More surgery:

  - gn-rust-correlation moved to genenetwork-rust.scm with new-style cargo-inputs
  - crates-io.scm import removed from genenetwork.scm and bioinformatics.scm
  - past-crates is now only referenced by crates-io.scm itself (dead file)
  - genenetwork2 builds successfully
  - All Rust packages (rust-qtlreaper, gn-rust-correlation) build from their new locations

3 files changed, 261 insertions, 7 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 83dd2b8..8b1a2db 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -9,7 +9,6 @@
   #:use-module (guix git-download)
   #:use-module (guix hg-download)
   #:use-module (guix build-system ant)
-  #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
@@ -21,7 +20,6 @@
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
-  #:use-module (gn packages crates-io)
   #:use-module (gn packages datastructures)
   #:use-module (gn packages maths)
   #:use-module (gn packages python)
@@ -40,7 +38,6 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages cran)
-  #:use-module (past-crates packages crates-io)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
diff --git a/gn/packages/genenetwork-rust.scm b/gn/packages/genenetwork-rust.scm
index 6189c72..54b8389 100644
--- a/gn/packages/genenetwork-rust.scm
+++ b/gn/packages/genenetwork-rust.scm
@@ -8,6 +8,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system cargo)
   #:use-module (guix gexp)
+  #:use-module (gnu packages maths)
   #:export (lookup-cargo-inputs))
 
 ;;; Crate sources for rust-qtlreaper (guix import crate -f Cargo.lock qtlreaper)
@@ -249,6 +250,169 @@
                 "1amb5i6gz7yjb0dnmz5y669674pqmwbj44p4yfxfv2ncgvk8x15q"))
 
 
+
+;;; Crate sources for gn-rust-correlation
+
+(define rust-gsl-6.0.0
+  (crate-source "GSL" "6.0.0"
+                "1kpiivagrsk9ags7d4k2521jwix0lqgnd3i8ayj3dfniszvcmgn9"))
+
+(define rust-gsl-sys-3.0.0
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "GSL-sys" "3.0.0"
+                "17dx066l1pbjwp9syjkzqb6fiajyb4wc814zqdfrj807rh6nfxs5"))
+
+(define rust-aho-corasick-1.1.4
+  (crate-source "aho-corasick" "1.1.4"
+                "00a32wb2h07im3skkikc495jvncf62jl6s96vwc7bhi70h9imlyx"))
+
+(define rust-assert-approx-eq-1.1.0
+  (crate-source "assert_approx_eq" "1.1.0"
+                "1zagfwfad5wssmr830gk3489f97ppczv6xs627jxniwm6ssdl1rw"))
+
+(define rust-bumpalo-3.20.2
+  (crate-source "bumpalo" "3.20.2"
+                "1jrgxlff76k9glam0akhwpil2fr1w32gbjdf5hpipc7ld2c7h82x"))
+
+(define rust-cast-0.3.0
+  (crate-source "cast" "0.3.0"
+                "1dbyngbyz2qkk0jn2sxil8vrz3rnpcj142y184p9l4nbl9radcip"))
+
+(define rust-cfg-if-1.0.4
+  (crate-source "cfg-if" "1.0.4"
+                "008q28ajc546z5p2hcwdnckmg0hia7rnx52fni04bwqkzyrghc4k"))
+
+(define rust-criterion-0.3.6
+  (crate-source "criterion" "0.3.6"
+                "13yd64ah93gkbdv7qq4cr6rhgl9979jjcjk3gkhnav1b7glns7dh"))
+
+(define rust-criterion-plot-0.4.5
+  (crate-source "criterion-plot" "0.4.5"
+                "0xhq0jz1603585h7xvm3s4x9irmifjliklszbzs4cda00y1cqwr6"))
+
+(define rust-csv-1.4.0
+  (crate-source "csv" "1.4.0"
