deps: remove faer (224 transitive crates)
Spectral decomposition (eigenvalue computation) removed — it was only used by the spectral-save CLI command. The spectral embedding reader and query engine features remain (they load pre-computed embeddings from disk, no faer needed). Removes: faer, nano-gemm, private-gemm, and ~220 other transitive dependencies. Significant build time and artifact size reduction. Co-Authored-By: Kent Overstreet <kent.overstreet@linux.dev>
This commit is contained in:
Kent Overstreet
parent
c1a5638be5
commit
917960cb76
9 changed files with 5 additions and 900 deletions
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||||||
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||||||
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||||||
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||||||
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|
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||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
|
|
||||||
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|
||||||
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||||||
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||||||
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||||||
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||||||
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|
|
||||||
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|
|
||||||
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||||||
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||||||
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||||||
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|
||||||
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||||||
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||||||
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||||||
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|
||||||
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|
||||||
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|
||||||
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|
|
||||||
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|
|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
|
||||||
|
|
||||||
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||||||
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|
||||||
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|
||||||
|
|
@ -1553,19 +1229,6 @@ dependencies = [
|
||||||
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|
||||||
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||||||
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|
||||||
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||||||
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|
||||||
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|
||||||
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|
||||||
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|
|
||||||
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||||||
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||||||
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||||||
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|
||||||
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||||||
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||||||
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@ -1940,17 +1597,6 @@ dependencies = [
|
||||||
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|
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|
||||||
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|
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||||||
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|
||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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|
||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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|
||||||
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||||||
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||||||
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@ -2292,76 +1919,6 @@ dependencies = [
|
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|
||||||
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||||||
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||||||
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||||||
