diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/4store.scm | 86 | ||||
| -rw-r--r-- | gn/packages/arrayfire.scm | 457 | ||||
| -rw-r--r-- | gn/packages/beignet.scm | 155 | ||||
| -rw-r--r-- | gn/packages/bioinformatics.scm | 973 | ||||
| -rw-r--r-- | gn/packages/bnw.scm | 90 | ||||
| -rw-r--r-- | gn/packages/clBLAS.scm | 162 | ||||
| -rw-r--r-- | gn/packages/clFFT.scm | 158 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 5623 | ||||
| -rw-r--r-- | gn/packages/cwl.scm | 1 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 505 | ||||
| -rw-r--r-- | gn/packages/glfw.scm | 83 | ||||
| -rw-r--r-- | gn/packages/hyphy.scm | 31 | ||||
| -rw-r--r-- | gn/packages/mongodb.scm | 74 | ||||
| -rw-r--r-- | gn/packages/ocl-icd.scm | 99 | ||||
| -rw-r--r-- | gn/packages/opencl-headers.scm | 63 | ||||
| -rw-r--r-- | gn/packages/openfyba.scm | 39 | ||||
| -rw-r--r-- | gn/packages/ratspub.scm | 75 | ||||
| -rw-r--r-- | gn/packages/ruby.scm | 47 | ||||
| -rw-r--r-- | gn/packages/sparql-query.scm | 87 | ||||
| -rw-r--r-- | gn/packages/statistics.scm | 4 | ||||
| -rw-r--r-- | gn/packages/yaj.scm | 1 |
21 files changed, 5053 insertions, 3760 deletions
diff --git a/gn/packages/4store.scm b/gn/packages/4store.scm deleted file mode 100644 index ec09112..0000000 --- a/gn/packages/4store.scm +++ /dev/null @@ -1,86 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Roel Janssen <roel@gnu.org> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages 4store) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) - #:use-module (guix utils) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (gnu packages) - #:use-module (gnu packages autotools) - #:use-module (gnu packages python) - #:use-module (gnu packages perl) - #:use-module (gnu packages rdf) - #:use-module (gnu packages pcre) - #:use-module (gnu packages avahi) - #:use-module (gnu packages gettext) - #:use-module (gnu packages glib) - #:use-module (gnu packages linux) - #:use-module (gnu packages readline) - #:use-module (gnu packages cyrus-sasl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages tls) - #:use-module (gnu packages file) - #:use-module (gnu packages xml)) - -(define-public 4store ; guix ready - (let ((commit "c5a56d7c7504551a1f2fff6c16c4d9a440e4a317")) - (package - (name "4store") - (version (string-append "1.1.6-0." (string-take commit 7))) - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/garlik/4store/archive/" - commit ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "12pn5masjrfp1d8v1dz47qga0ns8d03f2f5icnb9d6m1jfp8l38a")) - (patches (list (search-patch "4store-fix-buildsystem.patch"))))) - (build-system gnu-build-system) - (native-inputs - `(("perl" ,perl) - ("python" ,python-2) - ("file" ,file) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gnu-gettext) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs - `(("glib" ,glib) - ("rasqal" ,rasqal) - ("libxml2" ,libxml2) - ("raptor2" ,raptor2) - ("readline" ,readline) - ("avahi" ,avahi) - ("pcre" ,pcre) - ("cyrus-sasl" ,cyrus-sasl) - ("openssl" ,openssl) - ("util-linux" ,util-linux))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'configure 'generate-configure - (lambda _ - (zero? (system* "./autogen.sh"))))))) - (home-page "http://www.4store.org") - (synopsis "Clustered RDF storage and query engine") - (description "4store is a RDF/SPARQL store written in C, either single -machines or networked clusters.") - (license license:gpl3+)))) diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 39e7899..9cb86fa 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> +;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -19,342 +20,216 @@ (define-module (gn packages arrayfire) #:use-module (guix packages) #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) #:use-module (guix git-download) - #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (gnu packages) #:use-module (guix utils) #:use-module (gnu packages algebra) - #:use-module (gnu packages autotools) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages compression) - #:use-module (gnu packages curl) - #:use-module (gnu packages gawk) - #:use-module (gnu packages cmake) #:use-module (gnu packages boost) - #:use-module (gnu packages glib) - #:use-module (gnu packages image) - #:use-module (gnu packages video) - #:use-module (gnu packages textutils) - ;; #:use-module (gnu packages fftw) - ;; #:use-module (gnu packages fftw-openmpi) - in algebra - ;; #:use-module (gnu packages fftwf) - #:use-module (gnu packages gl) + #:use-module (gnu packages check) #:use-module (gnu packages gcc) - #:use-module (gnu packages gnupg) - #:use-module (gnu packages pkg-config) #:use-module (gnu packages maths) - #:use-module (gnu packages mpi) - #:use-module (gnu packages web) - #:use-module (gnu packages wget) - #:use-module (gnu packages python) - #:use-module (gnu packages ruby) - #:use-module (gnu packages xorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) + #:use-module (gnu packages opencl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python)) (define-public arrayfire (package (name "arrayfire") - (version "3.3.1") + (version "3.3.2") (source (origin - (method url-fetch) - (uri (string-append "http://arrayfire.com/arrayfire_source/arrayfire-full-" version - ".tar.bz2")) - (file-name (string-append name "-" version ".tar.bz2")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/arrayfire/arrayfire.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "045adww6dqmyz6kkfmq7xawi5v9a894yp5j9pzn6j568gi48pyqc")))) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gawk" ,gawk) - ("git" ,git) - ("glew" ,glew) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("boost" ,boost) - ("glfw" ,glfw) - ("compute" ,compute) - ("curl" ,curl) + "113ldnqsil4p84sayv7jh8vnn0nalxibhdyvvwp94vqk20kqg4lw")) + (patches (search-patches "arrayfire-lapack-detection.patch" + "arrayfire-newer-boost-compute.patch")))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("googletest" ,googletest) + ("assets" ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arrayfire/assets.git") + (commit "729c7b64039e6433ae5ee521658ba20147efcb02"))) ; March 4, 2019 + (file-name (git-file-name "arrayfire-assets" "submodule")) + (sha256 + (base32 + "05zg7m6zlwi3llbv7l5wd9qi9ppb9p3ad2i5xmqwvcbgx5ry4l2s")))) + ("threads" ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/alltheflops/threads.git") + (commit "5e778ce0a7f0f80af9d32ea3569df3dbec834f59"))) ; Dec 16, 2015 + (file-name (git-file-name "arrayfire-threads" "submodule")) + (sha256 + (base32 + "1rj2357r124b4ry0s467fz9hs4jxcyacliwprggvai85a39pqabx")))))) + (inputs + `(("boost" ,boost) ("clBLAS" ,clBLAS) ("clFFT" ,clFFT) - ("atlas" ,atlas) - ("dbus" ,dbus) - ("opencl-headers" ,opencl-headers) - ("ocl-icd" ,ocl-icd) - ("enca" ,enca) - ("eudev" ,eudev) - ("glew" ,glew) - ("glib" ,glib) - ("lapack" ,lapack) - ("scalapack" ,scalapack) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("libyajl" ,libyajl) - ("mesa-utils" ,mesa-utils) - ("python" ,python-2) - ("freeimage" ,freeimage) - ("freeglut" ,freeglut) - ("fftw" ,fftw) - ("fftwf" ,fftwf) ("fftw-openmpi" ,fftw-openmpi) - ("glew" ,glew) - ("glu" ,glu) + ("fftwf" ,fftwf) + ("ocl-icd" ,ocl-icd) ("openblas" ,openblas) - ("wget" ,wget) - ("cmake" ,cmake))) + ("opencl-headers" ,opencl-headers))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DBUILD_OPENCL=ON" "-DBUILD_CUDA=OFF" "-DBUILD_GRAPHICS=OFF" "-DUSE_SYSTEM_BOOST_COMPUTE=ON" "-DUSE_SYSTEM_CLBLAS=ON" "-DUSE_SYSTEM_CLFFT=ON") - #:tests? #t)) - (synopsis "ArrayFire: a general purpose GPU library. https://arrayfire.com") - (description "ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming simple.Now on Guix") - (home-page "http://arrayfire.com/") - (license (list license:gpl2 - license:gpl2+ - license:gpl3 - license:gpl3+)))) - -(define-public glfw - (package - (name "glfw") - (version "3.1.2") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/glfw/glfw/archive/" - version ".tar.gz")) - (sha256 - (base32 - "08pixv8hd5xsccf7l8cqcijjqaq4k4da8qbp77wggal2fq445ika")))) - (build-system cmake-build-system) - (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") - #:tests? #f)) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("git" ,git) - ("libtool" ,libtool) - ("libpthread-stubs" ,libpthread-stubs) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("enca" ,enca) - ("eudev" ,eudev) - ("glew" ,glew) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) - ("python" ,python-2))) - (home-page "http://www.glfw.org/") - (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) + `(#:configure-flags + '("-DBUILD_OPENCL=ON" + "-DBUILD_CUDA=OFF" + "-DBUILD_GRAPHICS=OFF" + "-DBUILD_TEST=OFF" ; building tests segfaults + "-DUSE_SYSTEM_CLBLAS=ON" + "-DUSE_SYSTEM_CLFFT=ON" + "-DUSE_SYSTEM_GTEST=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'add-more-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((assets (assoc-ref inputs "assets")) + (threads (assoc-ref inputs "threads"))) + (copy-recursively assets "assets") + (copy-recursively threads "src/backend/cpu/threads")) + #t)) + (add-after 'unpack 'fix-sources + (lambda _ + (substitute* "src/backend/opencl/blas.cpp" + ;; https://github.com/arrayfire/arrayfire/commit/90a9ffbce5c38352a365e03a634ffaf0d2fb9933 + (("#undef BLAS_FUNC_DEF") + "#undef BLAS_FUNC_DEF\n#undef BLAS_FUNC")) + (substitute* '("src/backend/cpu/blas.cpp" + "src/backend/opencl/cpu/cpu_blas.cpp") + ;; https://github.com/arrayfire/arrayfire/pull/2538/files + (("&cblas_##PREFIX##FUNC;") + "(FUNC##_func_def<TYPE>)&cblas_##PREFIX##FUNC;")) + #t))) + #:tests? #f)) ; Building the tests fail linking, so we build the examples as a test. + (home-page "https://arrayfire.com/") + (synopsis "High performance library for parallel computing") + (description + "ArrayFire is a high performance software library for parallel computing +with an easy-to-use API. Its array based function set makes parallel +programming simple.") + (license (list license:bsd-3 ; everything except CMakeModules folder + license:cc0)))) ; assets (define-public clBLAS (package (name "clBLAS") - (version "v2.10") + (version "2.12") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/clMathLibraries/clBLAS/archive/" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/clMathLibraries/clBLAS.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0adlb02lqzrklfybhnv4n0p37mvkvdi3vqiwa05x2mv05ywnr93j")))) + "154mz52r5hm0jrp5fqrirzzbki14c1jkacj75flplnykbl36ibjs")))) (build-system cmake-build-system) - (arguments `(#:tests? #f - #:configure-flags '("../clBLAS-2.10/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release" "-DBUILD_TEST=OFF"))) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("gfortran" ,gfortran) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("boost" ,boost) - ("enca" ,enca) - ("eudev" ,eudev) - ("fftw-openmpi" ,fftw-openmpi) - ("glew" ,glew) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("openmpi" ,openmpi) - ("ocl-icd" ,ocl-icd) + (arguments + `(#:tests? #f + #:configure-flags + (list "../source/src" + "-DUSE_SYSTEM_GTEST=ON" + ;"-DBoost_USE_STATIC_LIBS=OFF" ; this does not seem to apply + "-DBUILD_TEST=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "src/CMakeLists.txt" + (("Boost_USE_STATIC_LIBS ON") + "Boost_USE_STATIC_LIBS OFF")) + #t))))) + (native-inputs + `(("gfortran" ,gfortran) + ("openblas" ,openblas) ("opencl-headers" ,opencl-headers) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) ("python" ,python-2))) - (home-page "http://www.glfw.org/") - (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) + (inputs + `(("boost" ,boost) + ("ocl-icd" ,ocl-icd))) + (home-page "https://github.com/clMathLibraries/clBLAS") + (synopsis "Library containing BLAS functions written in OpenCL") + (description + "The primary goal of @code{clBLAS} is to make it easier for developers to +utilize the inherent performance and power efficiency benefits of heterogeneous +computing. @code{clBLAS} interfaces do not hide nor wrap @code{OpenCL} +interfaces, but rather leaves @code{OpenCL} state management to the control of +the user to allow for maximum performance and flexibility. The @code{clBLAS} +library does generate and enqueue optimized @code{OpenCL} kernels, relieving the +user from the task of writing, optimizing and maintaining kernel code themselves.") + (license license:asl2.0))) (define-public clFFT (package (name "clFFT") - (version "v2.10.1") + (version "2.12.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/clMathLibraries/clFFT/archive/" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/clMathLibraries/clFFT.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "19hrk1lf06kch8x9dpbdj0waycn2mldrmj2y4vzi7zn2gdfw6g73")))) + "134vb6214hn00qy84m4djg4hqs6hw19gkp8d0wlq8gb9m3mfx7na")))) (build-system cmake-build-system) - (arguments `(#:configure-flags '("../clFFT-2.10.1/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("enca" ,enca) - ("eudev" ,eudev) + (arguments + `(#:configure-flags '("../source/src" + "-DBUILD_TEST=ON" + "-DUSE_SYSTEM_GTEST=ON" + "-DBoost_USE_STATIC_LIBS=OFF") + #:test-target "Test")) + (native-inputs + `(("boost" ,boost) ("fftw-openmpi" ,fftw-openmpi) - ("glew" ,glew) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("openmpi" ,openmpi) - ("ocl-icd" ,ocl-icd) - ("opencl-headers" ,opencl-headers) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) - ("python" ,python-2))) - (home-page "http://www.glfw.org/") - (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) + ("fftwf" ,fftwf) + ("googletest" ,googletest))) + (inputs + `(("ocl-icd" ,ocl-icd) + ("opencl-headers" ,opencl-headers))) + (home-page "https://github.com/clMathLibraries/clFFT/") + (synopsis "Library containing FFT functions written in OpenCL") + (description "@code{clFFT} is a software library containing FFT functions +written in @code{OpenCL}. In addition to GPU devices, the library also supports +running on CPU devices to facilitate debugging and heterogeneous programming.") + (license license:asl2.0))) -(define-public compute +(define-public compute ; superceeded by boost-1.61+ (package (name "compute") - (version "v0.5") + (version "0.5") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/boostorg/compute/archive/" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/boostorg/compute.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1r16zd1wdnn9gx278mkvr13k3i79hr35v6vj0fn7v3n92ngwxnhd")))) + "0jc04k43br49hqgzrxfn3wfz2m94q1z45zfg5nahqb7p0lbfgwyx")))) (build-system cmake-build-system) - (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("enca" ,enca) - ("eudev" ,eudev) - ("fftw-openmpi" ,fftw-openmpi) - ("glew" ,glew) - ("boost" ,boost) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("openmpi" ,openmpi) - ("opencl-headers" ,opencl-headers) - ("ocl-icd" ,ocl-icd) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) - ("python" ,python-2))) - (home-page "http://boost.org") - (synopsis "Peer-reviewed portable C++ source libraries,BoostCompute") - (description "Peer-reviewed portable C++ source libraries,BoostCompute") - (license (list license:x11-style)))) - -(define-public ocl-icd - (package - (name "ocl-icd") - (version "2.2.9") - (source (origin - (method url-fetch) - (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) - (inputs `(("zip" ,zip) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("ruby" ,ruby) - ("libtool" ,libtool) - ("opencl-headers" ,opencl-headers) - ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") - (description "OpenCL implementations are provided as ICD (Installable Client Driver). - An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. - This free ICD Loader can load any (free or non free) ICD") - (license (list license:gpl2 license:ruby)))) - -(define-public opencl-headers -(let ((commit "c1770dc")) - (package - (name "opencl-headers") - (version (string-append "2.1-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/KhronosGroup/OpenCL-Headers.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck")))) - (propagated-inputs '()) - (inputs '()) - (native-inputs '()) - (build-system gnu-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (string-append - (assoc-ref outputs "out") - "/include/CL"))))))) - (synopsis "The Khronos OpenCL headers") - (description "This package provides the Khronos OpenCL headers") - (home-page "https://www.khronos.org/registry/cl/") - (license (list license:gpl2))))) + `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON" + "-DCMAKE_BUILD_TYPE=Release") + #:tests? #f)) ; tests require OpenCL device + (native-inputs + `(("boost" ,boost-for-mysql) ; 1.59.0 + ("opencl-headers" ,opencl-headers) + ("ocl-icd" ,ocl-icd))) + (home-page "http://boostorg.github.io/compute/") + (synopsis "C++ GPU Computing Library for OpenCL") + (description + "@code{Boost.Compute} is a GPU/parallel-computing library for C++ based on +@code{OpenCL}. The core library is a thin C++ wrapper over the @code{OpenCL +API} and provides access to compute devices, contexts, command queues and memory +buffers.") + (license license:boost1.0))) diff --git a/gn/packages/beignet.scm b/gn/packages/beignet.scm deleted file mode 100644 index c07fa61..0000000 --- a/gn/packages/beignet.scm +++ /dev/null @@ -1,155 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages beignet) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system cmake) - #:use-module (guix build-system gnu) - #:use-module (guix packages) - #:use-module (gnu packages) - #:use-module (guix utils) - #:use-module (gnu packages algebra) - #:use-module (gnu packages autotools) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages gawk) - #:use-module (gnu packages cmake) - #:use-module (gnu packages compression) - #:use-module (gnu packages glib) - #:use-module (gnu packages gnupg) - #:use-module (gnu packages llvm) - #:use-module (gnu packages libedit) - #:use-module (gnu packages video) - #:use-module (gnu packages textutils) - #:use-module (gnu packages gl) - #:use-module (gnu packages ruby) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages maths) - #:use-module (gnu packages web) - #:use-module (gnu packages ncurses) - #:use-module (gnu packages python) - #:use-module (gnu packages xorg) - #:use-module (gnu packages xdisorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) - -(define-public beignet - (package - (name "beignet") - (version "1.1.1") - (source (origin - (method url-fetch) - (uri (string-append "https://01.org/sites/default/files/beignet-" - version "-source.tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "068i5srqpncfw0kklxdyzxcm5w56pi91jp7pkv6cglzvnjgcdx4v")))) - (inputs `(("autoconf" ,autoconf) - ("llvm" ,llvm-3.5) - ("libpthread-stubs", libpthread-stubs) - ("clang" ,clang-3.5) - ("libdrm" ,libdrm) - ("libtool" ,libtool) - ("libsm" ,libsm) - ("libxfixes" ,libxfixes) - ("libxext" ,libxext) - ("libedit" ,libedit) - ("xextproto" ,xextproto) - ("python" ,python-2) - ("opencl-headers" ,opencl-headers) - ("glu" ,glu) - ("zlib" ,zlib) - ("pkg-config" ,pkg-config) - ("freeglut" ,freeglut) - ("mesa-utils" ,mesa-utils) - ("ncurses" ,ncurses) - ("ocl-icd" ,ocl-icd))) - (build-system cmake-build-system) - (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release" "-DCOMPILER=CLANG") #:tests? #f)) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "Intel's OpenCL framework") - (description "Intel's OpenCL framework that works with Intel IvyBridge GPUs and above") - (license license:gpl2))) - -(define-public ocl-icd - (package - (name "ocl-icd") - (version "2.2.9") - (source (origin - (method url-fetch) - (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) - (inputs `(("zip" ,zip) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("ruby" ,ruby) - ("libtool" ,libtool) - ("opencl-headers" ,opencl-headers) - ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") - (description "OpenCL implementations are provided as ICD (Installable Client Driver). - An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. - This free ICD Loader can load any (free or non free) ICD") - (license license:gpl2))) - -(define-public opencl-headers -(let ((commit "c1770dc")) - (package - (name "opencl-headers") - (version (string-append "2.1-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/KhronosGroup/OpenCL-Headers.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck")))) - (propagated-inputs '()) - (inputs '()) - (native-inputs '()) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (string-append - (assoc-ref outputs "out") - "/include/CL"))))))) - (synopsis "The Khronos OpenCL headers") - (description "This package provides the Khronos OpenCL headers") - (home-page "https://www.khronos.org/registry/cl/") - (license license:gpl2)))) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index bdd0322..ad4db7b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -7,60 +7,20 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system ant) - #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) - #:use-module (guix build-system perl) + #:use-module (guix build-system gnu) #:use-module (guix build-system python) - ;; #:use-module (guix build-system ruby) - #:use-module (guix build-system r) - #:use-module (guix build-system trivial) - #:use-module (gn packages statistics) - #:use-module (gnu packages autotools) - #:use-module (gnu packages algebra) - #:use-module (gnu packages base) + #:use-module (gnu packages) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages compression) - #:use-module (gnu packages databases) #:use-module (gnu packages check) - #:use-module (gnu packages cmake) - #:use-module (gnu packages compression) - #:use-module (gnu packages cpio) - #:use-module (gnu packages curl) - #:use-module (gnu packages documentation) - #:use-module (gnu packages datastructures) - #:use-module (gnu packages file) - #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) - #:use-module (gnu packages graphviz) - #:use-module (gnu packages java) - #:use-module (gnu packages linux) - #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) - #:use-module (gnu packages mpi) - #:use-module (gnu packages ncurses) - #:use-module (gnu packages node) - #:use-module (gnu packages parallel) - #:use-module (gnu packages pcre) #:use-module (gnu packages perl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages popt) - #:use-module (gnu packages protobuf) #:use-module (gnu packages python) - #:use-module (gnu packages ruby) - #:use-module (gnu packages statistics) - #:use-module (gnu packages tbb) - #:use-module (gnu packages textutils) - #:use-module (gnu packages time) - #:use-module (gnu packages tls) - #:use-module (gnu packages vim) - #:use-module (gnu packages web) - #:use-module (gnu packages xml) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages dlang) -; #:use-module (gn packages ldc) - #:use-module (gn packages shell) - #:use-module (srfi srfi-1)) + #:use-module (gnu packages python-xyz) + #:use-module (gnu packages statistics)) (define-public contra (package @@ -69,10 +29,15 @@ (source (origin (method url-fetch) (uri (string-append - "mirror://sourceforge/contra-cnv/CONTRA.v" version ".tar.gz")) + "mirror://sourceforge/contra-cnv/CONTRA.V" + (version-major+minor version) "/CONTRA.v" version ".tar.gz")) (sha256 (base32 - "0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91")))) + "0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file "BEDTools.v2.11.2.tar.gz") #t)))) (build-system gnu-build-system) (propagated-inputs `(("python" ,python-2) @@ -87,18 +52,16 @@ (delete 'configure) (delete 'build) ; We can use Guix's BEDtools instead. (replace 'install - (lambda _ - (let* ((out (assoc-ref %outputs "out")) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) (doc (string-append out "/share/doc/contra"))) - (mkdir-p bin) - (mkdir-p doc) - (and - (zero? (system* "cp" "--recursive" "scripts" bin)) - (zero? (system* "cp" "contra.py" bin)) - (zero? (system* "cp" "baseline.py" bin)) - ;; There's only a pre-built PDF available. - (zero? (system* "cp" "CONTRA_User_Guide.2.0.pdf" doc))))))))) + (copy-recursively "scripts" (string-append bin "/scripts")) + (install-file "contra.py" bin) + (install-file "baseline.py" bin) + ;; There's only a pre-built PDF available. + (install-file "CONTRA_User_Guide.2.0.pdf" doc)) + #t))))) (home-page "http://contra-cnv.sourceforge.net/") (synopsis "Tool for copy number variation (CNV) detection for targeted resequencing data") @@ -219,486 +182,6 @@ data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM). ") (license license:gpl2+))) -(define-public tabixpp - (package - (name "tabixpp") - (version "1.0.0") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/tabixpp/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "1s0lgks7qlvlhvcjhi2wm18nnza1bwcnic44ij7z8wfg88h4ivwn")))) - (build-system gnu-build-system) - (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) - (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - ;; The build phase needs overriding the location of htslib. - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (zero? - (system* "make" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "tabix++" bin))))))) - (home-page "https://github.com/ekg/tabixpp") - (synopsis "C++ wrapper around tabix project") - (description "This is a C++ wrapper around the Tabix project which abstracts -some of the details of opening and jumping in tabix-indexed files.") - (license license:expat))) - -;; This version works with FreeBayes while the released version doesn't. The -;; released creates a variable with the name "vcf" somewhere, which is also the -;; name of a namespace in vcflib. -(define-public tabixpp-freebayes - (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) - (package (inherit tabixpp) - (name "tabixpp-freebayes") - (version (string-append "0-1." (string-take commit 7))) - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/tabixpp/archive/" - commit ".tar.gz")) - (file-name (string-append name "-" version "-checkout.tar.gz")) - (sha256 - (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))))) - -(define-public smithwaterman - ;; TODO: Upgrading smithwaterman breaks FreeBayes. - (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) - (package - (name "smithwaterman") - (version (string-append "0-1." (string-take commit 7))) - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/smithwaterman/archive/" - commit ".tar.gz")) - (file-name (string-append name "-" version "-checkout.tar.gz")) - (sha256 - (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "smithwaterman" bin))))))) - (home-page "https://github.com/ekg/smithwaterman") - (synopsis "Implementation of the Smith-Waterman algorithm") - (description "Implementation of the Smith-Waterman algorithm.") - ;; The project contains a license file for the GPLv2. The source files - ;; do not contain a license notice, so GPLv2-only is assumed here. - (license license:gpl2)))) - -(define-public multichoose - (package - (name "multichoose") - (version "1.0.3") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/multichoose/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "0xy86vvr3qrs4l81qis7ia1q2hnqv0xcb4a1n60smxbhqqis5w3l")))) - (build-system gnu-build-system) - (native-inputs - `(("python" ,python-2) - ("node" ,node))) - (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - ;; TODO: There are Python modules for these programs too. - (install-file "multichoose" bin) - (install-file "multipermute" bin))))))) - (home-page "https://github.com/ekg/multichoose") - (synopsis "Library for efficient loopless multiset combination generation -algorithm") - (description "A library implements an efficient loopless multiset -combination generation algorithm which is (approximately) described in -\"Loopless algorithms for generating permutations, combinations, and other -combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM), -1973. (Algorithm 7.)") - (license license:expat))) - -(define-public fsom - (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3")) - (package - (name "fsom") - (version (string-append "0-1." (string-take commit 7))) - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/fsom/archive/" - "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz")) - (file-name (string-append name "-" version "-checkout.tar.gz")) - (sha256 - (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "fsom" bin))))))) - (home-page "https://github.com/ekg/fsom") - (synopsis "Program for managing SOM (Self-Organizing Maps) neural networks") - (description "Program for managing SOM (Self-Organizing Maps) neural networks.") - (license license:gpl3)))) - -(define-public filevercmp - (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) - (package - (name "filevercmp") - (version (string-append "0-1." (string-take commit 7))) - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/filevercmp/archive/" - commit ".tar.gz")) - (file-name "filevercmp-src.tar.gz") - (sha256 - (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "filevercmp" bin))))))) - (home-page "https://github.com/ekg/filevercmp") - (synopsis "Program to compare version strings") - (description "A program to compare version strings. It intends to be a -replacement for strverscmp.") - (license license:gpl3+)))) - -(define-public fastahack ; guix ready - (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) - (package - (name "fastahack") - (version (string-append "0-1." (string-take commit 7))) - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/fastahack/archive/" - commit ".tar.gz")) - (file-name (string-append name "-" version "-checkout.tar.gz")) - (sha256 - (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "fastahack" bin))))))) - (home-page "https://github.com/ekg/fastahack") - (synopsis "Program for indexing and sequence extraction from FASTA files") - (description "Fastahack is a small application for indexing and extracting -sequences and subsequences from FASTA files. The included Fasta.cpp library -provides a FASTA reader and indexer that can be embeddedinto applications which -would benefit from directly reading subsequences from FASTA files. The library -automatically handles index file generation and use.") - ;; There is no specific license for fastahack. - ;; A part of the program is licensed GPLv2. - (license (list license:non-copyleft license:gpl2))))) - -(define-public vcflib ; guix duplicat, see below? - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) - (package - (name "vcflib") - (version (string-append "1.0.2-1." (string-take commit 7))) - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/vcflib/vcflib/archive/" - "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz")) - (file-name "vcflib-5ac0913.tar.gz") - (sha256 - (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8")))) - (build-system gnu-build-system) - (native-inputs - `(("htslib" ,htslib) - ("zlib" ,zlib) - ("python" ,python-2) - ("perl" ,perl) - ("r" ,r) - ("node" ,node) - ("tabixpp-src" ,(package-source tabixpp-freebayes)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("multichoose-src" ,(package-source multichoose)) - ("fsom-src" ,(package-source fsom)) - ("filevercmp-src" ,(package-source filevercmp)) - ("fastahack-src" ,(package-source fastahack)) - ("intervaltree-src" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/ekg/intervaltree/archive/" - "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) - (file-name "intervaltree-src.tar.gz") - (sha256 - (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))))) - (arguments - `(#:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (zero? (system* "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "intervaltree-src" "intervaltree") - (unpack "fastahack-src" "fastahack") - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "multichoose-src" "multichoose") - (unpack "smithwaterman-src" "smithwaterman") - (unpack "tabixpp-src" "tabixpp"))))) - (add-after 'unpack-submodule-sources 'fix-makefile - (lambda* (#:key inputs #:allow-other-keys) - (substitute* '("Makefile") - (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) - (replace - 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "tabixpp" - (zero? (system* "make"))) - (zero? (system* "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - ;;(include (string-append (assoc-ref outputs "out") "/include")) - (lib (string-append (assoc-ref outputs "out") "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - ;; The header files do not correspond to libvcflib.a, therefore - ;; I left them out. - ;;(for-each (lambda (file) - ;; (install-file file include)) - ;; (find-files "src" "\\.h$")) - (install-file "libvcflib.a" lib))))))) - (home-page "https://github.com/vcflib/vcflib/") - (synopsis "Library for parsing and manipulating VCF files") - (description "Vcflib provides methods to manipulate and interpret -sequence variation as it can be described by VCF. It is both an API for parsing -and operating on records of genomic variation as it can be described by the VCF -format, and a collection of command-line utilities for executing complex -manipulations on VCF files.") - (license license:expat)))) - -(define-public bash-tap ; guix license issue - (package - (name "bash-tap") - (version "1.0.2") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/illusori/bash-tap/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "0qs1qi38bl3ns4mpagcawv618dsk2q1lgrbddgvs0wl3ia12cyz5")))) - (build-system trivial-build-system) - (native-inputs `(("source" ,source) - ("tar" ,tar) - ("gzip" ,gzip))) - (arguments - `(#:modules ((guix build utils)) - #:builder (begin - (use-modules (guix build utils)) - (let ((tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) - (path (string-append (assoc-ref %build-inputs "gzip") "/bin")) - (bin (string-append %output "/bin")) - (source (string-append (assoc-ref %build-inputs "source")))) - (setenv "PATH" path) - (mkdir-p bin) - (with-directory-excursion bin - (zero? (system* tar "xvf" source - "--strip-components=1" - "--no-anchored" - "bash-tap" - "bash-tap-bootstrap" - "bash-tap-mock"))))))) - (home-page "http://www.illusori.co.uk/projects/bash-tap/") - (synopsis "Bash port of a Test::More/Test::Builder-style TAP-compliant -test library") - (description "Bash TAP is a TAP-compliant Test::More-style testing library -for Bash shell scripts and functions. Along with the Test::More-style testing -helpers it provides helper functions for mocking commands and functions and -in-process output capturing.") - ;; The author didn't specify a license. - (license license:public-domain))) - -(define-public freebayes ; guix dependent package issues - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") - (revision "1")) - (package - (name "freebayes") - (version (string-append "1.0.2-" revision "." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/freebayes.git") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) - (build-system gnu-build-system) - (inputs - `(("zlib" ,zlib) - ("htslib" ,htslib))) - (native-inputs - `(("bc" ,bc) ; Needed for running tests. - ("samtools" ,samtools) ; Needed for running tests. - ("parallel" ,parallel) ; Needed for running tests. - ("procps" ,procps) ; Needed for running tests. - ("bamtools" ,bamtools) - ("cmake" ,cmake) - ("python" ,python-2) - ("node" ,node) - ("r" ,r) - ("perl" ,perl) - ("bamtools-src" ,(package-source bamtools)) - ("vcflib-src" ,(package-source vcflib)) - ;; These are submodules for the vcflib version used in freebayes - ("tabixpp-src" ,(package-source tabixpp-freebayes)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("multichoose-src" ,(package-source multichoose)) - ("fsom-src" ,(package-source fsom)) - ("filevercmp-src" ,(package-source filevercmp)) - ("fastahack-src" ,(package-source fastahack)) - ("intervaltree-src" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/ekg/intervaltree/archive/" - "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) - (file-name "intervaltree-src.tar.gz") - (sha256 - (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) - ;; These submodules are needed to run the tests. - ("bash-tap-src" ,(package-source bash-tap)) - ;; ,(origin - ;; (method url-fetch) - ;; (uri (string-append "https://github.com/illusori/bash-tap/archive/" - ;; "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz")) - ;; (file-name "bash-tap-src.tar.gz") - ;; (sha256 - ;; (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz")))) - ("test-simple-bash-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ingydotnet/test-simple-bash/archive/" - "124673ff204b01c8e96b7fc9f9b32ee35d898acc" ".tar.gz")) - (file-name "test-simple-bash-src.tar.gz") - (sha256 - (base32 "016xf3wbgqbav9dncvfdx5k0f10z5xwq8jdszajzmcvnhz5wis14")))))) - (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (zero? (system* "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "bamtools-src" "bamtools") - (unpack "vcflib-src" "vcflib") - ;;(unpack "intervaltree-src" "intervaltree") - (unpack "fastahack-src" "vcflib/fastahack") - (unpack "filevercmp-src" "vcflib/filevercmp") - (unpack "fsom-src" "vcflib/fsom") - (unpack "intervaltree-src" "vcflib/intervaltree") - (unpack "multichoose-src" "vcflib/multichoose") - (unpack "smithwaterman-src" "vcflib/smithwaterman") - (unpack "tabixpp-src" "vcflib/tabixpp") - (unpack "test-simple-bash-src" "test/test-simple-bash") - (unpack "bash-tap-src" "test/bash-tap"))))) - (add-after 'unpack-submodule-sources 'fix-makefile - (lambda* (#:key inputs #:allow-other-keys) - ;; We don't have the .git folder to get the version tag from. - ;; For this checkout of the code, it's v1.0.0. - (substitute* '("vcflib/Makefile") - (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (and - ;; Compile Bamtools before compiling the main project. - (with-directory-excursion "bamtools" - (system* "mkdir" "build") - (with-directory-excursion "build" - (and (zero? (system* "cmake" "../")) - (zero? (system* "make"))))) - ;; Compile vcflib before we compiling the main project. - (with-directory-excursion "vcflib" - (with-directory-excursion "tabixpp" - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (zero? - (system* "make" "HTS_HEADERS=" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) - (zero? (system* "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))) - (with-directory-excursion "src" - (zero? (system* "make")))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "bin/freebayes" bin) - (install-file "bin/bamleftalign" bin)))) - ;; There are three tests that fail. All because of the -P - ;; (--perl-regexp) option in grep, which is not compiled into the - ;; version of grep in Guix. - (replace 'check - (lambda* (#:key inputs #:allow-other-keys) - (system* "make" "test")))))) - (home-page "https://github.com/ekg/freebayes") - (synopsis "Haplotype-based variant detector") - (description "FreeBayes is a Bayesian genetic variant detector designed to -find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), -indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and -complex events (composite insertion and substitution events) smaller than the -length of a short-read sequencing alignment.") - (license license:expat)))) - (define-public plink2 (package (name "plink2") @@ -805,146 +288,18 @@ integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.") (license license:gpl3+)))) - -(define-public vcflib ; duplicate? See above - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) - (package - (name "vcflib") - (version (string-append "v1.0.2-" (string-take commit 7))) - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/vcflib/vcflib/archive/" - "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz")) - (file-name "vcflib-5ac0913.tar.gz") - (sha256 - (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8")))) - (build-system gnu-build-system) - (native-inputs - `(("htslib" ,htslib) - ("zlib" ,zlib) - ("python" ,python-2) - ("perl" ,perl) - ("tabixpp-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/tabixpp/archive/" - "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz")) - (file-name "tabixpp-src.tar.gz") - (sha256 - (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))) - ("intervaltree-src" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/ekg/intervaltree/archive/" - "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) - (file-name "intervaltree-src.tar.gz") - (sha256 - (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) - ("smithwaterman-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/smithwaterman/archive/" - "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz")) - (file-name "smithwaterman-src.tar.gz") - (sha256 - (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) - ("multichoose-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/multichoose/archive/" - "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz")) - (file-name "multichoose-src.tar.gz") - (sha256 - (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i")))) - ("fsom-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/fsom/archive/" - "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz")) - (file-name "fsom-src.tar.gz") - (sha256 - (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3")))) - ("filevercmp-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/filevercmp/archive/" - "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz")) - (file-name "filevercmp-src.tar.gz") - (sha256 - (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) - ("fastahack-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/fastahack/archive/" - "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz")) - (file-name "fastahack-src.tar.gz") - (sha256 - (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))))) - (arguments - `(#:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (zero? (system* "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "intervaltree-src" "intervaltree") - (unpack "fastahack-src" "fastahack") - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose") - (unpack "smithwaterman-src" "smithwaterman") - (unpack "tabixpp-src" "tabixpp"))))) - (add-after 'unpack-submodule-sources 'fix-makefile - (lambda* (#:key inputs #:allow-other-keys) - (substitute* '("Makefile") - (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) - (replace - 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "tabixpp" - (zero? (system* "make"))) - (zero? (system* "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (lib (string-append (assoc-ref outputs "out") "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - (install-file "libvcflib.a" lib))))))) - (home-page "https://github.com/vcflib/vcflib/") - (synopsis "Library for parsing and manipulating VCF files") - (description "Vcflib provides methods to manipulate and interpret -sequence variation as it can be described by VCF. It is both an API for parsing -and operating on records of genomic variation as it can be described by the VCF -format, and a collection of command-line utilities for executing complex -manipulations on VCF files.") - (license license:expat)))) - (define-public pindel (package (name "pindel") (version "0.2.5b8") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/genome/pindel/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/genome/pindel.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "06bsf0psxwf7h5p3j97xkh9k5qrwhxh6xn942y1j1m2inyhgs8bz")))) + (base32 "16a32fbgv1n58nfcxa1nyphrdrad80sgpinfa9p028n6plwycpww")))) (build-system gnu-build-system) (inputs `(("samtools" ,samtools) @@ -968,7 +323,7 @@ manipulations on VCF files.") ;; The second run actually compiles the program. Now Makefile.local ;; is available, and we should treat an exiting make with an error as ;; a true error. - (zero? (system* "make")))) + (invoke "make"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) @@ -979,13 +334,11 @@ manipulations on VCF files.") ;; There are multiple test targets, so in order to run all ;; tests, we must run the separate make targets. (replace 'check - (lambda* (#:key inputs #:allow-other-keys) - (and - (zero? (system* "make" "acceptance-tests")) - (zero? (system* "make" "coverage-tests")) - (zero? (system* "make" "cppcheck")) - (zero? (system* "make" "functional-tests")) - (zero? (system* "make" "regression-tests")))))))) + (lambda _ + (for-each (lambda (target) + (invoke "make" target)) + '("acceptance-tests" "coverage-tests" "cppcheck" + "functional-tests" "regression-tests"))))))) (home-page "https://github.com/genome/pindel") (synopsis "Structural variants detector for next-gen sequencing data") (description "Pindel can detect breakpoints of large deletions, medium sized @@ -1008,45 +361,251 @@ reads.") (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8")))) (build-system ant-build-system) (arguments - `(#:phases + `(#:tests? #f ; build.xml does not exist + #:phases (modify-phases %standard-phases (replace 'unpack (lambda _ (mkdir "source") (chdir "source") - (and - ;; Unpack the Java archive containing the source files. - (zero? (system* "jar" "xf" (assoc-ref %build-inputs "source"))) - ;; Remove existing compiled output. - (with-directory-excursion "net/sf/varscan/" - (for-each (lambda (file) - (unless (string= (string-take-right file 5) ".java") - (zero? (system* "rm" file)))) - (find-files "." #:directories? #f)))))) + ;; Unpack the Java archive containing the source files. + (invoke "jar" "xf" (assoc-ref %build-inputs "source")) + ;; Remove existing compiled output. + (with-directory-excursion "net/sf/varscan/" + (for-each (lambda (file) + (delete-file file)) + (find-files "." "^.java$" #:directories? #f))) + #t)) (replace 'build (lambda _ - (let ((classes '())) - (and - ;; Compile the source files. - (with-directory-excursion "net/sf/varscan/" - (for-each (lambda (file) - (when (string= (string-take-right file 5) ".java") - (zero? (system* "javac" file)) - (cons )) - (find-files "." #:directories? #f))) - ;; Construct the new Java archive. - (zero? (system* "jar" "cfm" "varscan-2.4.1.jar" - "META-INF/MANIFEST.MF" - "net/sf/varscan/*.java"))))))) + ;; Compile the source files. + (with-directory-excursion "net/sf/varscan/" + (for-each (lambda (file) + (invoke "javac" file)) + (find-files "." ".java$" #:directories? #f))) + ;; Construct the new Java archive. + (apply invoke "jar" "cfm" + (string-append "varscan-" ,version ".jar") + "META-INF/MANIFEST.MF" + (find-files "net/sf/varscan" ".java$")))) (replace 'install - (lambda _ - (let ((out (string-append (assoc-ref %outputs "out") + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (string-append (assoc-ref outputs "out") "/share/java/varscan/"))) - (mkdir-p out) - (install-file "varscan-2.4.1.jar" out))))))) - (home-page "http://dkoboldt.github.io/varscan/") + (install-file (string-append "varscan-" ,version ".jar") out)) + #t))))) + (home-page "https://dkoboldt.github.io/varscan/") (synopsis "Variant detection in massively parallel sequencing data") - (description "") + (description "Variant detection in massively parallel sequencing data.") ;; Free for non-commercial use by academic, government, and ;; non-profit/not-for-profit institutions (license license:non-copyleft))) + +(define-public edirect-gn + (package + (inherit edirect) + (name "edirect-gn") + (arguments + (substitute-keyword-arguments (package-arguments edirect) + ((#:phases phases) + `(modify-phases ,phases + ; (replace 'build + ; (lambda* (#:key inputs #:allow-other-keys) + ; (let ((go (string-append (assoc-ref inputs "go") "/bin/go"))) + ; (invoke go "build" "xtract.go")))) + (add-after 'unpack 'patch-programs + (lambda* (#:key inputs #:allow-other-keys) + (let ((gzip (assoc-ref inputs "gzip"))) + (substitute* '("index-bioc" + "pm-index" + "pm-invert" + "pm-stash" + "rchive.go" + "run-ncbi-converter") + (("gunzip") (string-append gzip "/bin/gunzip"))) + (substitute* (find-files "." "^e") + (("exec perl") "exec")) + (substitute* '("xtract" "rchive") + ;; or add current directory to PATH + ((".*PATH.*") ""))) + #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (xtract.linux (assoc-ref inputs "xtract.Linux")) + (rchive.linux (assoc-ref inputs "rchive.Linux"))) + (for-each + (lambda (file) + (install-file file bin)) + '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed" + "edirect.pl" "efetch" "epost" "fetch-pubmed" "ftp-cp" + "ftp-ls" "has-asp" "pm-prepare" "pm-refresh" "pm-stash" + "rchive" "xtract")) + (copy-file xtract.linux (string-append bin "/xtract.Linux")) + (copy-file rchive.linux (string-append bin "/rchive.Linux")) + (chmod (string-append bin "/xtract.Linux") #o555) + (chmod (string-append bin "/rchive.Linux") #o555)) + #t)) + (replace 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure 'edirect.pl' finds all perl inputs at runtime. + (let ((out (assoc-ref outputs "out")) + (path (getenv "PERL5LIB"))) + (for-each + (lambda (file) + (wrap-program (string-append out "/bin/" file) + `("PERL5LIB" ":" prefix (,path)))) + '("edirect.pl" "asp-ls" "ftp-cp" "ftp-ls"))) + #t)))))) + (inputs + `(("gzip" ,gzip) + ,@(package-inputs edirect))) + (native-inputs + `( + ;("go" ,go) + ("xtract.Linux" + ,(origin + (method url-fetch) + (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" + "versions/" (package-version edirect) "/xtract.Linux")) + (file-name (string-append "xtract.Linux-" (package-version edirect))) + (sha256 + (base32 + "0fx6arpn38spnwszmvkkpa3498qrrlglg2l9jw91icgqbyjjq9wq")))) + ("rchive.Linux" + ,(origin + (method url-fetch) + (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" + "versions/" (package-version edirect) "/rchive.Linux")) + (file-name (string-append "rchive.Linux-" (package-version edirect))) + (sha256 + (base32 + "134y0zprplqlplc6qmcjb97411bxkwghmq3z0qjgh0dgdbzjq1w3")))))) + (native-search-paths + ;; Ideally this should be set for LWP somewhere. + (list (search-path-specification + (variable "PERL_LWP_SSL_CA_FILE") + (file-type 'regular) + (separator #f) + (files '("/etc/ssl/certs/ca-certificates.crt"))))) + ;; Due to the precompiled binaries we download: + (supported-systems '("x86_64-linux")))) + +;; TODO: Unbundle zlib, bamtools, tclap +(define-public sniffles + (package + (name "sniffles") + (version "1.0.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fritzsedlazeck/Sniffles.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rkwqn1ycckfzrg2wdid4cqahq8q2jmmgi7vvl8qxgpsihqfbq0j")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file (string-append "../source/bin/sniffles-core-" + ,version "/sniffles") + (string-append out "/bin"))) + #t)) + (replace 'check + (lambda _ + (with-directory-excursion "../source/test_set" + (for-each make-file-writable (find-files ".")) + (invoke (string-append "../bin/sniffles-core-" ,version "/sniffles") + "-m" "reads_region.bam" "-v" "test.vcf"))))))) + (native-inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/fritzsedlazeck/Sniffles") + (synopsis "Structural variation caller using third generation sequencing") + (description + "Sniffles is a structural variation caller using third generation sequencing +(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence +from split-read alignments, high-mismatch regions, and coverage analysis.") + (license license:expat))) + +;; TODO: Unbundle Complete-Striped-Smith-Waterman-Library +(define-public ngmlr + (package + (name "ngmlr") + (version "0.2.7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/philres/ngmlr.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0lmsy8w0kxbyfnrln7lxgmnx3d82sv2b20n2yw5742rvfhq1v31n")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'patch-more-tools + (lambda* (#:key inputs #:allow-other-keys) + (let ((bed (assoc-ref inputs "bedtools")) + (sam (assoc-ref inputs "samtools"))) + (substitute* (find-files "test" "\\.sh$") + (("bedtools") (string-append bed "/bin/bedtools")) + (("samtools") (string-append sam "/bin/samtools"))) + #t))) + (replace 'check + (lambda _ + (with-directory-excursion "../source" + (invoke "sh" "test/test_travis.sh"))))))) + (native-inputs + `(("bedtools" ,bedtools) + ("samtools" ,samtools))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/philres/ngmlr") + (synopsis "Long-read mapper designed to align PacBio or Oxford Nanopore") + (description + "NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore +(standard and ultra-long) to a reference genome with a focus on reads that span +structural variations.") + (license license:expat))) + +(define-public svim + (package + (name "svim") + (version "1.2.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/eldariont/svim.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08j02in9jbq41b67dna1apnc3y30i37v44d1khml1xlx0iga720s")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "python3" "-m" "unittest" "discover" "-s" "src/")))))) + (propagated-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy) + ("minimap2" ,minimap2) + ("ngmlr" ,ngmlr) + ("samtools" ,samtools))) + (home-page "https://github.com/eldariont/svim") + (synopsis "Structural Variant Identification Method using Long Reads") + (description + "SVIM (pronounced SWIM) is a structural variant caller for long reads. It +is able to detect, classify and genotype five different classes of structural +variants. Unlike existing methods, SVIM integrates information from across the +genome to precisely distinguish similar events, such as tandem and interspersed +duplications and novel element insertions.") + (license license:gpl3))) diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm index 2c34256..7b6662c 100644 --- a/gn/packages/bnw.scm +++ b/gn/packages/bnw.scm @@ -2,12 +2,12 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix git-download) - #:use-module (guix build-system trivial) - #:use-module (gnu packages bash) + #:use-module (guix build-system gnu) #:use-module (gn packages graphviz) #:use-module (gn packages javascript) #:use-module (gn packages maths) #:use-module (gnu packages python) + #:use-module (gnu packages statistics) #:use-module (gn packages web)) (define-public bnw @@ -25,44 +25,45 @@ (sha256 (base32 "10qwykp2zcyxih6a52icvy30ps69qk4v3jgirmdpw1l15zi4p2wq")))) - (build-system trivial-build-system) + (build-system gnu-build-system) (arguments - `(#:modules ((guix build utils)) - #:builder - (begin - (use-modules (guix build utils)) - (let* ((out (assoc-ref %outputs "out")) - (source (assoc-ref %build-inputs "source")) - (bash (assoc-ref %build-inputs "bash")) - (graphviz (assoc-ref %build-inputs "graphviz")) - (octave (assoc-ref %build-inputs "octave")) - (python (assoc-ref %build-inputs "python")) - (jquery (assoc-ref %build-inputs "jquery")) - (awesome (assoc-ref %build-inputs "awesome")) - (cyto (assoc-ref %build-inputs "cytoscape")) - (cyto2 (assoc-ref %build-inputs "cytoscape-2")) - (cs-dagre (assoc-ref %build-inputs "cyto-dagre")) - (d3js (assoc-ref %build-inputs "d3js")) - (d3js-multi (assoc-ref %build-inputs "d3js-multi")) - (dagre (assoc-ref %build-inputs "dagre")) - (lodash (assoc-ref %build-inputs "lodash")) - (canvas-toblob (assoc-ref %build-inputs "canvas-toblob")) - (filesaver (assoc-ref %build-inputs "filesaver")) - (panzoom (assoc-ref %build-inputs "panzoom")) - (js-path "/share/genenetwork2/javascript/")) - (copy-recursively source out) - (for-each (lambda (file) - (patch-shebang file - (list (string-append bash "/bin") - (string-append octave "/bin") - (string-append python "/bin")))) - (find-files out ".*")) - (with-directory-excursion out + `(#:tests? #f ; no test suite + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'patch-source-shebangs 'patch--more-shebangs + (lambda* (#:key inputs #:allow-other-keys) + (let* ((bash (assoc-ref inputs "bash")) + (graphviz (assoc-ref inputs "graphviz")) + (octave (assoc-ref inputs "octave")) + (python (assoc-ref inputs "python")) + (rmath (assoc-ref inputs "rmath")) + (jquery (assoc-ref inputs "jquery")) + (awesome (assoc-ref inputs "awesome")) + (cyto (assoc-ref inputs "cytoscape")) + (cyto2 (assoc-ref inputs "cytoscape-2")) + (cs-dagre (assoc-ref inputs "cyto-dagre")) + (d3js (assoc-ref inputs "d3js")) + (d3js-multi (assoc-ref inputs "d3js-multi")) + (dagre (assoc-ref inputs "dagre")) + (lodash (assoc-ref inputs "lodash")) + (canvas-toblob (assoc-ref inputs "canvas-toblob")) + (filesaver (assoc-ref inputs "filesaver")) + (panzoom (assoc-ref inputs "panzoom")) + (js-path "/share/genenetwork2/javascript/")) + (for-each (lambda (file) + (patch-shebang file + (list (string-append bash "/bin") + (string-append octave "/bin") + (string-append python "/bin")))) + (find-files "." ".*")) (substitute* (append '("home.php") (find-files "sourcecodes" ".php") (find-files "sourcecodes/run_scripts" ".*")) (("/usr/bin/dot") (string-append graphviz "/bin/dot"))) + (substitute* "sourcecodes/build.sh" + (("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so"))) (substitute* "sourcecodes/layout_cyto.php" (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js") (string-append cyto js-path "cytoscape/cytoscape.min.js")) @@ -91,13 +92,26 @@ (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js") (string-append canvas-toblob js-path "canvas-toBlob/canvas-toBlob.js")) (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js") - (string-append filesaver js-path "filesaver/filesaver.js")))))))) - (native-inputs `(("source" ,source))) + (string-append filesaver js-path "filesaver/filesaver.js")))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (delete-file "sourcecodes/localscore/libRmath.so") + (copy-recursively "." out)) + #t)) + (replace 'build + (lambda _ + (with-directory-excursion "sourcecodes" + (substitute* "build.sh" + (("./localscore") "localscore")) + (chmod "k-best/src/buildk_poster.sh" #o755) + (invoke "sh" "build.sh"))))))) (inputs - `(("bash" ,bash-minimal) - ("graphviz" ,graphviz-2.26) + `(("graphviz" ,graphviz-2.26) ("octave" ,octave-3.4.3) ("python" ,python-2) + ("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version? ("jquery" ,web-jquery) ("awesome" ,web-font-awesome) ("cytoscape" ,javascript-cytoscape) diff --git a/gn/packages/clBLAS.scm b/gn/packages/clBLAS.scm deleted file mode 100644 index 1c838fb..0000000 --- a/gn/packages/clBLAS.scm +++ /dev/null @@ -1,162 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages clBLAS) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system gnu) - #:use-module (guix build-system cmake) - #:use-module (guix packages) - #:use-module (gnu packages algebra) - #:use-module (gnu packages autotools) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages base) - #:use-module (gnu packages curl) - #:use-module (gnu packages compression) - #:use-module (gnu packages gawk) - #:use-module (gnu packages cmake) - #:use-module (gnu packages boost) - #:use-module (gnu packages glib) - #:use-module (gnu packages image) - #:use-module (gnu packages video) - #:use-module (gnu packages textutils) - #:use-module (gnu packages gl) - #:use-module (gnu packages gcc) - #:use-module (gnu packages gnupg) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages maths) - #:use-module (gnu packages mpi) - #:use-module (gnu packages ruby) - #:use-module (gnu packages web) - #:use-module (gnu packages python) - #:use-module (gnu packages xorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) - -(define-public clBLAS - (package - (name "clBLAS") - (version "v2.10") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/clMathLibraries/clBLAS/archive/" - version ".tar.gz")) - (sha256 - (base32 - "0adlb02lqzrklfybhnv4n0p37mvkvdi3vqiwa05x2mv05ywnr93j")))) - (build-system cmake-build-system) - (arguments `(#:tests? #f - #:configure-flags '("../clBLAS-2.10/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release" "-DBUILD_TEST=OFF"))) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("gfortran" ,gfortran) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("boost" ,boost) - ("enca" ,enca) - ("eudev" ,eudev) - ("fftw-openmpi" ,fftw-openmpi) - ("glew" ,glew) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("openmpi" ,openmpi) - ("ocl-icd" ,ocl-icd) - ("opencl-headers" ,opencl-headers) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) - ("python" ,python-2))) - (home-page "http://www.glfw.org/") - (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) - -(define-public ocl-icd - (package - (name "ocl-icd") - (version "2.2.9") - (source (origin - (method url-fetch) - (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) - (inputs `(("zip" ,zip) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("ruby" ,ruby) - ("libtool" ,libtool) - ("opencl-headers" ,opencl-headers) - ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") - (description "OpenCL implementations are provided as ICD (Installable Client Driver). - An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. - This free ICD Loader can load any (free or non free) ICD") - (license (list license:gpl2 license:ruby)))) - -(define-public opencl-headers -(let ((commit "c1770dc")) - (package - (name "opencl-headers") - (version (string-append "2.1-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/KhronosGroup/OpenCL-Headers.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck")))) - (propagated-inputs '()) - (inputs '()) - (native-inputs '()) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (string-append - (assoc-ref outputs "out") - "/include/CL"))))))) - (synopsis "The Khronos OpenCL headers") - (description "This package provides the Khronos OpenCL headers") - (home-page "https://www.khronos.org/registry/cl/") - (license (list license:gpl2))))) diff --git a/gn/packages/clFFT.scm b/gn/packages/clFFT.scm deleted file mode 100644 index fb42c85..0000000 --- a/gn/packages/clFFT.scm +++ /dev/null @@ -1,158 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages clFFT) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system gnu) - #:use-module (guix build-system cmake) - #:use-module (guix packages) - #:use-module (gnu packages algebra) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages base) - #:use-module (gnu packages autotools) - #:use-module (gnu packages compression) - #:use-module (gnu packages curl) - #:use-module (gnu packages gawk) - #:use-module (gnu packages cmake) - #:use-module (gnu packages boost) - #:use-module (gnu packages glib) - #:use-module (gnu packages image) - #:use-module (gnu packages video) - #:use-module (gnu packages textutils) - #:use-module (gnu packages gl) - #:use-module (gnu packages gnupg) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages maths) - #:use-module (gnu packages mpi) - #:use-module (gnu packages ruby) - #:use-module (gnu packages web) - #:use-module (gnu packages python) - #:use-module (gnu packages xorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) - -(define-public clFFT - (package - (name "clFFT") - (version "v2.10.1") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/clMathLibraries/clFFT/archive/" - version ".tar.gz")) - (sha256 - (base32 - "19hrk1lf06kch8x9dpbdj0waycn2mldrmj2y4vzi7zn2gdfw6g73")))) - (build-system cmake-build-system) - (arguments `(#:configure-flags '("../clFFT-2.10.1/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("enca" ,enca) - ("eudev" ,eudev) - ("fftw-openmpi" ,fftw-openmpi) - ("glew" ,glew) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("openmpi" ,openmpi) - ("ocl-icd" ,ocl-icd) - ("opencl-headers" ,opencl-headers) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) - ("python" ,python-2))) - (home-page "http://www.glfw.org/") - (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) - -(define-public ocl-icd - (package - (name "ocl-icd") - (version "2.2.9") - (source (origin - (method url-fetch) - (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) - (inputs `(("zip" ,zip) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("ruby" ,ruby) - ("libtool" ,libtool) - ("opencl-headers" ,opencl-headers) - ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") - (description "OpenCL implementations are provided as ICD (Installable Client Driver). - An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. - This free ICD Loader can load any (free or non free) ICD") - (license (list license:gpl2 license:ruby)))) - -(define-public opencl-headers -(let ((commit "c1770dc")) - (package - (name "opencl-headers") - (version (string-append "2.1-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/KhronosGroup/OpenCL-Headers.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck")))) - (propagated-inputs '()) - (inputs '()) - (native-inputs '()) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (string-append - (assoc-ref outputs "out") - "/include/CL"))))))) - (synopsis "The Khronos OpenCL headers") - (description "This package provides the Khronos OpenCL headers") - (home-page "https://www.khronos.org/registry/cl/") - (license (list license:gpl2))))) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index abc69d9..9aaf002 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -5,10 +5,47 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system cargo) - #:use-module (gnu packages crates-io)) + #:use-module (gnu packages compression) + #:use-module (gnu packages crates-io) + #:use-module (gnu packages gcc) + #:use-module (gnu packages jemalloc) + #:use-module (gnu packages llvm) + #:use-module (gnu packages maths) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages ssh) + #:use-module (gnu packages tls) + #:use-module (gnu packages version-control)) ;; Please keep these packages sorted alphabetically +(define-public rust-accelerate-src + (package + (name "rust-accelerate-src") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "accelerate-src" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "17fiqyq7f9k41pbsyrvk9pxyx9z6fw399wq036cvwkbmb14xcpj1")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-libc" ,rust-libc)) + #:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'build)))) ; only available for macOS + (home-page "https://github.com/blas-lapack-rs/accelerate-src") + (synopsis + "The package provides a source of BLAS and LAPACK via the Accelerate framework.") + (description + "The package provides a source of BLAS and LAPACK via the Accelerate framework.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-addr2line (package (name "rust-addr2line") @@ -47,10 +84,65 @@ (license (list license:asl2.0 license:expat)))) +(define-public rust-addr2line-0.9 + (package + (inherit rust-addr2line) + (name "rust-addr2line") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "addr2line" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "17rlf04nx3g3rcy661v24ksnmpk6vqn680g5b5sp8lk20iih2xnx")))) + (arguments + `(#:cargo-inputs + (("rust-cpp-demangle" ,rust-cpp-demangle) + ("rust-fallible-iterator" + ,rust-fallible-iterator) + ("rust-gimli" ,rust-gimli) + ("rust-intervaltree" ,rust-intervaltree) + ("rust-lazycell" ,rust-lazycell) + ("rust-object" ,rust-object) + ("rust-rustc-demangle" ,rust-rustc-demangle) + ("rust-smallvec" ,rust-smallvec)) + #:cargo-development-inputs + (("rust-backtrace" ,rust-backtrace) + ("rust-clap" ,rust-clap) + ("rust-findshlibs" ,rust-findshlibs) + ("rust-memmap" ,rust-memmap) + ("rust-rustc-test" ,rust-rustc-test)))))) + +(define-public rust-adler32 + (package + (name "rust-adler32") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "adler32" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0p7fxlnks9l7p7rwfqi7aqgnk2bps5zc0rjiw00mdw19nnbjjlky")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs (("rust-rand" ,rust-rand-0.4)))) + (home-page "https://github.com/remram44/adler32-rs") + (synopsis + "It is an implementation of the Adler32 rolling hash algorithm in the Rust programming language.") + (description + "It is an implementation of the Adler32 rolling hash algorithm in the Rust programming language.") + (license (list license:bsd-3 + license:zlib)))) + (define-public rust-afl (package (name "rust-afl") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) @@ -58,7 +150,7 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0g2chc18ji7qxi0d03n2ai140qdcww958v5si6rcjnnhmri1vyfb")))) + "14k6hnwzqn7rrs0hs87vcfqj4334k9wff38d15378frlxpviaard")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -79,7 +171,7 @@ (define-public rust-aho-corasick (package (name "rust-aho-corasick") - (version "0.7.4") + (version "0.7.6") (source (origin (method url-fetch) @@ -87,7 +179,7 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "10p2yl9fz7a4zwc4kj4zpk0wcz64n4m5l0ng6zsa6zkxrcfamdrn")))) + "0b8dh20fhdc59dhhnfi89n2bi80a8zbagzd5c122hf1vv2amxysq")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -95,12 +187,37 @@ #:cargo-development-inputs (("rust-doc-comment" ,rust-doc-comment)))) (home-page "https://github.com/BurntSushi/aho-corasick") - (synopsis "Fast multiple substring searching.") + (synopsis "Fast multiple substring searching") (description "Fast multiple substring searching.") (license (list license:unlicense license:expat)))) +(define-public rust-aho-corasick-0.6 + (package + (inherit rust-aho-corasick) + (name "rust-aho-corasick") + (version "0.6.10") + (source + (origin + (method url-fetch) + (uri (crate-uri "aho-corasick" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "19f8v503ibvlyr824g5ynicrh1lsmp2i0zmpszr8lqay0qw3vkl1")))) + (arguments + `(#:cargo-inputs + (("rust-memchr" ,rust-memchr)) + #:cargo-development-inputs + (("rust-csv" ,rust-csv) + ("rust-docopt" ,rust-docopt) + ("rust-memmap" ,rust-memmap) + ("rust-quickcheck" ,rust-quickcheck) + ("rust-rand" ,rust-rand-0.5) + ("rust-serde" ,rust-serde) + ("rust-serde-derive" ,rust-serde-derive)))))) + (define-public rust-ansi-term (package (name "rust-ansi-term") @@ -147,6 +264,40 @@ `(#:cargo-inputs (("rust-winapi" ,rust-winapi)))))) +(define-public rust-argon2rs + (package + (name "rust-argon2rs") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "argon2rs" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "14mkgkrjd4b4zy92pflz6yb4j1wn2chbd8jczxknxbkdm2vb0rrz")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-blake2-rfc" ,rust-blake2-rfc) + ("rust-scoped-threadpool" ,rust-scoped-threadpool)) + #:cargo-development-inputs + (("rust-cargon" ,rust-cargon)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-Cargo-toml + (lambda _ + (substitute* "Cargo.toml" + (("path = \"benches/cargon\",") "")) + #t))))) + (home-page "https://github.com/bryant/argon2rs") + (synopsis "Rust library for the Argon2 hashing algorithm") + (description + "This is a purely Rust-based library that provides both variants of the +state-of-the-art Argon2 hashing algorithm, suitable for password hashing and +password-based key derivation.") + (license license:expat))) + (define-public rust-arrayvec (package (name "rust-arrayvec") @@ -185,19 +336,17 @@ (origin (method url-fetch) (uri (crate-uri "ascii" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1mn5az4hkxgjhwy157pr1nrfdb3qjpw8jw8v91m2i8wg59b21qwi")))) + (base32 + "1mn5az4hkxgjhwy157pr1nrfdb3qjpw8jw8v91m2i8wg59b21qwi")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-quickcheck" ,rust-quickcheck) - ("rust-serde" ,rust-serde) - ("rust-serde-test" ,rust-serde-test)))) - (home-page - "https://github.com/tomprogrammer/rust-ascii") + `(#:cargo-inputs + (("rust-quickcheck" ,rust-quickcheck-0.6) + ("rust-serde" ,rust-serde) + ("rust-serde-test" ,rust-serde-test)))) + (home-page "https://github.com/tomprogrammer/rust-ascii") (synopsis "ASCII-only equivalents to `char`, `str` and `String`.") (description @@ -236,56 +385,10 @@ (license (list license:asl2.0 license:expat)))) -(define-public rust-atty - (package - (name "rust-atty") - (version "0.2.13") - (source - (origin - (method url-fetch) - (uri (crate-uri "atty" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "140sswp1bwqwc4zk80bxkbnfb3g936hgrb77g9g0k1zcld3wc0qq")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-libc" ,rust-libc) - ("rust-winapi" ,rust-winapi)))) - (home-page "https://github.com/softprops/atty") - (synopsis "A simple interface for querying atty") - (description - "This package provides a simple interface for querying atty") - (license license:expat))) - -(define-public rust-autocfg ; guix upstreamable - (package - (name "rust-autocfg") - (version "0.1.5") - (source - (origin - (method url-fetch) - (uri (crate-uri "autocfg" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0asl6fnc35yk5l2rxwhp25v128jgm45dp754h9z8x51b6n90w4r2")))) - (build-system cargo-build-system) - (home-page "https://github.com/cuviper/autocfg") - (synopsis "Automatic cfg for Rust compiler features") - (description "Rust library for build scripts to automatically configure -code based on compiler support. Code snippets are dynamically tested to see -if the @code{rustc} will accept them, rather than hard-coding specific version -support.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-automod (package (name "rust-automod") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) @@ -294,7 +397,7 @@ support.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0pld582piq2d55z0j96zcs8izw3ml46f8h9y7sdyxg093yfvxl2h")))) + "17am5i7z7jpsrq9bm0wyhf4q9850g2kqvzl3ik900x5gc7brwv2a")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -311,7 +414,7 @@ support.") (define-public rust-average (package (name "rust-average") - (version "0.10.1") + (version "0.10.2") (source (origin (method url-fetch) @@ -320,7 +423,7 @@ support.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "077wbjzn2hwdjnglp8pjvirvsjgfgbgnlirwh5g2hk14xqx7f57l")))) + "16ib3vlfp3akpflha1m6598x3jfrgrh9qgrf9vvv11rfqirp22dx")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -377,40 +480,35 @@ support.") (define-public rust-backtrace (package (name "rust-backtrace") - (version "0.3.33") + (version "0.3.35") (source (origin (method url-fetch) (uri (crate-uri "backtrace" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1iiinw3c494lz8xb823ccl9zwifka9zsg44734wsd3xgr6dngyw8")))) + (base32 + "0mfwbb6832rh1za304w8x37bvs9fjbybpmmz0iksqfzsaf108w8k")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-addr2line" ,rust-addr2line) - ("rust-backtrace-sys" ,rust-backtrace-sys) - ("rust-cfg-if" ,rust-cfg-if) - ("rust-compiler-builtins" - ,rust-compiler-builtins) - ("rust-cpp-demangle" ,rust-cpp-demangle) - ("rust-findshlibs" ,rust-findshlibs) - ("rust-goblin" ,rust-goblin) - ("rust-goblin" ,rust-goblin) - ("rust-goblin" ,rust-goblin) - ("rust-goblin" ,rust-goblin) - ("rust-libc" ,rust-libc) - ("rust-memmap" ,rust-memmap) - ("rust-rustc-demangle" ,rust-rustc-demangle) - ("rust-rustc-serialize" ,rust-rustc-serialize) - ("rust-rustc-std-workspace-core" - ,rust-rustc-std-workspace-core) - ("rust-serde" ,rust-serde) - ("rust-winapi" ,rust-winapi)))) - (home-page - "https://github.com/rust-lang/backtrace-rs") + `(#:cargo-inputs + (("rust-addr2line" ,rust-addr2line-0.9) + ("rust-backtrace-sys" ,rust-backtrace-sys) + ("rust-cfg-if" ,rust-cfg-if) + ("rust-compiler-builtins" + ,rust-compiler-builtins) + ("rust-cpp-demangle" ,rust-cpp-demangle) + ("rust-findshlibs" ,rust-findshlibs) + ("rust-goblin" ,rust-goblin) + ("rust-libc" ,rust-libc) + ("rust-memmap" ,rust-memmap) + ("rust-rustc-demangle" ,rust-rustc-demangle) + ("rust-rustc-serialize" ,rust-rustc-serialize) + ("rust-rustc-std-workspace-core" + ,rust-rustc-std-workspace-core) + ("rust-serde" ,rust-serde) + ("rust-winapi" ,rust-winapi)))) + (home-page "https://github.com/rust-lang/backtrace-rs") (synopsis "A library to acquire a stack trace (backtrace) at runtime in a Rust program.") (description @@ -442,7 +540,7 @@ support.") #:cargo-development-inputs (("rust-cc" ,rust-cc)))) (home-page - "https://github.com/alexcrichton/backtrace-rs") + "https://github.com/rust-lang/backtrace-rs") (synopsis "Bindings to the libbacktrace gcc library") (description @@ -458,17 +556,16 @@ support.") (origin (method url-fetch) (uri (crate-uri "base-x" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0hv4y5cdhv6bk0ghk2434clw8v4mmk5cc9lsh6qrpri92zlfmx3n")))) + (base32 + "0hv4y5cdhv6bk0ghk2434clw8v4mmk5cc9lsh6qrpri92zlfmx3n")))) (build-system cargo-build-system) (arguments - `(#:cargo-development-inputs - (("rust-bencher" ,rust-bencher) - ("rust-json" ,rust-json) - ("rust-rand" ,rust-rand)))) + `(#:cargo-development-inputs + (("rust-bencher" ,rust-bencher) + ("rust-json" ,rust-json) + ("rust-rand" ,rust-rand-0.3)))) (home-page "https://github.com/OrKoN/base-x-rs") (synopsis "Encode/decode any base") (description "Encode/decode any base") @@ -495,7 +592,7 @@ support.") (("rust-criterion" ,rust-criterion) ("rust-rand" ,rust-rand)))) (home-page - "https://github.com/alicemaz/rust-base64") + "https://github.com/marshallpierce/rust-base64") (synopsis "encodes and decodes base64 as bytes or utf8") (description @@ -503,27 +600,25 @@ support.") (license (list license:asl2.0 license:expat)))) -(define-public rust-bencher ; guix upstreamable +(define-public rust-base64-0.9 (package - (name "rust-bencher") - (version "0.1.5") + (inherit rust-base64) + (name "rust-base64") + (version "0.9.3") (source (origin (method url-fetch) - (uri (crate-uri "bencher" version)) + (uri (crate-uri "base64" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1x8p2xblgqssay8cdykp5pkfc0np0jk5bs5cx4f5av097aav9zbx")))) - (build-system cargo-build-system) - (home-page "https://github.com/bluss/bencher/") - (synopsis "Port of the libtest benchmark runner to Rust stable") - (description "This package provides a port of the libtest (unstable Rust) -benchmark runner to Rust stable releases. Supports running benchmarks and -filtering based on the name. Benchmark execution works exactly the same way -and no more (caveat: black_box is still missing!).") - (license (list license:asl2.0 - license:expat)))) + "0hs62r35bgxslawyrn1vp9rmvrkkm76fqv0vqcwd048vs876r7a8")))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder)) + #:cargo-development-inputs + (("rust-safemem" ,rust-safemem) + ("rust-rand" ,rust-rand-0.4)))))) (define-public rust-bincode (package @@ -547,7 +642,7 @@ and no more (caveat: black_box is still missing!).") #:cargo-development-inputs (("rust-serde-bytes" ,rust-serde-bytes) ("rust-serde-derive" ,rust-serde-derive)))) - (home-page "https://github.com/TyOverby/bincode") + (home-page "https://github.com/servo/bincode") (synopsis "A binary serialization / deserialization strategy that uses Serde for transforming structs into bytes and vice versa!") (description @@ -557,7 +652,7 @@ and no more (caveat: black_box is still missing!).") (define-public rust-bindgen (package (name "rust-bindgen") - (version "0.50.0") + (version "0.51.0") (source (origin (method url-fetch) @@ -566,7 +661,7 @@ and no more (caveat: black_box is still missing!).") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1k4n1d002vrfn1mlpww3ib7f275yn4rpxfwkqpr9bym27zg17ab5")))) + "1l4sifn771v83q8wafyvmsrphjni8i8wvgdlddd09v35f3fhq9qq")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -589,7 +684,17 @@ and no more (caveat: black_box is still missing!).") #:cargo-development-inputs (("rust-clap" ,rust-clap) ("rust-diff" ,rust-diff) - ("rust-shlex" ,rust-shlex)))) + ("rust-shlex" ,rust-shlex)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-environmental-variable + (lambda* (#:key inputs #:allow-other-keys) + (let ((clang (assoc-ref inputs "libclang"))) + (setenv "LIBCLANG_PATH" + (string-append clang "/lib"))) + #t))))) + (inputs + `(("libclang" ,clang))) (home-page "https://rust-lang.github.io/rust-bindgen/") (synopsis @@ -625,26 +730,77 @@ and no more (caveat: black_box is still missing!).") (license (list license:asl2.0 license:expat)))) -(define-public rust-bitflags ; guix upstreamable +(define-public rust-blake2-rfc (package - (name "rust-bitflags") - (version "1.1.0") + (name "rust-blake2-rfc") + (version "0.2.18") (source (origin (method url-fetch) - (uri (crate-uri "bitflags" version)) + (uri (crate-uri "blake2-rfc" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1zc1qb1hwsnl2d8rhzicsv9kqd5b2hwbrscrcfw5as4sfr35659x")))) + "0034g47hyq2bzmk40895ill1mbnpmmjakdq3dmm9clidvl5m6vax")))) (build-system cargo-build-system) - (home-page "https://github.com/bitflags/bitflags") - (synopsis "Macro to generate structures which behave like bitflags") - (description "This package provides a macro to generate structures which -behave like a set of bitflags.") + (arguments + `(#:cargo-inputs + (("rust-arrayvec" ,rust-arrayvec) + ("rust-constant-time-eq" ,rust-constant-time-eq) + ("rust-clippy" ,rust-clippy)) + #:cargo-development-inputs + (("rust-data-encoding" ,rust-data-encoding)))) + (home-page "https://github.com/cesarb/blake2-rfc") + (synopsis "pure Rust implementation of BLAKE2 based on RFC 7693") + (description + "This is a pure Rust implementation of BLAKE2 based on RFC 7693. This +crate is limited to the features described in the RFC: only the @code{digest +length} and @code{key length} parameters can be used.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-blas-src + (package + (name "rust-blas-src") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "blas-src" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0cxln7bgwxbknaf3qbv4hscy9k53msax14x0szvvp680km3z9zs6")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-accelerate-src" ,rust-accelerate-src) + ("rust-intel-mkl-src" ,rust-intel-mkl-src) + ("rust-netlib-src" ,rust-netlib-src) + ("rust-openblas-src" ,rust-openblas-src)))) + (home-page + "https://github.com/blas-lapack-rs/blas-src") + (synopsis + "The package provides a BLAS source of choice.") + (description + "The package provides a BLAS source of choice.") (license (list license:asl2.0 license:expat)))) +(define-public rust-blas-src-0.2 + (package + (inherit rust-blas-src) + (name "rust-blas-src") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "blas-src" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0l9c1gjhld3ajalak1ipklxfjvwqyy3l7xl019spdbqlrk8r9f57")))))) + (define-public rust-blobby (package (name "rust-blobby") @@ -673,6 +829,33 @@ behave like a set of bitflags.") (license (list license:asl2.0 license:expat)))) +(define-public rust-bodyparser + (package + (name "rust-bodyparser") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "bodyparser" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0c1gynj9l7wv3mjrzr5jifmy0pjdwachfqz09aygdmmab3xan8zh")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-iron" ,rust-iron) + ("rust-persistent" ,rust-persistent) + ("rust-plugin" ,rust-plugin) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive)))) + (home-page "https://github.com/iron/body-parser") + (synopsis "Body parsing middleware for Iron.") + (description "Body parsing middleware for Iron.") + (license license:expat))) + (define-public rust-bumpalo (package (name "rust-bumpalo") @@ -693,7 +876,7 @@ behave like a set of bitflags.") ("rust-quickcheck" ,rust-quickcheck)))) (home-page "https://github.com/fitzgen/bumpalo") (synopsis - "A fast bump allocation arena for Rust.") + "Fast bump allocation arena for Rust") (description "This package provides a fast bump allocation arena for Rust.") (license (list license:asl2.0 @@ -749,7 +932,7 @@ behave like a set of bitflags.") ("rust-serde" ,rust-serde)) #:cargo-development-inputs (("rust-serde-test" ,rust-serde-test)))) - (home-page "https://github.com/carllerche/bytes") + (home-page "https://github.com/tokio-rs/bytes") (synopsis "Types and traits for working with bytes") (description @@ -777,7 +960,7 @@ behave like a set of bitflags.") ("rust-ppv-lite86" ,rust-ppv-lite86) ("rust-stream-cipher" ,rust-stream-cipher)) #:cargo-development-inputs - (("rust-hex-literal" ,rust-hex-literal)))) + (("rust-hex-literal" ,rust-hex-literal-0.1)))) (home-page "https://github.com/cryptocorrosion/cryptocorrosion") (synopsis "The ChaCha family of stream ciphers") @@ -786,35 +969,65 @@ behave like a set of bitflags.") (license (list license:asl2.0 license:expat)))) +(define-public rust-cargon + (package + (name "rust-cargon") + (version "0.0.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "cargon" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1cszlab7jk736p0lb50ag4l9nv72m7j41bwrmygl0lr4iz0350w2")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-gcc" ,rust-gcc)))) + (home-page "https://github.com/bryant/argon2rs") + (synopsis "Thin wrapper around the Argon2 C library") + (description + "This package provides a thin wrapper around the Argon2 C library. It is +used in argon2rs' bench suite.") + (license license:wtfpl2))) + (define-public rust-cc (package (name "rust-cc") - (version "1.0.38") + (version "1.0.41") (source (origin (method url-fetch) (uri (crate-uri "cc" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0imzcz53wg7m3gr6657yrikp7icyc2bpkvssnyd0xvj8imihqh6f")))) + (base32 + "1zxzd559dbbf1iwdzmkj7czapzccs17kqqmsj9ayijpdix5rrbld")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-rayon" ,rust-rayon)) + `(;#:cargo-inputs + ;(("rust-rayon" ,rust-rayon)) #:cargo-development-inputs (("rust-tempdir" ,rust-tempdir)) - #:tests? #f)) ; tests fail - (home-page - "https://github.com/alexcrichton/cc-rs") - (synopsis - "A build-time dependency for Cargo build scripts to assist in invoking the native - C compiler to compile native C code into a static archive to be linked into Rust - code.") - (description - "This package provides a build-time dependency for Cargo build scripts to assist in invoking the native - C compiler to compile native C code into a static archive to be linked into Rustcode.") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-optional-deps + (lambda _ + (substitute* "Cargo.toml.orig" + ((".*optional.*") "\n") + ((".*features.*") "") + ((".*parallel.*") "")) + (delete-file "Cargo.toml") + (copy-file "Cargo.toml.orig" "Cargo.toml") + #t))) + #:tests? #f)) ; Tests require cc-test from git repo. + (home-page "https://github.com/alexcrichton/cc-rs") + (synopsis "Invoke the native C compiler") + (description + "This package provides a build-time dependency for Cargo build scripts to +assist in invoking the native C compiler to compile native C code into a static +archive to be linked into Rustcode.") (license (list license:asl2.0 license:expat)))) @@ -836,7 +1049,17 @@ behave like a set of bitflags.") `(#:cargo-inputs (("rust-nom" ,rust-nom)) #:cargo-development-inputs - (("rust-clang-sys" ,rust-clang-sys)))) + (("rust-clang-sys" ,rust-clang-sys)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-environmental-variable + (lambda* (#:key inputs #:allow-other-keys) + (let ((clang (assoc-ref inputs "libclang"))) + (setenv "LIBCLANG_PATH" + (string-append clang "/lib"))) + #t))))) + (inputs + `(("libclang" ,clang))) (home-page "https://github.com/jethrogb/rust-cexpr") (synopsis "A C expression parser and evaluator") @@ -845,27 +1068,6 @@ behave like a set of bitflags.") (license (list license:asl2.0 license:expat)))) -(define-public rust-cfg-if ; guix upstreamable - (package - (name "rust-cfg-if") - (version "0.1.9") - (source - (origin - (method url-fetch) - (uri (crate-uri "cfg-if" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0csygklgz3ybpr0670rkip49zh76m43ar3k7xgypkzbzrwycx1ml")))) - (build-system cargo-build-system) - (home-page "https://github.com/alexcrichton/cfg-if") - (synopsis "Define an item depending on parameters") - (description "This package provides a macro to ergonomically define an item -depending on a large number of #[cfg] parameters. Structured like an -@code{if-else} chain, the first matching branch is the item that gets emitted.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-chrono (package (name "rust-chrono") @@ -921,7 +1123,7 @@ depending on a large number of #[cfg] parameters. Structured like an ("rust-serde" ,rust-serde) ("rust-serde-derive" ,rust-serde-derive)))) (home-page - "http://github.com/sagiegurari/ci_info") + "https://github.com/sagiegurari/ci_info") (synopsis "Provides current CI environment information.") (description @@ -958,7 +1160,7 @@ depending on a large number of #[cfg] parameters. Structured like an (string-append clang "/lib"))) #t))))) (inputs - `(("libclang" ,(@ (gnu packages llvm) clang)))) + `(("libclang" ,clang))) (home-page "https://github.com/KyleMayes/clang-sys") (synopsis "Rust bindings for libclang.") @@ -990,7 +1192,7 @@ depending on a large number of #[cfg] parameters. Structured like an ("rust-textwrap" ,rust-textwrap) ("rust-unicode-width" ,rust-unicode-width) ("rust-vec-map" ,rust-vec-map) - ("rust-yaml-rust" ,rust-yaml-rust)) + ("rust-yaml-rust" ,rust-yaml-rust-0.3)) #:cargo-development-inputs (("rust-lazy-static" ,rust-lazy-static) ("rust-regex" ,rust-regex) @@ -1002,34 +1204,6 @@ depending on a large number of #[cfg] parameters. Structured like an "This package provides a simple to use, efficient, and full-featured Command Line Argument Parser") (license license:expat))) -(define-public rust-clicolors-control - (package - (name "rust-clicolors-control") - (version "1.0.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "clicolors-control" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1y80cgarxhrd1bz5yjm81r444v6flvy36aaxrrsac0yhfd6gvavk")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-atty" ,rust-atty) - ("rust-lazy-static" ,rust-lazy-static) - ("rust-libc" ,rust-libc) - ("rust-winapi" ,rust-winapi)))) - (home-page - "https://github.com/mitsuhiko/clicolors-control") - (synopsis - "A common utility library to control CLI colorization") - (description - "This package provides a common utility library to control CLI colorization") - (license license:expat))) - (define-public rust-clippy (package (name "rust-clippy") @@ -1048,7 +1222,7 @@ depending on a large number of #[cfg] parameters. Structured like an `(#:cargo-development-inputs (("rust-term" ,rust-term)))) (home-page - "https://github.com/rust-lang-nursery/rust-clippy") + "https://github.com/rust-lang/rust-clippy") (synopsis "A bunch of helpful lints to avoid common pitfalls in Rust.") (description @@ -1056,30 +1230,6 @@ depending on a large number of #[cfg] parameters. Structured like an (license (list license:asl2.0 license:expat)))) -(define-public rust-cloudabi - (package - (name "rust-cloudabi") - (version "0.0.3") - (source - (origin - (method url-fetch) - (uri (crate-uri "cloudabi" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0kxcg83jlihy0phnd2g8c2c303px3l2p3pkjz357ll6llnd5pz6x")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-bitflags" ,rust-bitflags)))) - (home-page "https://nuxi.nl/cloudabi/") - (synopsis - "Low level interface to CloudABI. Contains all syscalls and related types.") - (description - "Low level interface to CloudABI. Contains all syscalls and related types.") - (license license:bsd-2))) - (define-public rust-cmake (package (name "rust-cmake") @@ -1121,10 +1271,9 @@ depending on a large number of #[cfg] parameters. Structured like an (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-rustc-std-workspace-core" - ,rust-rustc-std-workspace-core)) - #:cargo-development-inputs - (("rust-cc" ,rust-cc)))) + (("rust-cc" ,rust-cc) + ("rust-rustc-std-workspace-core" + ,rust-rustc-std-workspace-core)))) (home-page "https://github.com/rust-lang-nursery/compiler-builtins") (synopsis @@ -1134,6 +1283,45 @@ depending on a large number of #[cfg] parameters. Structured like an (license (list license:asl2.0 license:expat)))) +(define-public rust-compiletest-rs + (package + (name "rust-compiletest-rs") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "compiletest-rs" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0rvckrzk4bs3h9vsvf0z8rzhh59rddxcq5z5c0iyzv1daihci5sq")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-diff" ,rust-diff) + ("rust-filetime" ,rust-filetime) + ("rust-getopts" ,rust-getopts) + ("rust-libc" ,rust-libc) + ("rust-log" ,rust-log) + ("rust-miow" ,rust-miow) + ("rust-regex" ,rust-regex) + ("rust-rustfix" ,rust-rustfix) + ("rust-serde" ,rust-serde) + ("rust-serde-derive" ,rust-serde-derive) + ("rust-serde-json" ,rust-serde-json) + ("rust-winapi" ,rust-winapi) + ("rust-tempfile" ,rust-tempfile) + ("rust-tester" ,rust-tester)))) + (home-page "https://github.com/laumann/compiletest-rs") + (synopsis "Compiletest utility from the Rust compiler") + (description + "This project is an attempt at extracting the @code{compiletest} utility +from the Rust compiler. The @code{compiletest} utility is useful for library +and plugin developers, who want to include test programs that should fail to +compile, issue warnings or otherwise produce compile-time output.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-console (package (name "rust-console") @@ -1197,6 +1385,98 @@ depending on a large number of #[cfg] parameters. Structured like an "This crate provides a number of conversion traits with more specific semantics than those provided by 'as' or 'From'/'Into'.") (license license:expat))) +(define-public rust-cookie + (package + (name "rust-cookie") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "cookie" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1mdvqixahcywvqp0y8k2skkgbpfhsp0w73l9mz93dcrx1gq091l8")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-time" ,rust-time) + ("rust-base64" ,rust-base64) + ("rust-ring" ,rust-ring) + ("rust-url" ,rust-url)))) + (home-page + "https://github.com/alexcrichton/cookie-rs") + (synopsis "Crate for parsing HTTP cookie headers and managing a cookie jar. Supports signed and private (encrypted + signed) jars.") + (description "Crate for parsing HTTP cookie headers and managing a cookie jar. Supports signed and private (encrypted + signed) jars.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-cookie-store + (package + (name "rust-cookie-store") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "cookie_store" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0204vzqszkjs5j4bqf8rrzrjj9c6f1zdydsid8ndkc7h7bx1v90l")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cookie" ,rust-cookie) + ("rust-idna" ,rust-idna) + ("rust-log" ,rust-log) + ("rust-publicsuffix" ,rust-publicsuffix) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json) + ("rust-time" ,rust-time) + ("rust-try-from" ,rust-try-from) + ("rust-url" ,rust-url)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-pretty-assertions" ,rust-pretty-assertions)))) + (home-page + "https://github.com/pfernie/cookie_store") + (synopsis + "Implementation of Cookie storage and retrieval per [RFC6265](http://tools.ietf.org/html/rfc6265)") + (description + "Implementation of Cookie storage and retrieval per [RFC6265](http://tools.ietf.org/html/rfc6265)") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-cookie-store-0.7 + (package + (inherit rust-cookie-store) + (name "rust-cookie-store") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "cookie_store" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "174i9k9g62pfx7y1nqynywdpjplkl3j4hi3ck6bz2r996qzhnxa6")))) + (arguments + `(#:cargo-inputs + (("rust-cookie" ,rust-cookie) + ("rust-idna" ,rust-idna) + ("rust-log" ,rust-log) + ("rust-publicsuffix" ,rust-publicsuffix) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json) + ("rust-time" ,rust-time) + ("rust-try-from" ,rust-try-from) + ("rust-url" ,rust-url)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-pretty-assertions" ,rust-pretty-assertions)))))) + (define-public rust-core-arch (package (name "rust-core-arch") @@ -1216,7 +1496,7 @@ depending on a large number of #[cfg] parameters. Structured like an (("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test)))) (home-page - "https://github.com/rust-lang-nursery/stdsimd") + "https://github.com/rust-lang/stdarch") (synopsis "`core::arch` - Rust's core library architecture-specific intrinsics.") (description @@ -1224,6 +1504,36 @@ depending on a large number of #[cfg] parameters. Structured like an (license (list license:asl2.0 license:expat)))) +(define-public rust-core-foundation + (package + (name "rust-core-foundation") + (version "0.6.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "core-foundation" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0va97wf49c8dzm9c8pgyk1jn7z21rl0bj1syf2zz5m2z2hzy1f95")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-chrono" ,rust-chrono) + ("rust-core-foundation-sys" + ,rust-core-foundation-sys) + ("rust-libc" ,rust-libc) + ("rust-uuid" ,rust-uuid)))) + (home-page + "https://github.com/servo/core-foundation-rs") + (synopsis + "Bindings to Core Foundation for macOS") + (description + "Bindings to Core Foundation for macOS") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-cpp-demangle (package (name "rust-cpp-demangle") @@ -1232,11 +1542,10 @@ depending on a large number of #[cfg] parameters. Structured like an (origin (method url-fetch) (uri (crate-uri "cpp_demangle" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0a4hqsfc0sfdwy7pcr0rc1fjp2j47fxbkqfc2lfrbi4zlm5hq36k")))) + (base32 + "0a4hqsfc0sfdwy7pcr0rc1fjp2j47fxbkqfc2lfrbi4zlm5hq36k")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -1286,6 +1595,34 @@ depending on a large number of #[cfg] parameters. Structured like an "Library for retrieving and interacting with the crates.io index") (license license:asl2.0))) +(define-public rust-crc32fast + (package + (name "rust-crc32fast") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "crc32fast" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1c9dhkvf3brrzzplcijaywxi2w8wv5578i0ryhcm7x8dmzi5s4ms")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher) + ("rust-quickcheck" ,rust-quickcheck-0.6) + ("rust-rand" ,rust-rand-0.4)))) + (home-page "https://github.com/srijs/rust-crc32fast") + (synopsis + "Fast, SIMD-accelerated CRC32 (IEEE) checksum computation") + (description + "Fast, SIMD-accelerated CRC32 (IEEE) checksum computation") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-criterion (package (name "rust-criterion") @@ -1335,6 +1672,38 @@ depending on a large number of #[cfg] parameters. Structured like an (license (list license:asl2.0 license:expat)))) +(define-public rust-crossbeam + (package + (name "rust-crossbeam") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "crossbeam" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0g5jysq5x4gndc1v5sq9n3f1m97k7qihwdpigw6ar6knj14qm09d")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-crossbeam-channel" + ,rust-crossbeam-channel) + ("rust-crossbeam-deque" ,rust-crossbeam-deque) + ("rust-crossbeam-epoch" ,rust-crossbeam-epoch) + ("rust-crossbeam-queue" ,rust-crossbeam-queue) + ("rust-crossbeam-utils" ,rust-crossbeam-utils)) + #:cargo-development-inputs + (("rust-rand" ,rust-rand-0.6)))) + (home-page + "https://github.com/crossbeam-rs/crossbeam") + (synopsis "Tools for concurrent programming") + (description "Tools for concurrent programming") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-crossbeam-deque (package (name "rust-crossbeam-deque") @@ -1532,6 +1901,63 @@ depending on a large number of #[cfg] parameters. Structured like an `(#:cargo-inputs (("rust-cfg-if" ,rust-cfg-if)))))) +(define-public rust-csv + (package + (name "rust-csv") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "csv" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0zgq18xam24rbggm3ybmrygipa0mrr7rscf9r8hmi9vkzp6rql9p")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bstr" ,rust-bstr) + ("rust-csv-core" ,rust-csv-core) + ("rust-itoa" ,rust-itoa) + ("rust-ryu" ,rust-ryu) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-serde" ,rust-serde)))) + (home-page + "https://github.com/BurntSushi/rust-csv") + (synopsis + "Fast CSV parsing with support for serde.") + (description + "Fast CSV parsing with support for serde.") + (license (list license:unlicense + license:expat)))) + +(define-public rust-ct-logs + (package + (name "rust-ct-logs") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "ct-logs" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "04wiwiv4ghni3x2vni3z711mlz0ndqvh04vmdkbw3nr7zbsqcdjd")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-sct" ,rust-sct)))) + (home-page "https://github.com/ctz/ct-logs") + (synopsis + "Google's list of Certificate Transparency logs for use with sct crate") + (description + "Google's list of Certificate Transparency logs for use with sct crate") + (license (list license:asl2.0 + license:isc + license:expat)))) + (define-public rust-custom-derive (package (name "rust-custom-derive") @@ -1716,45 +2142,6 @@ depending on a large number of #[cfg] parameters. Structured like an "System-level helper functions for the dirs and directories crates.") (license #f))) -(define-public rust-discard ; guix upstreamable - (package - (name "rust-discard") - (version "1.0.4") - (source - (origin - (method url-fetch) - (uri (crate-uri "discard" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1h67ni5bxvg95s91wgicily4ix7lcw7cq0a5gy9njrybaibhyb91")))) - (build-system cargo-build-system) - (home-page "https://github.com/Pauan/rust-discard") - (synopsis "Allow for intentionally leaking memory") - (description "There are situations where you need to intentionally leak some -memory but not other memory. This package provides a discard trait which allows -for intentionally leaking memory") - (license license:expat))) - -(define-public rust-doc-comment ; guix upstreamable - (package - (name "rust-doc-comment") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (crate-uri "doc-comment" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "15rsqxgarfpb1yim9sbp9yfgj7p2dq6v51c6bq1a62paii9ylgcj")))) - (build-system cargo-build-system) - (home-page "https://github.com/GuillaumeGomez/doc-comment") - (synopsis "Macro to generate doc comments") - (description "This package provides a way to generate doc comments -from macros.") - (license license:expat))) - (define-public rust-docopt (package (name "rust-docopt") @@ -1781,25 +2168,35 @@ from macros.") (license (list license:unlicense license:expat)))) -(define-public rust-dtoa ; guix upstreamable +(define-public rust-duct (package - (name "rust-dtoa") - (version "0.4.4") + (name "rust-duct") + (version "0.12.0") (source (origin (method url-fetch) - (uri (crate-uri "dtoa" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "duct" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0phbm7i0dpn44gzi07683zxaicjap5064w62pidci4fhhciv8mza")))) + (base32 + "1vm1nzyi434h2zwix7c925qfa886ri1qx4nkq4hdrgkq7h9ayh1n")))) (build-system cargo-build-system) - (home-page "https://github.com/dtolnay/dtoa") - (synopsis "Fast functions for printing floating-point primitives") - (description "This crate provides fast functions for printing -floating-point primitives to an @code{io::Write}.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-inputs + (("rust-lazycell" ,rust-lazycell) + ("rust-libc" ,rust-libc) + ("rust-os-pipe" ,rust-os-pipe) + ("rust-shared-child" ,rust-shared-child)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://github.com/oconnor663/duct.rs") + (synopsis + "a library for creating shell pipelines") + (description + "a library for creating shell pipelines") + (license license:expat))) (define-public rust-either (package @@ -1854,6 +2251,242 @@ floating-point primitives to an @code{io::Write}.") (license (list license:asl2.0 license:expat)))) +(define-public rust-encoding + (package + (name "rust-encoding") + (version "0.2.33") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1v1ndmkarh9z3n5hk53da4z56hgk9wa5kcsm7cnx345raqw983bb")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-encoding-index-japanese" + ,rust-encoding-index-japanese) + ("rust-encoding-index-korean" + ,rust-encoding-index-korean) + ("rust-encoding-index-simpchinese" + ,rust-encoding-index-simpchinese) + ("rust-encoding-index-singlebyte" + ,rust-encoding-index-singlebyte) + ("rust-encoding-index-tradchinese" + ,rust-encoding-index-tradchinese)) + #:cargo-development-inputs + (("rust-getopts" ,rust-getopts)))) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Character encoding support for Rust") + (description + "Character encoding support for Rust") + (license license:expat))) + +(define-public rust-encoding-index-japanese + (package + (name "rust-encoding-index-japanese") + (version "1.20141219.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_index_japanese" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "148c1lmd640p1d7fzk0nv7892mbyavvwddgqvcsm78798bzv5s04")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-encoding-index-tests" + ,rust-encoding-index-tests)))) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Index tables for Japanese character encodings") + (description + "Index tables for Japanese character encodings") + (license license:cc0))) + +(define-public rust-encoding-index-korean + (package + (name "rust-encoding-index-korean") + (version "1.20141219.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_index_korean" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "10cxabp5ppygbq4y6y680856zl9zjvq7ahpiw8zj3fmwwsw3zhsd")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-encoding-index-tests" + ,rust-encoding-index-tests)))) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Index tables for Korean character encodings") + (description + "Index tables for Korean character encodings") + (license license:cc0))) + +(define-public rust-encoding-index-simpchinese + (package + (name "rust-encoding-index-simpchinese") + (version "1.20141219.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_index_simpchinese" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1xria2i7mc5dqdrpqxasdbxv1qx46jjbm53if3y1i4cvj2a72ynq")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-encoding-index-tests" + ,rust-encoding-index-tests)))) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Index tables for simple Chienese character encodings") + (description + "Index tables for simple Chienese character encodings") + (license license:cc0))) + +(define-public rust-encoding-index-singlebyte + (package + (name "rust-encoding-index-singlebyte") + (version "1.20141219.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_index_singlebyte" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0jp85bz2pprzvg9m95w4q0vibh67b6w3bx35lafay95jzyndal9k")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-encoding-index-tests" + ,rust-encoding-index-tests)))) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Index tables for various single-byte character encodings") + (description + "Index tables for various single-byte character encodings") + (license license:cc0))) + +(define-public rust-encoding-index-tests + (package + (name "rust-encoding-index-tests") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_index_tests" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0s85y091gl17ixass49bzaivng7w8p82p6nyvz2r3my9w4mxhim2")))) + (build-system cargo-build-system) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Helper macros used to test index tables for character encodings") + (description + "Helper macros used to test index tables for character encodings.") + (license license:cc0))) + +(define-public rust-encoding-index-tradchinese + (package + (name "rust-encoding-index-tradchinese") + (version "1.20141219.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_index_tradchinese" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "060ci4iz6xfvzk38syfbjvs7pix5hch3mvxkksswmqwcd3aj03px")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-encoding-index-tests" + ,rust-encoding-index-tests)))) + (home-page + "https://github.com/lifthrasiir/rust-encoding") + (synopsis "Index tables for traditional Chienese character encodings") + (description + "Index tables for traditional Chienese character encodings") + (license license:cc0))) + +(define-public rust-encoding-rs + (package + (name "rust-encoding-rs") + (version "0.8.17") + (source + (origin + (method url-fetch) + (uri (crate-uri "encoding_rs" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1v902qqnbd37vdq4rjvp6k05wmghrasfdcjy30gp1xpjg5f7hma1")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-packed-simd" ,rust-packed-simd) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-bincode" ,rust-bincode) + ("rust-serde-derive" ,rust-serde-derive) + ("rust-serde-json" ,rust-serde-json)))) + (home-page "https://docs.rs/encoding_rs/") + (synopsis + "A Gecko-oriented implementation of the Encoding Standard") + (description + "This package provides a Gecko-oriented implementation of the Encoding Standard") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-enum-as-inner + (package + (name "rust-enum-as-inner") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "enum-as-inner" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0zg3h7k3g1z7a9ayqy63sk302d4dg5g2h274ddv80mj4jxn2cn1x")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2) + ("rust-quote" ,rust-quote) + ("rust-syn" ,rust-syn)))) + (home-page "https://github.com/bluejekyll/enum-as-inner") + (synopsis "A deriving proc-macro for generating functions to automatically give access to the inner members of enum.") + (description "A deriving proc-macro for generating functions to automatically give access to the inner members of enum.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-env-logger (package (name "rust-env-logger") @@ -1884,6 +2517,38 @@ floating-point primitives to an @code{io::Write}.") (license (list license:asl2.0 license:expat)))) +(define-public rust-env-logger-0.5 + (package + (inherit rust-env-logger) + (name "rust-env-logger") + (version "0.5.13") + (source + (origin + (method url-fetch) + (uri (crate-uri "env_logger" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0f0c4i4c65jh8lci0afl5yg74ac0lbnpxcp81chj114zwg9a9c0m")))))) + +(define-public rust-env-logger-0.4 + (package + (inherit rust-env-logger) + (name "rust-env-logger") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "env_logger" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0nydz2lidsvx9gs0v2zcz68rzqx8in7fzmiprgsrhqh17vkj3prx")))) + (arguments + `(#:cargo-inputs + (("rust-log" ,rust-log) + ("rust-regex" ,rust-regex-0.2)))))) + (define-public rust-envmnt (package (name "rust-envmnt") @@ -1902,7 +2567,7 @@ floating-point primitives to an @code{io::Write}.") `(#:cargo-inputs (("rust-indexmap" ,rust-indexmap)))) (home-page - "http://github.com/sagiegurari/envmnt") + "https://github.com/sagiegurari/envmnt") (synopsis "Environment variables utility functions.") (description @@ -2013,7 +2678,7 @@ floating-point primitives to an @code{io::Write}.") (("rust-proc-macro2" ,rust-proc-macro2) ("rust-quote" ,rust-quote) ("rust-syn" ,rust-syn) - ("rust-synstructure" ,rust-synstructure)) + ("rust-synstructure" ,rust-synstructure-0.10)) #:cargo-development-inputs (("rust-failure" ,rust-failure)))) (home-page @@ -2023,52 +2688,165 @@ floating-point primitives to an @code{io::Write}.") (license (list license:asl2.0 license:expat)))) -(define-public rust-fallible-iterator ; guix upstreamable +(define-public rust-filetime (package - (name "rust-fallible-iterator") - (version "0.2.0") + (name "rust-filetime") + (version "0.2.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "filetime" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0sflihq2l77xjrza7yjalnxsc7dxzg25rhzcfbd9vmyfah5kimvb")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-libc" ,rust-libc) + ("rust-redox-syscall" ,rust-redox-syscall) + ("rust-winapi" ,rust-winapi)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://github.com/alexcrichton/filetime") + (synopsis + "Platform-agnostic accessors of timestamps in File metadata") + (description + "Platform-agnostic accessors of timestamps in File metadata") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-rustfix + (package + (name "rust-rustfix") + (version "0.4.6") (source (origin (method url-fetch) - (uri (crate-uri "fallible-iterator" version)) + (uri (crate-uri "rustfix" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01zn0ysnass3mmrhxk90584y713vjfq1x97mi4saac99g9vsql3i")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-failure" ,rust-failure) + ("rust-log" ,rust-log) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json)) + #:cargo-development-inputs + (("rust-difference" ,rust-difference) + ("rust-duct" ,rust-duct) + ("rust-env-logger" ,rust-env-logger) + ("rust-log" ,rust-log) + ("rust-proptest" ,rust-proptest) + ("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://github.com/rust-lang-nursery/rustfix") + (synopsis + "Automatically apply the suggestions made by rustc") + (description + "Automatically apply the suggestions made by rustc") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-flame + (package + (name "rust-flame") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "flame" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1xq759lsr8gqss7hva42azn3whgrbrs2sd9xpn92c5ickxm1fhs4")))) + "0c5bmhyimzxch3pmh0w3z9n57saasgix4bmbbksr9vp1c5j71hhz")))) (build-system cargo-build-system) - (home-page "https://github.com/sfackler/rust-fallible-iterator") - (synopsis "Fallible iterator traits") - (description "If the @code{std} or @code{alloc} features are enabled, this -crate provides implementations for @code{Box}, @code{Vec}, @code{BTreeMap}, and -@code{BTreeSet}. If the @code{std} feature is enabled, this crate additionally -provides implementations for @code{HashMap} and @code{HashSet}.") + (arguments + `(#:cargo-inputs + (("rust-lazy-static" ,rust-lazy-static) + ("rust-thread-id" ,rust-thread-id) + ("rust-serde" ,rust-serde) + ("rust-serde-derive" ,rust-serde-derive) + ("rust-serde-json" ,rust-serde-json)))) + (home-page "https://github.com/TyOverby/flame") + (synopsis "A cool flamegraph library for rust") + (description + "Flamegraphs are a great way to view profiling information. At a glance, they give you information about how much time your program spends in critical sections of your code giving you some much-needed insight into where optimizations may be needed.") (license (list license:asl2.0 license:expat)))) -(define-public rust-findshlibs +(define-public rust-flamer (package - (name "rust-findshlibs") - (version "0.5.0") + (name "rust-flamer") + (version "0.4.0") (source (origin (method url-fetch) - (uri (crate-uri "findshlibs" version)) + (uri (crate-uri "flamer" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1avszq3fn4ix7p6wjfdkli6fjyxccks1qhzja92a6kpxakd35drn")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-flame" ,rust-flame) + ("rust-quote" ,rust-quote) + ("rust-syn" ,rust-syn)))) + (home-page "https://github.com/llogiq/flamer") + (synopsis "A proc macro to insert appropriate flame::start_guard(_) calls (for use with flame)") + (description + "A proc macro to insert appropriate flame::start_guard(_) calls (for use with flame)") + (license license:asl2.0))) + +(define-public rust-flate2 + (package + (name "rust-flate2") + (version "1.0.