Updated (impg) to latest with dependencies

1 files changed, 156 insertions, 35 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 0c7dac3..6ff58b7 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -1669,7 +1669,7 @@
   (crate-source "zlib-rs" "0.6.2"
                 "1j1nf9nmmx9wcwf0mn22smpam7wb28sdz6fw6v8pwcq7227c8if7"))
 
-(define rust-fastga-rs-0.1.2.e7a6d93
+(define rust-fastga-rs-0.1.2.e5037d5
   ;; TODO REVIEW: Check bundled sources.
   (origin
     (method git-fetch)
@@ -1678,7 +1678,7 @@
     (file-name (git-file-name "rust-fastga-rs" "0.1.2.e7a6d93"))
     (sha256 (base32 "0s99i55j44rz3miywik3ms1l3mz6h63n5fmwvgjh4ywxw2k9r4p5"))))
 
-(define rust-gfasort-0.1.0.e23f45e
+(define rust-gfasort-0.1.0.b5fdb1d
   (origin
     (method git-fetch)
     (uri (git-reference (url "https://github.com/pangenome/gfasort")
@@ -1724,7 +1724,7 @@
     (file-name (git-file-name "rust-ragc" "0.1.1.e9e4a6f"))
     (sha256 (base32 "0ks74pgh0vjy4mzxvp7riq1rkf9zh9kqzhvvy8iys46zrbkxmhs7"))))
 
-(define rust-seqwish-0.1.3.a781924
+(define rust-seqwish-0.1.3.b65a7e0
   (origin
     (method git-fetch)
     (uri (git-reference (url "https://github.com/pangenome/seqwish")
@@ -1732,7 +1732,7 @@
     (file-name (git-file-name "rust-seqwish" "0.1.3.a781924"))
     (sha256 (base32 "17ii1659v5k1smnwzn7hm12dqw0l2zpflb20krwdb84xv75rnmgd"))))
 
-(define rust-sweepga-0.1.1.f591843
+(define rust-sweepga-0.1.1.29d2123
   (origin
     (method git-fetch)
     (uri (git-reference (url "https://github.com/pangenome/sweepga")
@@ -1740,7 +1740,7 @@
     (file-name (git-file-name "rust-sweepga" "0.1.1.f591843"))
     (sha256 (base32 "1clc295cvmis131aw5m2z5v8v16qfk7xxyawdx18iygwr5nbqbg9"))))
 
-(define rust-tpa-0.1.0.301dc3f
+(define rust-tpa-0.1.0.49f1801
   (origin
     (method git-fetch)
     (uri (git-reference (url "https://github.com/AndreaGuarracino/tpa")
@@ -1748,7 +1748,7 @@
     (file-name (git-file-name "rust-tpa" "0.1.0.301dc3f"))
     (sha256 (base32 "18v0g2845pgzj3y002q4y04rav28ccr5gjxck7bc92jlrcl75mjk"))))
 
-(define rust-tracepoints-0.1.0.b737734
+(define rust-tracepoints-0.1.0.66a5511
   (origin
     (method git-fetch)
     (uri (git-reference (url "https://github.com/AndreaGuarracino/tracepoints")
@@ -1756,6 +1756,70 @@
     (file-name (git-file-name "rust-tracepoints" "0.1.0.b737734"))
     (sha256 (base32 "0xyqvi01rvnmvwxbx6y413qjjci7d271xjpz1z0lkw1s2zc61h0c"))))
 