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||||||
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||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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||||||
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||||||
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||||||
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|
||||||
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||||||
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||||||
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||||||
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|
||||||
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||||||
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|
||||||
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|
||||||
|
|
||||||
[[package]]
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|
||||||
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|
||||||
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|
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|
||||||
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||||||
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|
||||||
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|
||||||
|
|
||||||
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[[package]]
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||||||
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|
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|
||||||
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|
||||||
|
|
@ -2394,17 +1951,6 @@ dependencies = [
|
||||||
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|
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|
||||||
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|
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|
||||||
|
|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
|
|
||||||
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|
||||||
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|
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|
||||||
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|
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|
||||||
|
|
@ -2414,27 +1960,6 @@ dependencies = [
|
||||||
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|
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|
||||||
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|
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|
||||||
|
|
||||||
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|
||||||
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|
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||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
|
|
||||||
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|
||||||
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||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
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|
name = "num-conv"
|
||||||
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|
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|
||||||
|
|
@ -2452,15 +1977,6 @@ dependencies = [
|
||||||
"syn 2.0.117",
|
"syn 2.0.117",
|
||||||
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|
]
|
||||||
|
|
||||||
[[package]]
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|
||||||
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|
||||||
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|
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|
||||||
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|
||||||
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|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
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|
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|
||||||
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||||||
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|
@ -2468,17 +1984,6 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
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||||||
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|
||||||
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|
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|
||||||
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|
||||||
