mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-26 22:38:07 -05:00
44d10b1f72
* gnu/packages/python.scm: Move hundreds of package definitions from here... * gnu/packages/python-xyz.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/benchmark.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/calendar.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/cluster.scm, gnu/packages/compression.scm, gnu/packages/connman.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/direct-connect.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/docker.scm, gnu/packages/ebook.scm, gnu/packages/elf.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/finance.scm, gnu/packages/fltk.scm, gnu/packages/fontutils.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/geo.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/ham-radio.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/kde-frameworks.scm, gnu/packages/key-mon.scm, gnu/packages/libffi.scm, gnu/packages/libreoffice.scm, gnu/packages/libusb.scm, gnu/packages/lirc.scm, gnu/packages/logging.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/mate.scm, gnu/packages/maths.scm, gnu/packages/medical.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/nutrition.scm, gnu/packages/openldap.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/photo.scm, gnu/packages/polkit.scm, gnu/packages/protobuf.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/qt.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm, gnu/packages/search.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/simulation.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wicd.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: Update module references.
398 lines
17 KiB
Scheme
398 lines
17 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
|
|
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
|
|
;;;
|
|
;;; 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 (gnu packages julia)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix download)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix git-download)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages algebra)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages elf)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages llvm)
|
|
#:use-module (gnu packages libevent)
|
|
#:use-module (gnu packages libunwind)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages multiprecision) ; mpfr
|
|
#:use-module (gnu packages pcre)
|
|
#:use-module (gnu packages perl)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages python-xyz)
|
|
#:use-module (gnu packages textutils)
|
|
#:use-module (gnu packages tls)
|
|
#:use-module (gnu packages version-control)
|
|
#:use-module (gnu packages wget)
|
|
#:use-module (ice-9 match))
|
|
|
|
(define libuv-julia
|
|
(let ((commit "52d72a52cc7ccd570929990f010ed16e2ec604c8")
|
|
(revision "5"))
|
|
(package (inherit libuv)
|
|
(name "libuv-julia")
|
|
(version (string-append "1.9.0-" revision "." (string-take commit 8)))
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/JuliaLang/libuv.git")
|
|
(commit commit)))
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
(sha256
|
|
(base32
|
|
"1daxh6ci6q7znxxajr3bm16dd53ragm0d681wf4kzg542qnjq3lh"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments libuv)
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(delete 'autogen)))))
|
|
(home-page "https://github.com/JuliaLang/libuv"))))
|
|
|
|
(define libunwind-for-julia
|
|
(package
|
|
(inherit libunwind)
|
|
(version "1.1-julia2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://s3.amazonaws.com/julialang/src/"
|
|
"libunwind-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
|
|
|
|
(define-public julia
|
|
(package
|
|
(name "julia")
|
|
(version "0.6.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://github.com/JuliaLang/julia/releases/download/v"
|
|
version "/julia-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0rd6lcc9sic10q1j3c6f9qr901i1c4554m93n2sz5b3mh37byqhw"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:test-target "test"
|
|
#:modules ((ice-9 match)
|
|
(guix build gnu-build-system)
|
|
(guix build utils))
|
|
|
|
;; Do not strip binaries to keep support for full backtraces.
|
|
;; See https://github.com/JuliaLang/julia/issues/17831
|
|
#:strip-binaries? #f
|
|
|
|
;; The DSOs use $ORIGIN to refer to each other, but (guix build
|
|
;; gremlin) doesn't support it yet, so skip this phase.
|
|
#:validate-runpath? #f
|
|
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure)
|
|
(add-after 'unpack 'prepare-deps
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(mkdir "deps/srccache")
|
|
(copy-file (assoc-ref inputs "dsfmt")
|
|
"deps/srccache/dsfmt-2.2.3.tar.gz")
|
|
(copy-file (assoc-ref inputs "objconv")
|
|
"deps/srccache/objconv.zip")
|
|
(copy-file (assoc-ref inputs "suitesparse")
|
|
"deps/srccache/SuiteSparse-4.4.5.tar.gz")
|
|
(copy-file (string-append (assoc-ref inputs "virtualenv")
|
|
"/bin/virtualenv")
|
|
"julia-env")
|
|
(copy-file (assoc-ref inputs "unicode-data")
|
|
"doc/UnicodeData.txt")
|
|
#t))
|
|
;; FIXME: Building the documentation requires Julia packages that
|
|
;; would be downloaded from the Internet. We should build them in a
|
|
;; separate build phase.