+;;; Updated git-sourced crate defs for impg f773342
+
+(define rust-fastga-rs-0.1.2.e5037d5
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/pangenome/fastga-rs")
+                        (commit "e5037d5ef818f0ed1eef68e5678324a3b6f9111a")))
+    (file-name (git-file-name "rust-fastga-rs" "0.1.2.e5037d5"))
+    (sha256 (base32 "19himg61r4r59pplpgv9ay903wv80pnm22hw0z87ddp6xivyj923"))))
+
+(define rust-gfasort-0.1.0.b5fdb1d
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/pangenome/gfasort")
+                        (commit "b5fdb1d2222cfd295288465aba007ef88603b665")))
+    (file-name (git-file-name "rust-gfasort" "0.1.0.b5fdb1d"))
+    (sha256 (base32 "1312nszzcdk4l8cc2i0sni6ib7pz31d173v1h12nr28736dyqax8"))))
+
+(define rust-seqwish-0.1.3.b65a7e0
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/pangenome/seqwish")
+                        (commit "b65a7e0a8b6d1a2fb9e2f69e43efc7b57d87bf28")))
+    (file-name (git-file-name "rust-seqwish" "0.1.3.b65a7e0"))
+    (sha256 (base32 "1bk3lpg18b7nmzqrrd673cjbnjkl168cg2n4xbshp0fa4v4kwfl0"))))
+
+(define rust-sweepga-0.1.1.29d2123
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/pangenome/sweepga")
+                        (commit "29d21238765abb1016d7d75c19666127faa962cb")))
+    (file-name (git-file-name "rust-sweepga" "0.1.1.29d2123"))
+    (sha256 (base32 "001b0q3c2rjjqnwmqdyh7sg1v3y2y1wxqvk1j1shf4wq8nii4gbc"))))
+
+(define rust-tpa-0.1.0.49f1801
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/AndreaGuarracino/tpa")
+                        (commit "49f1801f9e0108c211571fa2614e517009446afe")))
+    (file-name (git-file-name "rust-tpa" "0.1.0.49f1801"))
+    (sha256 (base32 "06i0lj24k62bm112ns6jymk4r3w5qcfi7ifdy0zxhkpg9ny91897"))))
+
+(define rust-tracepoints-0.1.0.66a5511
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/AndreaGuarracino/tracepoints")
+                        (commit "66a5511b0b84d8502f9d7c99efd150616ff2cae3")))
+    (file-name (git-file-name "rust-tracepoints" "0.1.0.66a5511"))
+    (sha256 (base32 "06rzivxfd1s2d181n34zh8m1qj4yp62ixw8gbnrddqmwj4k5snpy"))))
+
+;;;
+
+(define rust-terminal-size-0.4.4
+  (crate-source "terminal_size" "0.4.4"
+                "0x4839vhhpzacc42rqj2wjhivlhlggzz3890b0c5pmyb3j11n2i3"))
+
+(define rust-wfmash-rs-0.1.0.d47b7e3
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/pangenome/wfmash-rs")
+                        (commit "d47b7e3eba7f1d0f2bfdb72629cc667c2d5f8382")))
+    (file-name (git-file-name "rust-wfmash-rs" "0.1.0.d47b7e3"))
+    (sha256 (base32 "1r2akqsdh0196pgayzadyzikbsll2a3gnznfwgvndqwr0xnqgy4q"))))
+
 ;;;
 ;;; Additional crate sources for impg transitive dependencies.
 ;;;
@@ -2183,6 +2247,53 @@
   (crate-source "libz-sys" "1.1.23"
                 "1xy0l46gmhfyk28r9pm7njl0h7dh8l2vpiqw67kn043pyfxiil8m"))
 