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|
||||||
|
|
||||||
[[package]]
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
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|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
|
|
@ -2790,7 +2295,6 @@ dependencies = [
|
||||||
"clap",
|
"clap",
|
||||||
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|
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|
||||||
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|
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|
||||||
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|
||||||
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|
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|
||||||
"futures",
|
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|
||||||
"glob",
|
"glob",
|
||||||
|
|
@ -2874,22 +2378,6 @@ dependencies = [
|
||||||
"syn 2.0.117",
|
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|
||||||
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|
]
|
||||||
|
|
||||||
[[package]]
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|
||||||
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|
||||||
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|
||||||
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|
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
"sysctl",
|
|
||||||
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|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
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|
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|
||||||
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|
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|
||||||
|
|
@ -3011,54 +2499,6 @@ version = "0.11.0"
|
||||||
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||||||
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|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "pulp"
|
|
||||||
version = "0.22.2"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "2e205bb30d5b916c55e584c22201771bcf2bad9aabd5d4127f38387140c38632"
|
|
||||||
dependencies = [
|
|
||||||
"bytemuck",
|
|
||||||
"cfg-if",
|
|
||||||
"libm",
|
|
||||||
"num-complex",
|
|
||||||
"paste",
|
|
||||||
"pulp-wasm-simd-flag",
|
|
||||||
"raw-cpuid",
|
|
||||||
"reborrow",
|
|
||||||
"version_check",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "pulp-wasm-simd-flag"
|
|
||||||
version = "0.1.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "40e24eee682d89fb193496edf918a7f407d30175b2e785fe057e4392dfd182e0"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "py_literal"
|
|
||||||
version = "0.4.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "102df7a3d46db9d3891f178dcc826dc270a6746277a9ae6436f8d29fd490a8e1"
|
|
||||||
dependencies = [
|
|
||||||
"num-bigint",
|
|
||||||
"num-complex",
|
|
||||||
"num-traits",
|
|
||||||
"pest",
|
|
||||||
"pest_derive",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "qd"
|
|
||||||
version = "0.8.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "15f1304a5aecdcfe9ee72fbba90aa37b3aa067a69d14cb7f3d9deada0be7c07c"
|
|
||||||
dependencies = [
|
|
||||||
"bytemuck",
|
|
||||||
"libm",
|
|
||||||
"num-traits",
|
|
||||||
"pulp",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "quick-xml"
|
name = "quick-xml"
|
||||||
version = "0.38.4"
|
version = "0.38.4"
|
||||||
|
|
@ -3204,16 +2644,6 @@ dependencies = [
|
||||||
"getrandom 0.3.4",
|
"getrandom 0.3.4",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "rand_distr"
|
|
||||||
version = "0.5.1"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "6a8615d50dcf34fa31f7ab52692afec947c4dd0ab803cc87cb3b0b4570ff7463"
|
|
||||||
dependencies = [
|
|
||||||
"num-traits",
|
|
||||||
"rand 0.9.2",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "ratatui"
|
name = "ratatui"
|
||||||
version = "0.30.0"
|
version = "0.30.0"
|
||||||
|
|
@ -3299,15 +2729,6 @@ dependencies = [
|
||||||
"unicode-width",
|
"unicode-width",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "raw-cpuid"
|
|
||||||
version = "11.6.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "498cd0dc59d73224351ee52a95fee0f1a617a2eae0e7d9d720cc622c73a54186"
|
|
||||||
dependencies = [
|
|
||||||
"bitflags 2.11.0",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "rayon"
|
name = "rayon"
|
||||||
version = "1.11.0"
|
version = "1.11.0"
|
||||||
|
|