|
|
(add-after 'unpack 'disable-documentation
|
|
(lambda _
|
|
(substitute* "Makefile"
|
|
(("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
|
|
(string-append line "\n"))
|
|
(("src ui doc deps")
|
|
"src ui deps"))
|
|
#t))
|
|
(add-before 'check 'set-home
|
|
;; Some tests require a home directory to be set.
|
|
(lambda _ (setenv "HOME" "/tmp") #t))
|
|
(add-after 'unpack 'hardcode-soname-map
|
|
;; ./src/runtime_ccall.cpp creates a map from library names to paths
|
|
;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
|
|
;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(use-modules (ice-9 match))
|
|
(substitute* "src/runtime_ccall.cpp"
|
|
;; Patch out invocations of '/sbin/ldconfig' to avoid getting
|
|
;; error messages about missing '/sbin/ldconfig' on GuixSD.
|
|
(("popen\\(.*ldconfig.*\\);")
|
|
"NULL;\n")
|
|
|
|
;; Populate 'sonameMap'.
|
|
(("jl_read_sonames.*;")
|
|
(string-join
|
|
(map (match-lambda
|
|
((input libname soname)
|
|
(string-append
|
|
"sonameMap[\"" libname "\"] = "
|
|
"\"" (assoc-ref inputs input) "/lib/" soname "\";")))
|
|
'(("libc" "libc" "libc.so.6")
|
|
("pcre2" "libpcre2-8" "libpcre2-8.so")
|
|
("mpfr" "libmpfr" "libmpfr.so")
|
|
("openblas" "libblas" "libopenblas.so")
|
|
("arpack-ng" "libarpack" "libarpack.so")
|
|
("lapack" "liblapack" "liblapack.so")
|
|
("libgit2" "libgit2" "libgit2.so")
|
|
("gmp" "libgmp" "libgmp.so")
|
|
("openlibm" "libopenlibm" "libopenlibm.so")
|
|
("openspecfun" "libopenspecfun" "libopenspecfun.so")
|
|
("fftw" "libfftw3" "libfftw3_threads.so")
|
|
("fftwf" "libfftw3f" "libfftw3f_threads.so"))))))
|
|
(substitute* "base/fft/FFTW.jl"
|
|
(("const libfftw = Base.libfftw_name")
|
|
(string-append "const libfftw = \""
|
|
(assoc-ref inputs "fftw") "/lib/libfftw3_threads.so"
|
|
"\""))
|
|
(("const libfftwf = Base.libfftwf_name")
|
|
(string-append "const libfftwf = \""
|
|
(assoc-ref inputs "fftwf") "/lib/libfftw3f_threads.so"
|
|
"\"")))
|
|
(substitute* "base/math.jl"
|
|
(("const libm = Base.libm_name")
|
|
(string-append "const libm = \""
|
|
(assoc-ref inputs "openlibm")
|
|
"/lib/libopenlibm.so"
|
|
"\""))
|
|
(("const openspecfun = \"libopenspecfun\"")
|
|
(string-append "const openspecfun = \""
|
|
(assoc-ref inputs "openspecfun")
|
|
"/lib/libopenspecfun.so"
|
|
"\"")))
|
|
(substitute* "base/pcre.jl"
|
|
(("const PCRE_LIB = \"libpcre2-8\"")
|
|
(string-append "const PCRE_LIB = \""
|
|
(assoc-ref inputs "pcre2")
|
|
"/lib/libpcre2-8.so" "\"")))
|
|
#t))
|
|
(add-before 'build 'fix-include-and-link-paths
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
;; LIBUTF8PROC is a linker flag, not a build target. It is
|
|
;; included in the LIBFILES_* variable which is used as a
|
|
;; collection of build targets and a list of libraries to link
|
|
;; against.
