;;; 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)))