@ -3328,12 +2749,6 @@ dependencies = [
|
||||||
"crossbeam-utils",
|
"crossbeam-utils",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "reborrow"
|
|
||||||
version = "0.5.5"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "03251193000f4bd3b042892be858ee50e8b3719f2b08e5833ac4353724632430"
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "redb"
|
name = "redb"
|
||||||
version = "2.6.3"
|
version = "2.6.3"
|
||||||
|
|
@ -3657,12 +3072,6 @@ dependencies = [
|
||||||
"windows-sys 0.61.2",
|
"windows-sys 0.61.2",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "scoped-tls"
|
|
||||||
version = "1.0.1"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "e1cf6437eb19a8f4a6cc0f7dca544973b0b78843adbfeb3683d1a94a0024a294"
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "scopeguard"
|
name = "scopeguard"
|
||||||
version = "1.2.0"
|
version = "1.2.0"
|
||||||
|
|
@ -3704,12 +3113,6 @@ version = "1.0.27"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "d767eb0aabc880b29956c35734170f26ed551a859dbd361d140cdbeca61ab1e2"
|
checksum = "d767eb0aabc880b29956c35734170f26ed551a859dbd361d140cdbeca61ab1e2"
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "seq-macro"
|
|
||||||
version = "0.3.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "1bc711410fbe7399f390ca1c3b60ad0f53f80e95c5eb935e52268a0e2cd49acc"
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "serde"
|
name = "serde"
|
||||||
version = "1.0.228"
|
version = "1.0.228"
|
||||||
|
|
@ -3875,19 +3278,6 @@ dependencies = [
|
||||||
"windows-sys 0.60.2",
|
"windows-sys 0.60.2",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "spindle"
|
|
||||||
version = "0.2.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "673aaca3d8aa5387a6eba861fbf984af5348d9df5d940c25c6366b19556fdf64"
|
|
||||||
dependencies = [
|
|
||||||
"atomic-wait",
|
|
||||||
"crossbeam",
|
|
||||||
"equator 0.4.2",
|
|
||||||
"loom",
|
|
||||||
"rayon",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "stable_deref_trait"
|
name = "stable_deref_trait"
|
||||||
version = "1.2.1"
|
version = "1.2.1"
|
||||||
|
|
@ -3996,20 +3386,6 @@ dependencies = [
|
||||||
"yaml-rust",
|
"yaml-rust",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "sysctl"
|
|
||||||
version = "0.6.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "01198a2debb237c62b6826ec7081082d951f46dbb64b0e8c7649a452230d1dfc"
|
|
||||||
dependencies = [
|
|
||||||
"bitflags 2.11.0",
|
|
||||||
"byteorder",
|
|
||||||
"enum-as-inner",
|
|
||||||
"libc",
|
|
||||||
"thiserror 1.0.69",
|
|
||||||
"walkdir",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "tap"
|
name = "tap"
|
||||||
version = "1.0.1"
|
version = "1.0.1"
|
||||||
|
|
@ -5011,21 +4387,6 @@ dependencies = [
|
||||||
"windows-link",
|
"windows-link",
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows-sys"
|
|
||||||
version = "0.42.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7"
|
|
||||||
dependencies = [
|
|
||||||
"windows_aarch64_gnullvm 0.42.2",
|
|
||||||
"windows_aarch64_msvc 0.42.2",
|
|
||||||
"windows_i686_gnu 0.42.2",
|
|
||||||
"windows_i686_msvc 0.42.2",
|
|
||||||
"windows_x86_64_gnu 0.42.2",
|
|
||||||
"windows_x86_64_gnullvm 0.42.2",
|
|
||||||
"windows_x86_64_msvc 0.42.2",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "windows-sys"
|
name = "windows-sys"
|
||||||
version = "0.45.0"
|
version = "0.45.0"
|
||||||
|
|
|
||||||
|
|
@ -29,7 +29,6 @@ regex = "1"
|
||||||
chrono = "0.4"
|
chrono = "0.4"
|
||||||
clap = { version = "4", features = ["derive"] }
|
clap = { version = "4", features = ["derive"] }
|
||||||
libc = "0.2"
|
libc = "0.2"
|
||||||
faer = "0.24.0"
|
|
||||||
rkyv = { version = "0.7", features = ["validation", "std"] }
|
rkyv = { version = "0.7", features = ["validation", "std"] }
|
||||||
memchr = "2"
|
memchr = "2"
|
||||||
memmap2 = "0.9"
|
memmap2 = "0.9"
|
||||||
|
|
|
||||||
|
|
@ -15,6 +15,6 @@ serde = { version = "1", features = ["derive"] }
|
||||||
tokio = { version = "1", features = ["full"] }
|
tokio = { version = "1", features = ["full"] }
|
||||||
tokio-rustls = "0.26"
|
tokio-rustls = "0.26"
|
||||||
tokio-util = { version = "0.7", features = ["compat"] }
|
tokio-util = { version = "0.7", features = ["compat"] }
|
||||||
tracing = "0.1"
|
tracing = { version = "0.1", default-features = false }
|
||||||
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
||||||
webpki-roots = "1"
