Merge pull request #117881 from ninjin/juliaclean
julia: cleanup/reorganisation
This commit is contained in:
Michael Raskin
GitHub
commit
ae96c292c0
11 changed files with 39 additions and 260 deletions
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@ -88,13 +88,7 @@ stdenv.mkDerivation rec {
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;
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patches = [
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# Julia recompiles a precompiled file if the mtime stored *in* the
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# .ji file differs from the mtime of the .ji file. This
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# doesn't work in Nix because Nix changes the mtime of files in
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# the Nix store to 1. So patch Julia to accept mtimes of 1.
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./allow_nix_mtime.patch
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./diagonal-test.patch
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./use-system-utf8proc-julia-1.0.patch
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./patches/1.0/use-system-utf8proc-julia-1.0.patch
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];
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postPatch = ''
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@ -184,6 +178,8 @@ stdenv.mkDerivation rec {
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
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'';
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enableParallelBuilding = true;
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postInstall = ''
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# Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
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# as using a wrapper with LD_LIBRARY_PATH causes segmentation
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@ -1,161 +0,0 @@
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{ lib, stdenv, fetchurl, fetchzip, fetchFromGitHub
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# build tools
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, gfortran, m4, makeWrapper, patchelf, perl, which, python2
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, cmake
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# libjulia dependencies
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, libunwind, readline, utf8proc, zlib
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# standard library dependencies
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, curl, fftwSinglePrec, fftw, gmp, libgit2, mpfr, openlibm, openspecfun, pcre2
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# linear algebra
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, blas, lapack, arpack
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# Darwin frameworks
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, CoreServices, ApplicationServices
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}:
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assert (!blas.isILP64) && (!lapack.isILP64);
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with lib;
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let
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majorVersion = "1";
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minorVersion = "3";
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maintenanceVersion = "1";
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src_sha256 = "0q9a7yc3b235psrwl5ghyxgwly25lf8n818l8h6bkf2ymdbsv5p6";
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version = "${majorVersion}.${minorVersion}.${maintenanceVersion}";
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in
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stdenv.mkDerivation rec {
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pname = "julia";
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inherit version;
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src = fetchzip {
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url = "https://github.com/JuliaLang/julia/releases/download/v${majorVersion}.${minorVersion}.${maintenanceVersion}/julia-${majorVersion}.${minorVersion}.${maintenanceVersion}-full.tar.gz";
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sha256 = src_sha256;
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};
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prePatch = ''
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export PATH=$PATH:${cmake}/bin
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'';
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patches = [
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./use-system-utf8proc-julia-1.3.patch
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# Julia recompiles a precompiled file if the mtime stored *in* the
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# .ji file differs from the mtime of the .ji file. This
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# doesn't work in Nix because Nix changes the mtime of files in
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# the Nix store to 1. So patch Julia to accept mtimes of 1.