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "flate2" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1n2vagn0q5yim32hxkwi1cjgp3yn1dm45p7z8nw6lapywihhs9mi")))) + "10j6bpgpipywmrsxxmp1q48qd9vp1c4fs64y2hv02r48cfxgznia")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-lazy-static" ,rust-lazy-static) - ("rust-libc" ,rust-libc)))) + (("rust-crc32fast" ,rust-crc32fast) + ("rust-futures" ,rust-futures) + ("rust-libc" ,rust-libc) + ("rust-libz-sys" ,rust-libz-sys) + ("rust-miniz-sys" ,rust-miniz-sys) + ("rust-miniz-oxide" ,rust-miniz-oxide) + ("rust-miniz-oxide" ,rust-miniz-oxide) + ("rust-tokio-io" ,rust-tokio-io)) + #:cargo-development-inputs + (("rust-futures" ,rust-futures) + ("rust-quickcheck" ,rust-quickcheck) + ("rust-rand" ,rust-rand) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-tokio-threadpool" ,rust-tokio-threadpool)))) (home-page - "https://github.com/gimli-rs/findshlibs") + "https://github.com/alexcrichton/flate2-rs") (synopsis - "Find the set of shared libraries loaded in the current process with a cross platform API") + "Bindings to miniz.c for DEFLATE compression and decompression exposed as + Reader/Writer streams. Contains bindings for zlib, deflate, and gzip-based + streams.") (description - "Find the set of shared libraries loaded in the current process with a cross platform API") + "Bindings to miniz.c for DEFLATE compression and decompression exposed as + Reader/Writer streams. Contains bindings for zlib, deflate, and gzip-based + streams.") (license (list license:asl2.0 license:expat)))) @@ -2098,45 +2876,57 @@ provides implementations for @code{HashMap} and @code{HashSet}.") (license (list license:asl2.0 license:expat)))) -(define-public rust-fnv ; guix upstreamable +(define-public rust-foreign-types (package - (name "rust-fnv") - (version "1.0.6") + (name "rust-foreign-types") + (version "0.4.0") (source (origin (method url-fetch) - (uri (crate-uri "fnv" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "foreign-types" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1ww56bi1r5b8id3ns9j3qxbi7w5h005rzhiryy0zi9h97raqbb9g")))) + (base32 + "0ca4i38yrf9iy5k47lr1ylb3rvcbn36d81k5pr5kzf6kmj6p111n")))) (build-system cargo-build-system) - (home-page "https://github.com/servo/rust-fnv") - (synopsis "implementation of the Fowler-Noll-Vo hash function") - (description "The @code{fnv} hash function is a custom @code{Hasher} -implementation that is more efficient for smaller hash keys.") + (arguments + `(#:cargo-inputs + (("rust-foreign-types-macros" ,rust-foreign-types-macros) + ("rust-foreign-types-shared" ,rust-foreign-types-shared)))) + (home-page + "https://github.com/sfackler/foreign-types") + (synopsis + "A framework for Rust wrappers over C APIs.") + (description + "A framework for Rust wrappers over C APIs.") (license (list license:asl2.0 license:expat)))) -(define-public rust-fs-extra ; guix upstreamable +(define-public rust-foreign-types-macros (package - (name "rust-fs-extra") - (version "1.1.0") + (name "rust-foreign-types-macros") + (version "0.1.0") (source (origin (method url-fetch) - (uri (crate-uri "fs_extra" version)) + (uri (crate-uri "foreign-types-macros" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0x6675wdhsx277k1k1235jwcv38naf20d8kwrk948ds26hh4lajz")))) + (base32 + "16yjigjcsklcwy2ad32l24k1nwm9n3bsnyhxc3z9whjbsrj60qk6")))) (build-system cargo-build-system) - (home-page "https://github.com/webdesus/fs_extra") - (synopsis "Extra filesystem methods") - (description "Expanding opportunities standard library @code{std::fs} and -@code{std::io}. Recursively copy folders with recept information about -process and much more.") - (license license:expat))) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2) + ("rust-quote" ,rust-quote) + ("rust-syn" ,rust-syn)))) + (home-page "https://github.com/sfackler/foreign-types") + (synopsis "An internal crate used by foreign-types") + (description + "An internal crate used by foreign-types.") + (license (list license:asl2.0 + license:expat)))) (define-public rust-fst (package @@ -2155,7 +2945,7 @@ process and much more.") (arguments `(#:cargo-inputs (("rust-byteorder" ,rust-byteorder) - ("rust-memmap" ,rust-memmap)) + ("rust-memmap" ,rust-memmap-0.6)) #:cargo-development-inputs (("rust-fnv" ,rust-fnv) ("rust-fst-levenshtein" ,rust-fst-levenshtein) @@ -2214,7 +3004,7 @@ process and much more.") (arguments `(#:cargo-inputs (("rust-fst" ,rust-fst) - ("rust-regex-syntax" ,rust-regex-syntax) + ("rust-regex-syntax" ,rust-regex-syntax-0.3) ("rust-utf8-ranges" ,rust-utf8-ranges)))) (home-page "https://github.com/BurntSushi/fst") (synopsis @@ -2224,45 +3014,6 @@ process and much more.") (license (list license:unlicense license:expat)))) -(define-public rust-fuchsia-cprng ; guix upstreamable - (package - (name "rust-fuchsia-cprng") - (version "0.1.1") - (source - (origin - (method url-fetch) - (uri (crate-uri "fuchsia-cprng" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1fnkqrbz7ixxzsb04bsz9p0zzazanma8znfdqjvh39n14vapfvx0")))) - (build-system cargo-build-system) - (home-page "https://fuchsia.googlesource.com/fuchsia/+/master/garnet/public/rust/fuchsia-cprng") - (synopsis "Fuchsia cryptographically secure pseudorandom number generator") - (description "Rust crate for the Fuchsia cryptographically secure -pseudorandom number generator") - (license license:bsd-3))) - -(define-public rust-futures ; guix upstreamable - (package - (name "rust-futures") - (version "0.1.28") - (source - (origin - (method url-fetch) - (uri (crate-uri "futures" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0saq8ffjw1pwf1pzhw3kq1z7dfq6wpd8x93dnni6vbkc799kkp25")))) - (build-system cargo-build-system) - (home-page "https://github.com/rust-lang-nursery/futures-rs") - (synopsis "Implementation of zero-cost futures in Rust") - (description "An implementation of @code{futures} and @code{streams} -featuring zero allocations, composability, and iterator-like interfaces.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-futures-channel-preview (package (name "rust-futures-channel-preview") @@ -2284,7 +3035,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") ("rust-futures-sink-preview" ,rust-futures-sink-preview)))) (home-page - "https://rust-lang-nursery.github.io/futures-rs") + "https://rust-lang-nursery.github.io/futures-rs/") (synopsis "Channels for asynchronous communication using futures-rs.") (description @@ -2336,7 +3087,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") ,rust-futures-util-preview) ("rust-num-cpus" ,rust-num-cpus)))) (home-page - "https://rust-lang-nursery.github.io/futures-rs") + "https://rust-lang-nursery.github.io/futures-rs/") (synopsis "Executors for asynchronous tasks based on the futures-rs library.") (description @@ -2344,23 +3095,40 @@ featuring zero allocations, composability, and iterator-like interfaces.") (license (list license:asl2.0 license:expat)))) -(define-public rust-futures-io-preview ; guix upstreamable +(define-public rust-futures-preview (package - (name "rust-futures-io-preview") - (version "0.3.0-alpha.17") + (name "rust-futures-preview") + (version "0.3.0-alpha.18") (source (origin (method url-fetch) - (uri (crate-uri "futures-io-preview" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "futures-preview" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0fhvwhdb8ywjjbfng0ra1r8yyc9yzpyxg9sv3spb3f7w0lk40bh8")))) + (base32 + "1dg4qijba037xqykminifxpnjasabcjx9pwa3ww8wcmj9w6gka7g")))) (build-system cargo-build-system) - (home-page "https://rust-lang-nursery.github.io/futures-rs") - (synopsis "Async read and write traits for the futures library") - (description "This crate provides the @code{AsyncRead} and -@code{AsyncWrite} traits for the @code{futures-rs} library.") + (arguments + `(#:cargo-inputs + (("rust-futures-channel-preview" + ,rust-futures-channel-preview) + ("rust-futures-core-preview" + ,rust-futures-core-preview) + ("rust-futures-executor-preview" + ,rust-futures-executor-preview) + ("rust-futures-io-preview" + ,rust-futures-io-preview) + ("rust-futures-sink-preview" + ,rust-futures-sink-preview) + ("rust-futures-util-preview" + ,rust-futures-util-preview)))) + (home-page + "https://rust-lang-nursery.github.io/futures-rs") + (synopsis + "An implementation of futures and streams featuring zero allocations, composability, and iterator-like interfaces.") + (description + "An implementation of futures and streams featuring zero allocations, composability, and iterator-like interfaces.") (license (list license:asl2.0 license:expat)))) @@ -2387,7 +3155,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") ("rust-quote" ,rust-quote) ("rust-syn" ,rust-syn)))) (home-page - "https://rust-lang-nursery.github.io/futures-rs") + "https://rust-lang-nursery.github.io/futures-rs/") (synopsis "The `select!` macro for waiting on multiple different `Future`s at once and handling the first one to complete.") (description @@ -2414,7 +3182,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") (("rust-futures-core-preview" ,rust-futures-core-preview)))) (home-page - "https://rust-lang-nursery.github.io/futures-rs") + "https://rust-lang-nursery.github.io/futures-rs/") (synopsis "The asynchronous `Sink` trait for the futures-rs library.") (description @@ -2422,6 +3190,35 @@ featuring zero allocations, composability, and iterator-like interfaces.") (license (list license:asl2.0 license:expat)))) +(define-public rust-futures-timer + (package + (name "rust-futures-timer") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "futures-timer" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0l35r7nm8p43j0adkhybnwxzbjiqy0b00kgccjy3l513m9abb7lg")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures-preview" ,rust-futures-preview) + ("rust-pin-utils" ,rust-pin-utils)) + #:cargo-development-inputs + (("rust-runtime" ,rust-runtime)))) + (home-page + "https://github.com/alexcrichton/futures-timer") + (synopsis + "Timeouts and intervals for futures.") + (description + "Timeouts and intervals for futures.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-futures-util-preview (package (name "rust-futures-util-preview") @@ -2458,7 +3255,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") ("rust-slab" ,rust-slab) ("rust-tokio-io" ,rust-tokio-io)))) (home-page - "https://rust-lang-nursery.github.io/futures-rs") + "https://rust-lang-nursery.github.io/futures-rs/") (synopsis "Common utilities and extension traits for the futures-rs library.") (description @@ -2494,6 +3291,35 @@ featuring zero allocations, composability, and iterator-like interfaces.") (license (list license:asl2.0 license:expat)))) +(define-public rust-gcc + (package + (name "rust-gcc") + (version "0.3.55") + (source + (origin + (method url-fetch) + (uri (crate-uri "gcc" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1hng1sajn4r67hndvhjysswz8niayjwvcj42zphpxzhbz89kjpwg")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rayon" ,rust-rayon-0.8)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)) + ;#:tests? #f + )) ; tests fail + (home-page "https://github.com/alexcrichton/gcc-rs") + (synopsis "Library to compile C/C++ code into a Rust library/application") + (description + "This package provides a build-time dependency for Cargo build scripts to +assist in invoking the native C compiler to compile native C code into a static +archive to be linked into Rustcode.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-generic-array (package (name "rust-generic-array") @@ -2516,7 +3342,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") (("rust-bincode" ,rust-bincode) ("rust-serde-json" ,rust-serde-json)))) (home-page - "https://github.com/fizyk20/generic-array.git") + "https://github.com/fizyk20/generic-array") (synopsis "Generic types implementing functionality of arrays") (description @@ -2543,7 +3369,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") #:cargo-development-inputs (("rust-log" ,rust-log)))) (home-page - "https://github.com/rust-lang/getopts") + "https://github.com/rust-lang-nursery/getopts") (synopsis "getopts-like option parsing.") (description "getopts-like option parsing.") (license (list license:asl2.0 @@ -2608,9 +3434,18 @@ featuring zero allocations, composability, and iterator-like interfaces.") ("rust-serde-derive" ,rust-serde-derive) ("rust-tempdir" ,rust-tempdir) ("rust-thread-id" ,rust-thread-id) - ("rust-time" ,rust-time)))) - ;(inputs - ; `(("libgit" ,(@ (gnu packages version-control) libgit2)))) + ("rust-time" ,rust-time)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-openssl + (lambda* (#:key inputs #:allow-other-keys) + (let ((openssl (assoc-ref inputs "openssl"))) + (setenv "OPENSSL_DIR" openssl)) + (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1") + #t))))) + (inputs + `(("libgit" ,libgit2) + ("openssl" ,openssl))) (home-page "https://github.com/rust-lang/git2-rs") (synopsis @@ -2682,7 +3517,7 @@ featuring zero allocations, composability, and iterator-like interfaces.") (arguments `(#:cargo-development-inputs (("rust-tempdir" ,rust-tempdir)))) - (home-page "https://github.com/rust-lang/glob") + (home-page "https://github.com/rust-lang-nursery/glob") (synopsis "Support for matching file paths against Unix shell style patterns.") (description @@ -2734,29 +3569,51 @@ featuring zero allocations, composability, and iterator-like interfaces.") "An impish, cross-platform, ELF, Mach-o, and PE binary parsing and loading crate") (license license:expat))) -(define-public rust-heapsize +(define-public rust-h2 (package - (name "rust-heapsize") - (version "0.4.2") + (name "rust-h2") + (version "0.1.26") (source (origin (method url-fetch) - (uri (crate-uri "heapsize" version)) + (uri (crate-uri "h2" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0q94q9ppqjgrw71swiyia4hgby2cz6dldp7ij57nkvhd6zmfcy8n")))) + "0qn457y8xh03p7c7cpk76r22gqpyqxc58g5022j3iya7d0j4rcx5")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs (("rust-winapi" ,rust-winapi)))) - (home-page "https://github.com/servo/heapsize") + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder) + ("rust-bytes" ,rust-bytes) + ("rust-fnv" ,rust-fnv) + ("rust-futures" ,rust-futures) + ("rust-http" ,rust-http) + ("rust-indexmap" ,rust-indexmap) + ("rust-log" ,rust-log) + ("rust-slab" ,rust-slab) + ("rust-string" ,rust-string) + ("rust-tokio-io" ,rust-tokio-io)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-hex" ,rust-hex) + ("rust-quickcheck" ,rust-quickcheck) + ("rust-rand" ,rust-rand) + ("rust-rustls" ,rust-rustls) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-rustls" ,rust-tokio-rustls) + ("rust-walkdir" ,rust-walkdir) + ("rust-webpki" ,rust-webpki) + ("rust-webpki-roots" ,rust-webpki-roots)))) + (home-page "https://github.com/hyperium/h2") (synopsis - "Infrastructure for measuring the total runtime size of an object on the heap") + "A Tokio aware, HTTP/2.0 client & server implementation for Rust.") (description - "Infrastructure for measuring the total runtime size of an object on the heap") - (license (list license:asl2.0 - license:expat)))) + "A Tokio aware, HTTP/2.0 client & server implementation for Rust.") + (license license:expat))) (define-public rust-heck (package @@ -2784,26 +3641,6 @@ featuring zero allocations, composability, and iterator-like interfaces.") (license (list license:asl2.0 license:expat)))) -(define-public rust-hex ; guix upstreamable - (package - (name "rust-hex") - (version "0.3.2") - (source - (origin - (method url-fetch) - (uri (crate-uri "hex" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0xsdcjiik5j750j67zk42qdnmm4ahirk3gmkmcqgq7qls2jjcl40")))) - (build-system cargo-build-system) - (home-page "https://github.com/KokaKiwi/rust-hex") - (synopsis "Encode and decode data to/from hexadecimals") - (description "This crate allows for encoding and decoding data into/from -hexadecimal representation.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-hex-literal (package (name "rust-hex-literal") @@ -2830,6 +3667,24 @@ hexadecimal representation.") (license (list license:asl2.0 license:expat)))) +(define-public rust-hex-literal-0.1 + (package + (inherit rust-hex-literal) + (name "rust-hex-literal") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "hex-literal" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ffnn5g9q5xhdmzj2ic5hk9y18kyqflbmqcssqcya9gixs5r5hnx")))) + (arguments + `(#:cargo-inputs + (("rust-hex-literal-impl" ,rust-hex-literal-impl-0.1) + ("rust-proc-macro-hack" ,rust-proc-macro-hack)))))) + (define-public rust-hex-literal-impl (package (name "rust-hex-literal-impl") @@ -2855,6 +3710,113 @@ hexadecimal representation.") (license (list license:asl2.0 license:expat)))) +(define-public rust-hex-literal-impl-0.1 + (package + (inherit rust-hex-literal-impl) + (name "rust-hex-literal-impl") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "hex-literal-impl" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1nnxqhyn9l998ma04ip79bmpqv1as6003s03g26ynhrr471p022j")))) + (arguments + `(#:cargo-inputs + (("rust-proc-macro-hack" ,rust-proc-macro-hack-0.4)))))) + +(define-public rust-http + (package + (name "rust-http") + (version "0.1.18") + (source + (origin + (method url-fetch) + (uri (crate-uri "http" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1r5nlliz3340dqn1fanr4f13lxfqiwp9r1mhgw8lkr1rz5bcnarp")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-fnv" ,rust-fnv) + ("rust-itoa" ,rust-itoa)) + #:cargo-development-inputs + (("rust-doc-comment" ,rust-doc-comment) + ("rust-indexmap" ,rust-indexmap) + ("rust-quickcheck" ,rust-quickcheck-0.6) + ("rust-rand" ,rust-rand-0.4) + ("rust-seahash" ,rust-seahash) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json)))) + (home-page + "https://github.com/hyperium/http") + (synopsis + "A general purpose library of common HTTP types") + (description + "A general purpose library of common HTTP types") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-http-body + (package + (name "rust-http-body") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "http-body" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0b99404k4mw6a92hvyr0qwzkqv4f866ykg0x7913limjq5cwhhb7")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-futures" ,rust-futures) + ("rust-http" ,rust-http) + ("rust-tokio-buf" ,rust-tokio-buf)))) + (home-page + "https://github.com/hyperium/http-body") + (synopsis + "Trait representing an asynchronous, streaming, HTTP request or response body.") + (description + "Trait representing an asynchronous, streaming, HTTP request or response body.") + (license license:expat))) + +(define-public rust-httparse + (package + (name "rust-httparse") + (version "1.3.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "httparse" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1yf23ldnjwfkkhkca7f4w15mky9961gjz28dlwyybhphc7l9l5yd")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-pico-sys" ,rust-pico-sys)))) + (home-page + "https://github.com/seanmonstar/httparse") + (synopsis + "A push parser for the HTTP 1.x protocol.") + (description + "A push parser for the HTTP 1.x protocol.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-humantime (package (name "rust-humantime") @@ -2885,6 +3847,215 @@ hexadecimal representation.") (license (list license:asl2.0 license:expat)))) +(define-public rust-hyper + (package + (name "rust-hyper") + (version "0.12.33") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyper" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "13rc9js5n8b338lwif94v6mfni5cjjvxf2jcdsrlzvnqx6y4rd3w")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-futures" ,rust-futures) + ("rust-futures-cpupool" ,rust-futures-cpupool) + ("rust-h2" ,rust-h2) + ("rust-http" ,rust-http) + ("rust-http-body" ,rust-http-body) + ("rust-httparse" ,rust-httparse) + ("rust-iovec" ,rust-iovec) + ("rust-itoa" ,rust-itoa) + ("rust-log" ,rust-log) + ("rust-net2" ,rust-net2) + ("rust-time" ,rust-time) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-buf" ,rust-tokio-buf) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-tokio-reactor" ,rust-tokio-reactor) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-tokio-threadpool" ,rust-tokio-threadpool) + ("rust-tokio-timer" ,rust-tokio-timer) + ("rust-want" ,rust-want)) + #:cargo-development-inputs + (("rust-futures-timer" ,rust-futures-timer) + ("rust-num-cpus" ,rust-num-cpus) + ("rust-pretty-env-logger" + ,rust-pretty-env-logger) + ("rust-rustc-version" ,rust-rustc-version) + ("rust-serde" ,rust-serde) + ("rust-serde-derive" ,rust-serde-derive) + ("rust-serde-json" ,rust-serde-json) + ("rust-spmc" ,rust-spmc) + ("rust-tokio-fs" ,rust-tokio-fs) + ("rust-tokio-mockstream" ,rust-tokio-mockstream) + ("rust-url" ,rust-url)))) + (home-page "https://hyper.rs") + (synopsis "A fast and correct HTTP library.") + (description + "This package provides a fast and correct HTTP library.") + (license license:expat))) + +(define-public rust-hyper-0.10 + (package + (inherit rust-hyper) + (name "rust-hyper") + (version "0.10.16") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyper" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0wwjh9p3mzvg3fss2lqz5r7ddcgl1fh9w6my2j69d6k0lbcm41ha")))) + (arguments + `(#:cargo-inputs + (("rust-base64" ,rust-base64-0.9) + ("rust-httparse" ,rust-httparse) + ("rust-language-tags" ,rust-language-tags) + ("rust-log" ,rust-log-0.3) + ("rust-mime" ,rust-mime-0.2) + ("rust-num-cpus" ,rust-num-cpus) + ("rust-time" ,rust-time) + ("rust-traitobject" ,rust-traitobject) + ("rust-typeable" ,rust-typeable) + ("rust-unicase" ,rust-unicase) + ("rust-url" ,rust-url)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger)))))) + +(define-public rust-hyper-old-types + (package + (name "rust-hyper-old-types") + (version "0.11.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyper-old-types" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1i69sks0bwamzqdbx8ffgkssxffv6crdmwjgl47nr5pkxi8vx5k8")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-base64" ,rust-base64) + ("rust-bytes" ,rust-bytes) + ("rust-http" ,rust-http) + ("rust-httparse" ,rust-httparse) + ("rust-language-tags" ,rust-language-tags) + ("rust-log" ,rust-log) + ("rust-mime" ,rust-mime) + ("rust-percent-encoding" ,rust-percent-encoding) + ("rust-time" ,rust-time) + ("rust-unicase" ,rust-unicase)))) + (home-page "https://hyper.rs") + (synopsis "HTTP types from hyper 0.11.x") + (description "HTTP types from hyper 0.11.x") + (license license:expat))) + +(define-public rust-hyper-native-tls + (package + (name "rust-hyper-native-tls") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyper-native-tls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0s30y20qy0akzss91yxsq1x1q7rr04jy33i0cq72nx22yjc5advd")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-antidote" ,rust-antidote) + ("rust-hyper" ,rust-hyper) + ("rust-native-tls" ,rust-native-tls)))) + (home-page "https://github.com/sfackler/hyper-native-tls") + (synopsis "native-tls support for Hyper 0.10.") + (description "native-tls support for Hyper 0.10.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-hyper-rustls + (package + (name "rust-hyper-rustls") + (version "0.17.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyper-rustls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0li9xkzmqd40dbjbl9g0nbf2ka9y0q538ififyd30zsavz3qb7bi")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-ct-logs" ,rust-ct-logs) + ("rust-futures" ,rust-futures) + ("rust-hyper" ,rust-hyper) + ("rust-rustls" ,rust-rustls) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-tokio-rustls" ,rust-tokio-rustls) + ("rust-webpki" ,rust-webpki) + ("rust-webpki-roots" ,rust-webpki-roots)) + #:cargo-development-inputs + (("rust-tokio" ,rust-tokio) + ("rust-tokio-tcp" ,rust-tokio-tcp)))) + (home-page "https://github.com/ctz/hyper-rustls") + (synopsis + "Rustls+hyper integration for pure rust HTTPS") + (description + "Rustls+hyper integration for pure rust HTTPS") + (license (list license:asl2.0 + license:isc + license:expat)))) + +(define-public rust-hyper-tls + (package + (name "rust-hyper-tls") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyper-tls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0kqp4sz8613j6nv375wfj3gh95ff4nb6a3rb1f2vbx0almm0v01s")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-futures" ,rust-futures) + ("rust-hyper" ,rust-hyper) + ("rust-native-tls" ,rust-native-tls) + ("rust-tokio-io" ,rust-tokio-io)) + #:cargo-development-inputs + (("rust-tokio" ,rust-tokio)))) + (home-page "https://hyper.rs") + (synopsis + "Default TLS implementation for use with hyper") + (description + "Default TLS implementation for use with hyper") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-hyphenation (package (name "rust-hyphenation") @@ -3005,9 +4176,9 @@ hexadecimal representation.") (("rust-serde" ,rust-serde)) #:cargo-development-inputs (("rust-fnv" ,rust-fnv) - ("rust-itertools" ,rust-itertools) + ("rust-itertools" ,rust-itertools-0.7) ("rust-lazy-static" ,rust-lazy-static) - ("rust-quickcheck" ,rust-quickcheck) + ("rust-quickcheck" ,rust-quickcheck-0.6) ("rust-rand" ,rust-rand) ("rust-serde-test" ,rust-serde-test)))) (home-page "https://github.com/bluss/indexmap") @@ -3071,6 +4242,38 @@ hexadecimal representation.") "This package provides a snapshot testing library for Rust") (license license:asl2.0))) +(define-public rust-intel-mkl-src + (package + (name "rust-intel-mkl-src") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "intel-mkl-src" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "16kq725cl4rnvfpwq9x4rl83ylcqs7d0xryagx8ijm6bdblbfabc")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-failure" ,rust-failure) + ("rust-pkg-config" ,rust-pkg-config) + ("rust-reqwest" ,rust-reqwest) + ("rust-tar" ,rust-tar) + ("rust-xz2" ,rust-xz2)) + #:cargo-development-inputs + (("rust-libc" ,rust-libc)))) + (inputs + `(("pkg-config" ,pkg-config) + ("xz" ,xz))) + (home-page "https://github.com/termoshtt/rust-intel-mkl") + (synopsis "Redistribution of Intel MKL as a crate") + (description + "Redistribution of Intel @acronym{MKL, Math Kernel Library} as a crate.") + (license (list license:non-copyleft "Intel Simplified Software License" + license:expat)))) ; some wrapper codes + (define-public rust-intervaltree (package (name "rust-intervaltree") @@ -3096,29 +4299,65 @@ hexadecimal representation.") "This package provides a simple and generic implementation of an immutable interval tree.") (license license:expat))) -(define-public rust-iovec +(define-public rust-iron (package - (name "rust-iovec") - (version "0.1.2") + (name "rust-iron") + (version "0.6.1") (source (origin (method url-fetch) - (uri (crate-uri "iovec" version)) + (uri (crate-uri "iron" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "025vi072m22299z3fg73qid188z2iip7k41ba6v5v5yhwwby9rnv")))) + "1s4mf8395f693nhwsr0znw3j5frzn56gzllypyl50il85p50ily6")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-libc" ,rust-libc) - ("rust-winapi" ,rust-winapi)))) - (home-page "https://github.com/carllerche/iovec") + (("rust-hyper" ,rust-hyper-0.10) + ("rust-log" ,rust-log) + ("rust-mime-guess" ,rust-mime-guess) + ("rust-modifier" ,rust-modifier) + ("rust-num-cpus" ,rust-num-cpus) + ("rust-plugin" ,rust-plugin) + ("rust-typemap" ,rust-typemap) + ("rust-url" ,rust-url) + ("rust-hyper-native-tls" ,rust-hyper-native-tls)) + #:cargo-development-inputs + (("rust-mime" ,rust-mime) + ("rust-time" ,rust-time)))) + (home-page "https://github.com/iron/iron") + (synopsis "Extensible, Concurrency Focused Web Development in Rust.") + (description "Extensible, Concurrency Focused Web Development in Rust.") + (license license:expat))) + +(define-public rust-ipconfig + (package + (name "rust-ipconfig") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "ipconfig" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0gyqiqr4nk2dw9ild1aq3hnv6984sgydfdq7ki586q5ydwhzlyda")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-socket2" ,rust-socket2) + ("rust-widestring" ,rust-widestring) + ("rust-winapi" ,rust-winapi) + ("rust-winreg" ,rust-winreg)))) + (home-page + "https://github.com/liranringel/ipconfig") (synopsis - "Portable buffer type for scatter/gather I/O operations") + "Get network adapters information and network configuration for windows.") (description - "Portable buffer type for scatter/gather I/O operations") + "Get network adapters information and network configuration for windows.") (license (list license:asl2.0 license:expat)))) @@ -3141,8 +4380,8 @@ hexadecimal representation.") (("rust-either" ,rust-either)) #:cargo-development-inputs (("rust-permutohedron" ,rust-permutohedron) - ("rust-quickcheck" ,rust-quickcheck) - ("rust-rand" ,rust-rand)))) + ("rust-quickcheck" ,rust-quickcheck-0.7) + ("rust-rand" ,rust-rand-0.6)))) (home-page "https://github.com/bluss/rust-itertools") (synopsis @@ -3152,25 +4391,63 @@ hexadecimal representation.") (license (list license:asl2.0 license:expat)))) -(define-public rust-itoa ; guix upstreamable +(define-public rust-itertools-0.7 (package - (name "rust-itoa") - (version "0.4.4") + (inherit rust-itertools) + (name "rust-itertools") + (version "0.7.11") (source (origin (method url-fetch) - (uri (crate-uri "itoa" version)) + (uri (crate-uri "itertools" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0zvg2d9qv3avhf3d8ggglh6fdyw8kkwqg3r4622ly5yhxnvnc4jh")))) + "03cpsj26xmyamcalclqzr1i700vwx8hnbgxbpjvs354f8mnr8iqd")))) + (arguments + `(#:cargo-inputs + (("rust-either" ,rust-either)) + #:cargo-development-inputs + (("rust-permutohedron" ,rust-permutohedron) + ("rust-quickcheck" ,rust-quickcheck-0.5)))))) + +(define-public rust-jemalloc-ctl + (package + (name "rust-jemalloc-ctl") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "jemalloc-ctl" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1dx4mik2ww5ic4qqv5zx9dxq6pbkclxnxa9bscg4z4njkpzsa0n5")))) (build-system cargo-build-system) - (home-page "https://github.com/dtolnay/itoa") - (synopsis "Fast functions for printing integer primitives") - (description "This crate provides fast functions for printing integer -primitives to an @code{io::Write}.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-inputs + (("rust-jemalloc-sys" ,rust-jemalloc-sys) + ("rust-libc" ,rust-libc) + ("rust-paste" ,rust-paste)) + #:cargo-development-inputs + (("rust-jemallocator" ,rust-jemallocator)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-jemalloc + (lambda* (#:key inputs #:allow-other-keys) + (let ((jemalloc (assoc-ref inputs "jemalloc"))) + (setenv "JEMALLOC_OVERRIDE" + (string-append jemalloc "/lib/libjemalloc_pic.a"))) + #t))))) + (inputs + `(("jemalloc" ,jemalloc))) + (home-page "https://github.com/gnzlbg/jemallocator") + (synopsis + "A safe wrapper over jemalloc's control and introspection APIs") + (description + "This package provides a safe wrapper over jemalloc's control and introspection APIs") + (license #f))) (define-public rust-jemalloc-sys (package @@ -3180,22 +4457,34 @@ primitives to an @code{io::Write}.") (origin (method url-fetch) (uri (crate-uri "jemalloc-sys" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0ify9vlql01qhfxlj7d4p9jvcp90mj2h69nkbq7slccvbhzryfqd")))) + (base32 + "0ify9vlql01qhfxlj7d4p9jvcp90mj2h69nkbq7slccvbhzryfqd")) + ;(modules '((guix build utils))) + ;(snippet + ; '(begin + ; ;; unbundle jemalloc source + ; (delete-file-recursively "jemalloc") #t)) + )) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-libc" ,rust-libc) - ("rust-cc" ,rust-cc) - ("rust-fs-extra" ,rust-fs-extra)))) + `(#:cargo-inputs + (("rust-libc" ,rust-libc) + ("rust-cc" ,rust-cc) + ("rust-fs-extra" ,rust-fs-extra)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-jemalloc + (lambda* (#:key inputs #:allow-other-keys) + (let ((jemalloc (assoc-ref inputs "jemalloc"))) + (delete-file-recursively "jemalloc") + (setenv "JEMALLOC_OVERRIDE" + (string-append jemalloc "/lib/libjemalloc_pic.a"))) + #t))))) (inputs - `(("jemalloc" ,(@ (gnu packages jemalloc) jemalloc)) - ("rust-cc" ,rust-cc))) - (home-page - "https://github.com/gnzlbg/jemallocator") + `(("jemalloc" ,jemalloc))) + (home-page "https://github.com/gnzlbg/jemallocator") (synopsis "Rust FFI bindings to jemalloc") (description "Rust FFI bindings to jemalloc") (license (list license:asl2.0 @@ -3220,7 +4509,17 @@ primitives to an @code{io::Write}.") (("rust-jemalloc-sys" ,rust-jemalloc-sys) ("rust-libc" ,rust-libc)) #:cargo-development-inputs - (("rust-paste" ,rust-paste)))) + (("rust-paste" ,rust-paste)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-jemalloc + (lambda* (#:key inputs #:allow-other-keys) + (let ((jemalloc (assoc-ref inputs "jemalloc"))) + (setenv "JEMALLOC_OVERRIDE" + (string-append jemalloc "/lib/libjemalloc_pic.a"))) + #t))))) + (inputs + `(("jemalloc" ,jemalloc))) (home-page "https://github.com/gnzlbg/jemallocator") (synopsis "A Rust allocator backed by jemalloc") (description @@ -3228,48 +4527,35 @@ primitives to an @code{io::Write}.") (license (list license:asl2.0 license:expat)))) -(define-public rust-json ; guix upstreamable - (package - (name "rust-json") - (version "0.11.14") - (source - (origin - (method url-fetch) - (uri (crate-uri "json" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1hj8c6xj5c2aqqszi8naaflmcdbya1i9byyjrq4iybxjb4q91mq1")))) - (build-system cargo-build-system) - (home-page "https://github.com/maciejhirsz/json-rust") - (synopsis "JSON implementation in Rust") - (description "This crate provides a JSON implementation in Rust, reducing -friction with idiomatic Rust structs to ease interopability.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-lazy-static +(define-public rust-js-sys (package - (name "rust-lazy-static") - (version "1.3.0") + (name "rust-js-sys") + (version "0.3.27") (source (origin (method url-fetch) - (uri (crate-uri "lazy_static" version)) + (uri (crate-uri "js-sys" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "052ac27w189hrf1j3hz7sga46rp84zl2hqnzyihxv78mgzr2jmxw")))) + "1m6p0bdgdkhwwy6bvapl9z3bw9nq3li2x480anfffn3calm4zz0y")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs (("rust-spin" ,rust-spin)))) + `(#:cargo-inputs + (("rust-wasm-bindgen" ,rust-wasm-bindgen)) + #:cargo-development-inputs + (("rust-futures" ,rust-futures) + ("rust-wasm-bindgen-futures" + ,rust-wasm-bindgen-futures) + ("rust-wasm-bindgen-test" + ,rust-wasm-bindgen-test)))) (home-page - "https://github.com/rust-lang-nursery/lazy-static.rs") + "https://rustwasm.github.io/wasm-bindgen/") (synopsis - "A macro for declaring lazily evaluated statics in Rust.") + "Bindings for all JS global objects and functions in all JS environments like Node.js and browsers, built on `#[wasm_bindgen]` using the `wasm-bindgen` crate.") (description - "This package provides a macro for declaring lazily evaluated statics in Rust.") + "Bindings for all JS global objects and functions in all JS environments like Node.js and browsers, built on `#[wasm_bindgen]` using the `wasm-bindgen` crate.") (license (list license:asl2.0 license:expat)))) @@ -3333,31 +4619,34 @@ friction with idiomatic Rust structs to ease interopability.") (license (list license:asl2.0 license:expat)))) -(define-public rust-libc +(define-public rust-libflate (package - (name "rust-libc") - (version "0.2.60") + (name "rust-libflate") + (version "0.1.27") (source (origin (method url-fetch) - (uri (crate-uri "libc" version)) + (uri (crate-uri "libflate" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1sxmlcyb39v8awlq5ndaiiq2vja3mc4vf97nxz3qjy007xiq0knl")))) + (base32 + "1p8z839c5lpl0g01mf8iglys9lgcjxw6xjw56crhwp8z7gs5s4yr")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-rustc-std-workspace-core" - ,rust-rustc-std-workspace-core)))) - (home-page "https://github.com/rust-lang/libc") + `(#:cargo-inputs + (("rust-adler32" ,rust-adler32) + ("rust-crc32fast" ,rust-crc32fast) + ("rust-rle-decode-fast" ,rust-rle-decode-fast) + ("rust-take-mut" ,rust-take-mut)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap)))) + (home-page "https://github.com/sile/libflate") (synopsis - "Raw FFI bindings to platform libraries like libc.") + "A Rust implementation of DEFLATE algorithm and related formats (ZLIB, GZIP)") (description - "Raw FFI bindings to platform libraries like libc.") - (license (list license:asl2.0 - license:expat)))) + "This package provides a Rust implementation of DEFLATE algorithm and related formats (ZLIB, GZIP)") + (license license:expat))) (define-public rust-libgit2-sys (package @@ -3370,8 +4659,14 @@ friction with idiomatic Rust structs to ease interopability.") (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0y2mibmx7wy91s2kmb2gfb29mrqlqaxpy5wcwr8s1lwws7b9w5sc")))) + (base32 + "0y2mibmx7wy91s2kmb2gfb29mrqlqaxpy5wcwr8s1lwws7b9w5sc")) + ;(modules '((guix build utils))) + ;(snippet + ; '(begin + ; ;; unbundle jemalloc source + ; (delete-file-recursively "libgit2") #t)) + )) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -3381,9 +4676,22 @@ friction with idiomatic Rust structs to ease interopability.") ("rust-openssl-sys" ,rust-openssl-sys)) #:cargo-development-inputs (("rust-cc" ,rust-cc) - ("rust-pkg-config" ,rust-pkg-config)))) - ;(inputs - ; `(("libgit" ,(@ (gnu packages version-control) libgit2)))) + ("rust-pkg-config" ,rust-pkg-config)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-openssl + (lambda* (#:key inputs #:allow-other-keys) + (let ((openssl (assoc-ref inputs "openssl"))) + (setenv "OPENSSL_DIR" openssl)) + (delete-file-recursively "libgit2") + (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1") + (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1") + #t))))) + (inputs + `(("libgit" ,libgit2) + ("openssl" ,openssl) + ("pkg-config" ,pkg-config) + ("zlib" ,zlib))) (home-page "https://github.com/rust-lang/git2-rs") (synopsis @@ -3430,8 +4738,14 @@ friction with idiomatic Rust structs to ease interopability.") (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "17dz3xxy5bc73sr52maa6wdqmw1a0ymznrgfzlxid2rng101yshj")))) + (base32 + "17dz3xxy5bc73sr52maa6wdqmw1a0ymznrgfzlxid2rng101yshj")) + ;(modules '((guix build utils))) + ;(snippet + ; '(begin + ; ;; unbundle jemalloc source + ; (delete-file-recursively "libssh2") #t)) + )) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -3441,9 +4755,21 @@ friction with idiomatic Rust structs to ease interopability.") ("rust-vcpkg" ,rust-vcpkg)) #:cargo-development-inputs (("rust-cc" ,rust-cc) - ("rust-pkg-config" ,rust-pkg-config)))) - ;(inputs - ; `(("libssh2" ,(@ (gnu packages ssh) libssh2)))) + ("rust-pkg-config" ,rust-pkg-config)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-openssl + (lambda* (#:key inputs #:allow-other-keys) + (let ((openssl (assoc-ref inputs "openssl"))) + (setenv "OPENSSL_DIR" openssl)) + (delete-file-recursively "libssh2") + (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1") + #t))))) + (inputs + `(("libssh2" ,libssh2) + ("openssl" ,openssl) + ("pkg-config" ,pkg-config) + ("zlib" ,zlib))) (home-page "https://github.com/alexcrichton/ssh2-rs") (synopsis @@ -3453,7 +4779,6 @@ friction with idiomatic Rust structs to ease interopability.") (license (list license:asl2.0 license:expat)))) -;; TODO: Unbundle zlib (define-public rust-libz-sys (package (name "rust-libz-sys") @@ -3465,15 +4790,29 @@ friction with idiomatic Rust structs to ease interopability.