Milestone achieved: guix-bioinformatics no longer depends on guix-rust-past-crates. All Rust packages build with only -L . -L ../guix-past/modules.

3 files changed, 2 insertions, 326 deletions

diff --git a/README.org b/README.org
index 6a1dfd7..092c818 100644
--- a/README.org
+++ b/README.org
@@ -67,7 +67,7 @@ We run our own substitution server. Add the key to your machine as
 root with
 
 : guix archive --authorize < tux02-guix-substitutions-public-key.txt
-: guix build -L ~/guix-rust-past-crates/modules/ -L ~/guix-bioinformatics/ -L ~/guix-past/modules/  --substitute-urls="https://cuirass.genenetwork.org https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" hello
+: guix build -L ~/guix-bioinformatics/ -L ~/guix-past/modules/  --substitute-urls="https://cuirass.genenetwork.org https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" hello
 
 * An important note on AI
 
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
deleted file mode 100644
index 17eb20a..0000000
--- a/gn/packages/crates-io.scm
+++ /dev/null
@@ -1,324 +0,0 @@
-(define-module (gn packages crates-io)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system cargo)
-  #:use-module (past-crates packages crates-io)
-  #:use-module (gnu packages maths)
-  #:use-module (gnu packages python))
-
-(define-public rust-boomphf-0.5
-  (package
-    (name "rust-boomphf")
-    (version "0.5.9")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "boomphf" version))
-        (file-name
-         (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "0braniw72g9yq5006sfgc1g8d4317bb524c694jw6nggizrvg3sf"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8)
-        ("rust-log" ,rust-log-0.4)
-        ("rust-rayon" ,rust-rayon-1)
-        ("rust-serde" ,rust-serde-1)
-        ("rust-wyhash" ,rust-wyhash-0.5))
-       #:cargo-development-inputs
-       (("rust-bencher" ,rust-bencher-0.1)
-        ("rust-quickcheck" ,rust-quickcheck-1))))
-    (home-page "https://github.com/10XGenomics/rust-boomphf")
-    (synopsis "Scalable and Efficient Minimal Perfect Hash Functions")
-    (description "This package provides a Rust implementation of
-@url{https://arxiv.org/abs/1702.03154, fast and scalable minimal perfect hashing
-for massive key sets}.  It generates an @acronym{MPHF, minimal perfect hash
-functions} for a collection of hashable objects.")
-    (license license:expat)))
-
-(define-public rust-gfa-0.6
-  (package
-    (name "rust-gfa")
-    (version "0.6.2")
-    (source (origin
-              (method url-fetch)
-              (uri (crate-uri "gfa" version))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0ghmy4r0324s6vvmj9nmh326346nkwm7nybnpcpswnjvf02b85gw"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-bstr" ,rust-bstr-0.2)
-        ("rust-bytemuck" ,rust-bytemuck-1)
-        ("rust-lazy-static" ,rust-lazy-static-1)
-        ("rust-nom" ,rust-nom-5)
-        ("rust-regex" ,rust-regex-1)
-        ("rust-serde" ,rust-serde-1))
-        #:cargo-development-inputs
-        (("rust-criterion" ,rust-criterion-0.3))))
-    (home-page "https://github.com/pangenome/rs-gfa")
-    (synopsis
-     "Library for working with graphs in the GFA (Graphical Fragment Assembly) format")
-    (description
-     "Library for working with graphs in the GFA (Graphical Fragment Assembly) format")
-    (license license:expat)))
-
-(define-public rust-succinct-0.5
-  (package
-    (name "rust-succinct")
-    (version "0.5.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "succinct" version))
-        (file-name
-         (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "0654c9gq50x7djyf25zbzz3d2pc4x3z21wmjj3qbr6d9h4hbd63p"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-byteorder" ,rust-byteorder-1)
-        ("rust-num-traits" ,rust-num-traits-0.2))
-       #:cargo-development-inputs
-       (("rust-quickcheck" ,rust-quickcheck-0.9))))
-    (home-page "https://github.com/tov/succinct-rs")
-    (synopsis "Succinct data structures for Rust")
-    (description "This package provides succinct data structures for Rust.")