+                "0f7r2ip0rbi7k377c3xmsh9xd69sillffhpfmbgnvz3yrxl9vkaj"))
+
+(define rust-csv-core-0.1.13
+  (crate-source "csv-core" "0.1.13"
+                "10lppd3fdb1i5npgx9xqjs5mjmy2qbdi8n16i48lg03ak4k3qjkh"))
+
+(define rust-half-1.8.3
+  (crate-source "half" "1.8.3"
+                "00q4ki8ycdswapw6xn1q89vr7rzi1c8m99igps0lx1i1gzhyshqv"))
+
+(define rust-itertools-0.10.5
+  (crate-source "itertools" "0.10.5"
+                "0ww45h7nxx5kj6z2y6chlskxd1igvs4j507anr6dzg99x1h25zdh"))
+
+(define rust-js-sys-0.3.94
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "js-sys" "0.3.94"
+                "1nb4fr7c78mrrdhmg04nbac1zvd5z3panvqka8sy30nfh3py411f"))
+
+(define rust-lazy-static-1.5.0
+  (crate-source "lazy_static" "1.5.0"
+                "1zk6dqqni0193xg6iijh7i3i44sryglwgvx20spdvwk3r6sbrlmv"))
+
+(define rust-once-cell-1.21.4
+  (crate-source "once_cell" "1.21.4"
+                "0l1v676wf71kjg2khch4dphwh1jp3291ffiymr2mvy1kxd5kwz4z"))
+
+(define rust-oorandom-11.1.5
+  (crate-source "oorandom" "11.1.5"
+                "07mlf13z453fq01qff38big1lh83j8l6aaglf63ksqzzqxc0yyfn"))
+
+(define rust-paste-1.0.15
+  (crate-source "paste" "1.0.15"
+                "02pxffpdqkapy292harq6asfjvadgp1s005fip9ljfsn9fvxgh2p"))
+
+(define rust-pkg-config-0.3.32
+  (crate-source "pkg-config" "0.3.32"
+                "0k4h3gnzs94sjb2ix6jyksacs52cf1fanpwsmlhjnwrdnp8dppby"))
+
+(define rust-plotters-0.3.7
+  (crate-source "plotters" "0.3.7"
+                "0ixpy9svpmr2rkzkxvvdpysjjky4gw104d73n7pi2jbs7m06zsss"))
+
+(define rust-plotters-backend-0.3.7
+  (crate-source "plotters-backend" "0.3.7"
+                "0ahpliim4hrrf7d4ispc2hwr7rzkn6d6nf7lyyrid2lm28yf2hnz"))
+
+(define rust-plotters-svg-0.3.7
+  (crate-source "plotters-svg" "0.3.7"
+                "0w56sxaa2crpasa1zj0bhxzihlapqfkncggavyngg0w86anf5fji"))
+
+(define rust-regex-1.12.3
+  (crate-source "regex" "1.12.3"
+                "0xp2q0x7ybmpa5zlgaz00p8zswcirj9h8nry3rxxsdwi9fhm81z1"))
+
+(define rust-regex-automata-0.4.14
+  (crate-source "regex-automata" "0.4.14"
+                "13xf7hhn4qmgfh784llcp2kzrvljd13lb2b1ca0mwnf15w9d87bf"))
+
+(define rust-regex-syntax-0.8.10
+  (crate-source "regex-syntax" "0.8.10"
+                "02jx311ka0daxxc7v45ikzhcl3iydjbbb0mdrpc1xgg8v7c7v2fw"))
+
+(define rust-rustversion-1.0.22
+  (crate-source "rustversion" "1.0.22"
+                "0vfl70jhv72scd9rfqgr2n11m5i9l1acnk684m2w83w0zbqdx75k"))
+
+(define rust-ryu-1.0.23
+  (crate-source "ryu" "1.0.23"
+                "0zs70sg00l2fb9jwrf6cbkdyscjs53anrvai2hf7npyyfi5blx4p"))
+
+(define rust-same-file-1.0.6
+  (crate-source "same-file" "1.0.6"
+                "00h5j1w87dmhnvbv9l8bic3y7xxsnjmssvifw2ayvgx9mb1ivz4k"))
+
+(define rust-serde-cbor-0.11.2
+  (crate-source "serde_cbor" "0.11.2"
+                "1xf1bq7ixha30914pd5jl3yw9v1x6car7xgrpimvfvs5vszjxvrb"))
+
+(define rust-tinytemplate-1.2.1
+  (crate-source "tinytemplate" "1.2.1"
+                "1g5n77cqkdh9hy75zdb01adxn45mkh9y40wdr7l68xpz35gnnkdy"))
+
+(define rust-walkdir-2.5.0
+  (crate-source "walkdir" "2.5.0"
+                "0jsy7a710qv8gld5957ybrnc07gavppp963gs32xk4ag8130jy99"))
+
+(define rust-wasm-bindgen-0.2.117