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f")))) + "1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f")) + ;(modules '((guix build utils))) + ;(snippet + ; '(begin + ; ;; unbundle jemalloc source + ; (delete-file-recursively "src/zlib") #t)) + )) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-libc" ,rust-libc)) - #:cargo-development-inputs - (("rust-cc" ,rust-cc) + (("rust-libc" ,rust-libc) + ("rust-cc" ,rust-cc) ("rust-pkg-config" ,rust-pkg-config) - ("rust-vcpkg" ,rust-vcpkg)))) + ("rust-vcpkg" ,rust-vcpkg)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-vendored-zlib + (lambda _ + (delete-file-recursively "src/zlib") + #t))))) + (inputs + `(("pkg-config" ,pkg-config) + ("zlib" ,zlib))) (home-page "https://github.com/alexcrichton/libz-sys") (synopsis "Bindings to the system libz library (also known as zlib).") (description @@ -3510,6 +4849,25 @@ friction with idiomatic Rust structs to ease interopability.") (license (list license:asl2.0 license:expat)))) +(define-public rust-linked-hash-map-0.3 + (package + (inherit rust-linked-hash-map) + (name "rust-linked-hash-map") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "linked-hash-map" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1kaf95grvfqchxn8pl0854g8ab0fzl56217hndhhhz5qqm2j09kd")))) + (arguments + `(#:cargo-inputs + (("rust-clippy" ,rust-clippy) + ("rust-serde" ,rust-serde-0.8) + ("rust-serde-test" ,rust-serde-test)))))) ; 0.8 + (define-public rust-lipsum (package (name "rust-lipsum") @@ -3573,6 +4931,24 @@ friction with idiomatic Rust structs to ease interopability.") (license (list license:asl2.0 license:expat)))) +(define-public rust-lock-api-0.1 + (package + (inherit rust-lock-api) + (name "rust-lock-api") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "lock_api" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0b24q9mh258xa52ap636q1sxz0j5vrnp0hwbbh7ddjka3wwz3sv2")))) + (arguments + `(#:cargo-inputs + (("rust-owning-ref" ,rust-owning-ref) + ("rust-scopeguard" ,rust-scopeguard-0.3)))))) + (define-public rust-log (package (name "rust-log") @@ -3581,18 +4957,17 @@ friction with idiomatic Rust structs to ease interopability.") (origin (method url-fetch) (uri (crate-uri "log" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1cx51p86d9s1y2vbyi6jr4wj5cs7nryikygfcpbc42h7ajnvcxf2")))) + (base32 + "1cx51p86d9s1y2vbyi6jr4wj5cs7nryikygfcpbc42h7ajnvcxf2")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-cfg-if" ,rust-cfg-if) - ("rust-serde" ,rust-serde)) - #:cargo-development-inputs - (("rust-serde-test" ,rust-serde-test)))) + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-serde-test" ,rust-serde-test)))) (home-page "https://github.com/rust-lang/log") (synopsis "A lightweight logging facade for Rust") @@ -3601,64 +4976,162 @@ friction with idiomatic Rust structs to ease interopability.") (license (list license:asl2.0 license:expat)))) -(define-public rust-maplit ; guix upstreamable +(define-public rust-log-0.3 (package - (name "rust-maplit") - (version "1.0.1") + (inherit rust-log) + (name "rust-log") + (version "0.3.9") (source (origin (method url-fetch) - (uri (crate-uri "maplit" version)) + (uri (crate-uri "log" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hsczmvd6zkqgzqdjp5hfyg7f339n68w83n4pxvnsszrzssbdjq8")))) + "0jq23hhn5h35k7pa8r7wqnsywji6x3wn1q5q7lif5q536if8v7p1")))) + (arguments + `(#:cargo-inputs + (("rust-log" ,rust-log)))))) + +(define-public rust-loom + (package + (name "rust-loom") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "loom" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0w95rjw0sv3f5psaxlgfl4fsj6imjv16v2pap18alx2w7n2f8j24")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-futures-util-preview" + ,rust-futures-util-preview) + ("rust-generator" ,rust-generator) + ("rust-scoped-tls" ,rust-scoped-tls) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json)))) + (home-page "https://github.com/carllerche/loom") + (synopsis + "Permutation testing for concurrent code") + (description + "Permutation testing for concurrent code") + (license license:expat))) + +(define-public rust-lru-cache + (package + (name "rust-lru-cache") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "lru-cache" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "071viv6g2p3akwqmfb3c8vsycs5n7kr17b70l7la071jv0d4zqii")))) (build-system cargo-build-system) - (home-page "https://github.com/bluss/maplit") - (synopsis "Collection of Map macros") - (description "This crate provides a collection of @code{literal} macros for -@code{HashMap}, @code{HashSet}, @code{BTreeMap}, and @code{BTreeSet.}") + (arguments + `(#:cargo-inputs + (("rust-heapsize" ,rust-heapsize) + ("rust-linked-hash-map" ,rust-linked-hash-map)))) + (home-page + "https://github.com/contain-rs/lru-cache") + (synopsis + "A cache that holds a limited number of key-value pairs") + (description + "This package provides a cache that holds a limited number of key-value pairs") (license (list license:asl2.0 license:expat)))) -(define-public rust-matches ; guix upstreamable +(define-public rust-lzma-sys (package - (name "rust-matches") - (version "0.1.8") + (name "rust-lzma-sys") + (version "0.1.15") (source (origin (method url-fetch) - (uri (crate-uri "matches" version)) + (uri (crate-uri "lzma-sys" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "020axl4q7rk9vz90phs7f8jas4imxal9y9kxl4z4v7a6719mrz3z")))) + "14gyj256yh0wm77jbvmlc39v7lfn0navpfrja4alczarzlc8ir2k")))) (build-system cargo-build-system) - (home-page "https://github.com/SimonSapin/rust-std-candidates") - (synopsis "Macro to evaluate whether an expression matches a pattern.") - (description "This package provides a macro to evaluate, as a boolean, -whether an expression matches a pattern.") - (license license:expat))) + (arguments + `(#:cargo-inputs + (("rust-cc" ,rust-cc) + ("rust-libc" ,rust-libc) + ("rust-pkg-config" ,rust-pkg-config)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unbundle-xz + (lambda* (#:key inputs #:allow-other-keys) + (let ((xz (assoc-ref inputs "xz"))) + (delete-file-recursively "xz-5.2")) + #t))))) + (inputs + `(("pkg-config" ,pkg-config) + ("xz" ,xz))) + (home-page "https://github.com/alexcrichton/xz2-rs") + (synopsis "Bindings to liblzma for lzma and xz stream encoding/decoding") + (description + "Raw bindings to liblzma which contains an implementation of LZMA and xz +stream encoding/decoding.") + (license (list license:asl2.0 + license:expat)))) -(define-public rust-md5 ; guix upstreamable +(define-public rust-matrixmultiply (package - (name "rust-md5") - (version "0.6.1") + (name "rust-matrixmultiply") + (version "0.2.2") (source (origin (method url-fetch) - (uri (crate-uri "md5" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "matrixmultiply" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "17b2xm4h4cvxsdjsf3kdrzqv2za60kak961xzi5kmw6g6djcssvy")))) + (base32 + "16sgc1j87hmsqmhlqpqgcpbrb00f267ikbr55fhxla8nhwnxgznw")))) (build-system cargo-build-system) - (home-page "https://github.com/stainless-steel/md5") - (synopsis "MD5 hash function in Rust") - (description "The package provides the MD5 hash function.") + (arguments + `(#:cargo-inputs + (("rust-rawpointer" ,rust-rawpointer)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher) + ("rust-itertools" ,rust-itertools)))) + (home-page + "https://github.com/bluss/matrixmultiply/") + (synopsis "General matrix multiplication for f32 and f64 matrices.") + (description "General matrix multiplication for f32 and f64 matrices. Operates on matrices with general layout (they can use arbitrary row and column stride). Detects and uses AVX or SSE2 on x86 platforms transparently for higher performance. Uses a microkernel strategy, so that the implementation is easy to parallelize and optimize.") (license (list license:asl2.0 license:expat)))) +(define-public rust-matrixmultiply-0.1 + (package + (inherit rust-matrixmultiply) + (name "rust-matrixmultiply") + (version "0.1.15") + (source + (origin + (method url-fetch) + (uri (crate-uri "matrixmultiply" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "00p0fpjhm45qdzi37mgv7ggsy8b9gqvq4999yrbgyn1dxkf6gbfw")))) + (arguments + `(#:cargo-inputs + (("rust-rawpointer" ,rust-rawpointer)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher)))))) + (define-public rust-memchr (package (name "rust-memchr") @@ -3714,6 +5187,26 @@ whether an expression matches a pattern.") (license (list license:asl2.0 license:expat)))) +(define-public rust-memmap-0.6 + (package + (inherit rust-memmap) + (name "rust-memmap") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "memmap" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1zy6s0ni0lx9rjzq3gq2zz9r8zgjmbp02332g3gsj4fyhv4s5zz2")))) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc) + ("rust-winapi" ,rust-winapi)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))))) + (define-public rust-memoffset (package (name "rust-memoffset") @@ -3747,82 +5240,368 @@ whether an expression matches a pattern.") (origin (method url-fetch) (uri (crate-uri "memoffset" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1cvm2z7dy138s302ii7wlzcxbka5a8yfl5pl5di7lbdnw9hw578g")))))) + +(define-public rust-mime-0.2 + (package + (inherit rust-mime) + (name "rust-mime") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "mime" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1q1s1ax1gaz8ld3513nvhidfwnik5asbs1ma3hp6inp5dn56nqms")))) + (arguments + `(#:cargo-inputs + (("rust-log" ,rust-log-0.3) + ("rust-heapsize" ,rust-heapsize-0.3) + ("rust-serde" ,rust-serde-0.8)) + #:cargo-development-inputs + (("rust-serde-json" ,rust-serde-json-0.8)))))) + +(define-public rust-mime-guess + (package + (name "rust-mime-guess") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "mime_guess" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1cvm2z7dy138s302ii7wlzcxbka5a8yfl5pl5di7lbdnw9hw578g")))))) + "16c5ssgali30db6jh1cndy77dd1qgcykhshiyfyjvxxf94wx03hs")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-mime" ,rust-mime) + ("rust-unicase" ,rust-unicase)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion)))) + (home-page "https://github.com/abonander/mime_guess") + (synopsis + "MIME/MediaType guessing by file extension. Uses a static map of known file extension -> MIME type mappings.") + (description + "MIME/MediaType guessing by file extension. Uses a static map of known file extension -> MIME type mappings.") + (license license:expat))) -(define-public rust-no-panic +(define-public rust-miniz-oxide (package - (name "rust-no-panic") - (version "0.1.10") + (name "rust-miniz-oxide") + (version "0.3.2") (source (origin (method url-fetch) - (uri (crate-uri "no-panic" version)) + (uri (crate-uri "miniz_oxide" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "089gmyxg7kviimqn5nmghm5kngnmi77a0c6fbv0j67jxx7pjhq3r")))) + "041s41l5w7z8pkp93pdzn8rngxr93q4wxp034pr0cvc7bgway23i")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-adler32" ,rust-adler32)))) + (home-page + "https://github.com/Frommi/miniz_oxide/tree/master/miniz_oxide") + (synopsis + "DEFLATE compression and decompression library rewritten in Rust based on miniz") + (description + "DEFLATE compression and decompression library rewritten in Rust based on miniz") + (license license:expat))) + +(define-public rust-miniz-sys + (package + (name "rust-miniz-sys") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (crate-uri "miniz-sys" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "00l2r4anm8g35x0js2zfdnwfbrih9m43vphdpb77c5ga3kjkm7hy")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cc" ,rust-cc) + ("rust-libc" ,rust-libc)))) + (home-page "https://github.com/alexcrichton/flate2-rs") + (synopsis + "Bindings to the miniz.c library.") + (description + "Bindings to the miniz.c library.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-mio + (package + (name "rust-mio") + (version "0.6.19") + (source + (origin + (method url-fetch) + (uri (crate-uri "mio" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "08zzs227vrnyz5kvws6awzlgzb8zqpnihs71hkqlw07dlfb1kxc3")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-proc-macro2" ,rust-proc-macro2) - ("rust-quote" ,rust-quote) - ("rust-syn" ,rust-syn)) + (("rust-fuchsia-zircon" ,rust-fuchsia-zircon) + ("rust-fuchsia-zircon-sys" + ,rust-fuchsia-zircon-sys) + ("rust-iovec" ,rust-iovec) + ("rust-kernel32-sys" ,rust-kernel32-sys) + ("rust-libc" ,rust-libc) + ("rust-log" ,rust-log) + ("rust-miow" ,rust-miow-0.2) + ("rust-net2" ,rust-net2) + ("rust-slab" ,rust-slab) + ("rust-winapi" ,rust-winapi)) #:cargo-development-inputs - (("rust-tempfile" ,rust-tempfile)))) - (home-page "https://github.com/dtolnay/no-panic") + (("rust-bytes" ,rust-bytes) + ("rust-env-logger" ,rust-env-logger) + ("rust-tempdir" ,rust-tempdir)))) + (home-page "https://github.com/carllerche/mio") + (synopsis "Lightweight non-blocking IO") + (description "Lightweight non-blocking IO") + (license license:expat))) + +(define-public rust-mio-uds + (package + (name "rust-mio-uds") + (version "0.6.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "mio-uds" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "09gimdbnj7b9yca99pk8lxh9jhl79msj795c8fxi2sqr9slmfqln")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-iovec" ,rust-iovec) + ("rust-libc" ,rust-libc) + ("rust-mio" ,rust-mio)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://github.com/alexcrichton/mio-uds") (synopsis - "Attribute macro to require that the compiler prove a function can't ever panic.") + "Unix domain socket bindings for mio") (description - "Attribute macro to require that the compiler prove a function can't ever panic.") + "Unix domain socket bindings for mio") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-miow + (package + (name "rust-miow") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "miow" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "09ljvx6wg30f2xlv7b7hhpkw7k312n3hjgmrbhwzhz9x03ra0sir")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-socket2" ,rust-socket2) + ("rust-winapi" ,rust-winapi)) + #:cargo-development-inputs + (("rust-rand" ,rust-rand-0.4)))) + (home-page + "https://github.com/alexcrichton/miow") + (synopsis + "A zero overhead I/O library for Windows, focusing on IOCP and Async I/O abstractions.") + (description + "This package provides a zero overhead I/O library for Windows, focusing on IOCP and Async I/O abstractions.") (license (list license:asl2.0 license:expat)))) -(define-public rust-nodrop ; guix upstreamable +(define-public rust-miow-0.2 (package - (name "rust-nodrop") - (version "0.1.13") + (inherit rust-miow) + (name "rust-miow") + (version "0.2.1") (source (origin (method url-fetch) - (uri (crate-uri "nodrop" version)) + (uri (crate-uri "miow" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0if9ifn6rvar5jirx4b3qh4sl5kjkmcifycvzhxa9j3crkfng5ig")))) + "06g9b8sqlh5gxakwqq4rrib07afwanfnxgxajrldwcgk3hxjy7wc")))) + (arguments + `(#:cargo-inputs + (("rust-kernel32-sys" ,rust-kernel32-sys) + ("rust-net2" ,rust-net2) + ("rust-winapi" ,rust-winapi-0.2) + ("rust-ws2-32-sys" ,rust-ws2-32-sys)) + #:cargo-development-inputs + (("rust-rand" ,rust-rand-0.3)))))) + +(define-public rust-native-tls + (package + (name "rust-native-tls") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "native-tls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ki7cj4wzyd2nach4qdjly69sp7rs0yz3n3z2ii4mm1gqajg2bab")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-nodrop-union" ,rust-nodrop-union)))) - (home-page "https://github.com/bluss/arrayvec") - (synopsis "Wrapper type to inhibit drop (destructor)") - (description "This package provides a wrapper type to inhibit drop -(destructor). Use @code{std::mem::ManuallyDrop} instead!") + (("rust-lazy-static" ,rust-lazy-static) + ("rust-libc" ,rust-libc) + ("rust-log" ,rust-log) + ("rust-openssl" ,rust-openssl) + ("rust-openssl-probe" ,rust-openssl-probe) + ("rust-openssl-sys" ,rust-openssl-sys) + ("rust-schannel" ,rust-schannel) + ("rust-security-framework" ,rust-security-framework) + ("rust-security-framework-sys" ,rust-security-framework-sys) + ("rust-tempfile" ,rust-tempfile)) + #:cargo-development-inputs + (("rust-hex" ,rust-hex)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-openssl + (lambda* (#:key inputs #:allow-other-keys) + (let ((openssl (assoc-ref inputs "openssl"))) + (setenv "OPENSSL_DIR" openssl)) + #t))))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://github.com/sfackler/rust-native-tls") + (synopsis + "An abstraction over platform-specific TLS implementations.") + (description + "An abstraction over platform-specific TLS implementations.") (license (list license:asl2.0 license:expat)))) -(define-public rust-nodrop-union ; guix upstreamable +(define-public rust-ndarray (package - (name "rust-nodrop-union") - (version "0.1.10") + (name "rust-ndarray") + (version "0.12.1") (source (origin (method url-fetch) - (uri (crate-uri "nodrop-union" version)) + (uri (crate-uri "ndarray" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jsnkdn9l8jlmb9h4wssi76sxnyxwnyi00p6y1p2gdq7c1gdw2b7")))) + "0a5rfwcbqnvbwi3nw5sfz6kf0flhmjxs64s0b4kxc6lhmyl81wvw")))) (build-system cargo-build-system) - (home-page "https://github.com/bluss/arrayvec") - (synopsis "Wrapper type to inhibit drop (destructor)") - (description "This package provides a wrapper type to inhibit drop -(destructor). Implementation crate for nodrop, the untagged unions -implementation (which is unstable / requires nightly).") + (arguments + `(#:cargo-inputs + (("rust-itertools" ,rust-itertools-0.7) + ("rust-matrixmultiply" ,rust-matrixmultiply-0.1) + ("rust-num-complex" ,rust-num-complex) + ("rust-num-traits" ,rust-num-traits) + ("rust-blas-src" ,rust-blas-src-0.2) + ("rust-cblas-sys" ,rust-cblas-sys) + ("rust-rustc-serialize" ,rust-rustc-serialize) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-defmac" ,rust-defmac-0.1) + ("rust-quickcheck" ,rust-quickcheck-0.7) + ("rust-rawpointer" ,rust-rawpointer)))) + (home-page "https://github.com/rust-ndarray/ndarray") + (synopsis + "ndarray implements an n-dimensional container for general elements and for numerics.") + (description + "ndarray implements an n-dimensional container for general elements and for numerics.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-netlib-src + (package + (name "rust-netlib-src") + (version "0.7.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "netlib-src" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "112hwfw1zzdj10h3j213xxqjrq38iygb3nb3ijay65ycmrg819s4")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-cmake" ,rust-cmake) + ("rust-libc" ,rust-libc)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-lapack + (lambda _ + (delete-file-recursively "source") + (substitute* "Cargo.toml" + (("default .*") + "default = [\"system\"]\n")) + #t))))) + (inputs + `(("gfortran:lib" ,gfortran "lib") + ("lapack" ,lapack))) + (home-page "https://github.com/cmr/netlib-src") + (synopsis + "The package provides a source of BLAS and LAPACK via Netlib.") + (description + "The package provides a source of BLAS and LAPACK via Netlib.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-no-panic + (package + (name "rust-no-panic") + (version "0.1.10") + (source + (origin + (method url-fetch) + (uri (crate-uri "no-panic" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "089gmyxg7kviimqn5nmghm5kngnmi77a0c6fbv0j67jxx7pjhq3r")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2) + ("rust-quote" ,rust-quote) + ("rust-syn" ,rust-syn)) + #:cargo-development-inputs + (("rust-tempfile" ,rust-tempfile)))) + (home-page "https://github.com/dtolnay/no-panic") + (synopsis + "Attribute macro to require that the compiler prove a function can't ever panic.") + (description + "Attribute macro to require that the compiler prove a function can't ever panic.") (license (list license:asl2.0 license:expat)))) @@ -3858,111 +5637,126 @@ implementation (which is unstable / requires nightly).") "This package provides a byte-oriented, zero-copy, parser combinators library") (license license:expat))) -(define-public rust-num-cpus +(define-public rust-num-complex (package - (name "rust-num-cpus") - (version "1.10.1") + (name "rust-num-complex") + (version "0.2.3") (source (origin (method url-fetch) - (uri (crate-uri "num_cpus" version)) + (uri (crate-uri "num-complex" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0wrj3zvj6h3q26sqj9zxpd59frjb54n7jhjwf307clq31ic47vxw")))) + "1z6zjdzx1g1hj4y132ddy83d3p3zvw06igbf59npxxrzzcqwzc7w")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-libc" ,rust-libc)) + (("rust-num-traits" ,rust-num-traits) + ("rust-rand" ,rust-rand) + ("rust-serde" ,rust-serde)) #:cargo-development-inputs - (("rust-doc-comment" ,rust-doc-comment)))) + (("rust-autocfg" ,rust-autocfg)))) (home-page - "https://github.com/seanmonstar/num_cpus") - (synopsis "Get the number of CPUs on a machine.") + "https://github.com/rust-num/num-complex") + (synopsis + "Complex numbers implementation for Rust") (description - "Get the number of CPUs on a machine.") + "Complex numbers implementation for Rust") (license (list license:asl2.0 license:expat)))) -(define-public rust-num-integer +(define-public rust-object (package - (name "rust-num-integer") - (version "0.1.41") + (name "rust-object") + (version "0.13.0") (source (origin (method url-fetch) - (uri (crate-uri "num-integer" version)) + (uri (crate-uri "object" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "02dwjjpfbi16c71fq689s4sw3ih52cvfzr5z5gs6qpr5z0g58pmq")))) + "05gfh6da1aavksxxq52hpzy40yiqpwzra8lfk7pcc45qqrdw97nq")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-num-traits" ,rust-num-traits)) + (("rust-goblin" ,rust-goblin) + ("rust-scroll" ,rust-scroll) + ("rust-target-lexicon" ,rust-target-lexicon) + ("rust-uuid" ,rust-uuid) + ("rust-crc32fast" ,rust-crc32fast) + ("rust-flate2" ,rust-flate2) + ("rust-indexmap" ,rust-indexmap) + ("rust-parity-wasm" ,rust-parity-wasm)) #:cargo-development-inputs - (("rust-autocfg" ,rust-autocfg)))) - (home-page - "https://github.com/rust-num/num-integer") - (synopsis "Integer traits and functions") - (description "Integer traits and functions") + (("rust-memmap" ,rust-memmap)))) + (home-page "https://github.com/gimli-rs/object") + (synopsis + "A unified interface for parsing object file formats.") + (description + "A unified interface for parsing object file formats.") (license (list license:asl2.0 license:expat)))) -(define-public rust-num-iter +(define-public rust-odds (package - (name "rust-num-iter") - (version "0.1.39") + (name "rust-odds") + (version "0.3.1") (source (origin (method url-fetch) - (uri (crate-uri "num-iter" version)) + (uri (crate-uri "odds" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0bhk2qbr3261r6zvfc58lz4spfqjhvdripxgz5mks5rd85r55gbn")))) + "0rdnxa0na4897yb0svb3figz35g4imxjv61yfm2j21gbh5q8v8d9")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-num-integer" ,rust-num-integer) - ("rust-num-traits" ,rust-num-traits)) + (("rust-rawpointer" ,rust-rawpointer) + ("rust-rawslice" ,rust-rawslice) + ("rust-unchecked-index" ,rust-unchecked-index)) #:cargo-development-inputs - (("rust-autocfg" ,rust-autocfg)))) + (("rust-itertools" ,rust-itertools) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-memchr" ,rust-memchr) + ("rust-quickcheck" ,rust-quickcheck)))) (home-page - "https://github.com/rust-num/num-iter") + "https://github.com/bluss/odds") (synopsis - "External iterators for generic mathematics") + "Odds and ends") (description - "External iterators for generic mathematics") + "Odds and ends collection miscellania. Extra functionality for slices (`.find()`, `RevSlice`), strings and other things. Things in odds may move to more appropriate crates if we find them.") (license (list license:asl2.0 license:expat)))) -(define-public rust-num-traits +(define-public rust-openblas-src (package - (name "rust-num-traits") - (version "0.2.8") + (name "rust-openblas-src") + (version "0.7.0") (source (origin (method url-fetch) - (uri (crate-uri "num-traits" version)) + (uri (crate-uri "openblas-src" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0clvrm34rrqc8p6gq5ps5fcgws3kgq5knh7nlqxf2ayarwks9abb")))) + "1dyf7yh6rmkk7k3pgcp5p8248f08hhajkigw42bfwjw1d3jk6d8b")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-autocfg" ,rust-autocfg)))) + `(#:cargo-development-inputs + (("rust-libc" ,rust-libc)))) (home-page - "https://github.com/rust-num/num-traits") + "https://github.com/blas-lapack-rs/openblas-src") (synopsis - "Numeric traits for generic mathematics") + "The package provides a source of BLAS and LAPACK via OpenBLAS.") (description - "Numeric traits for generic mathematics") + "The package provides a source of BLAS and LAPACK via OpenBLAS.") (license (list license:asl2.0 license:expat)))) @@ -3990,17 +5784,49 @@ implementation (which is unstable / requires nightly).") ("rust-openssl-sys" ,rust-openssl-sys)) #:cargo-development-inputs (("rust-hex" ,rust-hex) - ("rust-tempdir" ,rust-tempdir)))) + ("rust-tempdir" ,rust-tempdir)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-openssl + (lambda* (#:key inputs #:allow-other-keys) + (let ((openssl (assoc-ref inputs "openssl"))) + (setenv "OPENSSL_DIR" openssl)) + #t))))) + (inputs + `(("openssl" ,openssl))) (home-page "https://github.com/sfackler/rust-openssl") (synopsis "OpenSSL bindings") (description "OpenSSL bindings") (license license:asl2.0))) +(define-public rust-openssl-probe + (package + (name "rust-openssl-probe") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "openssl-probe" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1pijrdifgsdwd45b08c2g0dsmnhz7c3kmagb70839ngrd7d29bvp")))) + (build-system cargo-build-system) + (home-page + "https://github.com/alexcrichton/openssl-probe") + (synopsis + "Tool for helping to find SSL certificate locations on the system for OpenSSL") + (description + "Tool for helping to find SSL certificate locations on the system for OpenSSL") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-openssl-src (package (name "rust-openssl-src") - (version "111.4.0+1.1.1c") + (version "111.5.0+1.1.1c") (source (origin (method url-fetch) @@ -4009,7 +5835,7 @@ implementation (which is unstable / requires nightly).") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "10s3hvkfk6bi4ba1ssvj914rjs31vs8plssy4kbvsa0w7idkqfkq")))) + "17h4jwa3n1i91h0q8g72c1d9xzm97bnkxn1s7rljyghp94zvzpjb")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-cc" ,rust-cc)))) @@ -4025,7 +5851,7 @@ implementation (which is unstable / requires nightly).") (define-public rust-openssl-sys (package (name "rust-openssl-sys") - (version "0.9.48") + (version "0.9.49") (source (origin (method url-fetch) @@ -4034,72 +5860,90 @@ implementation (which is unstable / requires nightly).") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1f05kxx8mai9ac16x1lk0404bymghbbj7vcbqrfwqfr52w131fmm")))) + "1168vivyqbzaxl48bvv9r1x714c03f5c1za8pv5x8fyj9gjxkypl")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-libc" ,rust-libc)) - #:cargo-development-inputs - (("rust-autocfg" ,rust-autocfg) - ("rust-cc" ,rust-cc) - ("rust-openssl-src" ,rust-openssl-src) - ("rust-pkg-config" ,rust-pkg-config) - ("rust-vcpkg" ,rust-vcpkg)))) + `(#:cargo-inputs + (("rust-autocfg" ,rust-autocfg) + ("rust-libc" ,rust-libc)) + #:cargo-development-inputs + (("rust-autocfg" ,rust-autocfg) + ("rust-cc" ,rust-cc) + ("rust-openssl-src" ,rust-openssl-src) + ("rust-pkg-config" ,rust-pkg-config) + ("rust-vcpkg" ,rust-vcpkg)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-openssl + (lambda* (#:key inputs #:allow-other-keys) + (let ((openssl (assoc-ref inputs "openssl"))) + (setenv "OPENSSL_DIR" openssl)) + #t))))) + (inputs + `(("openssl" ,openssl) + ("pkg-config" ,pkg-config))) (home-page "https://github.com/sfackler/rust-openssl") (synopsis "FFI bindings to OpenSSL") (description "FFI bindings to OpenSSL") (license license:expat))) -(define-public rust-rand-os +(define-public rust-ordermap (package - (name "rust-rand-os") - (version "0.2.0") + (name "rust-ordermap") + (version "0.4.2") (source (origin (method url-fetch) - (uri (crate-uri "rand_os" version)) + (uri (crate-uri "ordermap" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "06is69f8rfzs620g5b54k6cgy5yaycrsyqg55flyfrsf8g88733f")))) + "1m0vxmlm1x92m1ydgpddzg5mrfk3ddy8gk3r9dmpml18qrs9ch4i")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-getrandom" ,rust-getrandom) - ("rust-rand-core" ,rust-rand-core)))) - (home-page "https://crates.io/crates/rand_os") - (synopsis "OS backed Random Number Generator") - (description "OS backed Random Number Generator") + `(#:cargo-inputs + (("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-fnv" ,rust-fnv) + ("rust-itertools" ,rust-itertools-0.7) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-quickcheck" ,rust-quickcheck-0.6) + ("rust-rand" ,rust-rand-0.4) + ("rust-serde-test" ,rust-serde-test)))) + (home-page "https://github.com/bluss/ordermap") + (synopsis + "A hash table with consistent order and fast iteration. NOTE: This crate was renamed to indexmap. Please use it under its new name.") + (description + "A hash table with consistent order and fast iteration. NOTE: This crate was renamed to indexmap. Please use it under its new name.") + (properties `((superseded . ,rust-indexmap))) (license (list license:asl2.0 license:expat)))) -(define-public rust-rand-os-0.1 +(define-public rust-ordermap-0.3 (package - (inherit rust-rand-os) - (name "rust-rand-os") - (version "0.1.3") + (inherit rust-ordermap) + (name "rust-ordermap") + (version "0.3.5") (source (origin (method url-fetch) - (uri (crate-uri "rand_os" version)) + (uri (crate-uri "ordermap" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0wahppm0s64gkr2vmhcgwc0lij37in1lgfxg5rbgqlz0l5vgcxbv")))) + "0qr0a50l0qakbjcck93qdayd0xl8gzpp42x0n7b75cs4ybsx6vm8")))) (arguments `(#:cargo-inputs - (("rust-cloudabi" ,rust-cloudabi) - ("rust-fuchsia-cprng" ,rust-fuchsia-cprng) - ("rust-getrandom" ,rust-getrandom) - ("rust-libc" ,rust-libc) - ("rust-log" ,rust-log) - ("rust-rand-core" ,rust-rand-core-0.4) - ("rust-rdrand" ,rust-rdrand-0.4) - ("rust-stdweb" ,rust-stdweb) - ("rust-wasm-bindgen" ,rust-wasm-bindgen) - ("rust-winapi" ,rust-winapi)))))) + (("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-fnv" ,rust-fnv) + ("rust-itertools" ,rust-itertools-0.7) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-quickcheck" ,rust-quickcheck-0.6) + ("rust-rand" ,rust-rand-0.4) + ("rust-serde-test" ,rust-serde-test)))))) (define-public rust-packed-simd (package @@ -4133,6 +5977,32 @@ implementation (which is unstable / requires nightly).") (license (list license:asl2.0 license:expat)))) +(define-public rust-parity-wasm + (package + (name "rust-parity-wasm") + (version "0.40.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "parity-wasm" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0sp1nv5yjw2wpg2j7mjq3mhqqjqb85wmbxrgk27q2zvw7ddqmrky")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-time" ,rust-time)))) + (home-page + "https://github.com/paritytech/parity-wasm") + (synopsis + "WebAssembly binary format serialization/deserialization/interpreter") + (description + "WebAssembly binary format serialization/deserialization/interpreter") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-parking-lot (package (name "rust-parking-lot") @@ -4165,6 +6035,26 @@ implementation (which is unstable / requires nightly).") (license (list license:asl2.0 license:expat)))) +(define-public rust-parking-lot-0.7 + (package + (inherit rust-parking-lot) + (name "rust-parking-lot") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "parking_lot" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0dz32cqx9200n1lk3kwyb599vabfid3f8sj1aq85sw42s2pb8hdb")))) + (arguments + `(#:cargo-inputs + (("rust-lock-api" ,rust-lock-api-0.1) + ("rust-parking-lot-core" ,rust-parking-lot-core-0.4)) + #:cargo-development-inputs + (("rust-rand" ,rust-rand-0.6)))))) + (define-public rust-parking-lot-core (package (name "rust-parking-lot-core") @@ -4201,6 +6091,29 @@ implementation (which is unstable / requires nightly).") (license (list license:asl2.0 license:expat)))) +(define-public rust-parking-lot-core-0.4 + (package + (inherit rust-parking-lot-core) + (name "rust-parking-lot-core") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "parking_lot_core" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jcq8aq4wv9y5fip7jg12jdwjd5g5r3x857xdma8vcin769cgj4l")))) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc) + ("rust-rand" ,rust-rand-0.6) + ("rust-rustc-version" ,rust-rustc-version) + ("rust-winapi" ,rust-winapi) + ("rust-backtrace" ,rust-backtrace) + ("rust-petgraph" ,rust-petgraph) + ("rust-thread-id" ,rust-thread-id)))))) + (define-public rust-paste (package (name "rust-paste") @@ -4255,47 +6168,28 @@ implementation (which is unstable / requires nightly).") (license (list license:asl2.0 license:expat)))) -(define-public rust-peeking-take-while ; guix upstreamable +(define-public rust-persistent (package - (name "rust-peeking-take-while") - (version "0.1.2") - (source - (origin - (method url-fetch) - (uri (crate-uri "peeking_take_while" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "16bhqr6rdyrp12zv381cxaaqqd0pwysvm1q8h2ygihvypvfprc8r")))) - (build-system cargo-build-system) - (home-page "https://github.com/fitzgen/peeking_take_while") - (synopsis "Provides the peeking_take_while iterator adaptor method") - (description - "Like @code{Iterator::take_while}, but calls the predicate on a peeked -value. This allows you to use @code{Iterator::by_ref} and -@code{Iterator::take_while} together, and still get the first value for which -the @code{take_while} predicate returned false after dropping the @code{by_ref}.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-percent-encoding ; guix upstreamable - (package - (name "rust-percent-encoding") - (version "2.0.0") + (name "rust-persistent") + (version "0.4.0") (source (origin (method url-fetch) - (uri (crate-uri "percent-encoding" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "persistent" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0m6rkp3iy11la04p6z3492rns6n693pvmx585dvfmzzlzak2hkxs")))) + (base32 + "1iblxjjzd0h784l5y573nw5z3pdb3330k69hh413agagkh0a13wf")))) (build-system cargo-build-system) - (home-page "https://github.com/servo/rust-url/") - (synopsis "Percent encoding and decoding") - (description "This crate provides percent encoding and decoding.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-inputs + (("rust-iron" ,rust-iron) + ("rust-plugin" ,rust-plugin)))) + (home-page "https://github.com/iron/persistent") + (synopsis "A set of middleware for sharing server-global data in Iron.") + (description "A set of middleware for sharing server-global data in Iron.") + (license license:expat))) (define-public rust-pest (package @@ -4399,109 +6293,124 @@ the @code{take_while} predicate returned false after dropping the @code{by_ref}. (license (list license:asl2.0 license:expat)))) -(define-public rust-pin-utils ; guix upstreamable - (package - (name "rust-pin-utils") - (version "0.1.0-alpha.4") - (source - (origin - (method url-fetch) - (uri (crate-uri "pin-utils" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "11xmyx00n4m37d546by2rxb8ryxs12v55cc172i3yak1rqccd52q")))) - (build-system cargo-build-system) - (home-page "https://github.com/rust-lang-nursery/pin-utils") - (synopsis "Utilities for pinning") - (description "This crate provides utilities for pinning values on the stack.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-pkg-config +(define-public rust-petgraph (package - (name "rust-pkg-config") - (version "0.3.14") + (name "rust-petgraph") + (version "0.4.13") (source (origin (method url-fetch) - (uri (crate-uri "pkg-config" version)) + (uri (crate-uri "petgraph" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "135ia995lqzr0gxpk85h0bjxf82kj6hbxdx924sh9jdln6r8wvk7")))) + "0kyfmca854s54jk26g2x1kjb04c3k7cjilaxyr0if8lhxv8mjdlw")))) (build-system cargo-build-system) (arguments - `(#:cargo-development-inputs - (("rust-lazy-static" ,rust-lazy-static)))) - (inputs - `(("pkg-config" ,(@ (gnu packages pkg-config) pkg-config)))) + `(#:cargo-inputs + (("rust-fixedbitset" ,rust-fixedbitset) + ("rust-ordermap" ,rust-ordermap-0.3) + ("rust-quickcheck" ,rust-quickcheck) + ("rust-serde" ,rust-serde) + ("rust-serde-derive" ,rust-serde-derive)) + #:cargo-development-inputs + (("rust-defmac" ,rust-defmac) + ("rust-itertools" ,rust-itertools) + ("rust-odds" ,rust-odds) + ("rust-rand" ,rust-rand-0.3)))) (home-page - "https://github.com/alexcrichton/pkg-config-rs") + "https://github.com/bluss/petgraph") (synopsis - "A library to run the pkg-config system tool at build time in order to be used in Cargo build scripts.") + "Graph data structure library. Provides graph types and graph algorithms.") (description - "A library to run the pkg-config system tool at build time in order to be used in Cargo build scripts.") + "Graph data structure library. Provides graph types and graph algorithms.") (license (list license:asl2.0 license:expat)))) -(define-public rust-plain ; guix upstreamable +(define-public rust-pico-sys (package - (name "rust-plain") - (version "0.2.3") + (name "rust-pico-sys") + (version "0.0.1") (source (origin (method url-fetch) - (uri (crate-uri "plain" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "pico-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 (base32 - "19n1xbxb4wa7w891268bzf6cbwq4qvdb86bik1z129qb0xnnnndl")))) + "1q5pg0ms6szz6b5h26h4k40zb76zbwwjgyigac4wly9qngdj4yl5")))) (build-system cargo-build-system) - (home-page "https://github.com/randomites/plain") - (synopsis "Rust library that allows reinterpreting data safely") - (description "This package provides a small Rust library that allows users - to reinterpret data of certain types safely.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-inputs + (("rust-cc" ,rust-cc) + ("rust-libc" ,rust-libc)))) + (home-page "https://github.com/reem/rust-pico-sys.git") + (synopsis + "Bindings to the PicoHTTPParser.") + (description + "Bindings to the PicoHTTPParser.") + (license license:expat))) -(define-public rust-pocket-resources ; guix upstreamable +(define-public rust-pretty-env-logger (package - (name "rust-pocket-resources") - (version "0.3.2") + (name "rust-pretty-env-logger") + (version "0.3.1") (source (origin (method url-fetch) - (uri (crate-uri "pocket-resources" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "pretty_env_logger" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1n2i5vmi8fdbw89wm5nz1ws1z9f1qax911p6ksg4scmdg23z6df1")))) + (base32 + "0x4hyjlnvvhyk9m74iypzybm22w3dl2k8img4b956239n5vf8zki")))) (build-system cargo-build-system) - (home-page "https://github.com/tomaka/pocket-resources") - (synopsis "Include resources in your applications") - (description "This crate allows you to include resources in your -applications.") - (license license:expat))) + (arguments + `(#:cargo-inputs + (("rust-chrono" ,rust-chrono) + ("rust-env-logger" ,rust-env-logger) + ("rust-log" ,rust-log)))) + (home-page + "https://github.com/seanmonstar/pretty-env-logger") + (synopsis + "A simple logger built on top off env_logger. It is configured via an environment variable and writes to standard error with nice colored output for log levels.") + (description + "A simple logger built on top off env_logger. It is configured via an environment variable and writes to standard error with nice colored output for log levels.") + (license (list license:asl2.0 + license:expat)))) -(define-public rust-ppv-lite86 ; guix upstreamable +(define-public rust-pretty-assertions (package - (name "rust-ppv-lite86") - (version "0.2.5") + (name "rust-pretty-assertions") + (version "0.6.1") (source (origin (method url-fetch) - (uri (crate-uri "ppv-lite86" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "pretty_assertions" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "06snnv338w341nicfqba2jgln5dsla72ndkgrw7h1dfdb3vgkjz3")))) + (base32 + "09yl14gnmpygiqrdlsa64lcl4w6ydjl9m8jri6kgam0v9rjf309z")))) (build-system cargo-build-system) - (home-page "https://github.com/cryptocorrosion/cryptocorrosion") - (synopsis "Implementation of the crypto-simd API for x86") - (description "This crate provides an implementation of the crypto-simd API -for x86.") + (arguments + `(#:cargo-inputs + (("rust-ansi-term" ,rust-ansi-term) + ("rust-ctor" ,rust-ctor) + ("rust-difference" ,rust-difference) + ("rust-output-vt100" ,rust-output-vt100)))) + (home-page + "https://github.com/colin-kiegel/rust-pretty-assertions") + (synopsis + "When writing tests in Rust, you'll probably use assert_eq!