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./allow_nix_mtime.patch
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];
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postPatch = ''
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patchShebangs . contrib
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for i in backtrace cmdlineargs; do
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mv test/$i.jl{,.off}
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touch test/$i.jl
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done
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rm stdlib/Sockets/test/runtests.jl && touch stdlib/Sockets/test/runtests.jl
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rm stdlib/Distributed/test/runtests.jl && touch stdlib/Distributed/test/runtests.jl
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sed -e 's/Invalid Content-Type:/invalid Content-Type:/g' -i ./stdlib/LibGit2/test/libgit2.jl
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sed -e 's/Failed to resolve /failed to resolve /g' -i ./stdlib/LibGit2/test/libgit2.jl
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'';
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buildInputs = [
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arpack fftw fftwSinglePrec gmp libgit2 libunwind mpfr
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pcre2.dev blas lapack openlibm openspecfun readline utf8proc
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zlib
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]
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++ lib.optionals stdenv.isDarwin [CoreServices ApplicationServices]
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;
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nativeBuildInputs = [ curl gfortran m4 makeWrapper patchelf perl python2 which ];
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makeFlags =
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let
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arch = head (splitString "-" stdenv.system);
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march = {
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x86_64 = stdenv.hostPlatform.gcc.arch or "x86-64";
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i686 = "pentium4";
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aarch64 = "armv8-a";
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}.${arch}
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or (throw "unsupported architecture: ${arch}");
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# Julia requires Pentium 4 (SSE2) or better
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cpuTarget = { x86_64 = "x86-64"; i686 = "pentium4"; aarch64 = "generic"; }.${arch}
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or (throw "unsupported architecture: ${arch}");
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in [
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"ARCH=${arch}"
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"MARCH=${march}"
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"JULIA_CPU_TARGET=${cpuTarget}"
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"PREFIX=$(out)"
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"prefix=$(out)"
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"SHELL=${stdenv.shell}"
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(lib.optionalString (!stdenv.isDarwin) "USE_SYSTEM_BLAS=1")
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"USE_BLAS64=${if blas.isILP64 then "1" else "0"}"
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"USE_SYSTEM_LAPACK=1"
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"USE_SYSTEM_ARPACK=1"
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"USE_SYSTEM_FFTW=1"
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"USE_SYSTEM_GMP=1"
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"USE_SYSTEM_LIBGIT2=1"
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"USE_SYSTEM_LIBUNWIND=1"
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"USE_SYSTEM_MPFR=1"
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"USE_SYSTEM_OPENLIBM=1"
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"USE_SYSTEM_OPENSPECFUN=1"
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"USE_SYSTEM_PATCHELF=1"
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"USE_SYSTEM_PCRE=1"
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"PCRE_CONFIG=${pcre2.dev}/bin/pcre2-config"
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"PCRE_INCL_PATH=${pcre2.dev}/include/pcre2.h"
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"USE_SYSTEM_READLINE=1"
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"USE_SYSTEM_UTF8PROC=1"
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"USE_SYSTEM_ZLIB=1"
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"USE_BINARYBUILDER=0"
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];
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LD_LIBRARY_PATH = makeLibraryPath [
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arpack fftw fftwSinglePrec gmp libgit2 mpfr blas openlibm
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openspecfun pcre2 lapack
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];
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# Other versions of Julia pass the tests, but we are not sure why these fail.
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doCheck = false;
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checkTarget = "testall";
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# Julia's tests require read/write access to $HOME
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preCheck = ''
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export HOME="$NIX_BUILD_TOP"
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'';
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preBuild = ''
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sed -e '/^install:/s@[^ ]*/doc/[^ ]*@@' -i Makefile
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sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
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'';
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postInstall = ''
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# Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
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# as using a wrapper with LD_LIBRARY_PATH causes segmentation
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# faults when program returns an error:
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# $ julia -e 'throw(Error())'
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find $(echo $LD_LIBRARY_PATH | sed 's|:| |g') -maxdepth 1 -name '*.${if stdenv.isDarwin then "dylib" else "so"}*' | while read lib; do
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if [[ ! -e $out/lib/julia/$(basename $lib) ]]; then
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ln -sv $lib $out/lib/julia/$(basename $lib)
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fi
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done
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'';
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passthru = {
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inherit majorVersion minorVersion maintenanceVersion;
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site = "share/julia/site/v${majorVersion}.${minorVersion}";
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};
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meta = {
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description = "High-level performance-oriented dynamical language for technical computing";
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homepage = "https://julialang.org/";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ raskin rob garrison ];
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platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
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broken = stdenv.isi686;
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};
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}
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@ -33,13 +33,7 @@ stdenv.mkDerivation rec {
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};
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patches = [
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./use-system-utf8proc-julia-1.3.patch
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# Julia recompiles a precompiled file if the mtime stored *in* the
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# .ji file differs from the mtime of the .ji file. This
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# doesn't work in Nix because Nix changes the mtime of files in
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# the Nix store to 1. So patch Julia to accept mtimes of 1.
