diff options
Diffstat (limited to 'gn/packages/crates-io.scm')
| -rw-r--r-- | gn/packages/crates-io.scm | 454 |
1 files changed, 375 insertions, 79 deletions
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 1dc4f65..e500d86 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -7,11 +7,145 @@ #:use-module (guix build-system cargo) #:use-module (gnu packages crates-graphics) #:use-module (gnu packages crates-io) - #:use-module (gnu packages maths)) + #:use-module (gnu packages maths) + #:use-module (gnu packages python)) + +(define-public rust-bgzip-0.2 + (package + (name "rust-bgzip") + (version "0.2.1") + (source (origin + (method url-fetch) + (uri (crate-uri "bgzip" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1kssq4hp8csg27rhggabpfiyn9xp5rh5b8al63dghk11vqs7hk5j")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-flate2" ,rust-flate2-1) + ("rust-thiserror" ,rust-thiserror-1)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap-2) + ("rust-csv" ,rust-csv-1) + ("rust-tempfile" ,rust-tempfile-3)))) + (home-page "https://github.com/informationsea/bgzip-rs") + (synopsis "Rust implementation of bgzip") + (description "Rust implementation of bgzip") + (license license:expat))) + +(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-clap-lex-0.3 + (package + (name "rust-clap-lex") + (version "0.3.0") + (source (origin + (method url-fetch) + (uri (crate-uri "clap-lex" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1a4dzbnlxiamfsn0pnkhn7n9bdfjh66j9fxm6mmr7d227vvrhh8d")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-os-str-bytes" ,rust-os-str-bytes-6)))) + (home-page "https://github.com/clap-rs/clap/tree/master/clap_lex") + (synopsis "Minimal, flexible command line parser") + (description "Minimal, flexible command line parser") + (license (list license:expat license:asl2.0)))) + +(define-public rust-cuckoofilter-0.5 + (package + (name "rust-cuckoofilter") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (crate-uri "cuckoofilter" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "067fkr9dc118rqddr72xdldq05d31yyipvvyrmj9yrrik52ah45q")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t ; Not packaging dependencies + #:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1) + ;("rust-clippy" ,rust-clippy-0.0.302) + ;("rust-farmhash" ,rust-farmhash-1) + ("rust-fnv" ,rust-fnv-1) + ("rust-rand" ,rust-rand-0.7) + ("rust-serde" ,rust-serde-1) + ("rust-serde-bytes" ,rust-serde-bytes-0.11) + ("rust-serde-derive" ,rust-serde-derive-1)) + #:cargo-development-inputs + (("rust-serde-json" ,rust-serde-json-1)))) + (home-page "http://axiom.co") + (synopsis "Cuckoo Filter: Practically Better Than Bloom") + (description "Cuckoo Filter: Practically Better Than Bloom") + (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/chfi/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-handlegraph-0.7 (package - (inherit rust-handlegraph-0.3) (name "rust-handlegraph") (version "0.7.0-alpha.9") (source @@ -23,6 +157,7 @@ (sha256 (base32 "1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs")))) + (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-anyhow" ,rust-anyhow-1) @@ -36,7 +171,206 @@ ("rust-succinct" ,rust-succinct-0.5)) #:cargo-development-inputs (("rust-quickcheck" ,rust-quickcheck-0.9) - ("rust-rand" ,rust-rand-0.7)))))) + ("rust-rand" ,rust-rand-0.7)))) + (home-page "https://github.com/chfi/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) + (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-kstring-1 + (package + (name "rust-kstring") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "kstring" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1r4n9fa5scikqvl736nxghcfa6s3b07xz61w43hyzs2qb3wmd3nk")))) + (build-system cargo-build-system) + (arguments + `(;#:skip-build? #t ; Uses unstable features. + #:cargo-inputs + (("rust-document-features" ,rust-document-features-0.2) + ("rust-serde" ,rust-serde-1) + ("rust-static-assertions" ,rust-static-assertions-1)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3) + ("rust-proptest" ,rust-proptest-1)))) + (home-page "https://github.com/cobalt-org/kstring") + (synopsis "String optimized for map keys") + (description "Key String provides a Rust package optimized for map keys.") + (license (list license:expat license:asl2.0)))) + +(define-public rust-pyo3-0.14 + (package + (name "rust-pyo3") + (version "0.14.5") + (source (origin + (method url-fetch) + (uri (crate-uri "pyo3" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1j70b9bkncgpgnfxjxyvp4mk40rp55lk6qmacxm5c2k78y9hy41m")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-1) + ("rust-hashbrown" ,rust-hashbrown-0.11) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-indoc" ,rust-indoc-0.3) + ("rust-inventory" ,rust-inventory-0.1) + ("rust-libc" ,rust-libc-0.2) + ("rust-num-bigint" ,rust-num-bigint-0.4) + ("rust-num-complex" ,rust-num-complex-0.4) + ("rust-parking-lot" ,rust-parking-lot-0.11) + ("rust-paste" ,rust-paste-0.1) + ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.14) + ("rust-pyo3-macros" ,rust-pyo3-macros-0.14) + ("rust-serde" ,rust-serde-1) + ("rust-unindent" ,rust-unindent-0.1)) + #:cargo-development-inputs + (("rust-assert-approx-eq" ,rust-assert-approx-eq-1) + ("rust-criterion" ,rust-criterion-0.3) + ("rust-proptest" ,rust-proptest-0.10) + ("rust-rustversion" ,rust-rustversion-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-trybuild" ,rust-trybuild-1)))) + (inputs (list python)) + (home-page "https://github.com/pyo3/pyo3") + (synopsis "Rust bindings for the Python interpreter") + (description + "This package provides Rust bindings for Python, including tools for +creating native Python extension modules. Running and interacting with +Python code from a Rust binary is also supported.") + (license license:asl2.0))) + +(define-public rust-pyo3-build-config-0.14 + (package + (name "rust-pyo3-build-config") + (version "0.14.5") + (source (origin + (method url-fetch) + (uri (crate-uri "pyo3-build-config" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "13vkcl49b2x81azb613ss256k8pazrfc4fy4ny8pzgdciirn2afi")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-once-cell" ,rust-once-cell-1)))) + (home-page "https://github.com/pyo3/pyo3") + (synopsis "Build configuration for the PyO3 ecosystem") + (description "Build configuration for the PyO3 ecosystem") + (license license:asl2.0))) + +(define-public rust-pyo3-macros-0.14 + (package + (name "rust-pyo3-macros") + (version "0.14.5") + (source (origin + (method url-fetch) + (uri (crate-uri "pyo3-macros" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1a4fh24c5q85f31n2rwbqrai2bjprf9kzh6xvpgj8j3hblhwa2zw")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-pyo3-macros-backend" ,rust-pyo3-macros-backend-0.14) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://github.com/pyo3/pyo3") + (synopsis "Proc macros for PyO3 package") + (description "Proc macros for PyO3 package") + (license license:asl2.0))) + +(define-public rust-pyo3-macros-backend-0.14 + (package + (name "rust-pyo3-macros-backend") + (version "0.14.5") + (source (origin + (method url-fetch) + (uri (crate-uri "pyo3-macros-backend" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ps068jqyq1275zxxbzn6hyz9lkfz35az8waj6mzlji2jg2kyqki")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.14) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://github.com/pyo3/pyo3") + (synopsis "Code generation for PyO3 package") + (description "Code generation for PyO3 package") + (license license:asl2.0))) + +(define-public rust-quick-csv-0.1 + (package + (name "rust-quick-csv") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (crate-uri "quick-csv" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "131k8zzlplk2h62wz813jbvm0sk7v3mixwhhq34y9lmp3mqbgx7d")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-rustc-serialize" ,rust-rustc-serialize-0.3)))) + (home-page "https://github.com/tafia/quick-csv") + (synopsis "quick csv reader and decoder") + (description "quick csv reader and decoder") + (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-clap-for-jrep (package @@ -141,42 +475,42 @@ or any combination.") (description "Rust CLI tools for manipulation of Jupyter Notebooks.") (license #f)))) ; There is no license. -;; replace fields with those from upstream -(define-public rust-clap-3.1 +(define-public rust-clap-4 (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")))) + (version "4.0.9") + (source (origin + (method url-fetch) + (uri (crate-uri "clap" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1w0dxqzrh449s9l2k8g66pdsff02599bwi5mh0gny3227kcpsq1h")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs + `(#:skip-build? #t ; Not all inputs packaged. + #: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-clap-derive" ,rust-clap-derive-4) + ("rust-clap-lex" ,rust-clap-lex-0.3) + ("rust-once-cell" ,rust-once-cell-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)))) + ("rust-unicode-width" ,rust-unicode-width-0.1)) + ;#:cargo-development-inputs + ;(("rust-humantime" ,rust-humantime-2) + ; ("rust-rustversion" ,rust-rustversion-1) + ; ("rust-shlex" ,rust-shlex-1) + ; ("rust-snapbox" ,rust-snapbox-0.4) + ; ("rust-static-assertions" ,rust-static-assertions-1) + ; ("rust-trybuild" ,rust-trybuild-1) + ; ("rust-trycmd" ,rust-trycmd-0.13) + ; ("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9)) + )) (home-page "https://github.com/clap-rs/clap") (synopsis "A simple to use, efficient, and full-featured Command Line Argument Parser") @@ -185,19 +519,17 @@ or any combination.") Argument Parser") (license (list license:expat license:asl2.0)))) -;; ready to upstream, WITH rust-clap-derive -;; replace fields with those from upstream. -(define-public rust-clap-derive-3.1 +(define-public rust-clap-derive-4 (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")))) + (version "4.0.9") + (source (origin + (method url-fetch) + (uri (crate-uri "clap-derive" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02zhbbmyz3dpy9ml6xfp7i8p3ffj1djvkdnkg6gr6d0s5r4hg8x4")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -213,40 +545,6 @@ or any combination.") "Parse command line argument by defining a struct, derive crate.") (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 - `(#:skip-build? #t ; Not all inputs packaged - ;#: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") @@ -260,9 +558,7 @@ or any combination.") (base32 "1rwa5nzq8c5zg7lqmpkf7hyib415yxshd9amp911y8w1zss4s38p")))) (build-system cargo-build-system) (arguments - `(;#:skip-build? #t ; Not all inputs at correct versions? - ;#:tests? #f ; Skip tests for now - #:cargo-inputs + `(#:cargo-inputs (("rust-backtrace" ,rust-backtrace-0.3) ("rust-concolor" ,rust-concolor-0.0.8) ("rust-content-inspector" ,rust-content-inspector-0.2) @@ -302,7 +598,7 @@ or any combination.") (base32 "0wx4wd849bmkqj0gdi041gmpfpvlyhy2ha4zpin69yw9d9npl8cl")))) (build-system cargo-build-system) (arguments - `(;#:skip-build? #t ; Not all inputs packaged + `(#:skip-build? #t ; Not all inputs packaged ;#:tests? #f ; Skip tests for now #:cargo-inputs (("rust-combine" ,rust-combine-4) @@ -371,7 +667,7 @@ or any combination.") (license license:gpl3+))) (define-public gn-rust-correlation - (let ((commit "fd85c0f75e03f170b97fcedba26317e0832d087e") + (let ((commit "a22381e9830bac9a6848449279d258397217e251") (revision "0")) (package (name "gn-rust-correlation") @@ -385,7 +681,7 @@ or any combination.") (file-name (git-file-name name version)) (sha256 (base32 - "164z2abp8vassxi8bpf68wgiqjmafd6hzrkz4hj3wdhf4djiplrr")))) + "1cb197p8zmgxymzs9b7bygs0kg67809z6gc2svza909sxr9ac5ps")))) (build-system cargo-build-system) (native-inputs (list gsl)) |