(a, b) a lot. + + If such a test fails, it will present all the details of a and b. But you have to spot the differences yourself, which is not always straightforward, like here:") + (description + "When writing tests in Rust, you'll probably use assert_eq!(a, b) a lot. + + If such a test fails, it will present all the details of a and b. But you have to spot the differences yourself, which is not always straightforward, like here:") (license (list license:asl2.0 license:expat)))) @@ -4595,6 +6504,61 @@ invocations.") (license (list license:asl2.0 license:expat)))) +(define-public rust-proc-macro-hack-0.4 + (package + (inherit rust-proc-macro-hack) + (name "rust-proc-macro-hack") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "proc-macro-hack" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0fxn3qfhw76c518dfal2qqjwj5dbf0a1f7z0r5c4wd0igygg4fs6")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro-hack-impl" ,rust-proc-macro-hack-impl)) + #:cargo-development-inputs + (("rust-demo-hack" ,rust-demo-hack) + ("rust-demo-hack-impl" ,rust-demo-hack-impl)))))) + +(define-public rust-publicsuffix + (package + (name "rust-publicsuffix") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "publicsuffix" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "07ddqpri1xy7nxg5b7z8w49gw90rkn4qjvr423b4y7ngdnlcpzjs")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-error-chain" ,rust-error-chain) + ("rust-idna" ,rust-idna) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-regex" ,rust-regex) + ("rust-url" ,rust-url) + ("rust-native-tls" ,rust-native-tls)) + #:cargo-development-inputs + (("rust-rspec" ,rust-rspec)))) + (home-page + "https://github.com/rushmorem/publicsuffix") + (synopsis + "Robust domain name parsing and RFC compliant email address validation") + (description + "Robust domain name parsing and RFC compliant email address validation") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-pulldown-cmark (package (name "rust-pulldown-cmark") @@ -4656,26 +6620,6 @@ invocations.") "a collection of approximate quantile algorithms") (license license:expat))) -(define-public rust-quick-error ; guix upstreamable - (package - (name "rust-quick-error") - (version "1.2.2") - (source - (origin - (method url-fetch) - (uri (crate-uri "quick-error" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1w6kgwwv7p7zr0yyg5rb315lkk24bimywklwx7fsvsbwi10bjx4j")))) - (build-system cargo-build-system) - (home-page "http://github.com/tailhook/quick-error") - (synopsis "Macro which makes error types pleasant to write") - (description "This crate provides a macro which makes error types pleasant -to write.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-quickcheck (package (name "rust-quickcheck") @@ -4705,6 +6649,64 @@ to write.") (license (list license:unlicense license:expat)))) +(define-public rust-quickcheck-0.7 + (package + (inherit rust-quickcheck) + (name "rust-quickcheck") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "quickcheck" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "05pqzja6fwdyrs1za5vmxb9ifb993knmpdsrs1fs2wyz9qz7slyl")))) + (arguments + `(#:cargo-inputs + (("rust-env-logger" ,rust-env-logger-0.5) + ("rust-log" ,rust-log) + ("rust-rand" ,rust-rand-0.5) + ("rust-rand-core" ,rust-rand-core-0.2)))))) + +(define-public rust-quickcheck-0.6 + (package + (inherit rust-quickcheck) + (name "rust-quickcheck") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "quickcheck" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1dyazm2fcq0v9fscq1a7597zsvdl9f0j8c2bfj1jm2nlzz2sn6y0")))) + (arguments + `(#:cargo-inputs + (("rust-env-logger" ,rust-env-logger-0.5) + ("rust-log" ,rust-log) + ("rust-rand" ,rust-rand-0.4)))))) + +(define-public rust-quickcheck-0.5 + (package + (inherit rust-quickcheck) + (name "rust-quickcheck") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "quickcheck" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jzm1ygfbn4igaq14b9nipc8yvsn6c8panpgd1qiy5r2insjllyd")))) + (arguments + `(#:cargo-inputs + (("rust-env-logger" ,rust-env-logger-0.4) + ("rust-log" ,rust-log-0.3) + ("rust-rand" ,rust-rand-0.3)))))) + (define-public rust-rand (package (name "rust-rand") @@ -4889,7 +6891,7 @@ to write.") (define-public rust-rand-core (package (name "rust-rand-core") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) @@ -4898,13 +6900,12 @@ to write.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1jis94x9ri8xlxki2w2w5k29sjpfwgzkjylg7paganp74hrnhpk1")))) + "06bdvx08v3rkz451cm7z59xwwqn1rkfh6v9ay77b14f8dwlybgch")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-getrandom" ,rust-getrandom) - ("rust-serde" ,rust-serde) - ("rust-serde-derive" ,rust-serde-derive)))) + ("rust-serde" ,rust-serde)))) (home-page "https://crates.io/crates/rand_core") (synopsis "Core random number generator traits and tools for implementation.") @@ -4917,16 +6918,15 @@ to write.") (package (inherit rust-rand-core) (name "rust-rand-core") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (crate-uri "rand_core" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1h3dbrhi5qgflqnzzd86s48v1dn1l17bmdssi5q170whsm4sbryh")))) + "1p09ynysrq1vcdlmcqnapq4qakl2yd1ng3kxh3qscpx09k2a6cww")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -4942,8 +6942,7 @@ to write.") (origin (method url-fetch) (uri (crate-uri "rand_core" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "0jzdgszfa4bliigiy4hi66k7fs3gfwi2qxn8vik84ph77fwdwvvs")))) @@ -4952,6 +6951,24 @@ to write.") `(#:cargo-inputs (("rust-rand-core" ,rust-rand-core-0.4)))))) +(define-public rust-rand-core-0.2 + (package + (inherit rust-rand-core) + (name "rust-rand-core") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "rand_core" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0wikbw2a36bz8ywjyycjrd7db6ra3yzj14zs1ysxz2fiqhia8q8r")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rand-core" ,rust-rand-core-0.3)))))) + (define-public rust-rand-distr (package (name "rust-rand-distr") @@ -5118,6 +7135,56 @@ to write.") ("rust-rand-core" ,rust-rand-core-0.4) ("rust-winapi" ,rust-winapi)))))) +(define-public rust-rand-os + (package + (name "rust-rand-os") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "rand_os" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "06is69f8rfzs620g5b54k6cgy5yaycrsyqg55flyfrsf8g88733f")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-getrandom" ,rust-getrandom) + ("rust-rand-core" ,rust-rand-core)))) + (home-page "https://crates.io/crates/rand_os") + (synopsis "OS backed Random Number Generator") + (description "OS backed Random Number Generator") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-rand-os-0.1 + (package + (inherit rust-rand-os) + (name "rust-rand-os") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "rand_os" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0wahppm0s64gkr2vmhcgwc0lij37in1lgfxg5rbgqlz0l5vgcxbv")))) + (arguments + `(#:cargo-inputs + (("rust-cloudabi" ,rust-cloudabi) + ("rust-fuchsia-cprng" ,rust-fuchsia-cprng) + ("rust-getrandom" ,rust-getrandom) + ("rust-libc" ,rust-libc) + ("rust-log" ,rust-log) + ("rust-rand-core" ,rust-rand-core-0.4) + ("rust-rdrand" ,rust-rdrand-0.4) + ("rust-stdweb" ,rust-stdweb) + ("rust-wasm-bindgen" ,rust-wasm-bindgen) + ("rust-winapi" ,rust-winapi)))))) + (define-public rust-rand-pcg (package (name "rust-rand-pcg") @@ -5165,7 +7232,7 @@ to write.") (("rust-autocfg" ,rust-autocfg) ("rust-rand-core" ,rust-rand-core-0.4) ("rust-serde" ,rust-serde) - ("rust-serde" ,rust-serde-derive)) + ("rust-serde-derive" ,rust-serde-derive)) #:cargo-development-inputs (("rust-bincode" ,rust-bincode)))))) @@ -5215,7 +7282,7 @@ to write.") `(#:cargo-inputs (("rust-rand-core" ,rust-rand-core-0.3) ("rust-serde" ,rust-serde) - ("rust-serde" ,rust-serde-derive)) + ("rust-serde-derive" ,rust-serde-derive)) #:cargo-development-inputs (("rust-bincode" ,rust-bincode)))))) @@ -5330,6 +7397,29 @@ to write.") ("rust-serde" ,rust-serde) ("rust-serde-derive" ,rust-serde-derive)))))) +(define-public rust-rayon-0.8 + (package + (inherit rust-rayon) + (name "rust-rayon") + (version "0.8.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "rayon" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1j2l9x98ma63qkh9w8zik0vcpwqf9cvc2ynh66ibjp36nq4gw55n")))) + (arguments + `(#:cargo-inputs + (("rust-rayon-core" ,rust-rayon-core)) + #:cargo-development-inputs + (("rust-compiletest-rs" ,rust-compiletest-rs) + ("rust-docopt" ,rust-docopt) + ("rust-futures" ,rust-futures) + ("rust-rand" ,rust-rand-0.3) + ("rust-rustc-serialize" ,rust-rustc-serialize)))))) + (define-public rust-rayon-core (package (name "rust-rayon-core") @@ -5405,25 +7495,6 @@ to write.") `(#:cargo-inputs (("rust-rand-core" ,rust-rand-core-0.3)))))) -(define-public rust-redox-syscall ; guix upstreamable - (package - (name "rust-redox-syscall") - (version "0.1.56") - (source - (origin - (method url-fetch) - (uri (crate-uri "redox_syscall" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "110y7dyfm2vci4x5vk7gr0q551dvp31npl99fnsx2fb17wzwcf94")))) - (build-system cargo-build-system) - (home-page "https://gitlab.redox-os.org/redox-os/syscall") - (synopsis "Rust library to access raw Redox system calls") - (description "This package provides a Rust library to access raw Redox -system calls.") - (license license:expat))) - (define-public rust-redox-users (package (name "rust-redox-users") @@ -5450,7 +7521,7 @@ system calls.") "A Rust library to access Redox users and groups functionality") (description "This package provides a Rust library to access Redox users and groups functionality") - (license #f))) + (license license:expat))) (define-public rust-ref-cast (package @@ -5540,57 +7611,148 @@ system calls.") (license (list license:asl2.0 license:expat)))) -(define-public rust-regex-syntax +(define-public rust-regex-0.2 + (package + (inherit rust-regex) + (name "rust-regex") + (version "0.2.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "regex" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1163ir1k5zjspirfjl4wqbviwrxlhmfwy95xxb69y4irkv4snack")))) + (arguments + `(#:cargo-inputs + (("rust-aho-corasick" ,rust-aho-corasick-0.6) + ("rust-memchr" ,rust-memchr) + ("rust-regex-syntax" ,rust-regex-syntax) + ("rust-thread-local" ,rust-thread-local) + ("rust-utf8-ranges" ,rust-utf8-ranges)) + #:cargo-development-inputs + (("rust-lazy-static" ,rust-lazy-static) + ("rust-quickcheck" ,rust-quickcheck-0.6) + ("rust-rand" ,rust-rand-0.4)))))) + +(define-public rust-regex-syntax-0.3 (package + (inherit rust-regex-syntax) (name "rust-regex-syntax") - (version "0.6.10") + (version "0.3.9") (source (origin (method url-fetch) (uri (crate-uri "regex-syntax" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ms9hgdhhsxw9w920i7gipydvagf100bb56jbs192rz86ln01v7r")))) + (arguments + `(#:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck) ; 0.2 + ("rust-rand", rust-rand-0.3)))))) + +(define-public rust-reqwest + (package + (name "rust-reqwest") + (version "0.9.20") + (source + (origin + (method url-fetch) + (uri (crate-uri "reqwest" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0p47lf38yj2g2fnmvnraccqlxwk35zr76hlnqi8yva932nzqam6d")))) + "0y4wvzl3pspd8drr2hf9kk107cjw455cb6p529sh90x58dhqjv8g")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-ucd-util" ,rust-ucd-util)))) - (home-page "https://github.com/rust-lang/regex") - (synopsis "A regular expression parser.") + (("rust-base64" ,rust-base64) + ("rust-bytes" ,rust-bytes) + ("rust-cookie" ,rust-cookie) + ("rust-cookie-store" ,rust-cookie-store-0.7) + ("rust-encoding-rs" ,rust-encoding-rs) + ("rust-flate2" ,rust-flate2) + ("rust-futures" ,rust-futures) + ("rust-http" ,rust-http) + ("rust-hyper" ,rust-hyper) + ("rust-log" ,rust-log) + ("rust-mime" ,rust-mime) + ("rust-mime-guess" ,rust-mime-guess) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json) + ("rust-serde-urlencoded" ,rust-serde-urlencoded-0.5) + ("rust-time" ,rust-time) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-tokio-threadpool" ,rust-tokio-threadpool) + ("rust-tokio-timer" ,rust-tokio-timer) + ("rust-url" ,rust-url) + ("rust-uuid" ,rust-uuid) + ("rust-winreg" ,rust-winreg) + ("rust-hyper-old-types" ,rust-hyper-old-types) + ("rust-hyper-rustls" ,rust-hyper-rustls) + ("rust-hyper-tls" ,rust-hyper-tls) + ("rust-native-tls" ,rust-native-tls) + ("rust-rustls" ,rust-rustls) + ("rust-socks" ,rust-socks) + ("rust-tokio-rustls" ,rust-tokio-rustls) + ("rust-trust-dns-resolver" ,rust-trust-dns-resolver) + ("rust-webpki-roots" ,rust-webpki-roots)) + #:cargo-development-inputs + (("rust-bytes" ,rust-bytes) + ("rust-doc-comment" ,rust-doc-comment) + ("rust-env-logger" ,rust-env-logger) + ("rust-libflate" ,rust-libflate) + ("rust-serde" ,rust-serde) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-tcp" ,rust-tokio-tcp)))) + (home-page + "https://github.com/seanmonstar/reqwest") + (synopsis + "An ergonomic, batteries-included HTTP Client for Rust.") (description - "This package provides a regular expression parser.") + "An ergonomic, batteries-included HTTP Client for Rust.") (license (list license:asl2.0 license:expat)))) -(define-public rust-remove-dir-all +(define-public rust-ring (package - (name "rust-remove-dir-all") - (version "0.5.2") + (name "rust-ring") + (version "0.16.7") (source (origin (method url-fetch) - (uri (crate-uri "remove_dir_all" version)) + (uri (crate-uri "ring" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0bkrlyg26mgizpiy1yb2hhpgscxcag8r5fnckqsvk25608vzm0sa")))) + "0mzpk6zmvlvzy021fh8b3xs2zl6c8mqdqfwqn7zlvc07g8qyhskr")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-winapi" ,rust-winapi)) + (("rust-cc" ,rust-cc) + ("rust-libc" ,rust-libc) + ("rust-spin" ,rust-spin) + ("rust-untrusted" ,rust-untrusted) + ("rust-web-sys" ,rust-web-sys) + ("rust-winapi" ,rust-winapi) + ("rust-lazy-static" ,rust-lazy-static)) #:cargo-development-inputs - (("rust-doc-comment" ,rust-doc-comment)))) - (home-page - "https://github.com/XAMPPRocky/remove_dir_all.git") + (("rust-libc" ,rust-libc) + ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test)))) + (home-page "https://github.com/briansmith/ring") (synopsis - "A safe, reliable implementation of remove_dir_all for Windows") + "Safe, fast, small crypto using Rust") (description - "This package provides a safe, reliable implementation of remove_dir_all for Windows") - (license (list license:asl2.0 - license:expat)))) + "Safe, fast, small crypto using Rust") + (license (license:non-copyleft "file://LICENSE")))) (define-public rust-ron (package @@ -5620,6 +7782,36 @@ system calls.") (license (list license:asl2.0 license:expat)))) +(define-public rust-rspec + (package + (name "rust-rspec") + (version "1.0.0-beta.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "rspec" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1abfzwkbxlwahb243k8d3fp6i135lx1aqmbfl79w9zlpng182ndk")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-colored" ,rust-colored) + ("rust-derive-new" ,rust-derive-new) + ("rust-derive-builder" ,rust-derive-builder) + ("rust-expectest" ,rust-expectest) + ("rust-rayon" ,rust-rayon)) + #:cargo-development-inputs + (("rust-clippy" ,rust-clippy)))) + (home-page "https://mackwic.github.io/rspec") + (synopsis + "Write Rspec-like tests with stable rust") + (description + "Write Rspec-like tests with stable rust") + (license license:mpl2.0))) + (define-public rust-rustc-demangle (package (name "rust-rustc-demangle") @@ -5674,26 +7866,6 @@ system calls.") (license (list license:asl2.0 license:expat)))) -(define-public rust-rustc-std-workspace-core ; guix upstreamable - (package - (name "rust-rustc-std-workspace-core") - (version "1.0.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "rustc-std-workspace-core" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1309xhwyai9xpz128xrfjqkmnkvgjwddznmj7brbd8i8f58zamhr")))) - (build-system cargo-build-system) - (home-page "https://crates.io/crates/rustc-std-workspace-core") - (synopsis "Explicitly empty crate for rust-lang/rust integration") - (description "This crate provides an explicitly empty crate for -rust-lang/rust integration.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-rustc-test (package (name "rust-rustc-test") @@ -5751,118 +7923,69 @@ rust-lang/rust integration.") (license (list license:asl2.0 license:expat)))) -(define-public rust-ryu +(define-public rust-rustls (package - (name "rust-ryu") - (version "1.0.0") + (name "rust-rustls") + (version "0.16.0") (source (origin (method url-fetch) - (uri (crate-uri "ryu" version)) + (uri (crate-uri "rustls" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "15r9z2wzgbj04pks4jz7y6wif5xqhf1wqkl2nd7qrvn08ys68969")))) + "17n0fx3fpkg4fhpdplrdhkissnl003kj90vzbqag11vkpyqihnmj")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-no-panic" ,rust-no-panic)) + (("rust-base64" ,rust-base64) + ("rust-log" ,rust-log) + ("rust-ring" ,rust-ring) + ("rust-sct" ,rust-sct) + ("rust-webpki" ,rust-webpki)) #:cargo-development-inputs - (("rust-num-cpus" ,rust-num-cpus) - ("rust-rand" ,rust-rand)))) - (home-page "https://github.com/dtolnay/ryu") + (("rust-criterion" ,rust-criterion) + ("rust-env-logger" ,rust-env-logger) + ("rust-log" ,rust-log) + ("rust-tempfile" ,rust-tempfile) + ("rust-webpki-roots" ,rust-webpki-roots)))) + (home-page "https://github.com/ctz/rustls") (synopsis - "Fast floating point to string conversion") + "Rustls is a modern TLS library written in Rust.") (description - "Fast floating point to string conversion") + "Rustls is a modern TLS library written in Rust.") (license (list license:asl2.0 - license:boost1.0)))) + license:isc + license:expat)))) -(define-public rust-same-file +(define-public rust-ryu (package - (name "rust-same-file") - (version "1.0.5") + (name "rust-ryu") + (version "1.0.0") (source (origin (method url-fetch) - (uri (crate-uri "same-file" version)) + (uri (crate-uri "ryu" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "08a4zy10pjindf2rah320s6shgswk13mqw7s61m8i1y1xpf8spjq")))) + "15r9z2wzgbj04pks4jz7y6wif5xqhf1wqkl2nd7qrvn08ys68969")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-winapi-util" ,rust-winapi-util)))) - (home-page - "https://github.com/BurntSushi/same-file") + (("rust-no-panic" ,rust-no-panic)) + #:cargo-development-inputs + (("rust-num-cpus" ,rust-num-cpus) + ("rust-rand" ,rust-rand)))) + (home-page "https://github.com/dtolnay/ryu") (synopsis - "A simple crate for determining whether two file paths point to the same file.") + "Fast floating point to string conversion") (description - "This package provides a simple crate for determining whether two file paths point to the same file.") - (license (list license:unlicense - license:expat)))) - -(define-public rust-scoped-tls ; guix upstreamable - (package - (name "rust-scoped-tls") - (version "1.0.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "scoped-tls" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1hj8lifzvivdb1z02lfnzkshpvk85nkgzxsy2hc0zky9wf894spa")))) - (build-system cargo-build-system) - (home-page "https://github.com/alexcrichton/scoped-tls") - (synopsis "Rust library providing the old standard library's scoped_thread_local") - (description "This crate provides a library implementation of the standard -library's old @code{scoped_thread_local!} macro for providing scoped access to -@dfn{thread local storage} (TLS) so any type can be stored into TLS.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-scopeguard ; guix upstreamable - (package - (name "rust-scopeguard") - (version "1.0.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "scopeguard" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "03aay84r1f6w87ckbpj6cc4rnsxkxcfs13n5ynxjia0qkgjiabml")))) - (build-system cargo-build-system) - (home-page "https://github.com/bluss/scopeguard") - (synopsis "Scope guard which will run a closure even out of scope") - (description "This package provides a RAII scope guard that will run a -given closure when it goes out of scope, even if the code between panics -(assuming unwinding panic). Defines the macros @code{defer!}, -@code{defer_on_unwind!}, @code{defer_on_success!} as shorthands for guards -with one of the implemented strategies.") + "Fast floating point to string conversion") (license (list license:asl2.0 - license:expat)))) - -(define-public rust-scopeguard-0.3 - (package - (inherit rust-scopeguard) - (name "rust-scopeguard") - (version "0.3.3") - (source - (origin - (method url-fetch) - (uri (crate-uri "scopeguard" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "09sy9wbqp409pkwmqni40qmwa99ldqpl48pp95m1xw8sc19qy9cl")))))) + license:boost1.0)))) (define-public rust-scroll (package @@ -5921,6 +8044,33 @@ with one of the implemented strategies.") "This package provides a macros 1.1 derive implementation for Pread and Pwrite traits from the scroll crate") (license license:expat))) +(define-public rust-sct + (package + (name "rust-sct") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "sct" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0g4dz7las43kcpi9vqv9c6l1afjkdv3g3w3s7d2w7a7w77wjl173")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-ring" ,rust-ring) + ("rust-untrusted" ,rust-untrusted)))) + (home-page "https://github.com/ctz/sct.rs") + (synopsis + "Certificate transparency SCT verification library") + (description + "Certificate transparency SCT verification library") + (license (list license:asl2.0 + license:isc + license:expat)))) + (define-public rust-seahash ; guix upstreamable (package (name "rust-seahash") @@ -5940,6 +8090,40 @@ with one of the implemented strategies.") function with proven statistical guarantees.") (license license:expat))) +(define-public rust-security-framework + (package + (name "rust-security-framework") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "security-framework" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1hmdsdj061wk76g3fajbfjnw74p0q45hy8hfngp7diwy987kvrpf")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-core-foundation" ,rust-core-foundation) + ("rust-core-foundation-sys" + ,rust-core-foundation-sys) + ("rust-libc" ,rust-libc) + ("rust-security-framework-sys" + ,rust-security-framework-sys)) + #:cargo-development-inputs + (("rust-hex" ,rust-hex) + ("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://lib.rs/crates/security_framework") + (synopsis + "Security.framework bindings for macOS and iOS") + (description + "Security.framework bindings for macOS and iOS") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-select-rustc (package (name "rust-select-rustc") @@ -5999,25 +8183,6 @@ function with proven statistical guarantees.") (license (list license:asl2.0 license:expat)))) -(define-public rust-semver-parser ; guix upstreamable - (package - (name "rust-semver-parser") - (version "0.9.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "semver-parser" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1ahqhvgpzhcsd28id7xnrjv4419i9yyalhm7d7zi430qx0hi2vml")))) - (build-system cargo-build-system) - (home-page "https://github.com/steveklabnik/semver-parser") - (synopsis "Parsing of the semver spec") - (description "This package provides for parsing of the semver spec.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-semver-parser-0.7 (package (inherit rust-semver-parser) @@ -6027,11 +8192,10 @@ function with proven statistical guarantees.") (origin (method url-fetch) (uri (crate-uri "semver-parser" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "18vhypw6zgccnrlm5ps1pwa0khz7ry927iznpr88b87cagr1v2iq")))))) + (base32 + "18vhypw6zgccnrlm5ps1pwa0khz7ry927iznpr88b87cagr1v2iq")))))) (define-public rust-serde (package @@ -6060,6 +8224,23 @@ function with proven statistical guarantees.") (license (list license:asl2.0 license:expat)))) +(define-public rust-serde-0.8 + (package + (inherit rust-serde) + (name "rust-serde") + (version "0.8.23") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1j4ajipn0sf4ya0crgcb94s848qp7mfc35n6d0q2rf8rk5skzbcx")))) + (arguments + `(#:cargo-development-inputs + (("rust-clippy" ,rust-clippy)))))) + (define-public rust-serde-big-array (package (name "rust-serde-big-array") @@ -6206,20 +8387,27 @@ function with proven statistical guarantees.") (license (list license:asl2.0 license:expat)))) -(define-public rust-serde-json-1.0.39 +(define-public rust-serde-json-0.8 (package (inherit rust-serde-json) (name "rust-serde-json") - (version "1.0.39") + (version "0.8.6") (source (origin (method url-fetch) (uri (crate-uri "serde_json" version)) - (file-name - (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "03fl9l680gij0hrsr2csfm8nm858igvfy05czbdkzm54siqsl8ss")))))) + "0k3bclzbvzhiscjydqzym887i8mkh726xkf8isf3lln3xplx5xv7")))) + (arguments + `(#:cargo-inputs + (("rust-dtoa" ,rust-dtoa-0.2) + ("rust-itoa" ,rust-itoa) + ("rust-num-traits" ,rust-num-traits) + ("rust-serde" ,rust-serde-0.8) + ("rust-clippy" ,rust-clippy) + ("rust-linked-hash-map" ,rust-linked-hash-map)))))) (define-public rust-serde-stacker (package @@ -6278,6 +8466,57 @@ function with proven statistical guarantees.") (license (list license:asl2.0 license:expat)))) +(define-public rust-serde-urlencoded + (package + (name "rust-serde-urlencoded") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_urlencoded" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "15rcwfkff0md5i231m2ym5756ksw1mkh5b5g2rw72wsc5mzdgicy")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-dtoa" ,rust-dtoa) + ("rust-itoa" ,rust-itoa) + ("rust-serde" ,rust-serde) + ("rust-url" ,rust-url)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive)))) + (home-page "https://serde.rs") + (synopsis + "`x-www-form-urlencoded` meets Serde") + (description + "`x-www-form-urlencoded` meets Serde") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-serde-urlencoded-0.5 + (package + (inherit rust-serde-urlencoded) + (name "rust-serde-urlencoded") + (version "0.5.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_urlencoded" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0nhnzllx5xrij4x17g351n14md691r95mxr7sbpz4sl80n8xcbb4")))) + (arguments + `(#:cargo-inputs + (("rust-dtoa" ,rust-dtoa) + ("rust-itoa" ,rust-itoa) + ("rust-serde" ,rust-serde) + ("rust-url" ,rust-url-1)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive)))))) + (define-public rust-serde-yaml (package (name "rust-serde-yaml") @@ -6369,45 +8608,6 @@ function with proven statistical guarantees.") "Minimal implementation of SHA1 for Rust.") (license license:bsd-3))) -(define-public rust-shlex ; guix upstreamable - (package - (name "rust-shlex") - (version "0.1.1") - (source - (origin - (method url-fetch) - (uri (crate-uri "shlex" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1lmv6san7g8dv6jdfp14m7bdczq9ss7j7bgsfqyqjc3jnjfippvz")))) - (build-system cargo-build-system) - (home-page "https://github.com/comex/rust-shlex") - (synopsis "Split a string into shell words, like Python's shlex") - (description "This crate provides a method to split a string into shell -words, like Python's shlex.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-slab ; guix upstreamable - (package - (name "rust-slab") - (version "0.4.2") - (source - (origin - (method url-fetch) - (uri (crate-uri "slab" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1y59xsa27jk84sxzswjk60xcjf8b4fm5960jwpznrrcmasyva4f1")))) - (build-system cargo-build-system) - (home-page "https://github.com/carllerche/slab") - (synopsis "Pre-allocated storage for a uniform data type") - (description "This create provides a pre-allocated storage for a uniform -data type.") - (license license:expat))) - (define-public rust-sleef-sys (package (name "rust-sleef-sys") @@ -6464,25 +8664,142 @@ data type.") license:mpl2.0 license:expat)))) -(define-public rust-spin ; guix upstreamable +(define-public rust-smallvec (package - (name "rust-spin") - (version "0.5.0") + (name "rust-smallvec") + (version "0.6.10") (source (origin (method url-fetch) - (uri (crate-uri "spin" version)) + (uri (crate-uri "smallvec" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1dyl43rgzny79jjpgzi07y0ly2ggx1xwsn64csxj0j91bsf6lq5b")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-bincode" ,rust-bincode)))) + (home-page + "https://github.com/servo/rust-smallvec") + (synopsis + "'Small vector' optimization for Rust: store up to a small number of items on the stack") + (description + "'Small vector' optimization for Rust: store up to a small number of items on the stack") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-socket2 + (package + (name "rust-socket2") + (version "0.3.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "socket2" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "11bdcz04i106g4q7swkll0qxrb4287srqd2k3aq2q6i22zjlvdz8")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-libc" ,rust-libc) + ("rust-redox-syscall" ,rust-redox-syscall) + ("rust-winapi" ,rust-winapi)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://github.com/alexcrichton/socket2-rs") + (synopsis + "Utilities for handling networking sockets with a maximal amount of configuration possible intended.") + (description + "Utilities for handling networking sockets with a maximal amount of configuration possible intended.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-socks + (package + (name "rust-socks") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "socks" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1hnbw4c4j7dn9n3bd1v7ddkdzlxlzkfw3z29da1nxlj6jgx4r9p6")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder) + ("rust-libc" ,rust-libc) + ("rust-winapi" ,rust-winapi) + ("rust-ws2-32-sys" ,rust-ws2-32-sys)))) + (home-page "https://github.com/sfackler/rust-socks") + (synopsis + "SOCKS proxy support for Rust.") + (description + "SOCKS proxy support for Rust.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-sourcefile + (package + (name "rust-sourcefile") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "sourcefile" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0m9clchsj0rf13bggsgvbv9haiy0f6rhvnvkpvkk8720a5pkydj4")))) + "1lwa6973zs4bgj29my7agfjgk4nw9hp6j7dfnr13nid85fw7rxsb")))) (build-system cargo-build-system) - (home-page "https://github.com/mvdnes/spin-rs.git") - (synopsis "Synchronization primitives based on spinning") - (description "This crate provides synchronization primitives based on -spinning. They may contain data, are usable without @code{std},and static -initializers are available.") - (license license:expat))) + (arguments + `(#:cargo-development-inputs + (("rust-tempfile" ,rust-tempfile)))) + (home-page "https://github.com/derekdreery/sourcefile-rs") + (synopsis + "A library for concatenating source from multiple files, whilst keeping track of where each new file and line starts.") + (description + "A library for concatenating source from multiple files, whilst keeping track of where each new file and line starts.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-spmc + (package + (name "rust-spmc") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "spmc" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1rgcqgj6b3d0cshi7277akr2xk0cx11rkmviaahy7a3pla6l5a02")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-loom" ,rust-loom)))) + (home-page + "https://github.com/seanmonstar/spmc") + (synopsis + "Simple SPMC channel") + (description + "Simple SPMC channel") + (license (list license:asl2.0 + license:expat)))) (define-public rust-stacker (package @@ -6625,51 +8942,6 @@ initializers are available.") (license (list license:asl2.0 license:expat)))) -(define-public rust-stdweb-internal-runtime ; guix upstreamable - (package - (name "rust-stdweb-internal-runtime") - (version "0.1.4") - (source - (origin - (method url-fetch) - (uri (crate-uri "stdweb-internal-runtime" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1nhpyra7glbwcpakhpj5a3d7h7kx1ynif473nzshmk226m91f8ym")))) - (build-system cargo-build-system) - (home-page "https://github.com/koute/stdweb") - (synopsis "Internal runtime for the @code{stdweb} crate") - (description "This crate provides internal runtime for the @code{stdweb} -crate.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-stdweb-internal-test-macro - (package - (name "rust-stdweb-internal-test-macro") - (version "0.1.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "stdweb-internal-test-macro" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "12rrm7p77xnm3xacgn3rgniiyyjb4gq7902wpbljsvbx045z69l2")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-proc-macro2" ,rust-proc-macro2) - ("rust-quote" ,rust-quote)))) - (home-page "https://github.com/koute/stdweb") - (synopsis "Internal crate of the `stdweb` crate") - (description - "Internal crate of the `stdweb` crate") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-stream-cipher (package (name "rust-stream-cipher") @@ -6695,50 +8967,28 @@ crate.") (license (list license:asl2.0 license:expat)))) -(define-public rust-streaming-stats +(define-public rust-string (package - (name "rust-streaming-stats") - (version "0.2.2") + (name "rust-string") + (version "0.2.1") (source (origin (method url-fetch) - (uri (crate-uri "streaming-stats" version)) + (uri (crate-uri "string" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0l7xz4g6709s80zqpvlhrg0qhgz64r94cwhmfsg8xhabgznbp2px")))) + "0vaxz85ja52fn66akgvggb29wqa5bpj3y38syykpr1pbrjzi8hfj")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-num-traits" ,rust-num-traits)))) + `(#:cargo-inputs (("rust-bytes" ,rust-bytes)))) (home-page - "https://github.com/BurntSushi/rust-stats") + "https://github.com/carllerche/string") (synopsis - "Experimental crate for computing basic statistics on streams.") + "A UTF-8 encoded string with configurable byte storage.") (description - "Experimental crate for computing basic statistics on streams.") - (license (list license:unlicense - license:expat)))) - -(define-public rust-strsim ; guix upstreamable - (package - (name "rust-strsim") - (version "0.9.2") - (source - (origin - (method url-fetch) - (uri (crate-uri "strsim" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1xphwhf86yxxmcpvm4mikj8ls41f6nf7gqyjm98b74mfk81h6b03")))) - (build-system cargo-build-system) - (home-page "https://github.com/dguo/strsim-rs") - (synopsis "Rust implementations of string similarity metrics") - (description "This crate includes implementations of string similarity -metrics. It includes Hamming, Levenshtein, OSA, Damerau-Levenshtein, Jaro, -and Jaro-Winkler.") + "This package provides a UTF-8 encoded string with configurable byte storage.") (license license:expat))) (define-public rust-strsim-0.8 @@ -6829,7 +9079,7 @@ and Jaro-Winkler.") `(#:cargo-inputs (("rust-proc-macro2" ,rust-proc-macro2) ("rust-quote" ,rust-quote) - ("rust-unicode-xid" ,rust-unicode-xid)) + ("rust-unicode-xid" ,rust-unicode-xid-0.1)) #:cargo-development-inputs (("rust-insta" ,rust-insta) ("rust-rayon" ,rust-rayon) @@ -6862,7 +9112,7 @@ and Jaro-Winkler.") (("rust-proc-macro2" ,rust-proc-macro2) ("rust-quote" ,rust-quote) ("rust-syn" ,rust-syn) - ("rust-unicode-xid" ,rust-unicode-xid)) + ("rust-unicode-xid" ,rust-unicode-xid-0.1)) #:cargo-development-inputs (("rust-synstructure-test-traits" ,rust-synstructure-test-traits)))) @@ -6874,24 +9124,91 @@ and Jaro-Winkler.") "Helper methods and macros for custom derives") (license license:expat))) -(define-public rust-synstructure-test-traits ; guix upstreamable +(define-public rust-synstructure-0.10 (package - (name "rust-synstructure-test-traits") - (version "0.1.0") + (inherit rust-synstructure) + (name "rust-synstructure") + (version "0.10.2") (source (origin (method url-fetch) - (uri (crate-uri "synstructure_test_traits" version)) + (uri (crate-uri "synstructure" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1b3fs2b9kc1gy9dilaxqjbdl4z0mlrbbxjzkprdx953rif1c3q66")))) + "0grirdkgh2wl4hf9a3nbiazpgccxgq54kn52ms0xrr6njvgkwd82")))) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2) + ("rust-quote" ,rust-quote) + ("rust-syn" ,rust-syn) + ("rust-unicode-xid" ,rust-unicode-xid-0.1)) + #:cargo-development-inputs + (("rust-synstructure-test-traits" + ,rust-synstructure-test-traits)))))) + +(define-public rust-tar + (package + (name "rust-tar") + (version "0.4.26") + (source + (origin + (method url-fetch) + (uri (crate-uri "tar" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1lr6v3cpkfxd2lk5ll2jd8wr1xdskwj35smnh5sfb8xvzzxnn6dk")))) (build-system cargo-build-system) - (home-page "https://crates.io/crates/synstructure_test_traits") - (synopsis "Helper test traits for synstructure doctests") + (arguments + `(#:cargo-inputs + (("rust-filetime" ,rust-filetime) + ("rust-libc" ,rust-libc) + ("rust-redox-syscall" ,rust-redox-syscall) + ("rust-xattr" ,rust-xattr)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))) + (home-page + "https://github.com/alexcrichton/tar-rs") + (synopsis + "A Rust implementation of a TAR file reader and writer. This library does not + currently handle compression, but it is abstract over all I/O readers and + writers. Additionally, great lengths are taken to ensure that the entire + contents are never required to be entirely resident in memory all at once.") (description - "This package provides helper test traits for synstructure doctests.") - (license license:expat))) + "This package provides a Rust implementation of a TAR file reader and writer. This library does not + currently handle compression, but it is abstract over all I/O readers and + writers. Additionally, great lengths are taken to ensure that the entire + contents are never required to be entirely resident in memory all at once.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-target-lexicon + (package + (name "rust-target-lexicon") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "target-lexicon" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jrdch22pvm8r9fwx6d051l4yhac16lq6sn4q5fc6ic95fcb82hv")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-failure" ,rust-failure) + ("rust-failure-derive" ,rust-failure-derive) + ("rust-serde-json" ,rust-serde-json)))) + (home-page "https://github.com/CraneStation/target-lexicon") + (synopsis + "This is a library for managing targets for compilers and related tools.") + (description + "This is a library for managing targets for compilers and related tools.") + (license license:asl2.0))) ; with LLVM exception (define-public rust-tempdir (package @@ -6980,7 +9297,7 @@ and Jaro-Winkler.") (define-public rust-term-size (package (name "rust-term-size") - (version "1.0.0-beta1") + (version "0.3.1") (source (origin (method url-fetch) @@ -6989,12 +9306,12 @@ and Jaro-Winkler.