",
  "portable-atomic",
  "unicode-width",
  "web-time",
 ]
 
+[[package]]
+name = "indicatif"
+version = "0.18.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9433806cd6b4ec1aba79c021c7e4c58fb4c3b9977c085062e611ac929998fb0c"
+dependencies = [
+ "console 0.16.4",
+ "portable-atomic",
+ "unicode-width",
+ "unit-prefix",
+ "web-time",
+]
+
 [[package]]
 name = "infer"
 version = "0.19.0"
@@ -1326,12 +1390,9 @@ dependencies = [
 
 [[package]]
 name = "kodama"
-version = "0.2.3"
+version = "0.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a44f3a71a44fbf49ce38152db7dc9adf959d4fe5c29344cd1858bdbda8d9091"
-dependencies = [
- "num-traits",
-]
+checksum = "f868feceed4703c842925c14232667c5f29c8059d0354154b2d06ec3bf9daf82"
 
 [[package]]
 name = "lazy_static"
@@ -1365,6 +1426,12 @@ dependencies = [
  "pkg-config",
 ]
 
+[[package]]
+name = "linux-raw-sys"
+version = "0.4.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d26c52dbd32dccf2d10cac7725f8eae5296885fb5703b261f7d0a0739ec807ab"
+
 [[package]]
 name = "linux-raw-sys"
 version = "0.12.1"
@@ -1695,7 +1762,7 @@ version = "0.1.0"
 dependencies = [
  "crossbeam-channel",
  "hwlocality",
- "indicatif",
+ "indicatif 0.17.11",
  "ndarray",
  "obicompactvec",
  "obikpartitionner",
@@ -1720,7 +1787,7 @@ version = "1.1.44"
 dependencies = [
  "clap",
  "csv",
- "indicatif",
+ "indicatif 0.18.6",
  "kodama",
  "obidebruinj",
  "obifastwrite",
@@ -1737,7 +1804,9 @@ dependencies = [
  "obitaxonomy",
  "pprof",
  "rayon",
+ "serde",
  "serde_json",
+ "serde_yaml",
  "speedytree",
  "tracing",
  "tracing-subscriber",
@@ -1749,7 +1818,7 @@ version = "0.1.0"
 dependencies = [
  "cacheline-ef",
  "epserde",
- "indicatif",
+ "indicatif 0.17.11",
  "memmap2",
  "niffler 3.0.0",
  "obicompactvec",
@@ -1853,7 +1922,7 @@ dependencies = [
  "memmap2",
  "niffler 3.0.0",
  "obikseq",
- "rustix",
+ "rustix 1.1.4",
  "serde",
  "serde_json",
  "tempfile",
@@ -1863,7 +1932,8 @@ dependencies = [
 name = "obisys"
 version = "0.1.0"
 dependencies = [
- "indicatif",
+ "fs4",
+ "indicatif 0.17.11",
  "libc",
  "sysinfo",
  "tracing",
@@ -2017,10 +2087,11 @@ dependencies = [
 
 [[package]]
 name = "pprof"
-version = "0.13.0"
+version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef5c97c51bd34c7e742402e216abdeb44d415fbe6ae41d56b114723e953711cb"
+checksum = "38a01da47675efa7673b032bf8efd8214f1917d89685e07e395ab125ea42b187"
 dependencies = [
+ "aligned-vec",
  "backtrace",
  "cfg-if",
  "findshlibs",
@@ -2028,15 +2099,15 @@ dependencies = [
  "log",
  "nix 0.26.4",
  "once_cell",
- "parking_lot",
  "prost",
  "prost-build",
  "prost-derive",
  "sha2",
  "smallvec",
+ "spin",
  "symbolic-demangle",
  "tempfile",
- "thiserror 1.0.69",
+ "thiserror 2.0.18",
 ]
 
 [[package]]
@@ -2386,6 +2457,19 @@ dependencies = [
  "semver",
 ]
 
+[[package]]
+name = "rustix"
+version = "0.38.44"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fdb5bc1ae2baa591800df16c9ca78619bf65c0488b41b96ccec5d11220d8c154"
+dependencies = [
+ "bitflags 2.11.1",
+ "errno",
+ "libc",
+ "linux-raw-sys 0.4.15",
+ "windows-sys 0.59.0",
+]
+
 [[package]]
 name = "rustix"
 version = "1.1.4"
@@ -2395,7 +2479,7 @@ dependencies = [
  "bitflags 2.11.1",
  "errno",
  "libc",
- "linux-raw-sys",
+ "linux-raw-sys 0.12.1",
  "windows-sys 0.61.2",
 ]
 
@@ -2521,6 +2605,19 @@ dependencies = [
  "zmij",
 ]
 
+[[package]]
+name = "serde_yaml"
+version = "0.9.34+deprecated"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6a8b1a1a2ebf674015cc02edccce75287f1a0130d394307b36743c2f5d504b47"
+dependencies = [
+ "indexmap",
+ "itoa",
+ "ryu",
+ "serde",
+ "unsafe-libyaml",
+]
+
 [[package]]
 name = "sha2"
 version = "0.10.9"
@@ -2588,6 +2685,15 @@ dependencies = [
  "rb_tree",
 ]
 
+[[package]]
+name = "spin"
+version = "0.10.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "023a211cb3138dbc438680b32560ad89f699977624c9f8dbb95a47d5b4c07dd3"
+dependencies = [
+ "lock_api",
+]
+
 [[package]]
 name = "stable_deref_trait"
 version = "1.2.1"
@@ -2736,7 +2842,7 @@ dependencies = [
  "fastrand",
  "getrandom 0.3.4",
  "once_cell",
- "rustix",
+ "rustix 1.1.4",
  "windows-sys 0.61.2",
 ]
 
@@ -2920,6 +3026,18 @@ version = "0.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ebc1c04c71510c7f702b52b7c350734c9ff1295c464a03335b00bb84fc54f853"
 
+[[package]]
+name = "unit-prefix"
+version = "0.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "81e544489bf3d8ef66c953931f56617f423cd4b5494be343d9b9d3dda037b9a3"
+
+[[package]]
+name = "unsafe-libyaml"
+version = "0.2.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "673aac59facbab8a9007c7f6108d11f63b603f7cabff99fabf650fea5c32b861"
+
 [[package]]
 name = "untrusted"
 version = "0.9.0"
@@ -3421,7 +3539,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32e45ad4206f6d2479085147f02bc2ef834ac85886624a23575ae137c8aa8156"
 dependencies = [
  "libc",
- "rustix",
+ "rustix 1.1.4",
 ]
 
 [[package]]