gn: Update gfaffix to 0.1.3

2 files changed, 368 insertions, 6 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 01e4c59..e8df572 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -462,7 +462,7 @@ reads.")
 (define-public gfaffix
   (package
     (name "gfaffix")
-    (version "0.1.2.2")
+    (version "0.1.3")
     (source
       (origin
         (method git-fetch)
@@ -471,7 +471,7 @@ reads.")
                (commit version)))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1sh244yyhkaxbd635qjyig0wyxc57h8r1pwvs1vgdvlniw6h2cxy"))
+         (base32 "1biss5qv6ag1dfkn1nspwd528hpzgn8i4jydvbv2z7yv7sc685rh"))
         (modules '((guix build utils)))
         (snippet
          '(begin
@@ -479,8 +479,9 @@ reads.")
               (("^handlegraph.*") "handlegraph = \"0.7\"\n"))))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs
-       (("rust-clap" ,rust-clap-3)
+     `(#:install-source? #f
+       #:cargo-inputs
+       (("rust-clap" ,rust-clap-3.1)
         ("rust-rustc-hash" ,rust-rustc-hash-1)
         ("rust-regex" ,rust-regex-1)
         ("rust-handlegraph" ,rust-handlegraph-0.7)
@@ -495,8 +496,7 @@ reads.")
              (let ((handlebar-version ,(package-version rust-handlegraph-0.7)))
                (substitute* "Cargo.toml"
                  (("\"0.7\"")
-                  (string-append "{ version = \"" handlebar-version "\" }")))
-               #t))))))
+                  (string-append "{ version = \"" handlebar-version "\" }")))))))))
     (home-page "https://github.com/marschall-lab/GFAffix")
     (synopsis "Identify walk-preserving shared affixes in variation graphs")
     (description
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 2d14065..e8b7722 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -140,3 +140,365 @@ or any combination.")
       (description "Rust CLI tools for manipulation of Jupyter Notebooks.")
       (license #f)))) ; There is no license.
 
+(define-public rust-clap-3.1
+  (package
+    (name "rust-clap")
+    (version "3.1.6")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "clap" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "08q1hkksfixybnrwrpm44xq028wbn9yr2hnzrax9hihyq8v39jfq"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Skip the tests for now
+       #:cargo-inputs
+       (("rust-atty" ,rust-atty-0.2)
+        ("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-clap-derive" ,rust-clap-derive-3.1)
+        ("rust-indexmap" ,rust-indexmap-1)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-os-str-bytes" ,rust-os-str-bytes-6)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-strsim" ,rust-strsim-0.10)
+        ("rust-termcolor" ,rust-termcolor-1)
+        ("rust-terminal-size" ,rust-terminal-size-0.1)
+        ("rust-textwrap" ,rust-textwrap-0.15)
+        ("rust-unicase" ,rust-unicase-2)
+        ("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-rustversion" ,rust-rustversion-1)
+       ; ("rust-trybuild" ,rust-trybuild-1)
+       ; ("rust-trycmd" ,rust-trycmd-0.12))
+       ))
+    (home-page "https://github.com/clap-rs/clap")
+    (synopsis
+      "A simple to use, efficient, and full-featured 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 rust-clap-derive-3.1
+  (package
+    (name "rust-clap-derive")
+    (version "3.1.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "clap-derive" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "05mz2y6k73wc1gvv9r4mllfqslzvlwkvx77lk7769ag1xlwd15fs"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-heck" ,rust-heck-0.4)
+        ("rust-proc-macro-error" ,rust-proc-macro-error-1)
+        ("rust-proc-macro2" ,rust-proc-macro2-1)
+        ("rust-quote" ,rust-quote-1)
+        ("rust-syn" ,rust-syn-1))))
+    (home-page "https://github.com/clap-rs/clap/tree/master/clap_derive")
+    (synopsis
+      "Parse command line argument by defining a struct, derive crate.")