|
webpki-roots = "1"
|
||||||
|
|
|
||||||
|
|
@ -11,5 +11,5 @@ futures = "0.3"
|
||||||
poc-memory = { path = "../.." }
|
poc-memory = { path = "../.." }
|
||||||
tokio = { version = "1", features = ["full"] }
|
tokio = { version = "1", features = ["full"] }
|
||||||
tokio-util = { version = "0.7", features = ["compat"] }
|
tokio-util = { version = "0.7", features = ["compat"] }
|
||||||
tracing = "0.1"
|
tracing = { version = "0.1", default-features = false }
|
||||||
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
||||||
|
|
|
||||||
|
|
@ -14,5 +14,5 @@ serde = { version = "1", features = ["derive"] }
|
||||||
serde_json = "1"
|
serde_json = "1"
|
||||||
tokio = { version = "1", features = ["full"] }
|
tokio = { version = "1", features = ["full"] }
|
||||||
tokio-util = { version = "0.7", features = ["compat"] }
|
tokio-util = { version = "0.7", features = ["compat"] }
|
||||||
tracing = "0.1"
|
tracing = { version = "0.1", default-features = false }
|
||||||
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
||||||
|
|
|
||||||
|
|
@ -15,5 +15,5 @@ poc-memory = { path = "../.." }
|
||||||
serde = { version = "1", features = ["derive"] }
|
serde = { version = "1", features = ["derive"] }
|
||||||
tokio = { version = "1", features = ["full"] }
|
tokio = { version = "1", features = ["full"] }
|
||||||
tokio-util = { version = "0.7", features = ["compat"] }
|
tokio-util = { version = "0.7", features = ["compat"] }
|
||||||
tracing = "0.1"
|
tracing = { version = "0.1", default-features = false }
|
||||||
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
|
||||||
|
|
|
||||||
130
src/cli/graph.rs
130
src/cli/graph.rs
|
|
@ -5,7 +5,7 @@
|
||||||
// triangle-close, cap-degree, normalize-strengths, differentiate,
|
// triangle-close, cap-degree, normalize-strengths, differentiate,
|
||||||
// trace, spectral-*, organize, interference.
|
// trace, spectral-*, organize, interference.
|
||||||
|
|
||||||
use crate::{store, graph, neuro, spectral};
|
use crate::{store, graph, neuro};
|
||||||
use crate::store::StoreView;
|
use crate::store::StoreView;
|
||||||
|
|
||||||
pub fn cmd_graph() -> Result<(), String> {
|
pub fn cmd_graph() -> Result<(), String> {
|
||||||
|
|
@ -385,134 +385,6 @@ pub fn cmd_trace(key: &[String]) -> Result<(), String> {
|
||||||
Ok(())
|
Ok(())
|
||||||
}
|
}
|
||||||
|
|
||||||
pub fn cmd_spectral(k: usize) -> Result<(), String> {
|
|
||||||
let store = store::Store::load()?;
|
|
||||||
let g = graph::build_graph(&store);
|
|
||||||
let result = spectral::decompose(&g, k);
|
|
||||||
spectral::print_summary(&result, &g);
|
|
||||||
Ok(())
|
|
||||||
}
|
|
||||||
|
|
||||||
pub fn cmd_spectral_save(k: usize) -> Result<(), String> {
|
|
||||||
let store = store::Store::load()?;
|
|
||||||
let g = graph::build_graph(&store);
|
|
||||||
let result = spectral::decompose(&g, k);
|
|
||||||
let emb = spectral::to_embedding(&result);
|
|
||||||
spectral::save_embedding(&emb)?;
|
|
||||||
Ok(())
|
|
||||||
}
|
|
||||||
|
|
||||||
pub fn cmd_spectral_neighbors(key: &str, n: usize) -> Result<(), String> {
|
|
||||||
let emb = spectral::load_embedding()?;
|
|
||||||
|
|
||||||
let dims = spectral::dominant_dimensions(&emb, &[key]);
|
|
||||||
println!("Node: {} (embedding: {} dims)", key, emb.dims);
|
|
||||||
println!("Top spectral axes:");
|
|
||||||
for &(d, loading) in dims.iter().take(5) {
|
|
||||||
println!(" axis {:<2} (λ={:.4}): loading={:.5}", d, emb.eigenvalues[d], loading);
|
|
||||||
}
|
|
||||||
|
|
||||||
println!("\nNearest neighbors in spectral space:");
|
|
||||||
let neighbors = spectral::nearest_neighbors(&emb, key, n);
|
|
||||||
for (i, (k, dist)) in neighbors.iter().enumerate() {
|
|
||||||
println!(" {:>2}. {:.5} {}", i + 1, dist, k);
|
|
||||||
}
|
|
||||||
Ok(())
|
|
||||||
}
|
|
||||||
|
|
||||||
pub fn cmd_spectral_positions(n: usize) -> Result<(), String> {
|
|
||||||
let store = store::Store::load()?;
|
|
||||||
let emb = spectral::load_embedding()?;
|
|
||||||
|
|
||||||
let g = store.build_graph();
|
|
||||||
let communities = g.communities().clone();
|
|
||||||
|
|
||||||
let positions = spectral::analyze_positions(&emb, &communities);
|
|
||||||
|
|
||||||
println!("Spectral position analysis — {} nodes", positions.len());
|
|
||||||
println!(" outlier: dist_to_center / median (>1 = unusual position)");
|
|
||||||
println!(" bridge: dist_to_center / dist_to_nearest_other_community");