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "13w9cqjhzh3mmx6zami8lxyf42xx53yy866zxhxqcm71k637v8d8")))) + "09wk3173ngmb710qs9rwgibq4w250q8lgnwjvb9cypc1vdk9lnwy")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-clippy" ,rust-clippy) - ;("rust-kernel32-sys" ,rust-kernel32-sys) ; windows + ("rust-kernel32-sys" ,rust-kernel32-sys) ("rust-libc" ,rust-libc) ("rust-winapi" ,rust-winapi)))) (home-page @@ -7006,51 +9323,29 @@ and Jaro-Winkler.") (license (list license:asl2.0 license:expat)))) -(define-public rust-termcolor - (package - (name "rust-termcolor") - (version "1.0.5") - (source - (origin - (method url-fetch) - (uri (crate-uri "termcolor" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0vjfsn1a8zvqhnrbygrz1id6yckwv1dncw3w4zj65qdx0f00kmln")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-wincolor" ,rust-wincolor)))) - (home-page "https://github.com/BurntSushi/termcolor") - (synopsis "Library for writing colored text to a terminal") - (description "This package provides a simple cross platform library for -writing colored text to a terminal.") - (license (list license:unlicense - license:expat)))) - -(define-public rust-termios +(define-public rust-test-assembler (package - (name "rust-termios") - (version "0.3.1") + (name "rust-test-assembler") + (version "0.1.5") (source (origin (method url-fetch) - (uri (crate-uri "termios" version)) + (uri (crate-uri "test-assembler" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "09any1p4jp4bphvb5ikagnvwjc3xn2djchy96nkpa782xb2j1dkj")))) + "1sdx9hk0dk3z9crm8834ysyxsi92chls8arpd0gs796kis6lik2w")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs (("rust-libc" ,rust-libc)))) + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder)))) (home-page - "https://github.com/dcuddeback/termios-rs") + "https://github.com/luser/rust-test-assembler") (synopsis - "Safe bindings for the termios library.") + "A set of types for building complex binary streams.") (description - "Safe bindings for the termios library.") + "This package provides a set of types for building complex binary streams.") (license license:expat))) (define-public rust-textwrap @@ -7095,30 +9390,6 @@ writing colored text to a terminal.") and handle Unicode characters correctly.") (license license:expat))) -(define-public rust-thread-local - (package - (name "rust-thread-local") - (version "0.3.6") - (source - (origin - (method url-fetch) - (uri (crate-uri "thread_local" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "06rzik99p8c5js8238yhc8rk6np543ylb1dy9nrw5v80j0r3xdf6")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-lazy-static" ,rust-lazy-static)))) - (home-page - "https://github.com/Amanieu/thread_local-rs") - (synopsis "Per-object thread-local storage") - (description "Per-object thread-local storage") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-time (package (name "rust-time") @@ -7203,6 +9474,33 @@ writing colored text to a terminal.") "An event-driven, non-blocking I/O platform for writing asynchronous I/O backed applications.") (license license:expat))) +(define-public rust-tokio-buf + (package + (name "rust-tokio-buf") + (version "0.2.0-alpha.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "tokio-buf" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1bz2yb77kxq4006j6cjdkl14n21pi0c0mdw20ywj9yd70y7lap2z")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-either" ,rust-either)) + #:cargo-development-inputs + (("rust-tokio-mock-task" ,rust-tokio-mock-task)))) + (home-page "https://tokio.rs") + (synopsis + "Asynchronous stream of byte buffers") + (description + "Asynchronous stream of byte buffers") + (license license:expat))) + (define-public rust-tokio-codec (package (name "rust-tokio-codec") @@ -7229,6 +9527,55 @@ writing colored text to a terminal.") "Utilities for encoding and decoding frames.") (license license:expat))) +(define-public rust-tokio-core + (package + (name "rust-tokio-core") + (version "0.1.17") + (source + (origin + (method url-fetch) + (uri (crate-uri "tokio-core" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0wbgg59mxfvrhzv97y56nh3gmnmw3jj9dhgkmvz27410jjxzpvxf")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bytes" ,rust-bytes) + ("rust-futures" ,rust-futures) + ("rust-iovec" ,rust-iovec) + ("rust-log" ,rust-log) + ("rust-mio" ,rust-mio) + ("rust-scoped-tls" ,rust-scoped-tls-0.1) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-tokio-reactor" ,rust-tokio-reactor) + ("rust-tokio-timer" ,rust-tokio-timer)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-flate2" ,rust-flate2) + ("rust-futures-cpupool" ,rust-futures-cpupool) + ("rust-http" ,rust-http) + ("rust-httparse" ,rust-httparse) + ("rust-libc" ,rust-libc) + ("rust-num-cpus" ,rust-num-cpus) + ("rust-serde" ,rust-serde) + ("rust-serde-derive" ,rust-serde-derive) + ("rust-serde-json" ,rust-serde-json) + ("rust-time" ,rust-time)))) + (home-page "https://tokio.rs") + (synopsis + "Core I/O and event loop primitives for asynchronous I/O in Rust. Foundation for + the rest of the tokio crates.") + (description + "Core I/O and event loop primitives for asynchronous I/O in Rust. Foundation for + the rest of the tokio crates.") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-tokio-current-thread (package (name "rust-tokio-current-thread") @@ -7339,6 +9686,38 @@ writing colored text to a terminal.") "Core I/O primitives for asynchronous I/O in Rust.") (license license:expat))) +(define-public rust-tokio-io-pool + (package + (name "rust-tokio-io-pool") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "tokio-io-pool" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "17lrjj7lcw13wchpbvr8cynmypd29h40clf9qxabh6fxva40kwm5")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures" ,rust-futures) + ("rust-num-cpus" ,rust-num-cpus) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-executor" ,rust-tokio-executor)) + #:cargo-development-inputs + (("rust-tokio-current-thread" + ,rust-tokio-current-thread)))) + (home-page + "https://github.com/jonhoo/tokio-io-pool") + (synopsis + "Alternative tokio thread pool for executing short, I/O-heavy futures efficiently") + (description + "Alternative tokio thread pool for executing short, I/O-heavy futures efficiently") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-tokio-reactor (package (name "rust-tokio-reactor") @@ -7361,7 +9740,7 @@ writing colored text to a terminal.") ("rust-log" ,rust-log) ("rust-mio" ,rust-mio) ("rust-num-cpus" ,rust-num-cpus) - ("rust-parking-lot" ,rust-parking-lot) + ("rust-parking-lot" ,rust-parking-lot-0.7) ("rust-slab" ,rust-slab) ("rust-tokio-executor" ,rust-tokio-executor) ("rust-tokio-io" ,rust-tokio-io) @@ -7377,27 +9756,101 @@ writing colored text to a terminal.") "Event loop that drives Tokio I/O resources.") (license license:expat))) -(define-public rust-tokio-mock-task +(define-public rust-tokio-mockstream (package - (name "rust-tokio-mock-task") - (version "0.1.1") + (name "rust-tokio-mockstream") + (version "1.1.0") (source (origin (method url-fetch) - (uri (crate-uri "tokio-mock-task" version)) + (uri (crate-uri "tokio-mockstream" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1y7q83qfk9ljjfvs82b453pmz9x1v3d6kr4x55j8mal01s6790dw")))) + "0mg1i39cl8x32wxwbn74hlirks8a6f3g0gfzkb0n0zwbxwvc9gs1")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs (("rust-futures" ,rust-futures)))) + `(#:cargo-inputs + (("rust-futures" ,rust-futures) + ("rust-tokio-io" ,rust-tokio-io)) + #:cargo-development-inputs + (("rust-bytes" ,rust-bytes)))) (home-page - "https://github.com/carllerche/tokio-mock-task") - (synopsis "Mock a Tokio task") - (description "Mock a Tokio task") - (license license:expat))) + "https://github.com/aatxe/tokio-mockstream") + (synopsis + "A fake stream for testing network applications backed by buffers.") + (description + "A fake stream for testing network applications backed by buffers.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-tokio-openssl + (package + (name "rust-tokio-openssl") + (version "0.4.0-alpha.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "tokio-openssl" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0zzhb720bmjkcg5q53yp9mimx8frnbrk9il6rya16zc6pwmzbfw8")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-openssl" ,rust-openssl) + ("rust-tokio-io" ,rust-tokio-io)) + #:cargo-development-inputs + (("rust-futures-preview" ,rust-futures-preview) + ("rust-tokio" ,rust-tokio)))) + (home-page + "https://github.com/alexcrichton/tokio-openssl") + (synopsis + "An implementation of SSL streams for Tokio backed by OpenSSL") + (description + "An implementation of SSL streams for Tokio backed by OpenSSL") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-tokio-rustls + (package + (name "rust-tokio-rustls") + (version "0.12.0-alpha.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "tokio-rustls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0vmjqdpvvwi5xga8lrp9pr29i7jd77zzlbbv4vi2mnsqxjafdcji")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures-core-preview" + ,rust-futures-core-preview) + ("rust-rustls" ,rust-rustls) + ("rust-smallvec" ,rust-smallvec) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-webpki" ,rust-webpki)) + #:cargo-development-inputs + (("rust-futures-util-preview" + ,rust-futures-util-preview) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-tokio" ,rust-tokio) + ("rust-webpki-roots" ,rust-webpki-roots)))) + (home-page + "https://github.com/quininer/tokio-rustls") + (synopsis + "Asynchronous TLS/SSL streams for Tokio using Rustls.") + (description + "Asynchronous TLS/SSL streams for Tokio using Rustls.") + (license (list license:asl2.0 + license:expat)))) (define-public rust-tokio-sync (package @@ -7522,6 +9975,31 @@ writing colored text to a terminal.") (description "Timer facilities for Tokio") (license license:expat))) +(define-public rust-tokio-tls + (package + (name "rust-tokio-tls") + (version "0.3.0-alpha.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "tokio-tls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1z9bbxkd646lsn1fr1a5znxdz8afbpy31iq1knxd424v57lxf29p")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-native-tls" ,rust-native-tls) + ("rust-tokio-io" ,rust-tokio-io)))) + (home-page "https://tokio.rs") + (synopsis + "An implementation of TLS/SSL streams for Tokio giving an implementation of TLS for nonblocking I/O streams.") + (description + "An implementation of TLS/SSL streams for Tokio giving an implementation of TLS for nonblocking I/O streams.") + (license license:expat))) + (define-public rust-tokio-udp (package (name "rust-tokio-udp") @@ -7616,28 +10094,250 @@ writing colored text to a terminal.") (license (list license:asl2.0 license:expat)))) -(define-public rust-tracing-core +(define-public rust-trust-dns-https (package - (name "rust-tracing-core") - (version "0.1.2") + (name "rust-trust-dns-https") + (version "0.4.0") (source (origin (method url-fetch) - (uri (crate-uri "tracing-core" version)) + (uri (crate-uri "trust-dns-https" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "01fa73wzw2m5ybi3kkd52dgrw97mgc3i6inmhwys46ab28giwnxi")))) + "1ypkbgm5p7smjfkca3gaszhvknbr2ykf8skw8pyvpn0sq95lv5ia")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-lazy-static" ,rust-lazy-static)))) - (home-page "https://tokio.rs") + (("rust-bytes" ,rust-bytes) + ("rust-data-encoding" ,rust-data-encoding) + ("rust-failure" ,rust-failure) + ("rust-futures" ,rust-futures) + ("rust-h2" ,rust-h2) + ("rust-http" ,rust-http) + ("rust-log" ,rust-log) + ("rust-rustls" ,rust-rustls) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-reactor" ,rust-tokio-reactor) + ("rust-tokio-rustls" ,rust-tokio-rustls) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-trust-dns-proto" ,rust-trust-dns-proto) + ("rust-trust-dns-rustls" ,rust-trust-dns-rustls) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-reactor" ,rust-tokio-reactor) + ("rust-tokio-rustls" ,rust-tokio-rustls) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-trust-dns-proto" ,rust-trust-dns-proto) + ("rust-trust-dns-rustls" ,rust-trust-dns-rustls) + ("rust-typed-headers" ,rust-typed-headers) + ("rust-webpki" ,rust-webpki) + ("rust-webpki-roots" ,rust-webpki-roots)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-tokio" ,rust-tokio)))) + (home-page "http://www.trust-dns.org/index.html") + (synopsis + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use DNS over HTTPS.") + (description + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use DNS over HTTPS.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-trust-dns-native-tls + (package + (name "rust-trust-dns-native-tls") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "trust-dns-native-tls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0dkwfqxjjmbikm3mav71zjymgy8wmqr4mca64x49qzknvc4qwy6z")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures" ,rust-futures) + ("rust-native-tls" ,rust-native-tls) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-tokio-tls" ,rust-tokio-tls) + ("rust-trust-dns-proto" ,rust-trust-dns-proto)) + #:cargo-development-inputs + (("rust-tokio" ,rust-tokio)))) + (home-page "http://www.trust-dns.org/index.html") + (synopsis + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use native-tls for TLS.") + (description + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use native-tls for TLS.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-trust-dns-openssl + (package + (name "rust-trust-dns-openssl") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "trust-dns-openssl" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "19qxi4y33wd2g55r4v9d6b06d20bdhqhvsrsmbpz5ir3i7l5psp7")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures" ,rust-futures) + ("rust-openssl" ,rust-openssl) + ("rust-tokio-openssl" ,rust-tokio-openssl) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-trust-dns-proto" ,rust-trust-dns-proto)) + #:cargo-development-inputs + (("rust-openssl" ,rust-openssl) + ("rust-tokio" ,rust-tokio)))) + (home-page "http://www.trust-dns.org/index.html") + (synopsis + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use tokio-openssl for TLS.") + (description + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use tokio-openssl for TLS.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-trust-dns-proto + (package + (name "rust-trust-dns-proto") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "trust-dns-proto" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1f9xjyz7fsa83dj00zif7lmljd4x420c0vmniinhb7c35777wi85")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-data-encoding" ,rust-data-encoding) + ("rust-enum-as-inner" ,rust-enum-as-inner) + ("rust-failure" ,rust-failure) + ("rust-futures" ,rust-futures) + ("rust-idna" ,rust-idna) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-log" ,rust-log) + ("rust-openssl" ,rust-openssl) + ("rust-rand" ,rust-rand) + ("rust-ring" ,rust-ring) + ("rust-serde" ,rust-serde) + ("rust-smallvec" ,rust-smallvec) + ("rust-socket2" ,rust-socket2) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-io" ,rust-tokio-io) + ("rust-tokio-reactor" ,rust-tokio-reactor) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-tokio-timer" ,rust-tokio-timer) + ("rust-tokio-udp" ,rust-tokio-udp) + ("rust-url" ,rust-url)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-tokio" ,rust-tokio)))) + (home-page "http://www.trust-dns.org/index.html") + (synopsis + "Trust-DNS is a safe and secure DNS library. This is the foundational DNS protocol library for all Trust-DNS projects.") + (description + "Trust-DNS is a safe and secure DNS library. This is the foundational DNS protocol library for all Trust-DNS projects.") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-trust-dns-resolver + (package + (name "rust-trust-dns-resolver") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "trust-dns-resolver" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0cjkz3rcisk7v354l5hqb3j5x9x389pjqd6da6h8skvqxr0kl6yb")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-failure" ,rust-failure) + ("rust-futures" ,rust-futures) + ("rust-ipconfig" ,rust-ipconfig) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-log" ,rust-log) + ("rust-lru-cache" ,rust-lru-cache) + ("rust-resolv-conf" ,rust-resolv-conf) + ("rust-rustls" ,rust-rustls) + ("rust-serde" ,rust-serde) + ("rust-smallvec" ,rust-smallvec) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-tokio-udp" ,rust-tokio-udp) + ("rust-trust-dns-https" ,rust-trust-dns-https) + ("rust-trust-dns-native-tls" + ,rust-trust-dns-native-tls) + ("rust-trust-dns-openssl" + ,rust-trust-dns-openssl) + ("rust-trust-dns-proto" ,rust-trust-dns-proto) + ("rust-trust-dns-rustls" ,rust-trust-dns-rustls) + ("rust-webpki-roots" ,rust-webpki-roots)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger) + ("rust-tokio" ,rust-tokio) + ("rust-tokio-io" ,rust-tokio-io)))) + (home-page "http://www.trust-dns.org/index.html") + (synopsis + "Trust-DNS is a safe and secure DNS library. This Resolver library uses the Client library to perform all DNS queries. The Resolver is intended to be a high-level library for any DNS record resolution see Resolver and AsyncResolver for supported resolution types. The Client can be used for other queries. + ") + (description + "Trust-DNS is a safe and secure DNS library. This Resolver library uses the Client library to perform all DNS queries. The Resolver is intended to be a high-level library for any DNS record resolution see Resolver and AsyncResolver for supported resolution types. The Client can be used for other queries. + ") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-trust-dns-rustls + (package + (name "rust-trust-dns-rustls") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "trust-dns-rustls" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0glpggq31764q7lp19h5l6implsr7ik015qkm5rg7pqwy93krsb3")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures" ,rust-futures) + ("rust-log" ,rust-log) + ("rust-rustls" ,rust-rustls) + ("rust-tokio-rustls" ,rust-tokio-rustls) + ("rust-tokio-tcp" ,rust-tokio-tcp) + ("rust-trust-dns-proto" ,rust-trust-dns-proto) + ("rust-webpki" ,rust-webpki)) + #:cargo-development-inputs + (("rust-openssl" ,rust-openssl) + ("rust-tokio" ,rust-tokio)))) + (home-page "http://www.trust-dns.org/index.html") (synopsis - "Core primitives for application-level tracing.") + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use rustls for TLS.") (description - "Core primitives for application-level tracing.") + "Trust-DNS is a safe and secure DNS library. This is an extension for the Trust-DNS client to use rustls for TLS.") (license (list license:asl2.0 license:expat)))) @@ -7671,71 +10371,87 @@ writing colored text to a terminal.") (license (list license:asl2.0 license:expat)))) -(define-public rust-typenum ; guix upstreamable +(define-public rust-typed-arena (package - (name "rust-typenum") - (version "1.10.0") + (name "rust-typed-arena") + (version "1.5.0") (source (origin (method url-fetch) - (uri (crate-uri "typenum" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "typed-arena" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0sc1jirllfhdi52z1xv9yqzxzpk6v7vadd13n7wvs1wnjipn6bb1")))) + (base32 + "0im62vrmyzbr8xq66bcyr86ka4z2x8psn9z4982bq4fc8v1zaw3z")))) (build-system cargo-build-system) - (home-page "https://github.com/paholg/typenum") - (synopsis "Rust library for type-level numbers evaluated at compile time") - (description "Typenum is a Rust library for type-level numbers evaluated at -compile time. It currently supports bits, unsigned integers, and signed -integers. It also provides a type-level array of type-level numbers, but its -implementation is incomplete.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-development-inputs + (("rust-criterion" ,rust-criterion)))) + (home-page + "https://github.com/SimonSapin/rust-typed-arena") + (synopsis + "The arena, a fast but limited type of allocator") + (description + "The arena, a fast but limited type of allocator") + (license license:expat))) -(define-public rust-ucd-trie +(define-public rust-typed-headers (package - (name "rust-ucd-trie") - (version "0.1.2") + (name "rust-typed-headers") + (version "0.1.1") (source (origin (method url-fetch) - (uri (crate-uri "ucd-trie" version)) + (uri (crate-uri "typed-headers" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1hh6kyzh5xygwy96wfmsf8v8czlzhps2lgbcyhj1xzy1w1xys04g")))) + "0g40nlq5iw0zxhwb7nfmfbr9m86abgwwhxwhzrm10nfq6bsmlvxx")))) (build-system cargo-build-system) (arguments - `(#:cargo-development-inputs - (("rust-lazy-static" ,rust-lazy-static)))) - (home-page - "https://github.com/BurntSushi/ucd-generate") + `(#:cargo-inputs + (("rust-base64" ,rust-base64) + ("rust-bytes" ,rust-bytes) + ("rust-chrono" ,rust-chrono) + ("rust-http" ,rust-http) + ("rust-mime" ,rust-mime)))) + (home-page "https://github.com/sfackler/typed-headers") (synopsis - "A trie for storing Unicode codepoint sets and maps.") + "Typed HTTP header serialization and deserialization.") (description - "This package provides a trie for storing Unicode codepoint sets and maps.") + "Typed HTTP header serialization and deserialization.") (license (list license:asl2.0 license:expat)))) -(define-public rust-ucd-util ; guix upstreamable +(define-public rust-unicode-bidi (package - (name "rust-ucd-util") - (version "0.1.5") + (name "rust-unicode-bidi") + (version "0.3.4") (source (origin (method url-fetch) - (uri (crate-uri "ucd-util" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "unicode-bidi" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0x088q5z0m09a2jqcfgsnq955y8syn1mgn35cl78qinkxm4kp6zs")))) + "1malx8ljgm7v1gbaazkn7iicy5wj0bwcyadj3l727a38ch6bvwj9")))) (build-system cargo-build-system) - (home-page "https://github.com/BurntSushi/ucd-generate") - (synopsis "library for working with the Unicode character database") - (description "This package provides a small utility library for working -with the Unicode character database.") + (arguments + `(#:cargo-inputs + (("rust-matches" ,rust-matches) + ("rust-flame" ,rust-flame) + ("rust-flamer" ,rust-flamer) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-serde-test" ,rust-serde-test)))) + (home-page "https://github.com/servo/unicode-bidi") + (synopsis + "Implementation of the Unicode Bidirectional Algorithm") + (description + "Implementation of the Unicode Bidirectional Algorithm") (license (list license:asl2.0 license:expat)))) @@ -7793,46 +10509,6 @@ with the Unicode character database.") (license (list license:asl2.0 license:expat)))) -(define-public rust-unicode-width ; guix upstreamable - (package - (name "rust-unicode-width") - (version "0.1.5") - (source - (origin - (method url-fetch) - (uri (crate-uri "unicode-width" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "09k5lipygardwy0660jhls08fsgknrazzivmn804gps53hiqc8w8")))) - (build-system cargo-build-system) - (home-page "https://github.com/unicode-rs/unicode-width") - (synopsis "Determine displayed width according to Unicode rules") - (description "This crate allows you to determine displayed width of -@code{char} and @code{str} types according to Unicode Standard Annex #11 rules.") - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-unindent ; guix upstreamable - (package - (name "rust-unindent") - (version "0.1.3") - (source - (origin - (method url-fetch) - (uri (crate-uri "unindent" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1x21ilf78aqcq9xzb9b7i628wm10rhk0jp0chlv06rkc690l8jw3")))) - (build-system cargo-build-system) - (home-page "https://github.com/dtolnay/indoc") - (synopsis "Remove a column of leading whitespace from a string") - (description "This crate allows you to remove a column of leading -whitespace from a string.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-url (package (name "rust-url") @@ -7865,6 +10541,61 @@ whitespace from a string.") (license (list license:asl2.0 license:expat)))) +(define-public rust-url-1 + (package + (inherit rust-url) + (name "rust-url") + (version "1.7.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "url" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0nim1c90mxpi9wgdw2xh8dqd72vlklwlzam436akcrhjac6pqknx")))) + (arguments + `(#:cargo-inputs + (("rust-idna" ,rust-idna) + ("rust-matches" ,rust-matches) + ("rust-percent-encoding" ,rust-percent-encoding) + ("rust-encoding" ,rust-encoding) + ("rust-heapsize" ,rust-heapsize) + ("rust-rustc-serialize" ,rust-rustc-serialize) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher) + ("rust-rustc-serialize" ,rust-rustc-test) + ("rust-rustc-test" ,rust-rustc-test) + ("rust-serde-json" ,rust-serde-json)))))) + +(define-public rust-urlencoded + (package + (name "rust-urlencoded") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "urlencoded" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1qrkblcj3gpz256d5fci9g9ig20mxlavy25gj6p612qi740zalha")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bodyparser" ,rust-bodyparser) + ("rust-iron" ,rust-iron) + ("rust-plugin" ,rust-plugin) + ("rust-url" ,rust-url)))) + (home-page "https://github.com/iron/urlencoded") + (synopsis + "URL Encoded middleware for the Iron web framework. Decode URL Encoded data from GET request queries and POST request bodies.") + (description + "URL Encoded middleware for the Iron web framework. Decode URL Encoded data from GET request queries and POST request bodies.") + (license license:expat))) + (define-public rust-utf8-ranges (package (name "rust-utf8-ranges") @@ -8013,33 +10744,33 @@ whitespace from a string.") updated when the crate version changes.") (license license:expat))) -(define-public rust-walkdir +(define-public rust-want (package - (name "rust-walkdir") - (version "2.2.9") + (name "rust-want") + (version "0.3.0") (source (origin (method url-fetch) - (uri (crate-uri "walkdir" version)) + (uri (crate-uri "want" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "07ppalpvxkf8cnqr64np422792y4z5bs9m8b4nrflh5rm17wjn4n")))) + "181b2zmwfq389x9n2g1n37cvcvvdand832zz6v8i1l8wrdlaks0w")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-same-file" ,rust-same-file) - ("rust-winapi" ,rust-winapi) - ("rust-winapi-util" ,rust-winapi-util)) + (("rust-log" ,rust-bytes) + ("rust-try-lock" ,rust-try-lock)) #:cargo-development-inputs - (("rust-doc-comment" ,rust-doc-comment)))) - (home-page - "https://github.com/BurntSushi/walkdir") - (synopsis "Recursively walk a directory.") - (description "Recursively walk a directory.") - (license (list license:unlicense - license:expat)))) + (("rust-tokio-executor" ,rust-tokio-executor) + ("rust-tokio-sync" ,rust-tokio-sync)))) + (home-page "https://github.com/seanmonstar/want") + (synopsis + "Detect when another Future wants a result.") + (description + "Detect when another Future wants a result.") + (license license:expat))) (define-public rust-wasm-bindgen (package @@ -8102,6 +10833,44 @@ whitespace from a string.") (license (list license:asl2.0 license:expat)))) +(define-public rust-wasm-bindgen-futures + (package + (name "rust-wasm-bindgen-futures") + (version "0.3.27") + (source + (origin + (method url-fetch) + (uri (crate-uri "wasm-bindgen-futures" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "073p71skp91d9v2wczl6k7z9p0w25vn43br2v2g1ncbc6hvhnhl3")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if) + ("rust-futures" ,rust-futures) + ("rust-futures-channel-preview" + ,rust-futures-channel-preview) + ("rust-futures-util-preview" + ,rust-futures-util-preview) + ("rust-js-sys" ,rust-js-sys) + ("rust-lazy-static" ,rust-lazy-static) + ("rust-wasm-bindgen" ,rust-wasm-bindgen) + ("rust-web-sys" ,rust-web-sys)) + #:cargo-development-inputs + (("rust-wasm-bindgen-test" + ,rust-wasm-bindgen-test)))) + (home-page + "https://rustwasm.github.io/wasm-bindgen/") + (synopsis + "Bridging the gap between Rust Futures and JavaScript Promises") + (description + "Bridging the gap between Rust Futures and JavaScript Promises") + (license (list license:asl2.0 + license:expat)))) + (define-public rust-wasm-bindgen-macro (package (name "rust-wasm-bindgen-macro") @@ -8165,26 +10934,6 @@ whitespace from a string.") (license (list license:asl2.0 license:expat)))) -(define-public rust-wasm-bindgen-shared ; guix upstreamable - (package - (name "rust-wasm-bindgen-shared") - (version "0.2.48") - (source - (origin - (method url-fetch) - (uri (crate-uri "wasm-bindgen-shared" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "08rnfhjyk0f6liv8n4rdsvhx7r02glkhcbj2lp9lcbkbfpad9hnr")))) - (build-system cargo-build-system) - (home-page "https://rustwasm.github.io/wasm-bindgen/") - (synopsis "Shared support between wasm-bindgen and wasm-bindgen cli") - (description "This package provides shared support between -@code{wasm-bindgen} and @code{wasm-bindgen} cli, an internal dependency.") - (license (list license:asl2.0 - license:expat)))) - (define-public rust-wasm-bindgen-test (package (name "rust-wasm-bindgen-test") @@ -8220,182 +10969,242 @@ whitespace from a string.") (license (list license:asl2.0 license:expat)))) -(define-public rust-wasm-bindgen-test-macro +(define-public rust-wasm-bindgen-webidl (package - (name "rust-wasm-bindgen-test-macro") - (version "0.2.48") + (name "rust-wasm-bindgen-webidl") + (version "0.2.50") (source (origin (method url-fetch) - (uri (crate-uri "wasm-bindgen-test-macro" version)) + (uri (crate-uri "wasm-bindgen-webidl" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0n28mr6vncf1k1qr2b5bvfxq4jvqkjdzq0z0ab6w2f5d6v8q3q3l")))) + "057zak44nyrawipgi37m451fjkxz6ix5rzcw11d699rgpy4x4lxy")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-proc-macro2" ,rust-proc-macro2) - ("rust-quote" ,rust-quote)))) + (("rust-failure" ,rust-failure) + ("rust-heck" ,rust-heck) + ("rust-log" ,rust-log) + ("rust-proc-macro2" ,rust-proc-macro2) + ("rust-quote" ,rust-quote) + ("rust-syn" ,rust-syn) + ("rust-wasm-bindgen-backend" + ,rust-wasm-bindgen-backend) + ("rust-weedle" ,rust-weedle)))) (home-page - "https://github.com/rustwasm/wasm-bindgen") + "https://rustwasm.github.io/wasm-bindgen/") (synopsis - "Internal testing macro for wasm-bindgen") + "Support for parsing WebIDL specific to wasm-bindgen") (description - "Internal testing macro for wasm-bindgen") + "Support for parsing WebIDL specific to wasm-bindgen") (license (list license:asl2.0 license:expat)))) -(define-public rust-which +(define-public rust-web-sys (package - (name "rust-which") - (version "2.0.1") + (name "rust-web-sys") + (version "0.3.27") (source (origin (method url-fetch) - (uri (crate-uri "which" version)) + (uri (crate-uri "web-sys" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0r7i793sc0xqnd2fxnqbksj7j1kx65bwn81b8z49750v4c8cnymm")))) + "0lccdl3ihqh70s48dzvzpm09gpwvdjyw4wksk848dm0a41vw8db4")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-failure" ,rust-failure) - ("rust-libc" ,rust-libc)) + (("rust-js-sys" ,rust-js-sys) + ("rust-wasm-bindgen" ,rust-wasm-bindgen)) #:cargo-development-inputs - (("rust-tempdir" ,rust-tempdir)))) + (("rust-env-logger" ,rust-env-logger) + ("rust-failure" ,rust-failure) + ("rust-futures" ,rust-futures) + ("rust-sourcefile" ,rust-sourcefile) + ("rust-wasm-bindgen-futures" + ,rust-wasm-bindgen-futures) + ("rust-wasm-bindgen-test" + ,rust-wasm-bindgen-test) + ("rust-wasm-bindgen-webidl" + ,rust-wasm-bindgen-webidl)))) (home-page - "https://github.com/harryfei/which-rs.git") + "https://rustwasm.github.io/wasm-bindgen/web-sys/index.html") (synopsis - "A Rust equivalent of Unix command \"which\". Locate installed execuable in cross platforms.") + "Bindings for all Web APIs, a procedurally generated crate from WebIDL") (description - "This package provides a Rust equivalent of Unix command \"which\". Locate installed execuable in cross platforms.") - (license license:expat))) + "Bindings for all Web APIs, a procedurally generated crate from WebIDL") + (license (list license:asl2.0 + license:expat)))) -(define-public rust-winapi +(define-public rust-webpki (package - (name "rust-winapi") - (version "0.3.7") + (name "rust-webpki") + (version "0.21.0") (source (origin (method url-fetch) - (uri (crate-uri "winapi" version)) + (uri (crate-uri "webpki" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0w7pbhcl087lkggxdflfp2i92rq89ahsfdkjkv44fgmiy9m3h3pi")))) + "1d41gfai89q7drm92mgmh6fk57nikv2vqsa773i100dcf3kn9rnp")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-winapi-i686-pc-windows-gnu" - ,rust-winapi-i686-pc-windows-gnu) - ("rust-winapi-x86-64-pc-windows-gnu" - ,rust-winapi-x86-64-pc-windows-gnu)))) - (home-page - "https://github.com/retep998/winapi-rs") + (("rust-ring" ,rust-ring) + ("rust-untrusted" ,rust-untrusted)) + #:cargo-development-inputs + (("rust-base64" ,rust-base64)))) + (home-page "https://github.com/briansmith/webpki") (synopsis - "Raw FFI bindings for all of Windows API.") + "webpki is a library that validates Web PKI (TLS/SSL) certificates. webpki is designed to provide a full implementation of the client side of the Web PKI to a diverse range of applications and devices, including embedded (IoT) applications, mobile apps, desktop applications, and server infrastructure. webpki is intended to not only be the best implementation of the Web PKI, but to also precisely define what the Web PKI is.") (description - "Raw FFI bindings for all of Windows API.") - (license (list license:asl2.0 - license:expat)))) + "webpki is a library that validates Web PKI (TLS/SSL) certificates. webpki is designed to provide a full implementation of the client side of the Web PKI to a diverse range of applications and devices, including embedded (IoT) applications, mobile apps, desktop applications, and server infrastructure. webpki is intended to not only be the best implementation of the Web PKI, but to also precisely define what the Web PKI is.") + (license license:isc))) ; I think -(define-public rust-winapi-i686-pc-windows-gnu ; guix upstreamable? +(define-public rust-webpki-roots (package - (name "rust-winapi-i686-pc-windows-gnu") - (version "0.4.0") + (name "rust-webpki-roots") + (version "0.17.0") (source (origin (method url-fetch) - (uri (crate-uri "winapi-i686-pc-windows-gnu" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "webpki-roots" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "1dmpa6mvcvzz16zg6d5vrfy4bxgg541wxrcip7cnshi06v38ffxc")))) + (base32 + "12vi8dh0yik0h4f0b9dnlw5i3gxyky7iblbksh6zcq4xvlvswqm2")))) (build-system cargo-build-system) - (home-page "https://github.com/retep998/winapi-rs") - (synopsis "Import libraries for the i686-pc-windows-gnu target") - (description "This crate provides import libraries for the -i686-pc-windows-gnu target. Please don't use this crate directly, depend on -@code{winapi} instead.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-inputs (("rust-webpki" ,rust-webpki)))) + (home-page "https://github.com/ctz/webpki-roots") + (synopsis + "Mozilla's CA root certificates for use with webpki") + (description + "Mozilla's CA root certificates for use with webpki") + (license license:mpl2.0))) -(define-public rust-winapi-util +(define-public rust-which (package - (name "rust-winapi-util") - (version "0.1.2") + (name "rust-which") + (version "2.0.1") (source (origin (method url-fetch) - (uri (crate-uri "winapi-util" version)) + (uri (crate-uri "which" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1j839dc6y8vszvrsb7yk0qvs0w6asnahxzbyans37vnsw6vbls3i")))) + "0r7i793sc0xqnd2fxnqbksj7j1kx65bwn81b8z49750v4c8cnymm")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs (("rust-winapi" ,rust-winapi)))) + `(#:cargo-inputs + (("rust-failure" ,rust-failure) + ("rust-libc" ,rust-libc)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir)))) (home-page - "https://github.com/BurntSushi/winapi-util") + "https://github.com/harryfei/which-rs.git") (synopsis - "A dumping ground for high level safe wrappers over winapi.") + "A Rust equivalent of Unix command \"which\". Locate installed execuable in cross platforms.") (description - "This package provides a dumping ground for high level safe wrappers over winapi.") - (license (list license:unlicense - license:expat)))) + "This package provides a Rust equivalent of Unix command \"which\". Locate installed execuable in cross platforms.") + (license license:expat))) -(define-public rust-winapi-x86-64-pc-windows-gnu ; guix upstreamable? +(define-public rust-winreg (package - (name "rust-winapi-x86-64-pc-windows-gnu") - (version "0.4.0") + (name "rust-winreg") + (version "0.6.2") (source (origin (method url-fetch) - (uri (crate-uri "winapi-x86_64-pc-windows-gnu" version)) - (file-name (string-append name "-" version ".tar.gz")) + (uri (crate-uri "winreg" version)) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 - "0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki")))) + (base32 + "1jdcqr6zmvwyrp87h48miasfdvv16gjsb60rc8dy2kqwb3mnv65j")))) (build-system cargo-build-system) - (home-page "https://github.com/retep998/winapi-rs") - (synopsis "Import libraries for the x86_64-pc-windows-gnu target") - (description "This package provides import libraries for the -x86_64-pc-windows-gnu target. Please don't use this crate directly, depend on -@code{winapi} instead.") - (license (list license:asl2.0 - license:expat)))) + (arguments + `(#:cargo-inputs + (("rust-winapi" ,rust-winapi) + ("rust-chrono" ,rust-chrono) + ("rust-serde" ,rust-serde)) + #:cargo-development-inputs + (("rust-rand" ,rust-rand-0.3) + ("rust-serde-derive" ,rust-serde-derive)))) + (home-page "https://github.com/gentoo90/winreg-rs") + (synopsis + "Rust bindings to MS Windows Registry API.") + (description + "Rust bindings to MS Windows Registry API.") + (license license:expat))) -(define-public rust-wincolor +(define-public rust-xattr (package - (name "rust-wincolor") - (version "1.0.1") + (name "rust-xattr") + (version "0.2.2") (source (origin (method url-fetch) - (uri (crate-uri "wincolor" version)) + (uri (crate-uri "xattr" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1fp9sxq63kw3vjjcjrl3f7px082pplzxcr3qza2n2pa6mq0xj7jn")))) + "0k556fb6f5jc907975j9c8iynl2fqz3rf0w6fiig83i4yi0kfk14")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-winapi" ,rust-winapi) - ("rust-winapi-util" ,rust-winapi-util)))) + (("rust-libc" ,rust-libc)) + #:cargo-development-inputs + (("rust-tempfile" ,rust-tempfile)))) (home-page - "https://github.com/BurntSushi/termcolor/tree/master/wincolor") - (synopsis - "A simple Windows specific API for controlling text color in a Windows console.") + "https://github.com/Stebalien/xattr") + (synopsis "unix extended filesystem attributes") + (description "unix extended filesystem attributes") + (license (list license:asl2.0 + license:expat)))) + +(define-public rust-xz2 + (package + (name "rust-xz2") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "xz2" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0v4jb0193gx8s1kvd2ajsgh0ffmwhqhfmrrw1n1h2z7w6jgqcyf1")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures" ,rust-futures) + ("rust-lzma-sys" ,rust-lzma-sys) + ("rust-tokio-io" ,rust-tokio-io)) + #:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck-0.7) + ("rust-rand" ,rust-rand-0.5) + ("rust-tokio-core" ,rust-tokio-core)))) + (inputs + `(("pkg-config" ,pkg-config) + ("xz" ,xz))) + (home-page "https://github.com/alexcrichton/xz2-rs") + (synopsis "Rust bindings to liblzma providing Read/Write streams") (description - "This package provides a simple Windows specific API for controlling text color in a Windows console.") - (license (list license:unlicense + "Rust bindings to liblzma providing Read/Write streams as well as low-level +in-memory encoding/decoding.") + (license (list license:asl2.0 license:expat)))) (define-public rust-yaml-rust @@ -8416,7 +11225,7 @@ x86_64-pc-windows-gnu target. Please don't use this crate directly, depend on `(#:cargo-inputs (("rust-linked-hash-map" ,rust-linked-hash-map)) #:cargo-development-inputs - (("rust-quickcheck" ,rust-quickcheck)))) + (("rust-quickcheck" ,rust-quickcheck-0.7)))) (home-page "http://chyh1990.github.io/yaml-rust/") (synopsis "The missing YAML 1.2 parser for rust") @@ -8424,3 +11233,21 @@ x86_64-pc-windows-gnu target. Please don't use this crate directly, depend on "The missing YAML 1.2 parser for rust") (license (list license:asl2.0 license:expat)))) + +(define-public rust-yaml-rust-0.3 + (package + (inherit rust-yaml-rust) + (name "rust-yaml-rust") + (version "0.3.