+;;; New crate sources for impg f773342
+
+
+(define rust-anstream-1.0.0
+  (crate-source "anstream" "1.0.0"
+                "13d2bj0xfg012s4rmq44zc8zgy1q8k9yp7yhvfnarscnmwpj2jl2"))
+
+(define rust-anstyle-1.0.14
+  (crate-source "anstyle" "1.0.14"
+                "0030szmgj51fxkic1hpakxxgappxzwm6m154a3gfml83lq63l2wl"))
+
+(define rust-anstyle-parse-1.0.0
+  (crate-source "anstyle-parse" "1.0.0"
+                "03hkv2690s0crssbnmfkr76kw1k7ah2i6s5amdy9yca2n8w7zkjj"))
+
+(define rust-clap-4.6.0
+  (crate-source "clap" "4.6.0"
+                "0l8k0ja5rf4hpn2g98bqv5m6lkh2q6b6likjpmm6fjw3cxdsz4xi"))
+
+(define rust-clap-builder-4.6.0
+  (crate-source "clap_builder" "4.6.0"
+                "17q6np22yxhh5y5v53y4l31ps3hlaz45mvz2n2nicr7n3c056jki"))
+
+(define rust-clap-derive-4.6.0
+  (crate-source "clap_derive" "4.6.0"
+                "0snapc468s7n3avr33dky4y7rmb7ha3qsp9l0k5vh6jacf5bs40i"))
+
+(define rust-clap-lex-1.1.0
+  (crate-source "clap_lex" "1.1.0"
+                "1ycqkpygnlqnndghhcxjb44lzl0nmgsia64x9581030yifxs7m68"))
+
+(define rust-cmake-0.1.58
+  (crate-source "cmake" "0.1.58"
+                "0y06zxw5sv1p5vvpp5rz1qwbrq7ccawrl09nqy5ahx1a5418mxy0"))
+
+(define rust-colorchoice-1.0.5
+  (crate-source "colorchoice" "1.0.5"
+                "0w75k89hw39p0mnnhlrwr23q50rza1yjki44qvh2mgrnj065a1qx"))
+
+(define rust-env-filter-1.0.1
+  (crate-source "env_filter" "1.0.1"
+                "1vvf9xhaxm0m78bp23b8j3cbv1vm5vffn3gaas27mc64rhm0rs9j"))
+
+(define rust-env-logger-0.11.10
+  (crate-source "env_logger" "0.11.10"
+                "0smmk1hqzk7z91rg7fdq98d03gh9kidkd0ymim43zb4n457w0886"))
+
 (define-cargo-inputs lookup-cargo-inputs
   (gfainject =>
     (list rust-adler-1.0.2
@@ -2531,7 +2642,7 @@
           rust-env-logger-0.11.9
           rust-equivalent-1.0.2
           rust-errno-0.3.14
-          rust-fastga-rs-0.1.2.e7a6d93
+          rust-fastga-rs-0.1.2.e5037d5
           rust-fastrand-2.3.0
           rust-find-msvc-tools-0.1.9
           rust-flate2-1.1.9
@@ -2546,7 +2657,7 @@
           rust-getrandom-0.2.16
           rust-getrandom-0.3.3
           rust-gfa-0.10.1
-          rust-gfasort-0.1.0.e23f45e
+          rust-gfasort-0.1.0.b5fdb1d
           rust-glob-0.3.3
           rust-gzp-1.0.1
           rust-handlegraph-0.7.0-alpha.9.3ac575e
@@ -2654,7 +2765,7 @@
           rust-block-buffer-0.10.4
           rust-generic-array-0.14.7
           rust-cpufeatures-0.2.17
-          rust-seqwish-0.1.3.a781924
+          rust-seqwish-0.1.3.b65a7e0
           rust-serde-1.0.228
           rust-serde-core-1.0.228
           rust-serde-derive-1.0.228
@@ -2668,7 +2779,7 @@
           rust-strsim-0.11.1
           rust-strum-macros-0.26.4
           rust-succinct-0.5.2
-          rust-sweepga-0.1.1.f591843
+          rust-sweepga-0.1.1.29d2123
           rust-syn-1.0.109
           rust-syn-2.0.117
           rust-synstructure-0.13.2
@@ -2680,8 +2791,8 @@
           rust-thiserror-impl-1.0.69
           rust-thiserror-impl-2.0.16
           rust-tinystr-0.8.2
-          rust-tpa-0.1.0.301dc3f
-          rust-tracepoints-0.1.0.b737734
+          rust-tpa-0.1.0.49f1801
+          rust-tracepoints-0.1.0.66a5511
           rust-typenum-1.19.0
           rust-unicode-ident-1.0.24
           rust-unicode-width-0.2.2
@@ -2854,6 +2965,8 @@
           rust-wit-bindgen-rust-0.51.0
           rust-wit-bindgen-rust-macro-0.51.0
           rust-wit-component-0.244.0
+          rust-terminal-size-0.4.4
+          rust-wfmash-rs-0.1.0.d47b7e3
           rust-wit-parser-0.244.0))
   (gfaffix =>
     (list rust-adler2-2.0.1
@@ -3360,8 +3473,8 @@ sequences to accelerate the alignment process.")
 ;;;
 