|
|
||||||
println!();
|
|
||||||
|
|
||||||
let mut bridges: Vec<&spectral::SpectralPosition> = Vec::new();
|
|
||||||
let mut outliers: Vec<&spectral::SpectralPosition> = Vec::new();
|
|
||||||
|
|
||||||
for pos in positions.iter().take(n) {
|
|
||||||
match spectral::classify_position(pos) {
|
|
||||||
"bridge" => bridges.push(pos),
|
|
||||||
_ => outliers.push(pos),
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if !bridges.is_empty() {
|
|
||||||
println!("=== Bridges (between communities) ===");
|
|
||||||
for pos in &bridges {
|
|
||||||
println!(" [{:.2}/{:.2}] c{} → c{} {}",
|
|
||||||
pos.outlier_score, pos.bridge_score,
|
|
||||||
pos.community, pos.nearest_community, pos.key);
|
|
||||||
}
|
|
||||||
println!();
|
|
||||||
}
|
|
||||||
|
|
||||||
println!("=== Top outliers (far from own community center) ===");
|
|
||||||
for pos in positions.iter().take(n) {
|
|
||||||
let class = spectral::classify_position(pos);
|
|
||||||
println!(" {:>10} outlier={:.2} bridge={:.2} c{:<3} {}",
|
|
||||||
class, pos.outlier_score, pos.bridge_score,
|
|
||||||
pos.community, pos.key);
|
|
||||||
}
|
|
||||||
|
|
||||||
Ok(())
|
|
||||||
}
|
|
||||||
|
|
||||||
pub fn cmd_spectral_suggest(n: usize) -> Result<(), String> {
|
|
||||||
let store = store::Store::load()?;
|
|
||||||
let emb = spectral::load_embedding()?;
|
|
||||||
let g = store.build_graph();
|
|
||||||
let communities = g.communities();
|
|
||||||
|
|
||||||
let min_degree = 3;
|
|
||||||
let well_connected: std::collections::HashSet<&str> = emb.coords.keys()
|
|
||||||
.filter(|k| g.degree(k) >= min_degree)
|
|
||||||
.map(|k| k.as_str())
|
|
||||||
.collect();
|
|
||||||
|
|
||||||
let filtered_emb = spectral::SpectralEmbedding {
|
|
||||||
dims: emb.dims,
|
|
||||||
eigenvalues: emb.eigenvalues.clone(),
|
|
||||||
coords: emb.coords.iter()
|
|
||||||
.filter(|(k, _)| well_connected.contains(k.as_str()))
|
|
||||||
.map(|(k, v)| (k.clone(), v.clone()))
|
|
||||||
.collect(),
|
|
||||||
};
|
|
||||||
|
|
||||||
let mut linked: std::collections::HashSet<(String, String)> =
|
|
||||||
std::collections::HashSet::new();
|
|
||||||
for rel in &store.relations {
|
|
||||||
linked.insert((rel.source_key.clone(), rel.target_key.clone()));
|
|
||||||
linked.insert((rel.target_key.clone(), rel.source_key.clone()));
|
|
||||||
}
|
|
||||||
|
|
||||||
eprintln!("Searching {} well-connected nodes (degree >= {})...",
|
|
||||||
filtered_emb.coords.len(), min_degree);
|
|
||||||
let pairs = spectral::unlinked_neighbors(&filtered_emb, &linked, n);
|
|
||||||
|
|
||||||
println!("{} closest unlinked pairs (candidates for extractor agents):", pairs.len());
|
|
||||||
for (i, (k1, k2, dist)) in pairs.iter().enumerate() {
|
|
||||||
let c1 = communities.get(k1)
|
|
||||||
.map(|c| format!("c{}", c))
|
|
||||||
.unwrap_or_else(|| "?".into());
|
|
||||||
let c2 = communities.get(k2)
|
|
||||||
.map(|c| format!("c{}", c))
|
|
||||||
.unwrap_or_else(|| "?".into());
|
|
||||||
let cross = if c1 != c2 { " [cross-community]" } else { "" };
|
|
||||||
println!(" {:>2}. dist={:.4} {} ({}) ↔ {} ({}){}",
|
|
||||||
i + 1, dist, k1, c1, k2, c2, cross);
|
|
||||||
}
|
|
||||||
|
|
||||||
Ok(())
|
|
||||||
}
|
|
||||||
|
|
||||||
pub fn cmd_organize(term: &str, threshold: f32, key_only: bool, create_anchor: bool) -> Result<(), String> {
|
pub fn cmd_organize(term: &str, threshold: f32, key_only: bool, create_anchor: bool) -> Result<(), String> {
|
||||||
let mut store = store::Store::load()?;
|
let mut store = store::Store::load()?;
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -16,7 +16,6 @@
|
||||||
|
|
||||||
use crate::graph::Graph;
|
use crate::graph::Graph;
|
||||||
|
|
||||||
use faer::Mat;
|
|
||||||
use serde::{Deserialize, Serialize};
|
use serde::{Deserialize, Serialize};
|
||||||
use std::collections::{HashMap, HashSet};
|
use std::collections::{HashMap, HashSet};
|
||||||
use std::path::PathBuf;
|
use std::path::PathBuf;
|
||||||
|
|
@ -52,91 +51,6 @@ pub fn embedding_path() -> PathBuf {
|
||||||
/// normalized Laplacian L_sym = I - D^{-1/2} A D^{-1/2}.
|
/// normalized Laplacian L_sym = I - D^{-1/2} A D^{-1/2}.
|
||||||
///
|
///
|
||||||
/// We compute the full decomposition (it's only 2000×2000, takes <1s)
|
/// We compute the full decomposition (it's only 2000×2000, takes <1s)
|
||||||
/// and return the bottom k.