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./allow_nix_mtime.patch
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./patches/1.5/use-system-utf8proc-julia-1.3.patch
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];
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postPatch = ''
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@ -129,6 +123,8 @@ stdenv.mkDerivation rec {
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
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'';
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enableParallelBuilding = true;
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postInstall = ''
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# Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
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# as using a wrapper with LD_LIBRARY_PATH causes segmentation
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24
pkgs/development/compilers/julia/README.md
Normal file
24
pkgs/development/compilers/julia/README.md
Normal file
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@ -0,0 +1,24 @@
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Julia
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=====
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[Julia][julia], as a full-fledged programming language with an extensive
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standard library that covers numerical computing, can be somewhat challenging to
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package. This file aims to provide pointers which could not easily be included
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as comments in the expressions themselves.
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[julia]: https://julialang.org
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For Nixpkgs, the manual is as always your primary reference, and for the Julia
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side of things you probably want to familiarise yourself with the [README
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][readme], [build instructions][build], and [release process][release_process].
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Remember that these can change between Julia releases, especially if the LTS and
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release branches have deviated greatly. A lot of the build process is
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underdocumented and thus there is no substitute for digging into the code that
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controls the build process. You are very likely to need to use the test suite to
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locate and address issues and in the end passing it, while only disabling a
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minimal set of broken or incompatible tests you think you have a good reason to
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disable, is your best bet at arriving at a solid derivation.
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[readme]: https://github.com/JuliaLang/julia/blob/master/README.md
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[build]: https://github.com/JuliaLang/julia/blob/master/doc/build/build.md
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[release_process]: https://julialang.org/blog/2019/08/release-process
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@ -1,25 +0,0 @@
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From f79775378a9eeec5b99f18cc95735b12d172aba3 Mon Sep 17 00:00:00 2001
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From: Tom McLaughlin <pyro777@gmail.com>
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Date: Wed, 12 Dec 2018 13:01:32 -0800
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Subject: [PATCH] Patch to make work better with nix
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---
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base/loading.jl | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/base/loading.jl b/base/loading.jl
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index 51201b98b6..b40c0690f6 100644
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--- a/base/loading.jl
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+++ b/base/loading.jl
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@@ -1384,7 +1384,7 @@ function stale_cachefile(modpath::String, cachefile::String)
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# Issue #13606: compensate for Docker images rounding mtimes
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# Issue #20837: compensate for GlusterFS truncating mtimes to microseconds
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ftime = mtime(f)
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- if ftime != ftime_req && ftime != floor(ftime_req) && ftime != trunc(ftime_req, digits=6)
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+ if ftime != ftime_req && ftime != floor(ftime_req) && ftime != trunc(ftime_req, digits=6) && ftime != 1.0
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@debug "Rejecting stale cache file $cachefile (mtime $ftime_req) because file $f (mtime $ftime) has changed"
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return true
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end
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--
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2.17.1
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@ -1,27 +0,0 @@
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From 9eb180c523b877a53b9e1cf53a4d5e6dad3d7bfe Mon Sep 17 00:00:00 2001
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From: Lars Jellema <lars.jellema@gmail.com>
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Date: Sat, 19 Sep 2020 13:52:20 +0200
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Subject: [PATCH] Use approximate comparisons for diagonal tests
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---
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stdlib/LinearAlgebra/test/diagonal.jl | 4 ++--
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1 file changed, 2 insertions(+), 2 deletions(-)
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diff --git a/stdlib/LinearAlgebra/test/diagonal.jl b/stdlib/LinearAlgebra/test/diagonal.jl
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index e420d5bc6d..7f1b5d0aec 100644
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--- a/stdlib/LinearAlgebra/test/diagonal.jl
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+++ b/stdlib/LinearAlgebra/test/diagonal.jl
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@@ -450,8 +450,8 @@ end
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M = randn(T, 5, 5)
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MM = [randn(T, 2, 2) for _ in 1:2, _ in 1:2]
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for transform in (identity, adjoint, transpose, Adjoint, Transpose)
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- @test lmul!(transform(D), copy(M)) == *(transform(Matrix(D)), M)
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- @test rmul!(copy(M), transform(D)) == *(M, transform(Matrix(D)))
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+ @test lmul!(transform(D), copy(M)) ≈ *(transform(Matrix(D)), M)
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+ @test rmul!(copy(M), transform(D)) ≈ *(M, transform(Matrix(D)))
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@test lmul!(transform(DD), copy(MM)) == *(transform(fullDD), MM)
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@test rmul!(copy(MM), transform(DD)) == *(MM, transform(fullDD))
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end
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--
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2.28.0
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@ -1,22 +0,0 @@
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#!/usr/bin/env nix-shell
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#!nix-shell -i python3 -p python3 python3Packages.requests
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import os
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import re
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import requests
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import subprocess
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latest = requests.get("https://api.github.com/repos/JuliaLang/julia/releases/latest").json()["tag_name"]
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assert latest[0] == "v"
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major, minor, patch = latest[1:].split(".")