 (define-public impg
-  (let ((commit "748bd5e43ff81ac7bedc28b6e79b9c3b2aa08486")
-        (revision "0"))
+  (let ((commit "f773342a75da244f05bc93663857b77c3bc8a9f7")
+        (revision "1"))
     (package
       (name "impg")
       (version (git-version "0.4.1" revision commit))
@@ -3374,7 +3487,7 @@ sequences to accelerate the alignment process.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1j1xgh0kv7hm8xfla2bg11iq9nm9lry6awcm84iqczvvy4vf26i2"))))
+                  "0ap5mz2k14d42gfd28bj7zwliacxgx246dqkvj4kjsf9fyrh91jl"))))
       (build-system cargo-build-system)
       (arguments
        (list
@@ -3405,26 +3518,26 @@ sequences to accelerate the alignment process.")
                   (("git = \"https://github.com/pangenome/onecode-rs\", rev = \"38182c7acf7cccc53509176b1d11001ae6ff2642\"")
                    "path = \"guix-vendor/rust-onecode-0.1.0.38182c7-checkout\", version = \"0.1.0\"")
                   ;; tpa
-                  (("git = \"https://github.com/AndreaGuarracino/tpa\", rev = \"301dc3ff53482d993c065217dbcd8abb6ffff2d9\"")
-                   "path = \"guix-vendor/rust-tpa-0.1.0.301dc3f-checkout\", version = \"0.1.0\"")
+                  (("git = \"https://github.com/AndreaGuarracino/tpa\", rev = \"49f1801f9e0108c211571fa2614e517009446afe\"")
+                   "path = \"guix-vendor/rust-tpa-0.1.0.49f1801-checkout\", version = \"0.1.0\"")
                   ;; lib_wfa2
-                  (("git = \"https://github.com/AndreaGuarracino/lib_wfa2\", rev = \"0fe1ebfb7a364226f3d8d7b84b703611168435c6\"")
+                  (("git = \"https://github.com/AndreaGuarracino/lib_wfa2\", rev = \"8859b6a214141968f37d9bcb22552408318adda0\"")
                    "path = \"guix-vendor/rust-lib-wfa2-0.1.0.0fe1ebf-checkout\", version = \"0.1.0\"")
                   ;; tracepoints
-                  (("git = \"https://github.com/AndreaGuarracino/tracepoints\", rev = \"b73773433561fb36f21136776a7297c5877ab593\"")
-                   "path = \"guix-vendor/rust-tracepoints-0.1.0.b737734-checkout\", version = \"0.1.0\"")
+                  (("git = \"https://github.com/AndreaGuarracino/tracepoints\", rev = \"66a5511b0b84d8502f9d7c99efd150616ff2cae3\"")
+                   "path = \"guix-vendor/rust-tracepoints-0.1.0.66a5511-checkout\", version = \"0.1.0\"")
                   ;; handlegraph
                   (("git = \"https://github.com/[^\"]+/rs-handlegraph\", rev = \"3ac575e4216ce16a16667503a8875e469a40a97a\"")
                    "path = \"guix-vendor/rust-handlegraph-0.7.0-alpha.9.3ac575e-checkout\", version = \"0.7.0-alpha.9\"")
                   ;; sweepga
-                  (("git = \"https://github.com/pangenome/sweepga\", rev = \"f5918434c1abadfad594b40392ad7c43e0da4af8\", default-features = false")
-                   "path = \"guix-vendor/rust-sweepga-0.1.1.f591843-checkout\", version = \"0.1.1\", default-features = false")
+                  (("git = \"https://github.com/pangenome/sweepga\", rev = \"29d21238765abb1016d7d75c19666127faa962cb\", default-features = false")
+                   "path = \"guix-vendor/rust-sweepga-0.1.1.29d2123-checkout\", version = \"0.1.1\", default-features = false")
                   ;; seqwish
-                  (("git = \"https://github.com/pangenome/seqwish\", rev = \"a781924a1074f8177a24f8caa2b9be07d746acb0\"")
-                   "path = \"guix-vendor/rust-seqwish-0.1.3.a781924-checkout\", version = \"0.1.3\"")
+                  (("git = \"https://github.com/pangenome/seqwish\", branch = \"rust-2\"")
+                   "path = \"guix-vendor/rust-seqwish-0.1.3.b65a7e0-checkout\", version = \"0.1.3\"")
                   ;; gfasort
-                  (("git = \"https://github.com/pangenome/gfasort\", rev = \"e23f45e\"")
-                   "path = \"guix-vendor/rust-gfasort-0.1.0.e23f45e-checkout\", version = \"0.1.0\""))))
+                  (("git = \"https://github.com/pangenome/gfasort\", rev = \"b5fdb1d\"")
+                   "path = \"guix-vendor/rust-gfasort-0.1.0.b5fdb1d-checkout\", version = \"0.1.0\""))))
             (add-before 'build 'fix-vendored-git-deps
               (lambda _
                 ;; Two different onecode revisions (38182c7 and f531f5b) both
@@ -3435,25 +3548,27 @@ sequences to accelerate the alignment process.")
                   (("version = \"0.1.0\"")
                    "version = \"0.1.0-alt\""))
                 ;; sweepga has git deps on fastga-rs, onecode, ragc-core
-                (substitute* "guix-vendor/rust-sweepga-0.1.1.f591843-checkout/Cargo.toml"
+                (substitute* "guix-vendor/rust-sweepga-0.1.1.29d2123-checkout/Cargo.toml"
                   (("fastga-rs = \\{ git = \"[^\"]*\"[^}]*\\}")
-                   "fastga-rs = { path = \"../rust-fastga-rs-0.1.2.e7a6d93-checkout\", version = \"0.1.2\" }")
+                   "fastga-rs = { path = \"../rust-fastga-rs-0.1.2.e5037d5-checkout\", version = \"0.1.2\" }")
                   (("onecode = \\{ git = \"[^\"]*\"[^}]*\\}")
                    "onecode = { path = \"../rust-onecode-0.1.0.f531f5b-checkout\", version = \"0.1.0-alt\" }")
                   (("ragc-core = \\{ git = \"[^\"]*\"[^}]*\\}")
-                   "ragc-core = { path = \"../../ragc-workspace/ragc-core\" }"))
+                   "ragc-core = { path = \"../../ragc-workspace/ragc-core\" }")
+                  (("wfmash-rs = \\{ git = \"[^\"]*\"[^}]*\\}")
+                   "wfmash-rs = { path = \"../rust-wfmash-rs-0.1.0.d47b7e3-checkout\", version = \"0.1.0\" }"))
                 ;; tpa has git deps on lib_wfa2 and tracepoints
-                (substitute* "guix-vendor/rust-tpa-0.1.0.301dc3f-checkout/Cargo.toml"
+                (substitute* "guix-vendor/rust-tpa-0.1.0.49f1801-checkout/Cargo.toml"
                   (("lib_wfa2 = \\{ git = \"[^\"]*\"[^}]*\\}")
                    "lib_wfa2 = { path = \"../rust-lib-wfa2-0.1.0.0fe1ebf-checkout\", version = \"0.1.0\" }")
                   (("tracepoints = \\{ git = \"[^\"]*\"[^}]*\\}")
-                   "tracepoints = { path = \"../rust-tracepoints-0.1.0.b737734-checkout\", version = \"0.1.0\" }"))
+                   "tracepoints = { path = \"../rust-tracepoints-0.1.0.66a5511-checkout\", version = \"0.1.0\" }"))
                 ;; tracepoints has git dep on lib_wfa2
-                (substitute* "guix-vendor/rust-tracepoints-0.1.0.b737734-checkout/Cargo.toml"
+                (substitute* "guix-vendor/rust-tracepoints-0.1.0.66a5511-checkout/Cargo.toml"
                   (("lib_wfa2 = \\{ git = \"[^\"]*\"[^}]*\\}")
                    "lib_wfa2 = { path = \"../rust-lib-wfa2-0.1.0.0fe1ebf-checkout\", version = \"0.1.0\" }"))
                 ;; fastga-rs has git dep on onecode (the f531f5b rev)
-                (substitute* "guix-vendor/rust-fastga-rs-0.1.2.e7a6d93-checkout/Cargo.toml"
+                (substitute* "guix-vendor/rust-fastga-rs-0.1.2.e5037d5-checkout/Cargo.toml"
                   (("onecode = \\{ git = \"[^\"]*\"[^}]*\\}")
                    "onecode = { path = \"../rust-onecode-0.1.0.f531f5b-checkout\", version = \"0.1.0-alt\" }"))))
             (add-before 'build 'fix-seqwish-lockfile
@@ -3461,7 +3576,7 @@ sequences to accelerate the alignment process.")
               ;; 4.5.60.  Delete its lockfile so cargo metadata succeeds.
               (lambda _
                 (delete-file
-                 "guix-vendor/rust-seqwish-0.1.3.a781924-checkout/Cargo.lock")))
+                 "guix-vendor/rust-seqwish-0.1.3.b65a7e0-checkout/Cargo.lock")))
             (add-before 'build 'patch-home-msrv
               ;; home 0.5.12 declares rust-version = "1.88" but Guix ships
               ;; rustc 1.85.1.
@@ -3521,12 +3636,18 @@ sequences to accelerate the alignment process.")
                    "(_flags2 as u32)"))))
             (add-before 'build 'patch-include-paths-to-spoa
               (lambda _
+                ;; wfmash-rs tries to build wfmash from source via cmake+FetchContent.
+                ;; Skip by making build.rs find system wfmash or a pre-existing binary.
+                (substitute* "guix-vendor/rust-wfmash-rs-0.1.0.d47b7e3-checkout/build.rs"
+                  (("if !wfmash_src.join\\(\"CMakeLists.txt\"\\).exists\\(\\)")
+                   "if true"))
                 (substitute* "guix-vendor/rust-spoa-rs-0.1.0.6f4f102-checkout/build.rs"
                   (("spoa/include") #$(file-append spoa "/include"))
                   (("^ *out_dir\\.display.*$") "")
                   (("\\{\\}/build/lib\",") #$(file-append spoa "/lib\""))))))))
       (native-inputs (list pkg-config cmake-minimal clang))
-      (inputs (cons* spoa
+      (inputs (cons* htslib
+                     spoa
                      wfa2-lib-static
                      zlib
                      (list zstd "lib")