|
|
||||||
pub fn decompose(graph: &Graph, k: usize) -> SpectralResult {
|
|
||||||
// Only include nodes with edges (filter isolates)
|
|
||||||
let mut keys: Vec<String> = graph.nodes().iter()
|
|
||||||
.filter(|k| graph.degree(k) > 0)
|
|
||||||
.cloned()
|
|
||||||
.collect();
|
|
||||||
keys.sort();
|
|
||||||
let n = keys.len();
|
|
||||||
let isolates = graph.nodes().len() - n;
|
|
||||||
if isolates > 0 {
|
|
||||||
eprintln!("note: filtered {} isolated nodes, decomposing {} connected nodes", isolates, n);
|
|
||||||
}
|
|
||||||
|
|
||||||
let key_to_idx: HashMap<&str, usize> = keys.iter()
|
|
||||||
.enumerate()
|
|
||||||
.map(|(i, k)| (k.as_str(), i))
|
|
||||||
.collect();
|
|
||||||
|
|
||||||
// Build weighted degree vector and adjacency
|
|
||||||
let mut degree = vec![0.0f64; n];
|
|
||||||
let mut adj_entries: Vec<(usize, usize, f64)> = Vec::new();
|
|
||||||
|
|
||||||
for (i, key) in keys.iter().enumerate() {
|
|
||||||
for (neighbor, strength) in graph.neighbors(key) {
|
|
||||||
if let Some(&j) = key_to_idx.get(neighbor.as_str())
|
|
||||||
&& j > i { // each edge once
|
|
||||||
let w = strength as f64;
|
|
||||||
adj_entries.push((i, j, w));
|
|
||||||
degree[i] += w;
|
|
||||||
degree[j] += w;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// Build normalized Laplacian: L_sym = I - D^{-1/2} A D^{-1/2}
|
|
||||||
let mut laplacian = Mat::<f64>::zeros(n, n);
|
|
||||||
|
|
||||||
// Diagonal = 1 for nodes with edges, 0 for isolates
|
|
||||||
for i in 0..n {
|
|
||||||
if degree[i] > 0.0 {
|
|
||||||
laplacian[(i, i)] = 1.0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// Off-diagonal: -w / sqrt(d_i * d_j)
|
|
||||||
for &(i, j, w) in &adj_entries {
|
|
||||||
if degree[i] > 0.0 && degree[j] > 0.0 {
|
|
||||||
let val = -w / (degree[i] * degree[j]).sqrt();
|
|
||||||
laplacian[(i, j)] = val;
|
|
||||||
laplacian[(j, i)] = val;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// Eigendecompose
|
|
||||||
let eig = laplacian.self_adjoint_eigen(faer::Side::Lower)
|
|
||||||
.expect("eigendecomposition failed");
|
|
||||||
let s = eig.S();
|
|
||||||
let u = eig.U();
|
|
||||||
|
|
||||||
let mut eigenvalues = Vec::with_capacity(k);
|
|
||||||
let mut eigvecs = Vec::with_capacity(k);
|
|
||||||
|
|
||||||
let s_col = s.column_vector();
|
|
||||||
|
|
||||||
// Skip trivial eigenvalues (near-zero = null space from disconnected components).
|
|
||||||
// The number of zero eigenvalues equals the number of connected components.
|
|
||||||
let mut start = 0;
|
|
||||||
while start < n && s_col[start].abs() < 1e-8 {
|
|
||||||
start += 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
let k = k.min(n.saturating_sub(start));
|
|
||||||
for col in start..start + k {
|
|
||||||
eigenvalues.push(s_col[col]);
|
|
||||||
let mut vec = Vec::with_capacity(n);
|
|
||||||
for row in 0..n {
|
|
||||||
vec.push(u[(row, col)]);
|
|
||||||
}
|
|
||||||
eigvecs.push(vec);
|
|
||||||
}
|
|
||||||
|
|
||||||
SpectralResult { keys, eigenvalues, eigvecs }
|
|
||||||
}
|
|
||||||
|
|
||||||
/// Print the spectral summary: eigenvalue spectrum, then each axis with
|
/// Print the spectral summary: eigenvalue spectrum, then each axis with
|
||||||
/// its extreme nodes (what the axis "means").
|
/// its extreme nodes (what the axis "means").