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assert major == "1"
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# When a new minor version comes out we'll have to refactor/copy this update script.
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assert minor == "5"
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sha256 = subprocess.check_output(["nix-prefetch-url", "--unpack", f"https://github.com/JuliaLang/julia/releases/download/v{major}.{minor}.{patch}/julia-{major}.{minor}.{patch}-full.tar.gz"], text=True).strip()
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nix_path = os.path.join(os.path.dirname(__file__), "1.5.nix")
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nix0 = open(nix_path, "r").read()
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nix1 = re.sub("maintenanceVersion = \".*\";", f"maintenanceVersion = \"{patch}\";", nix0)
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nix2 = re.sub("src_sha256 = \".*\";", f"src_sha256 = \"{sha256}\";", nix1)
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open(nix_path, "w").write(nix2)
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@ -337,8 +337,10 @@ mapAliases ({
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kodiPlain = kodi;
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kodiPlainWayland = kodi-wayland;
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jellyfin_10_5 = throw "Jellyfin 10.5 is no longer supported and contains a security vulnerability. Please upgrade to a newer version."; # added 2021-04-26
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julia_07 = throw "julia_07 is deprecated in favor of julia_10 LTS"; # added 2020-09-15
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julia_11 = throw "julia_11 is deprecated in favor of latest Julia version"; # added 2020-09-15
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julia_07 = throw "julia_07 has been deprecated in favor of the latest LTS version"; # added 2020-09-15
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julia_1 = throw "julia_1 has been deprecated in favor of julia_10 as it was ambiguous"; # added 2021-03-13
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julia_11 = throw "julia_11 has been deprecated in favor of the latest stable version"; # added 2020-09-15
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julia_13 = throw "julia_13 has been deprecated in favor of the latest stable version"; # added 2021-03-13
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kdeconnect = plasma5Packages.kdeconnect-kde; # added 2020-10-28
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kdiff3-qt5 = kdiff3; # added 2017-02-18
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keepass-keefox = keepass-keepassrpc; # backwards compatibility alias, added 2018-02
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@ -10986,21 +10986,17 @@ in
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julia_10 = callPackage ../development/compilers/julia/1.0.nix {
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gmp = gmp6;
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inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
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inherit (darwin.apple_sdk.frameworks) ApplicationServices CoreServices;
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libgit2 = libgit2_0_27;
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};
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julia_13 = callPackage ../development/compilers/julia/1.3.nix {
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gmp = gmp6;
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inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
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};
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julia_15 = callPackage ../development/compilers/julia/1.5.nix {
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inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
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inherit (darwin.apple_sdk.frameworks) ApplicationServices CoreServices;
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};
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julia_1 = julia_10;
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julia = julia_15;
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julia-lts = julia_10;
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julia-stable = julia_15;
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julia = julia-lts;
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jwasm = callPackage ../development/compilers/jwasm { };
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