+    (description
+      "Parse command line argument by defining a struct, derive crate.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-os-str-bytes-6
+  (package
+    (name "rust-os-str-bytes")
+    (version "6.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "os-str-bytes" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0r5z5xds2wzzqlqjaw96dpjsz5nqyzc1rflm4mh09aa32qyl88lf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-memchr" ,rust-memchr-2)
+        ("rust-print-bytes" ,rust-print-bytes-0.5)
+        ("rust-uniquote" ,rust-uniquote-3))
+       #:cargo-development-inputs
+       (("rust-getrandom" ,rust-getrandom-0.2))))
+    (home-page "https://github.com/dylni/os_str_bytes")
+    (synopsis
+     "Utilities for converting between byte sequences and platform-native strings")
+    (description
+     "Utilities for converting between byte sequences and platform-native strings")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-textwrap-0.15
+  (package
+    (name "rust-textwrap")
+    (version "0.15.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "textwrap" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "1yw513k61lfiwgqrfvsjw1a5wpvm0azhpjr2kr0jhnq9c56is55i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; Skip tests for now
+       #:cargo-inputs
+       (("rust-hyphenation" ,rust-hyphenation-0.8)
+        ("rust-smawk" ,rust-smawk-0.3)
+        ("rust-terminal-size" ,rust-terminal-size-0.1)
+        ("rust-unicode-linebreak" ,rust-unicode-linebreak-0.1)
+        ("rust-unicode-width" ,rust-unicode-width-0.1))
+       ;#:cargo-development-inputs
+       ;(("rust-criterion" ,rust-criterion-0.3)
+       ; ("rust-lipsum" ,rust-lipsum-0.8)
+       ; ("rust-termion" ,rust-termion-1)
+       ; ("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9)
+       ; ("rust-version-sync" ,rust-version-sync-0.9))
+       ))
+    (home-page "https://github.com/mgeisler/textwrap")
+    (synopsis
+      "Powerful library for word wrapping, indenting, and dedenting strings")
+    (description
+      "Powerful library for word wrapping, indenting, and dedenting strings")
+    (license license:expat)))
+
+(define-public rust-trycmd-0.12
+  (package
+    (name "rust-trycmd")
+    (version "0.12.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "trycmd" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "1rwa5nzq8c5zg7lqmpkf7hyib415yxshd9amp911y8w1zss4s38p"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-concolor" ,rust-concolor-0.0.8)
+        ("rust-content-inspector" ,rust-content-inspector-0.2)
+        ("rust-difflib" ,rust-difflib-0.4)
+        ("rust-dunce" ,rust-dunce-1)
+        ("rust-escargot" ,rust-escargot-0.5)
+        ("rust-glob" ,rust-glob-0.3)
+        ("rust-humantime" ,rust-humantime-2)
+        ("rust-humantime-serde" ,rust-humantime-serde-1)
+        ("rust-normalize-line-endings" ,rust-normalize-line-endings-0.3)
+        ("rust-os-pipe" ,rust-os-pipe-1)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-schemars" ,rust-schemars-0.8)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-serde-json" ,rust-serde-json-1)
+        ("rust-shlex" ,rust-shlex-1)
+        ("rust-tempfile" ,rust-tempfile-3)
+        ("rust-toml-edit" ,rust-toml-edit-0.12)
+        ("rust-wait-timeout" ,rust-wait-timeout-0.2)
+        ("rust-walkdir" ,rust-walkdir-2)
+        ("rust-yansi" ,rust-yansi-0.5))))
+    (home-page "https://github.com/assert-rs/trycmd")
+    (synopsis "Snapshot testing for a herd of CLI tests")
+    (description "Snapshot testing for a herd of CLI tests")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-smawk-0.3
+  (package
+    (name "rust-smawk")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "smawk" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0hv0q1mw1r1brk7v3g4a80j162p7g1dri4bdidykrakzfqjd4ypn"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-ndarray" ,rust-ndarray-0.14))
+       #:cargo-development-inputs
+       (("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-rand" ,rust-rand-0.8)
+        ("rust-rand-chacha" ,rust-rand-chacha-0.3)
+        ("rust-version-sync" ,rust-version-sync-0.9))))
+    (home-page "https://github.com/mgeisler/smawk")
+    (synopsis "Functions for finding row-minima in a totally monotone matrix.")
+    (description
+      "This package provides functions for finding row-minima in a totally monotone
+matrix.")