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "yaml-rust" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "14m9dzwb8fb05f4jjb4nqp49rxd9c5vcmwpv3a04d2y5iphncqz6")))) + (arguments + `(#:cargo-inputs + (("rust-clippy" ,rust-clippy) + ("rust-linked-hash-map" ,rust-linked-hash-map-0.3)))))) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 245af84..84251a4 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -7,6 +7,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages python) #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages node) #:use-module (gnu packages rdf) #:use-module (gnu packages serialization) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 553fbd7..5f18c69 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -6,60 +6,34 @@ #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) - #:use-module (guix build-system gnu) #:use-module (guix build-system cargo) - #:use-module (guix build-system cmake) - #:use-module (guix build-system perl) #:use-module (guix build-system python) - ;; #:use-module (guix build-system ruby) - #:use-module (guix build-system r) #:use-module (guix build-system trivial) #:use-module (gnu packages) - #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) - #:use-module (gnu packages boost) - #:use-module (gnu packages compression) + #:use-module (gnu packages bootstrap) #:use-module (gnu packages check) #:use-module (gnu packages cran) - #:use-module (gn packages crates-io) - #:use-module (gnu packages crates-io) + #:use-module (gnu packages compression) #:use-module (gnu packages databases) - #:use-module (gnu packages cpio) - #:use-module (gn packages elixir) - #:use-module (gnu packages file) - #:use-module (gnu packages gcc) - #:use-module (gnu packages graphviz) - #:use-module (gnu packages java) - #:use-module (gnu packages linux) - #:use-module (gnu packages dlang) - #:use-module (gnu packages machine-learning) - #:use-module (gnu packages maths) - #:use-module (gnu packages ncurses) - #:use-module (gnu packages perl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages popt) - #:use-module (gnu packages protobuf) - #:use-module (gnu packages python-crypto) #:use-module (gnu packages python) + #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) - #:use-module (gnu packages tbb) - #:use-module (gnu packages textutils) + #:use-module (gnu packages version-control) #:use-module (gnu packages vim) #:use-module (gnu packages web) - #:use-module (gnu packages xml) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages version-control) #:use-module (gn packages bioinformatics) + #:use-module (gn packages crates-io) + #:use-module (gn packages elixir) #:use-module (gn packages gemma) #:use-module (gn packages javascript) #:use-module (gn packages phewas) #:use-module (gn packages python) #:use-module (gn packages python24) - #:use-module (gn packages statistics) - #:use-module (srfi srfi-1)) + #:use-module (gn packages statistics)) (define-public my-deploy (package @@ -224,8 +198,7 @@ location of a putative QTL.") "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja")))) (build-system python-build-system) (arguments - `( - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-tests @@ -248,11 +221,11 @@ location of a putative QTL.") (license license:gpl2+)))) (define-public rust-qtlreaper - (let ((commit "eacf6ff1c3d1cd16084a70a7a425bd77080c15de") + (let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3") (revision "1")) (package (name "rust-qtlreaper") - (version (git-version "0.1.3" revision commit)) + (version "0.1.4") (source (origin (method git-fetch) @@ -262,7 +235,7 @@ location of a putative QTL.") (file-name (git-file-name name version)) (sha256 (base32 - "0gr2z54i11zz94ra4w06fhfnwnmmhl5xyc8qhlk0v2qq18yfi7ji")))) + "0h70aalsplmc6xn1w7ha102n3bsi3gqkbnbrjvjm2za37c07gv0g")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -270,27 +243,8 @@ location of a putative QTL.") ("rust-structopt" ,rust-structopt) ("rust-rayon" ,rust-rayon-1.0) ("rust-serde" ,rust-serde) - ("rust-serde-json" ,rust-serde-json)) - #:phases - (modify-phases %standard-phases - (add-after 'configure 'regenerate-cargo-lock - (lambda _ - (delete-file "Cargo.lock") - (invoke "cargo" "generate-lockfile"))) - (add-after 'patch-generated-file-shebangs 'patch-cargo-checksums - (lambda _ - (use-modules (guix build cargo-utils)) - (for-each - (lambda (filename) - (use-modules (guix build cargo-utils)) - (delete-file filename) - (let* ((dir (dirname filename))) - (display (string-append - "patch-cargo-checksums: generate-checksums for " - dir "\n")) - (generate-checksums dir))) - (find-files "guix-vendor" ".cargo-checksum.json")) - #t))))) + ("rust-serde-json" ,rust-serde-json) + ("rust-ndarray" ,rust-ndarray)))) (home-page "https://github.com/chfi/rust-qtlreaper") (synopsis "Reimplementation of genenetwork/QTLReaper in Rust") (description "Reimplementation of genenetwork/QTLReaper in Rust") @@ -311,62 +265,62 @@ location of a putative QTL.") (sha256 (base32 "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) - (propagated-inputs `( ;; propagated for development purposes - ("python" ,python-2) ;; probably superfluous - ("coreutils" ,coreutils) - ("git" ,git) - ("vim" ,vim) - ("which" ,which) - ("grep" ,grep) - ("r" ,r) - ("r-ctl" ,r-ctl) - ("r-phewas" ,r-phewas) - ("r-qtl" ,r-qtl) - ("r-wgcna" ,r-wgcna) - ("redis" ,redis) - ("mysql" ,mysql) - ("gemma" ,gemma-gn2-git) - ("gemma-wrapper" ,gemma-wrapper) - ("genenetwork2-files-small" ,genenetwork2-files-small) - ("plink-ng-gn" ,plink-ng-gn) - ("pylmm-gn2" ,pylmm-gn2) - ("nginx" ,nginx) - ("python2-flask" ,python2-flask) - ("gunicorn" ,gunicorn) - ("python2-pillow" ,python2-pillow) - ("python2-cssselect" ,python2-cssselect) - ("python2-elasticsearch" ,python2-elasticsearch) - ("python2-htmlgen" ,python2-htmlgen) - ("python2-jinja2" ,python2-jinja2) - ("python2-sqlalchemy" ,python2-sqlalchemy) - ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) - ("python2-setuptools" ,python2-setuptools) - ("python2-scipy" ,python2-scipy) - ("python2-lxml" ,python2-lxml) - ("python2-mechanize" ,python2-mechanize) - ("python2-mysqlclient" ,python2-mysqlclient) - ("python2-numarray" ,python2-numarray) - ("python2-numpy" ,python2-numpy) - ("python2-pandas" ,python2-pandas) - ("python2-parallel" ,python2-parallel) - ("python2-parameterized" ,python2-parameterized) - ("python2-passlib" ,python2-passlib) - ("python2-redis" ,python2-redis) - ("python2-requests" ,python2-requests) - ("python2-requests" ,python2-requests) - ("python2-rpy2" ,python2-rpy2) - ("python2-scipy" ,python2-scipy) - ("python2-simplejson" ,python2-simplejson) - ("python2-pyyaml" ,python2-pyyaml) - ("python2-unittest2" ,python2-unittest2) - ("python2-xlsxwriter" ,python2-xlsxwriter) - ("python2-qtlreaper" ,python2-qtlreaper) - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - - )) + (propagated-inputs + `(;; propagated for development purposes + ("python" ,python-2) ;; probably superfluous + ("coreutils" ,coreutils) + ("git" ,git) + ("vim" ,vim) + ("which" ,which) + ("grep" ,grep) + ("r" ,r) + ("r-ctl" ,r-ctl) + ("r-phewas" ,r-phewas) + ("r-qtl" ,r-qtl) + ("r-wgcna" ,r-wgcna) + ("redis" ,redis) + ("mysql" ,mysql) + ("gemma" ,gemma-gn2-git) + ("gemma-wrapper" ,gemma-wrapper) + ("genenetwork2-files-small" ,genenetwork2-files-small) + ("plink-ng-gn" ,plink-ng-gn) + ("pylmm-gn2" ,pylmm-gn2) + ("nginx" ,nginx) + ("python2-flask" ,python2-flask) + ("gunicorn" ,gunicorn) + ("python2-pillow" ,python2-pillow) + ("python2-cssselect" ,python2-cssselect) + ("python2-elasticsearch" ,python2-elasticsearch) + ("python2-htmlgen" ,python2-htmlgen) + ("python2-jinja2" ,python2-jinja2) + ("python2-sqlalchemy" ,python2-sqlalchemy) + ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) + ("python2-setuptools" ,python2-setuptools) + ("python2-scipy" ,python2-scipy) + ("python2-lxml" ,python2-lxml) + ("python2-mechanize" ,python2-mechanize) + ("python2-mysqlclient" ,python2-mysqlclient) + ("python2-numarray" ,python2-numarray) + ("python2-numpy" ,python2-numpy) + ("python2-pandas" ,python2-pandas) + ("python2-parallel" ,python2-parallel) + ("python2-parameterized" ,python2-parameterized) + ("python2-passlib" ,python2-passlib) + ("python2-redis" ,python2-redis) + ("python2-requests" ,python2-requests) + ("python2-requests" ,python2-requests) + ("python2-rpy2" ,python2-rpy2) + ("python2-scipy" ,python2-scipy) + ("python2-simplejson" ,python2-simplejson) + ("python2-pyyaml" ,python2-pyyaml) + ("python2-unittest2" ,python2-unittest2) + ("python2-xlsxwriter" ,python2-xlsxwriter) + ("python2-qtlreaper" ,python2-qtlreaper) + ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) + ("javascript-cytoscape" ,javascript-cytoscape) + ("javascript-panzoom" ,javascript-cytoscape-panzoom) + ("javascript-qtip" ,javascript-cytoscape-qtip) + )) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -374,37 +328,38 @@ location of a putative QTL.") (modify-phases %standard-phases (delete 'reset-gzip-timestamps) (add-after 'unpack 'fix-paths-scripts - (lambda* _ + (lambda _ (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python2") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which")) ; three wiches in a row! - )#t)) + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python2") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which")) ; three wiches in a row! + ) + #t)) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) - (let* ( - (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) - (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) + (let* ( + (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) + (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + ) - (substitute* '("etc/default_settings.py") - (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) - ) - )))) + (substitute* '("etc/default_settings.py") + (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) + (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) + ) + )))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") @@ -437,20 +392,17 @@ location of a putative QTL.") (let* ((out (assoc-ref %outputs "out")) (name "gn2_data_s") (tarfn (string-append name ".tar")) - (targetdir (string-append out "/share/genenetwork2/")) - ) + (targetdir (string-append out "/share/genenetwork2/"))) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) - (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) - ) + (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))) (and - (zero? (system* lz4unpack source "-d" tarfn)) - (zero? (system* tar "xf" tarfn)) - (mkdir-p targetdir) - (copy-recursively name targetdir) - )))))) + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir))))))) (home-page "http://genenetwork.org/") (synopsis "Small file archive to run on genenetwork") (description "Genenetwork genotype and mapping files.") @@ -477,8 +429,7 @@ location of a putative QTL.") #:builder (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) - (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) - ) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))) (and (mkdir "db") (zero? (system* unzip source "-d" "db")) (chdir "db")))))) @@ -494,15 +445,16 @@ location of a putative QTL.") (package (name "python-reaper") (version (string-append "0.0.1-" - (string-take commit 7))) + (string-take commit 7))) (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/fredmanglis/reaper.git") - (commit commit))) - (sha256 - (base32 - "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/fredmanglis/reaper.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r")))) (build-system python-build-system) (arguments `(#:tests? #f)) @@ -514,133 +466,132 @@ written in C") (define-public genenetwork3 (let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd") - (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) + (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) (package (name "genenetwork3") (version (string-append "2.10rc5-" (string-take commit 7) )) (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/fredmanglis/genenetwork2.git") - ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") - ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") - (commit commit))) - (file-name (string-append name "-" version)) - (sha256 - (base32 - "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" - ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz" - )))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/fredmanglis/genenetwork2.git") + ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") + ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" + ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz" + )))) (propagated-inputs ;; propagated for development purposes - `( ;; Agnostic to Python - ("r" ,r) - ("git" ,git) - ("vim" ,vim) - ("grep" ,grep) - ("which" ,which) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("redis" ,redis) - ("mysql" ,mysql) - ("nginx" ,nginx) - ("r-wgcna" ,r-wgcna) - ;; ("r-phewas" ,r-phewas) - ("coreutils" ,coreutils) - ("gemma" ,gemma-gn2-git) - ("plink-ng-gn" ,plink-ng-gn) - ("python-lxml" ,python-lxml) ;; used for the tests - ("gemma-wrapper" ,gemma-wrapper) - ("python-unittest" ,python-unittest2) ;; used for the tests - ("python-parameterized" ,python-parameterized) ;; used for the tests - ("genenetwork2-files-small" ,genenetwork2-files-small) - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - - ;; With Python3 support - ("gunicorn" ,gunicorn) - ("python-rpy2" ,python-rpy2) - ("python-flask" ,python-flask) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-redis" ,python-redis) - ("python-scipy" ,python-scipy) - ("python-pillow" ,python-pillow) - ("python-reaper" ,python-reaper) - ("python-pyyaml" ,python-pyyaml) - ("python-jinja2" ,python-jinja2) - ("python-pandas" ,python-pandas) - ("python-htmlgen" ,python-htmlgen) - ("python-passlib" ,python-passlib) - ("python-wrapper" ,python-wrapper) - ("python-requests" ,python-requests) - ("python-cssselect" ,python-cssselect) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-simplejson" ,python-simplejson) - ("python-xlsxwriter" ,python-xlsxwriter) - ("python-mysqlclient" ,python-mysqlclient) - ("python-elasticsearch" ,python-elasticsearch) - ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) + `(;; Agnostic to Python + ("r" ,r) + ("git" ,git) + ("vim" ,vim) + ("grep" ,grep) + ("which" ,which) + ("r-ctl" ,r-ctl) + ("r-qtl" ,r-qtl) + ("redis" ,redis) + ("mysql" ,mysql) + ("nginx" ,nginx) + ("r-wgcna" ,r-wgcna) + ;; ("r-phewas" ,r-phewas) + ("coreutils" ,coreutils) + ("gemma" ,gemma-gn2-git) + ("plink-ng-gn" ,plink-ng-gn) + ("python-lxml" ,python-lxml) ;; used for the tests + ("gemma-wrapper" ,gemma-wrapper) + ("python-unittest" ,python-unittest2) ;; used for the tests + ("python-parameterized" ,python-parameterized) ;; used for the tests + ("genenetwork2-files-small" ,genenetwork2-files-small) + ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) + ("javascript-cytoscape" ,javascript-cytoscape) + ("javascript-panzoom" ,javascript-cytoscape-panzoom) + ("javascript-qtip" ,javascript-cytoscape-qtip) + ;; With Python3 support + ("gunicorn" ,gunicorn) + ("python-rpy2" ,python-rpy2) + ("python-flask" ,python-flask) + ("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-redis" ,python-redis) + ("python-scipy" ,python-scipy) + ("python-pillow" ,python-pillow) + ("python-reaper" ,python-reaper) + ("python-pyyaml" ,python-pyyaml) + ("python-jinja2" ,python-jinja2) + ("python-pandas" ,python-pandas) + ("python-htmlgen" ,python-htmlgen) + ("python-passlib" ,python-passlib) + ("python-wrapper" ,python-wrapper) + ("python-requests" ,python-requests) + ("python-cssselect" ,python-cssselect) + ("python-sqlalchemy" ,python-sqlalchemy) + ("python-setuptools" ,python-setuptools) + ("python-simplejson" ,python-simplejson) + ("python-xlsxwriter" ,python-xlsxwriter) + ("python-mysqlclient" ,python-mysqlclient) + ("python-elasticsearch" ,python-elasticsearch) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) - ;; Without Python3 support - ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program - ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program - ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) - ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions - )) + ;; Without Python3 support + ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program + ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program + ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) + ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions + )) (build-system python-build-system) (arguments `(#:phases - (modify-phases - %standard-phases - (delete 'reset-gzip-timestamps) - (add-after - 'unpack 'fix-paths-scripts - (lambda* _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - (add-before - 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ((datafiles - (string-append - (assoc-ref inputs "genenetwork2-files-small") - "/share/genenetwork2" )) - ;; (pylmmcmd - ;; (string-append - ;; (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd - (string-append - (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd - (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) + (modify-phases + %standard-phases + (delete 'reset-gzip-timestamps) + (add-after + 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))) + #t)) + (add-before + 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((datafiles + (string-append + (assoc-ref inputs "genenetwork2-files-small") + "/share/genenetwork2" )) + ;; (pylmmcmd + ;; (string-append + ;; (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + (plink2cmd + (string-append + (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd + (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) - (substitute* - '("etc/default_settings.py") - (("^GENENETWORK_FILES +=.*") - (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - (("^PYLMM_COMMAND =.*") - (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") - (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") - (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n"))))))) - #:tests? #f)) ; no 'setup.py test' + (substitute* + '("etc/default_settings.py") + (("^GENENETWORK_FILES +=.*") + (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) + (("^PYLMM_COMMAND =.*") + (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) + (("^PLINK_COMMAND =.*") + (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") + (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n"))))))) + #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") diff --git a/gn/packages/glfw.scm b/gn/packages/glfw.scm deleted file mode 100644 index 6eb3a75..0000000 --- a/gn/packages/glfw.scm +++ /dev/null @@ -1,83 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages glfw) - #:use-module ((guix licenses)) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (guix build-system cmake) - #:use-module (guix packages) - #:use-module (gnu packages algebra) - #:use-module (gnu packages autotools) - #:use-module (gnu packages curl) - #:use-module (gnu packages gawk) - #:use-module (gnu packages cmake) - #:use-module (gnu packages boost) - #:use-module (gnu packages glib) - #:use-module (gnu packages image) - #:use-module (gnu packages video) - #:use-module (gnu packages textutils) - #:use-module (gnu packages gl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages maths) - #:use-module (gnu packages web) - #:use-module (gnu packages databases) - #:use-module (gnu packages python) - #:use-module (gnu packages xorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) - -(define-public glfw ; guix opengl - (package - (name "glfw") - (version "3.1.2") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/glfw/glfw/archive/" - version ".tar.gz")) - (sha256 - (base32 - "08pixv8hd5xsccf7l8cqcijjqaq4k4da8qbp77wggal2fq445ika")))) - (build-system cmake-build-system) - (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") #:tests? #f)) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cmake" ,cmake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) - (inputs `(("curl" ,curl) - ("dbus" ,dbus) - ("enca" ,enca) - ("eudev" ,eudev) - ("glew" ,glew) - ("libcap" ,libcap) - ("libjpeg" ,libjpeg) - ("libltdl" ,libltdl) - ("libtiff" ,libtiff) - ("mesa-utils" ,mesa-utils) - ("randrproto" ,randrproto) - ("libxrandr" ,libxrandr) - ("xineramaproto" ,xineramaproto) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor) - ("mysql" ,mysql) - ("python" ,python-2))) - (home-page "http://www.glfw.org/") - (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list gpl2)))) diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm index 1a34c98..d0e9127 100644 --- a/gn/packages/hyphy.scm +++ b/gn/packages/hyphy.scm @@ -19,36 +19,43 @@ (define-module (gn packages hyphy) #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system cmake) #:use-module (guix packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages curl) #:use-module (gnu packages mpi) - #:use-module (gnu packages python)) + #:use-module (gnu packages python) + #:use-module (gnu packages tls)) +;; TODO: Unbundle sqlite, gtest (define-public hyphy ; guix: check (package (name "hyphy") - (version "2.2.6") + (version "2.5.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/veg/hyphy/archive/" version - ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/veg/hyphy.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "00i3609nywb1xfq50p3kvfbvahql241ciq23jrf67z0yp4y5l5a9")))) + "1fvmwg2rxkz3abhhldiir69vmyc4i85vdvy64bizgxd0g2k2bikm")))) (inputs - `(("python" ,python-2) + `(("curl" ,curl) + ("fftw-openmpi" ,fftw-openmpi) ("openmpi" ,openmpi) - ("fftw-openmpi" ,fftw-openmpi))) + ("openssl" ,openssl) + ("python" ,python-2))) (build-system cmake-build-system) (arguments - '(#:make-flags '("MPI") + '(#:make-flags '("MPI") ; Add "GTEST" for tests, currently fails to compile. #:configure-flags (list "-DCMAKE_BUILD_TYPE=Release" (string-append "-DINSTALL_PREFIX=" (assoc-ref %outputs "out"))) - #:tests? #f)) + #:tests? #f + #:test-target "HYPHYGTEST")) (synopsis "hyphy: an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.") diff --git a/gn/packages/mongodb.scm b/gn/packages/mongodb.scm deleted file mode 100644 index 79c2b75..0000000 --- a/gn/packages/mongodb.scm +++ /dev/null @@ -1,74 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Roel Janssen <roel@gnu.org> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages mongodb) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) - #:use-module (guix utils) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (gnu packages) - #:use-module (gnu packages perl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages python)) - -(define-public mongodb ; guix fix tests and maybe non-free - (package - (name "mongodb") - (version "3.3.3") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/mongodb/mongo/archive/r" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "01v16j8xbry7m7apwlhiqhgx3zyyk2kadyk2sr9m6k20wnh5j24y")) - (patches (list (search-patch "mongodb-add-version-file.patch"))))) - (build-system gnu-build-system) - (native-inputs - `(("scons" ,scons) - ("python" ,python-2) - ("perl" ,perl))) - (arguments - `(#:tests? #f ; There is no 'check' target. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase - (add-after 'unpack 'scons-propagate-environment - (lambda _ - ;; Modify the SConstruct file to arrange for - ;; environment variables to be propagated. - (substitute* "SConstruct" - (("^env = Environment\\(") - "env = Environment(ENV=os.environ, ")))) - (replace 'build - (lambda _ - (zero? (system* "scons" "mongod" "mongo" "mongos")))) - (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))) - (install-file "mongod" bin) - (install-file "mongos" bin) - (install-file "mongo" bin))))))) - (home-page "https://www.mongodb.org/") - (synopsis "High performance and high availability document database") - (description "Mongo is a high-performance, high availability, -schema-free document-oriented database. A key goal of MongoDB is to bridge -the gap between key/value stores (which are fast and highly scalable) and -traditional RDBMS systems (which are deep in functionality).") - (license (list license:agpl3 license:asl2.0)))) diff --git a/gn/packages/ocl-icd.scm b/gn/packages/ocl-icd.scm deleted file mode 100644 index 79b4853..0000000 --- a/gn/packages/ocl-icd.scm +++ /dev/null @@ -1,99 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages ocl-icd) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (gnu packages) - #:use-module (gnu packages autotools) - #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages linux) - #:use-module (gnu packages textutils) - #:use-module (gnu packages base) - #:use-module (gnu packages compression) - #:use-module (gnu packages gnupg) - #:use-module (gnu packages ruby) - #:use-module (guix git-download)) - -(define-public ocl-icd - (package - (name "ocl-icd") - (version "2.2.9") - (source (origin - (method url-fetch) - (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) - (inputs `(("zip" ,zip) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("ruby" ,ruby) - ("libtool" ,libtool) - ("opencl-headers" ,opencl-headers) - ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") - (description "OpenCL implementations are provided as ICD (Installable Client Driver). - An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. - This free ICD Loader can load any (free or non free) ICD") - (license license:gpl2))) - - (define-public opencl-headers -(let ((commit "c1770dc")) - (package - (name "opencl-headers") - (version (string-append "2.1-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/KhronosGroup/OpenCL-Headers.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck")))) - (propagated-inputs '()) - (inputs '()) - (native-inputs '()) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (string-append - (assoc-ref outputs "out") - "/include/CL"))))))) - (synopsis "The Khronos OpenCL headers") - (description "This package provides the Khronos OpenCL headers") - (home-page "https://www.khronos.org/registry/cl/") - (license license:gpl2)))) diff --git a/gn/packages/opencl-headers.scm b/gn/packages/opencl-headers.scm deleted file mode 100644 index bddd136..0000000 --- a/gn/packages/opencl-headers.scm +++ /dev/null @@ -1,63 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages opencl-headers) - #:use-module ((guix licenses)) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix packages) - #:use-module (guix build-system gnu) - #:use-module (gnu packages gl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages xorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) - -(define-public opencl-headers -(let ((commit "c1770dc")) - (package - (name "opencl-headers") - (version (string-append "2.1-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/KhronosGroup/OpenCL-Headers.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck")))) - (propagated-inputs '()) - (inputs '()) - (native-inputs '()) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (string-append - (assoc-ref outputs "out") - "/include/CL"))))))) - (synopsis "The Khronos OpenCL headers") - (description "This package provides the Khronos OpenCL headers") - (home-page "https://www.khronos.org/registry/cl/") - (license gpl2)))) diff --git a/gn/packages/openfyba.scm b/gn/packages/openfyba.scm index bfc50b7..c1a1c90 100644 --- a/gn/packages/openfyba.scm +++ b/gn/packages/openfyba.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> +;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -18,44 +19,40 @@ (define-module (gn packages openfyba) #:use-module ((guix licenses)) - #:use-module (gnu packages) - #:use-module (gnu packages autotools) #:use-module (guix packages) - #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) - #:use-module (gnu packages linux) - #:use-module (gnu packages textutils) - #:use-module (gnu packages base) - ;;#:use-module (gnu packages tls) + #:use-module (gnu packages autotools) #:use-module (gnu packages compression) - #:use-module (gnu packages gnupg) - #:use-module (gnu packages bootstrap) - #:use-module (guix git-download)) + #:use-module (gnu packages gnupg)) (define-public openfyba (package (name "openfyba") (version "4.1.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/kartverket/fyba/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/kartverket/fyba.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0ya1agi78d386skq353dk400fl11q6whfqmv31qrkn4g5vamixlr")))) + "0zxw4pf3s7rb9g8209i3rj0v5jjw1vb79knd5mzvw9drpl9bbgpl")))) (inputs `(("zip" ,zip) ("autoconf" ,autoconf) ("automake" ,automake) ("libtool" ,libtool) ("libgcrypt" ,libgcrypt))) (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ + (for-each make-file-writable (find-files "." ".*")) + (invoke "autoreconf" "-vfi")))))) (home-page "http://labs.kartverket.no/sos/") (synopsis "source code release of the FYBA library") (description "OpenFYBA is the source code release of the FYBA library.") - (license (list gpl2)))) + (license gpl2))) diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm new file mode 100644 index 0000000..7164229 --- /dev/null +++ b/gn/packages/ratspub.scm @@ -0,0 +1,75 @@ +(define-module (gn packages ratspub) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix git-download) + #:use-module (guix build-system python) + #:use-module (gn packages javascript) + #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) + #:use-module (gn packages web)) + +(define-public ratspub + (let ((commit "19bc3078c06bef3c10c55dc6e69018e595d07d17") + (revision "1")) + (package + (name "ratspub") + (version (git-version "0.0.0" revision commit)) ; June 1, 2019 + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chen42/ratspub.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1v05rrjmiwrjmjspn487hd39403vb452hmk2l1l55rkm26781hwk")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; no test suite + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (add-after 'unpack 'patch-javascript-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((cytoscape (assoc-ref inputs "cytoscape")) + (bootstrap (assoc-ref inputs "bootstrap"))) + (substitute* "templates/cytoscape.html" + (("script src=.*") + (string-append "script src=\"" cytoscape + "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js\"></script>\n"))) + (substitute* "templates/layout.html" + (("https://stackpath.bootstrapcdn.com/bootstrap/.*") + (string-append bootstrap "/share/web/bootstrap/css/bootstrap.min.css\">\n")))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (copy-recursively "static" (string-append out "/static")) + (copy-recursively "templates" (string-append out "/templates")) + (install-file "server.py" out)) + #t)) + (add-after 'install 'wrap-executable + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out "/server.py") + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("python-flask" ,python-flask) + ("python-nltk" ,python-nltk))) + (native-inputs + `(("cytoscape" ,javascript-cytoscape) + ("bootstrap" ,web-bootstrap))) + (home-page "http://rats.pub/") + (synopsis "Relationship with Addiction Through Searches of PubMed") + (description + "RatsPub searches PubMed to find sentences that contain the query terms +(i.e., gene symbols) and drug addiction-related keywords. These gene-keyword +relationships are presented as an interactive graph that can efficiently answer +the question \"What do we know about these genes and addiction?\". Data from +@acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association +Studies} catalog are also included in the search to better answer this +question.") + (license #f)))) diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm index e46616c..8dfb1d2 100644 --- a/gn/packages/ruby.scm +++ b/gn/packages/ruby.scm @@ -292,53 +292,6 @@ a history.") "https://github.com/pjotrp/bioruby-logger-plugin") (license #f))) -(define-public bio-table ; guix maybe ready -(package - (name "bio-table") - (version "1.0.0") - (source - (origin - (method url-fetch) - (uri (rubygems-uri "bio-table" version)) - (sha256 - (base32 - "1jlpls734kd41rffn2y2747nr14k5rwgaj2g3k48i9xgsfcmrn6r")))) - (build-system ruby-build-system) - (propagated-inputs - `(("ruby-bio-logger" ,ruby-bio-logger))) - (arguments - `(#:tests? #f)) ;; no bundler - (synopsis - "Functions and tools for tranforming and changing tab delimited and comma separated table files - useful for Excel sheets and SQL/RDF output") - (description - "Functions and tools for tranforming and changing tab delimited and comma separated table files - useful for Excel sheets and SQL/RDF output") - (home-page - "http://github.com/pjotrp/bioruby-table") - (license license:expat))) - - -(define-public bio-vcf ; guix maybe ready -(package - (name "bio-vcf") - (version "0.9.2") - (source - (origin - (method url-fetch) - (uri (rubygems-uri "bio-vcf" version)) - (sha256 - (base32 - "1007bn0w8l11q867lxsyqnk0vgvv12skvk9gyglv7g44knr5vh4j")))) - (build-system ruby-build-system) - (arguments - `(#:tests? #f)) ;; no bundler/cucumber - (synopsis - "Smart lazy multi-threaded parser for VCF format with useful filtering and output rewriting (JSON, RDF etc.)") - (description - "Smart lazy multi-threaded parser for VCF format with useful filtering and output rewriting (JSON, RDF etc.)") - (home-page - "http://github.com/pjotrp/bioruby-vcf") - (license license:expat))) - (define-public ruby-faraday (package (name "ruby-faraday") diff --git a/gn/packages/sparql-query.scm b/gn/packages/sparql-query.scm deleted file mode 100644 index dd6f553..0000000 --- a/gn/packages/sparql-query.scm +++ /dev/null @@ -1,87 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Roel Janssen <roel@gnu.org> -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. - -(define-module (gn packages sparql-query) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) - #:use-module (guix utils) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (gnu packages) - #:use-module (gnu packages compression) - #:use-module (gnu packages curl) - #:use-module (gnu packages glib) - #:use-module (gnu packages readline) - #:use-module (gnu packages ncurses) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages xml)) - -(define-public sparql-query - (package - (name "sparql-query") - (version "1.1") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/tialaramex/sparql-query/archive/" - version ".tar.gz")) - (sha256 - (base32 "0yq3k20472rv8npcc420q9ab6idy584g5y0q501d360k5q0ggr8w")) - (file-name (string-append name "-" version ".tar.gz")))) - (build-system gnu-build-system) - (inputs - `(("readline" ,readline) - ("ncurses" ,ncurses) - ("glib" ,glib) - ("libxml2" ,libxml2) - ("curl" ,curl))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (arguments - `(#:tests? #t - #:make-flags '("CC=gcc") - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'remove-git-dependency - (lambda _ - (substitute* "Makefile" - (("^gitrev :=.*$") "gitrev = \"v1.0-3-gb015131\"")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (install-file "sparql-query" bin) - (system* "ln" "--symbolic" - (string-append bin "/sparql-query") - (string-append bin "/sparql-update"))))) - (replace 'check - (lambda _ - (and - ;; The make-flags seem to get ignored here. - (zero? (system* "make" "CC=gcc" "scan-test")) - (zero? (system* "./scan-test")))))))) - (home-page "https://github.com/tialaramex/sparql-query/") - (synopsis "Command-line tool for accessing SPARQL endpoints over HTTP") - (description "sparql-query is a command-line tool for accessing SPARQL -endpoints over HTTP. It has been intentionally designed to 'feel' similar to -tools for interrogating SQL databases. For example, you can enter a query over -several lines, using a semi-colon at the end of a line to indicate the end of -your query. It also supports readline so that you can more easily recall and -edit previous queries, even across sessions. It can be used non-interactively, -for example from a shell script.") - (license license:gpl2+))) diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index edc9ab7..134213a 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -318,7 +318,7 @@ for use in genome-wide association studies (GWAS).") (define-public r-ctl ; guix: ready (package (name "r-ctl") - (version "1.0.0-0") + (version "1.0.0-2") (source (origin (method url-fetch) @@ -326,7 +326,7 @@ for use in genome-wide association studies (GWAS).") version ".tar.gz")) (sha256 (base32 - "12hrrql9wz43s1d3sfyzlqzx7ajrl3hvf96776ik6icbm8by8h6j")))) + "1gpb43zn411l476dby2g38qkcvh2fsdcvbkr9jb274l1154km1xm")))) (build-system r-build-system) (inputs `( ("r-qtl" ,r-qtl) diff --git a/gn/packages/yaj.scm b/gn/packages/yaj.scm index 662d83a..dc19f0f 100644 --- a/gn/packages/yaj.scm +++ b/gn/packages/yaj.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages check) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) |