-    (license (list license:expat license:asl2.0))))
-
-(define-public rust-handlegraph-0.7.0-alpha.9
-  (package
-    (name "rust-handlegraph")
-    (version "0.7.0-alpha.9")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "handlegraph" version))
-        (file-name
-         (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32
-          "1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-anyhow" ,rust-anyhow-1)
-        ("rust-boomphf" ,rust-boomphf-0.5)
-        ("rust-bstr" ,rust-bstr-0.2)
-        ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5)
-        ("rust-fnv" ,rust-fnv-1)
-        ("rust-gfa" ,rust-gfa-0.10)
-        ("rust-log" ,rust-log-0.4)
-        ("rust-rayon" ,rust-rayon-1)
-        ("rust-succinct" ,rust-succinct-0.5))
-       #:cargo-development-inputs
-       (("rust-quickcheck" ,rust-quickcheck-0.9)
-        ("rust-rand" ,rust-rand-0.7))))
-    (home-page "https://github.com/pangenome/rs-handlegraph")
-    (synopsis "Library for use in variation graphs")
-    (description
-     "This package provides a Rust implementation of VG handle graph.")
-    (license license:expat)))
-
-(define-public rust-handlegraph-0.3
-  (package
-    (inherit rust-handlegraph-0.7.0-alpha.9)
-    (name "rust-handlegraph")
-    (version "0.3.0")
-    (source (origin
-              (method url-fetch)
-              (uri (crate-uri "handlegraph" version))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1sj100w4lpj7798pws85qrfrzsily5hhzh6j118rwf56sgic1yml"))))
-    (arguments
-     `(#:cargo-inputs
-       (("rust-bstr" ,rust-bstr-0.2)
-        ("rust-gfa" ,rust-gfa-0.6))))))
-
-(define-public rust-clap-for-jrep
-  (package
-    (name "rust-clap")
-    (version "2.33.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "clap" version))
-       (file-name
-        (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1nf6ld3bims1n5vfzhkvcb55pdzh04bbhzf8nil5vvw05nxzarsh"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:tests? #f ; doctest fails with newer Rust (dangerous_implicit_autorefs)
-       #:cargo-inputs
-       (("rust-atty" ,rust-atty-0.2)
-        ("rust-bitflags" ,rust-bitflags-1)
-        ("rust-clap-derive" ,rust-clap-derive-3)
-        ("rust-indexmap" ,rust-indexmap-1)
-        ("rust-os-str-bytes" ,rust-os-str-bytes-2)
-        ("rust-strsim" ,rust-strsim-0.10)
-        ("rust-termcolor" ,rust-termcolor-1)
-        ("rust-ansi-term" ,rust-ansi-term-0.11)
-        ("rust-terminal-size" ,rust-terminal-size-0.1)
-        ("rust-textwrap" ,rust-textwrap-0.12)
-        ("rust-unicode-width" ,rust-unicode-width-0.1)
-        ("rust-vec-map" ,rust-vec-map-0.8)
-        ("rust-yaml-rust" ,rust-yaml-rust-0.4))
-       #:cargo-development-inputs
-       (("rust-criterion" ,rust-criterion-0.3)
-        ("rust-lazy-static" ,rust-lazy-static-1)
-        ("rust-regex" ,rust-regex-1)
-        ("rust-version-sync" ,rust-version-sync-0.8))))
-    (home-page "https://clap.rs/")
-    (synopsis "Command Line Argument Parser")
-    (description
-     "This package provides a simple to use, efficient, and full-featured
-Command Line Argument Parser.")
-    (license (list license:expat license:asl2.0))))
-
-(define-public jrep
-  (package
-    (name "jrep")
-    (version "0.1.3")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/joshua-laughner/jrep")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0syvlc93w26v856hp5l8ik615dfrvax6hdfzw5kqhaww3siqjaj9"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-clap" ,rust-clap-for-jrep)
-        ("rust-exitcode" ,rust-exitcode-1)
-        ("rust-term" ,rust-term-0.7)
-        ("rust-regex" ,rust-regex-1)
-        ("rust-serde" ,rust-serde-1)
-        ("rust-serde-json" ,rust-serde-json-1))))
-    (home-page "https://github.com/joshua-laughner/jrep/")
-    (synopsis "grep for Jupyter notebooks")
-    (description
-"@code{jrep} is @code{grep} for Jupyter notebooks.  It is a command line
-program that can search across multiple notebooks for specific text,
-but limit itself to certain types of cells, source text, output data,
-or any combination.")