|
|
(substitute* "src/flisp/Makefile"
|
|
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
|
|
"$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
|
|
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
|
|
"$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
|
|
|
|
;; The REPL must be linked with libuv.
|
|
(substitute* "ui/Makefile"
|
|
(("JLDFLAGS \\+= ")
|
|
(string-append "JLDFLAGS += "
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/lib/libuv.so ")))
|
|
|
|
(substitute* "base/Makefile"
|
|
(("\\$\\(build_includedir\\)/uv-errno.h")
|
|
(string-append (assoc-ref inputs "libuv")
|
|
"/include/uv-errno.h")))
|
|
#t))
|
|
(add-before 'build 'replace-default-shell
|
|
(lambda _
|
|
(substitute* "base/client.jl"
|
|
(("/bin/sh") (which "sh")))
|
|
#t))
|
|
(add-after 'unpack 'hardcode-paths
|
|
(lambda _
|
|
(substitute* "base/interactiveutil.jl"
|
|
(("`which") (string-append "`" (which "which")))
|
|
(("`wget") (string-append "`" (which "wget"))))
|
|
#t))
|
|
(add-before 'check 'disable-broken-tests
|
|
(lambda _
|
|
;; Adjust expected error messages to match what current libgit2
|
|
;; provides.
|
|
(substitute* "test/libgit2.jl"
|
|
(("Invalid Content-Type") "invalid Content-Type")
|
|
(("Failed to resolve path") "failed to resolve path"))
|
|
|
|
(substitute* "test/choosetests.jl"
|
|
;; These tests fail, probably because some of the input
|
|
;; binaries have been stripped and thus backtraces don't look
|
|
;; as expected.
|
|
(("\"backtrace\",") "")
|
|
(("\"compile\",") "")
|
|
(("\"replutil\",") "")
|
|
(("\"cmdlineargs\",") "")
|
|
;; FIXME: This test fails with the following error:
|
|
;; Error in testset file:
|
|
;; Test Failed
|
|
;; Expression: download("ba\0d", "good")
|
|
;; Expected: ArgumentError
|
|
;; Thrown: Base.UVError
|
|
(("\"file\",") ""))
|
|
#t)))
|
|
#:make-flags
|
|
(list
|
|
(string-append "prefix=" (assoc-ref %outputs "out"))
|
|
|
|
;; Passing the MARCH flag is necessary to build binary substitutes for
|
|
;; the supported architectures.
|
|
,(match (or (%current-target-system)
|
|
(%current-system))
|
|
("x86_64-linux" "MARCH=x86-64")
|
|
("i686-linux" "MARCH=pentium4")
|
|
("aarch64-linux" "MARCH=armv8-a")
|
|
;; Prevent errors when querying this package on unsupported
|
|
;; platforms, e.g. when running "guix package --search="
|
|
(_ "MARCH=UNSUPPORTED"))
|
|
|
|
"CONFIG_SHELL=bash" ;needed to build bundled libraries
|
|
"USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no
|
|
;build system for a shared library.
|
|
"USE_SYSTEM_LAPACK=1"
|
|
"USE_SYSTEM_BLAS=1"
|
|
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
|
|
|
|
"USE_SYSTEM_FFTW=1"
|
|
"LIBFFTWNAME=libfftw3"
|
|
"LIBFFTWFNAME=libfftw3f"
|
|
|
|
;; TODO: Suitesparse does not install shared libraries, so we cannot
|
|
;; use the suitesparse package.
|
|
;; "USE_SYSTEM_SUITESPARSE=1"
|
|
;; (string-append "SUITESPARSE_INC=-I "
|
|
;; (assoc-ref %build-inputs "suitesparse")
|
|
;; "/include")
|
|
|
|
"USE_GPL_LIBS=1" ;proudly
|
|
"USE_SYSTEM_UTF8PROC=1"
|
|
(string-append "UTF8PROC_INC="
|
|
(assoc-ref %build-inputs "utf8proc")
|
|
"/include")
|
|
"USE_SYSTEM_LLVM=1"
|
|
"USE_LLVM_SHLIB=0" ; FIXME: fails when set to 1
|
|
|
|
"USE_SYSTEM_LIBUNWIND=1"
|
|
"USE_SYSTEM_LIBUV=1"
|
|
(string-append "LIBUV="
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/lib/libuv.so")
|
|
(string-append "LIBUV_INC="
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/include")
|
|
"USE_SYSTEM_PATCHELF=1"
|
|
"USE_SYSTEM_PCRE=1"
|
|
"USE_SYSTEM_OPENLIBM=1"
|
|
"USE_SYSTEM_GMP=1"
|
|
"USE_SYSTEM_MPFR=1"
|
|
"USE_SYSTEM_ARPACK=1"
|
|
"USE_SYSTEM_LIBGIT2=1"
|
|
"USE_SYSTEM_OPENSPECFUN=1")))
|
|
(inputs
|
|
`(("llvm" ,llvm-3.9.1)
|
|
|
|
;; The bundled version is 3.3.0 so stick to that version. With other
|
|
;; versions, we get test failures in 'linalg/arnoldi' as described in
|
|
;; <https://bugs.gnu.org/30282>.
|
|
("arpack-ng" ,arpack-ng-3.3.0)
|
|
|
|
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
|
|
("lapack" ,lapack)
|
|
("openblas" ,openblas) ;Julia does not build with Atlas
|
|
("libunwind" ,libunwind-for-julia)
|
|
("openlibm" ,openlibm)
|
|
("openspecfun" ,openspecfun)
|
|
("libgit2" ,libgit2)
|
|
("fftw" ,fftw)
|
|
("fftwf" ,fftwf)
|
|
("fortran" ,gfortran)
|
|
("libuv" ,libuv-julia)
|
|
("pcre2" ,pcre2)
|
|
("utf8proc" ,utf8proc)
|
|
("mpfr" ,mpfr)
|
|
("wget" ,wget)
|
|
("which" ,which)
|
|
("zlib" ,zlib)
|
|
("gmp" ,gmp)
|
|
("virtualenv" ,python2-virtualenv)
|
|
;; FIXME: The following inputs are downloaded from upstream to allow us
|
|
;; to use the lightweight Julia release tarball. Ideally, these inputs
|
|
;; would eventually be replaced with proper Guix packages.
|
|
|
|
;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
|
|
("suitesparse"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
|
|
(sha256
|
|
(base32
|
|
"1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
|
|
("objconv"
|
|
,(origin
|
|
(method url-fetch)
|
|
;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
|
|
(uri "https://www.agner.org/optimize/objconv.zip")
|
|
(file-name "objconv-2018-10-07.zip")
|
|
(sha256
|
|
(base32
|
|
"0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
|
|
("dsfmt"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
|
|
"SFMT/dSFMT-src-2.2.3.tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
|
|
(native-inputs
|
|
`(("openssl" ,openssl)
|
|
("perl" ,perl)
|
|
("patchelf" ,patchelf)
|
|
("pkg-config" ,pkg-config)
|
|
("python" ,python-2)
|
|
("unicode-data"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "http://www.unicode.org/Public/9.0.0/ucd/UnicodeData.txt")
|
|
(sha256
|
|
(base32
|
|
"13zfannnr6sa6s27ggvcvzmh133ndi38pfyxsssvjmw2s8ac9pv8"))))))
|
|
;; Julia is not officially released for ARM and MIPS.
|
|
;; See https://github.com/JuliaLang/julia/issues/10639
|
|
(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
|
|
(home-page "https://julialang.org/")
|
|
(synopsis "High-performance dynamic language for technical computing")
|
|
(description
|
|
"Julia is a high-level, high-performance dynamic programming language for
|
|
technical computing, with syntax that is familiar to users of other technical
|
|
computing environments. It provides a sophisticated compiler, distributed
|
|
parallel execution, numerical accuracy, and an extensive mathematical function
|
|
library.")
|
|
(license license:expat)))
|