+  (crate-source "wasm-bindgen" "0.2.117"
+                "1c6hi55mq70546hrvrx7wa27sn3yvf04gg6hf8riwn8mnhdzql85"))
+
+(define rust-wasm-bindgen-macro-0.2.117
+  (crate-source "wasm-bindgen-macro" "0.2.117"
+                "1gl6gqy60khhyqv354m0kmgk541sass8kzymxim7hi6zbaizkgbz"))
+
+(define rust-wasm-bindgen-macro-support-0.2.117
+  (crate-source "wasm-bindgen-macro-support" "0.2.117"
+                "1wlza8xdr18cac2wm3ahxdwx1nnqa01m0d3jf3kd9dmsy8z6kafw"))
+
+(define rust-wasm-bindgen-shared-0.2.117
+  (crate-source "wasm-bindgen-shared" "0.2.117"
+                "0frxrdi1w0cswv8v7n1972hd23nbwm8hr7a2dhdq8bbd59l9l4ir"))
+
+(define rust-web-sys-0.3.94
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "web-sys" "0.3.94"
+                "02nxnhv349r2gcy8w71cjj6nimww1g2zy20y8r4hhbxi75z04w6d"))
+
+(define rust-winapi-util-0.1.11
+  (crate-source "winapi-util" "0.1.11"
+                "08hdl7mkll7pz8whg869h58c1r9y7in0w0pk8fm24qc77k0b39y2"))
+
+(define rust-windows-link-0.2.1
+  (crate-source "windows-link" "0.2.1"
+                "1rag186yfr3xx7piv5rg8b6im2dwcf8zldiflvb22xbzwli5507h"))
+
+(define rust-windows-sys-0.61.2
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "windows-sys" "0.61.2"
+                "1z7k3y9b6b5h52kid57lvmvm05362zv1v8w0gc7xyv5xphlp44xf"))
+
 (define-cargo-inputs lookup-cargo-inputs
   (qtlreaper =>
     (list rust-ansi-term-0.12.1
@@ -311,6 +475,83 @@
           rust-winapi-x86-64-pc-windows-gnu-0.4.0
           rust-zmij-1.0.21
           ))
+  (correlation_rust =>
+    (list rust-aho-corasick-1.1.4
+          rust-assert-approx-eq-1.1.0
+          rust-atty-0.2.14
+          rust-autocfg-1.5.0
+          rust-bitflags-1.3.2
+          rust-bumpalo-3.20.2
+          rust-cast-0.3.0
+          rust-cfg-if-1.0.4
+          rust-clap-2.34.0
+          rust-crossbeam-deque-0.8.6
+          rust-crossbeam-epoch-0.9.18
+          rust-crossbeam-utils-0.8.21
+          rust-criterion-0.3.6
+          rust-criterion-plot-0.4.5
+          rust-csv-1.4.0
+          rust-csv-core-0.1.13
+          rust-either-1.15.0
+          rust-gsl-6.0.0
+          rust-gsl-sys-3.0.0
+          rust-half-1.8.3
+          rust-heck-0.3.3
+          rust-hermit-abi-0.1.19
+          rust-itertools-0.10.5
+          rust-itoa-1.0.18
+          rust-js-sys-0.3.94
+          rust-lazy-static-1.5.0
+          rust-libc-0.2.184
+          rust-memchr-2.8.0
+          rust-num-traits-0.2.19
+          rust-once-cell-1.21.4
+          rust-oorandom-11.1.5
+          rust-paste-1.0.15
+          rust-pkg-config-0.3.32
+          rust-plotters-0.3.7
+          rust-plotters-backend-0.3.7
+          rust-plotters-svg-0.3.7
+          rust-proc-macro2-1.0.106
+          rust-quote-1.0.45
+          rust-rayon-1.11.0
+          rust-rayon-core-1.13.0
+          rust-regex-1.12.3
+          rust-regex-automata-0.4.14
+          rust-regex-syntax-0.8.10
+          rust-rustversion-1.0.22
+          rust-ryu-1.0.23
+          rust-same-file-1.0.6
+          rust-serde-1.0.228
+          rust-serde-cbor-0.11.2
+          rust-serde-core-1.0.228
+          rust-serde-derive-1.0.228