+    (license license:expat)))
+
+(define-public rust-unicode-linebreak-0.1
+  (package
+    (name "rust-unicode-linebreak")
+    (version "0.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicode-linebreak" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0grq6bsn967q4vpifld53s7a140nlmpq5vy8ghgr73f4n2mdqlis"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-regex" ,rust-regex-1))))
+    (home-page "https://github.com/axelf4/unicode-linebreak")
+    (synopsis "Implementation of the Unicode Line Breaking Algorithm")
+    (description "Implementation of the Unicode Line Breaking Algorithm")
+    (license license:asl2.0)))
+
+(define-public rust-lipsum-0.8
+  (package
+    (name "rust-lipsum")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "lipsum" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0sn5k0hgx099x2qdx0xlx8a5b74sfc55qnbyrhnh72baqxqp5vj2"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-rand" ,rust-rand-0.8)
+        ("rust-rand-chacha" ,rust-rand-chacha-0.3))
+       #:cargo-development-inputs
+       (("rust-version-sync" ,rust-version-sync-0.9))))
+    (home-page "https://github.com/mgeisler/lipsum/")
+    (synopsis
+      "Lipsum is a lorem ipsum text generation library. Use this if you need
+some filler text for your application.
+
+The text is generated using a simple Markov chain, which you can also
+instantiate to generate your own pieces of pseudo-random text.
+")
+    (description
+      "Lipsum is a lorem ipsum text generation library.  Use this if you need some
+filler text for your application.
+
+The text is generated using a simple Markov chain, which you can also
+instantiate to generate your own pieces of pseudo-random text.")
+    (license license:expat)))
+
+(define-public rust-print-bytes-0.5
+  (package
+    (name "rust-print-bytes")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "print-bytes" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0d4i9y3jx1chi6w97a8rgdbwm9g3cppr53rw53zl6fcaq31qx0b6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; Skip tests for now
+       #:cargo-inputs
+       (("rust-winapi" ,rust-winapi-0.3))
+       ;#:cargo-development-inputs
+       ;(("rust-os-str-bytes" ,rust-os-str-bytes-4))
+       ))
+    (home-page "https://github.com/dylni/print_bytes")
+    (synopsis "Print bytes as losslessly as possible")
+    (description "Print bytes as losslessly as possible")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-uniquote-3
+  (package
+    (name "rust-uniquote")
+    (version "3.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "uniquote" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "1bkl0n41yvs415mqny4b434kr456ysnb3dhic1zrrzppwx95jvxa"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dylni/uniquote")
+    (synopsis "Quote strings for clear display in output")
+    (description "Quote strings for clear display in output")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-ndarray-0.14
+  (package
+    (name "rust-ndarray")
+    (version "0.14.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ndarray" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "011wqzmrd9gpfcfvy1xfbskqfiahn96pmi2d0r9x34d682amq3bc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-approx" ,rust-approx-0.4)
+        ;("rust-blas-src" ,rust-blas-src-0.6)
+        ("rust-cblas-sys" ,rust-cblas-sys-0.1)
+        ("rust-matrixmultiply" ,rust-matrixmultiply-0.2)
+        ("rust-num-complex" ,rust-num-complex-0.3)
+        ("rust-num-integer" ,rust-num-integer-0.1)
+        ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-rawpointer" ,rust-rawpointer-0.2)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs
+       (("rust-approx" ,rust-approx-0.4)
+        ("rust-defmac" ,rust-defmac-0.2)
+        ("rust-itertools" ,rust-itertools-0.9)
+        ("rust-quickcheck" ,rust-quickcheck-0.9))))
+    (home-page "https://github.com/rust-ndarray/ndarray")
+    (synopsis
+      "An n-dimensional array for general elements and for numerics. Lightweight array views and slicing; views support chunking and splitting.")
+    (description
+      "An n-dimensional array for general elements and for numerics.  Lightweight array
+views and slicing; views support chunking and splitting.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-version-sync-0.9
+  (package
+    (name "rust-version-sync")
+    (version "0.9.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "version-sync" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "1w0v20p6k13yhfmgmcwhgy3371znyqcn83lhrf47swq7xhf81l4r"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1)
+        ("rust-pulldown-cmark" ,rust-pulldown-cmark-0.8)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-semver" ,rust-semver-1)
+        ("rust-syn" ,rust-syn-1)
+        ("rust-toml" ,rust-toml-0.5)
+        ("rust-url" ,rust-url-2))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))
+    (home-page "https://github.com/mgeisler/version-sync")
+    (synopsis
+      "Crate for ensuring that version numbers in README files and other files are kept in sync with the crate version.")
+    (description
+      "Crate for ensuring that version numbers in README files and other files are kept
+in sync with the crate version.")
+    (license license:expat)))
+