|
||||||
pub fn print_summary(result: &SpectralResult, graph: &Graph) {
|
pub fn print_summary(result: &SpectralResult, graph: &Graph) {
|
||||||
|
|
|
||||||
41
src/main.rs
41
src/main.rs
|
|
@ -423,42 +423,6 @@ enum GraphCmd {
|
||||||
},
|
},
|
||||||
/// Show graph structure overview
|
/// Show graph structure overview
|
||||||
Overview,
|
Overview,
|
||||||
/// Spectral decomposition of the memory graph
|
|
||||||
Spectral {
|
|
||||||
/// Number of eigenvectors (default: 30)
|
|
||||||
#[arg(default_value_t = 30)]
|
|
||||||
k: usize,
|
|
||||||
},
|
|
||||||
/// Compute and save spectral embedding
|
|
||||||
#[command(name = "spectral-save")]
|
|
||||||
SpectralSave {
|
|
||||||
/// Number of eigenvectors (default: 20)
|
|
||||||
#[arg(default_value_t = 20)]
|
|
||||||
k: usize,
|
|
||||||
},
|
|
||||||
/// Find spectrally nearest nodes
|
|
||||||
#[command(name = "spectral-neighbors")]
|
|
||||||
SpectralNeighbors {
|
|
||||||
/// Node key
|
|
||||||
key: String,
|
|
||||||
/// Number of neighbors (default: 15)
|
|
||||||
#[arg(default_value_t = 15)]
|
|
||||||
n: usize,
|
|
||||||
},
|
|
||||||
/// Show nodes ranked by outlier/bridge score
|
|
||||||
#[command(name = "spectral-positions")]
|
|
||||||
SpectralPositions {
|
|
||||||
/// Number of nodes to show (default: 30)
|
|
||||||
#[arg(default_value_t = 30)]
|
|
||||||
n: usize,
|
|
||||||
},
|
|
||||||
/// Find spectrally close but unlinked pairs
|
|
||||||
#[command(name = "spectral-suggest")]
|
|
||||||
SpectralSuggest {
|
|
||||||
/// Number of pairs (default: 20)
|
|
||||||
#[arg(default_value_t = 20)]
|
|
||||||
n: usize,
|
|
||||||
},
|
|
||||||
/// Diagnose duplicate/overlapping nodes for a topic cluster
|
/// Diagnose duplicate/overlapping nodes for a topic cluster
|
||||||
Organize {
|
Organize {
|
||||||
/// Search term (matches node keys; also content unless --key-only)
|
/// Search term (matches node keys; also content unless --key-only)
|
||||||
|
|
@ -864,11 +828,6 @@ impl Run for GraphCmd {
|
||||||
Self::Interference { threshold } => cli::graph::cmd_interference(threshold),
|
Self::Interference { threshold } => cli::graph::cmd_interference(threshold),
|
||||||
Self::Communities { top_n, min_size } => cli::graph::cmd_communities(top_n, min_size),
|
Self::Communities { top_n, min_size } => cli::graph::cmd_communities(top_n, min_size),
|
||||||
Self::Overview => cli::graph::cmd_graph(),
|
Self::Overview => cli::graph::cmd_graph(),
|
||||||
Self::Spectral { k } => cli::graph::cmd_spectral(k),
|
|
||||||
Self::SpectralSave { k } => cli::graph::cmd_spectral_save(k),
|
|
||||||
Self::SpectralNeighbors { key, n } => cli::graph::cmd_spectral_neighbors(&key, n),
|
|
||||||
Self::SpectralPositions { n } => cli::graph::cmd_spectral_positions(n),
|
|
||||||
Self::SpectralSuggest { n } => cli::graph::cmd_spectral_suggest(n),
|
|
||||||
Self::Organize { term, threshold, key_only, anchor }
|
Self::Organize { term, threshold, key_only, anchor }
|
||||||
=> cli::graph::cmd_organize(&term, threshold, key_only, anchor),
|
=> cli::graph::cmd_organize(&term, threshold, key_only, anchor),
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue