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guix/gnu/packages/julia.scm
Tobias Geerinckx-Rice f6e031ab36
gnu: julia: Update to 1.5.3. 
* gnu/packages/julia.scm (julia): Update to 1.5.3.
(libuv-julia): Update to 1fcc6d66f9df74189c74d3d390f02202bb7db953.
(julia-patch): Update version.  No change to patches.
2020-11-13 19:43:25 +01:00

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; 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 curl)
#: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 ssh)
#: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 "1fcc6d66f9df74189c74d3d390f02202bb7db953")
(revision "2"))
;; When upgrading Julia, also upgrade this. Get the commit from
;; https://github.com/JuliaLang/julia/blob/v1.5.2/deps/libuv.version
(package
(inherit libuv)
(name "libuv-julia")
(version (git-version "2.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/libuv")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji"))))
(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-julia
;; The Julia projects requires their patched version.
;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
(package
(inherit libunwind)
(name "libunwind-julia")
(version "1.3.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://savannah/libunwind/libunwind-"
version ".tar.gz"))
(sha256
(base32
"1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
(patches
(list
(julia-patch "libunwind-prefer-extbl"
"0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
(julia-patch "libunwind-static-arm"
"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
(home-page "https://github.com/JuliaLang/tree/master/deps/")))
(define (julia-patch-url version name)
(string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
"/deps/patches/" name ".patch"))
(define (julia-patch name sha)
(let ((version "1.5.3"))
(origin (method url-fetch)
(uri (julia-patch-url version name))
(sha256 (base32 sha))
(file-name name))))
(define llvm-julia
(package
(inherit llvm-9)
(name "llvm-julia")
(source (origin
(inherit (package-source llvm-9))
;; Those patches are inside the Julia source repo.
;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
;; but they are required to build Julia.
;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
(patches
(map (match-lambda
((name hash)
(julia-patch name hash)))
(list
'("llvm-D27629-AArch64-large_model_6.0.1"
"1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
'("llvm8-D34078-vectorize-fdiv"
"19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
'("llvm-7.0-D44650"
"1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
'("llvm9-D50010-VNCoercion-ni"
"1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx")
'("llvm-exegesis-mingw"
"0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
'("llvm-test-plugin-mingw"
"12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
'("llvm7-revert-D44485"
"0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
'("llvm-8.0-D66657-codegen-degenerate"
"1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
'("llvm-8.0-D71495-vectorize-freduce"
"1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
'("llvm-D75072-SCEV-add-type"
"029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z")
'("llvm-9.0-D65174-limit-merge-stores"
"04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0")
'("llvm9-D71443-PPC-MC-redef-symbol"
"1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy")
'("llvm-9.0-D78196"
"08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns")
'("llvm-julia-tsan-custom-as"
"0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s")
'("llvm-9.0-D85499"
"0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm"))))
(patch-flags '("-p1"))))
(arguments
(substitute-keyword-arguments (package-arguments llvm-9)
((#:configure-flags flags)
`(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
"-DCMAKE_BUILD_TYPE=Release"
;; Build a native compiler and the NVPTX backend (NVIDIA) since
;; Julia insists on it, nothing more. This reduces build times and
;; disk usage.
,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target))
"-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX"
"-DLLVM_INSTALL_UTILS=ON"
"-DLLVM_BUILD_TESTS=ON"
"-DLLVM_ENABLE_FFI=ON"
"-DLLVM_ENABLE_RTTI=ON"
;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
"-DLLVM_ENABLE_DUMP=ON"
"-DLLVM_LINK_LLVM_DYLIB=ON"))))))
(define-public libwhich
(package
(name "libwhich")
(version "1.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vtjnash/libwhich")
;; fixes linux-vdso.so related tests
(commit "87cffe10080c98e7b5786c5166e420bf1ada1d41")))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1bpa0fcqpa3ai3hm8mz0p13bf76fsq53wsfcx5qw302zh22108xr"))))
(arguments
`(#:make-flags
(list (string-append "CC=" ,(cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'check 'set-ld-library-path
(lambda* (#:key native-inputs inputs #:allow-other-keys)
(setenv "LD_LIBRARY_PATH"
(string-append (assoc-ref (or native-inputs inputs) "zlib")
"/lib"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "libwhich" (string-append out "/bin")))
#t)))))
(native-inputs
;; used for tests
`(("zlib" ,zlib)))
(build-system gnu-build-system)
(home-page "https://github.com/vtjnash/libwhich")
(synopsis "Like @code{which}, for dynamic libraries")
(description "@code{libwhich} is like @code{which}, but for dynamic
libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(license license:expat)))
(define-public julia
(package
(name "julia")
(version "1.5.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/JuliaLang/julia/releases/download/v"
version "/julia-" version ".tar.gz"))
(sha256
(base32
"1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy"))
(patches
(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(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 $ORIGIN to refer to each other, but (guix build
;; gremlin) doesn't support it yet, so skip this phase.
#:validate-runpath? #f
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
;; needed by libwhich
(setenv "LD_LIBRARY_PATH"
(string-join (map (lambda (pkg)
(string-append (assoc-ref inputs pkg)
"/lib"))
'("arpack-ng" "curl" "dsfmt"
"gmp" "lapack"
"libssh2" "libgit2"
"mbedtls" "mpfr"
"openblas" "openlibm" "pcre2"
"suitesparse"))
":"))
#t))
;; FIXME: Building the documentation requires Julia packages that
;; would be downloaded from the Internet. We should build them in a
;; separate build phase.
(add-after 'unpack 'disable-documentation
(lambda _
(substitute* "Makefile"
(("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
(string-append line "\n"))
(("src ui doc deps")
"src ui deps"))
#t))
(add-after 'unpack 'use-system-libwhich
(lambda* (#:key inputs #:allow-other-keys)
;; don't build it
(substitute* "deps/Makefile"
(("DEP_LIBS \\+= libwhich") ""))
;; call our version
(substitute* "base/Makefile"
(("\\$\\$\\(build_depsbindir\\)/libwhich")
(string-append (assoc-ref inputs "libwhich") "/bin/libwhich")))
#t))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #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\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
"$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
"$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(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-before 'build 'fix-precompile
(lambda _
(substitute* "base/loading.jl"
(("something(Base.active_project(), \"\")") "\"\""))
#t))
(add-before 'check 'disable-broken-tests
(lambda _
(substitute* "test/choosetests.jl"
(("tests = testnames")
;; Those failings are not deterministic. They depends on the
;; running order. I think it depends on the number of
;; runners, disabling it for now
;; https://github.com/JuliaLang/julia/issues/34330
"tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",\"precompile\",
\"client\",\"stacktraces\"]),
testnames)"))
;; Marking the test as broken as it's a known bug:
;; https://github.com/JuliaLang/julia/issues/32377
(substitute* "stdlib/REPL/test/replcompletions.jl"
(("@test count") "@test_broken count"))
;; Dates has a similar bug:
;; https://github.com/JuliaLang/julia/issues/34655
(substitute* "stdlib/Dates/test/io.jl"
(("\"Dates.Date") "\"Date")
(("\"Dates.Time") "\"Time"))
;; Upstream bug I found when packaging
;; https://github.com/JuliaLang/julia/issues/35785
(substitute* "test/file.jl"
(("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d"))
;; Deprecation test fails with --depwarn=no
;; https://github.com/JuliaLang/julia/issues/37673
(substitute* "test/Makefile"
(("./runtests.jl") "--depwarn=error ./runtests.jl"))
#t))
(add-after 'install 'make-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(program "julia"))
(with-directory-excursion bin
(wrap-program program
`("JULIA_LOAD_PATH" ":" prefix
("" "$JULIA_LOAD_PATH")))
(wrap-program program
`("JULIA_DEPOT_PATH" ":" prefix
("" "$JULIA_DEPOT_PATH"))))
#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
;; list of "USE_SYSTEM_*" is here:
;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
"USE_SYSTEM_DSFMT=1"
"USE_SYSTEM_P7ZIP=1"
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
"LIBBLAS=-lopenblas"
"LIBBLASNAME=libopenblas"
"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"
"LLVM_VER=9.0.1"
"USE_LLVM_SHLIB=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_MBEDTLS=1"
"USE_SYSTEM_LIBSSH2=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_ZLIB=1")))
(inputs
`(("llvm" ,llvm-julia)
("p7zip" ,p7zip)
;; 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-julia)
("openlibm" ,openlibm)
("mbedtls" ,mbedtls-apache)
("curl" ,curl)
("libgit2" ,libgit2-0.28)
("libssh2" ,libssh2)
("fortran" ,gfortran)
("libuv" ,libuv-julia)
("pcre2" ,pcre2)
("utf8proc" ,utf8proc)
("mpfr" ,mpfr)
("wget" ,wget)
("which" ,which)
("zlib" ,zlib)
("gmp" ,gmp)
("suitesparse" ,suitesparse)
;; Find dependencies versions here:
;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
("libwhich" ,libwhich)
("dsfmt" ,dsfmt)))
(native-inputs
`(("openssl" ,openssl)
("perl" ,perl)
("patchelf" ,patchelf)
("pkg-config" ,pkg-config)
("python" ,python-2)))
(native-search-paths
(list (search-path-specification
(variable "JULIA_LOAD_PATH")
(files (list "share/julia/packages/")))
(search-path-specification
(variable "JULIA_DEPOT_PATH")
(files (list "share/julia/")))))
;; 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)))
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