-    (license license:gpl3+)))
-
-(define-public notebook-tools
-  (let ((commit "a9db1f4f90f6df72d28bf1235ca16b988d7b86be")
-        (revision "0"))
-    (package
-      (name "notebook-tools")
-      (version commit)
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/CADLabs/notebook-tools")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0mmvqjfcsa6fq12rpay9w6ra1q8ijhmm1raqzi4d70y7wsbd20lw"))))
-      (build-system cargo-build-system)
-      (arguments
-       `(#:cargo-inputs
-         (("rust-clap" ,rust-clap-3)
-          ("rust-exitcode" ,rust-exitcode-1)
-          ("rust-term" ,rust-term-0.7)
-          ("rust-regex" ,rust-regex-1)
-          ("rust-serde" ,rust-serde-1)
-          ("rust-serde-json" ,rust-serde-json-1))))
-      (home-page "https://github.com/CADLabs/notebook-tools")
-      (synopsis "Rust CLI tools for manipulation of Jupyter Notebooks")
-      (description "Rust CLI tools for manipulation of Jupyter Notebooks.")
-      (license #f)))) ; There is no license.
-
-(define-public rust-gsl-sys
-  (package
-    (name "rust-gsl-sys")
-    (version "3.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "GSL-sys" version))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32 "17dx066l1pbjwp9syjkzqb6fiajyb4wc814zqdfrj807rh6nfxs5"))))
-    (build-system cargo-build-system)
-    (native-inputs
-     (list gsl))
-    (arguments
-     `(#:cargo-inputs
-       (("rust-libc" ,rust-libc-0.2)
-	("rust-pkg-config"  ,rust-pkg-config-0.3))))
-    (home-page "https://github.com/GuillaumeGomez/rust-GSL")
-    (synopsis "A rust binding for the GSL (the GNU scientific library)")
-    (description "This is the FFI counter-part of the Rust GSL crate. It is better to use the GSL crate directly rather than this one (unless something is missing the Rust binding!).")
-    (license license:expat)))
-
-(define-public rust-gsl
-  (package
-    (name "rust-gsl")
-    (version "6.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "GSL" version))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32 "1kpiivagrsk9ags7d4k2521jwix0lqgnd3i8ayj3dfniszvcmgn9"))))
-    (build-system cargo-build-system)
-    (native-inputs
-     (list gsl))
-    (arguments
-     `(#:tests? #false
-       #:cargo-inputs
-       (("GSL-sys" ,rust-gsl-sys)
-	("paste"  ,rust-paste-1))))
-    (home-page "https://github.com/GuillaumeGomez/rust-GSL")
-    (synopsis "A rust binding for the GSL (the GNU scientific library)")
-    (description "This package is wrapper for gsl")
-    (license license:gpl3+)))
-
-(define-public gn-rust-correlation
-  (let ((commit "48604d86471df965f189e46580578b24191add0e")
-        (revision "0"))
-    (package
-      (name "gn-rust-correlation")
-      (version (git-version "0.1.4" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/Alexanderlacuna/correlation_rust.git")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "1x7zz0ldf9bmb4lmj3yrhbgcqanc64pl03dimrx5aw7cap006pjw"))))
-      (build-system cargo-build-system)
-      (native-inputs (list gsl))
-      (arguments
-       `(#:cargo-inputs (("rust-serde" ,rust-serde-1)
-                         ("rust-serde-json" ,rust-serde-json-1)
-                         ("GSL" ,rust-gsl)
-                         ("rust-assert-approx-eq" ,rust-assert-approx-eq-1))
-         #:cargo-development-inputs (("rust-criterion" ,rust-criterion-0.3))))
-      (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/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 1399f24..0c7dac3 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -3414,7 +3414,7 @@ sequences to accelerate the alignment process.")
                   (("git = \"https://github.com/AndreaGuarracino/tracepoints\", rev = \"b73773433561fb36f21136776a7297c5877ab593\"")
                    "path = \"guix-vendor/rust-tracepoints-0.1.0.b737734-checkout\", version = \"0.1.0\"")
                   ;; handlegraph
-                  (("git = \"https://github.com/pangenome/rs-handlegraph\", rev = \"3ac575e4216ce16a16667503a8875e469a40a97a\"")
+                  (("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")