+          rust-serde-json-1.0.149
+          rust-strsim-0.8.0
+          rust-structopt-0.2.18
+          rust-structopt-derive-0.2.18
+          rust-syn-0.15.44
+          rust-syn-2.0.117
+          rust-textwrap-0.11.0
+          rust-tinytemplate-1.2.1
+          rust-unicode-ident-1.0.24
+          rust-unicode-segmentation-1.13.2
+          rust-unicode-width-0.1.14
+          rust-unicode-xid-0.1.0
+          rust-vec-map-0.8.2
+          rust-walkdir-2.5.0
+          rust-wasm-bindgen-0.2.117
+          rust-wasm-bindgen-macro-0.2.117
+          rust-wasm-bindgen-macro-support-0.2.117
+          rust-wasm-bindgen-shared-0.2.117
+          rust-web-sys-0.3.94
+          rust-winapi-0.3.9
+          rust-winapi-i686-pc-windows-gnu-0.4.0
+          rust-winapi-util-0.1.11
+          rust-winapi-x86-64-pc-windows-gnu-0.4.0
+          rust-windows-link-0.2.1
+          rust-windows-sys-0.61.2
+          rust-zmij-1.0.21))
 )
 
 (define-public rust-qtlreaper
@@ -332,3 +573,22 @@
      "Rust-qtlreaper is a Rust implementation of QTL Reaper for mapping
 quantitative trait loci (QTL) in genetic datasets.")
     (license license:agpl3+)))
+
+(define-public gn-rust-correlation
+  (let ((commit "48604d86471df965f189e46580578b24191add0e")
+        (revision "0"))
+    (package
+      (name "gn-rust-correlation")
+      (version (git-version "0.1.4" revision commit))
+      ;; Use local source with updated Cargo.lock for modern Rust.
+      (source (local-file "/fast/pjotr/tmp/claude/factory/correlation_rust"
+                          #:recursive? #t))
+      (build-system cargo-build-system)
+      (native-inputs (list gsl))
+      (arguments (list #:install-source? #f))
+      (inputs (cargo-inputs 'correlation_rust
+                            #:module '(gn packages genenetwork-rust)))
+      (home-page "https://github.com/Alexanderlacuna/correlation_rust")
+      (synopsis "Re-implementation of genenetwork/correlation in Rust")
+      (description "Re-implementation of genenetwork/correlation in Rust.")
+      (license #f))))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index c1b3f83..d8c83ac 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -7,7 +7,6 @@
   #:use-module (guix download)
   #:use-module (guix git)
   #:use-module (guix git-download)
-  #:use-module (guix build-system cargo)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
@@ -24,7 +23,6 @@
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cran)
-  #:use-module (past-crates packages crates-io)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages ghostscript)
@@ -52,7 +50,6 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages serialization)
   #:use-module (gn packages bioinformatics)
-  #:use-module (gn packages crates-io)
   #:use-module (gn packages gemma)
   #:use-module (gn packages javascript)
   #:use-module (gn packages node)
@@ -106,7 +103,7 @@
              python-mysqlclient-2.2.7
              python-numpy
              python-pandas
-             python-pingouin-without-tests
+             python-pingouin
              python-plotly
              python-pyld
              python-pymonad